Starting phenix.real_space_refine on Mon Feb 19 23:36:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w85_32352/02_2024/7w85_32352_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w85_32352/02_2024/7w85_32352.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w85_32352/02_2024/7w85_32352.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w85_32352/02_2024/7w85_32352.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w85_32352/02_2024/7w85_32352_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w85_32352/02_2024/7w85_32352_neut.pdb" } resolution = 2.94 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= 0.020 sd= 0.096 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: 5 Type Number sf(0) Gaussians Ni 42 6.56 5 S 504 5.16 5 C 51504 2.51 5 N 13920 2.21 5 O 15552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 24": "OD1" <-> "OD2" Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 63": "OE1" <-> "OE2" Residue "A ASP 71": "OD1" <-> "OD2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 191": "OD1" <-> "OD2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 425": "OD1" <-> "OD2" Residue "A PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 437": "OD1" <-> "OD2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B ASP 71": "OD1" <-> "OD2" Residue "B ASP 78": "OD1" <-> "OD2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 191": "OD1" <-> "OD2" Residue "B GLU 235": "OE1" <-> "OE2" Residue "B TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 358": "OE1" <-> "OE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 425": "OD1" <-> "OD2" Residue "B PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 437": "OD1" <-> "OD2" Residue "B GLU 438": "OE1" <-> "OE2" Residue "B GLU 450": "OE1" <-> "OE2" Residue "C ASP 24": "OD1" <-> "OD2" Residue "C PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "C ASP 71": "OD1" <-> "OD2" Residue "C ASP 78": "OD1" <-> "OD2" Residue "C ARG 111": "NH1" <-> "NH2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 191": "OD1" <-> "OD2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "C TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 358": "OE1" <-> "OE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 425": "OD1" <-> "OD2" Residue "C PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 437": "OD1" <-> "OD2" Residue "C GLU 438": "OE1" <-> "OE2" Residue "C GLU 450": "OE1" <-> "OE2" Residue "D ASP 24": "OD1" <-> "OD2" Residue "D PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 63": "OE1" <-> "OE2" Residue "D ASP 71": "OD1" <-> "OD2" Residue "D ASP 78": "OD1" <-> "OD2" Residue "D ARG 111": "NH1" <-> "NH2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 191": "OD1" <-> "OD2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 358": "OE1" <-> "OE2" Residue "D TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 425": "OD1" <-> "OD2" Residue "D PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 437": "OD1" <-> "OD2" Residue "D GLU 438": "OE1" <-> "OE2" Residue "D GLU 450": "OE1" <-> "OE2" Residue "E ASP 24": "OD1" <-> "OD2" Residue "E PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 63": "OE1" <-> "OE2" Residue "E ASP 71": "OD1" <-> "OD2" Residue "E ASP 78": "OD1" <-> "OD2" Residue "E ARG 111": "NH1" <-> "NH2" Residue "E GLU 113": "OE1" <-> "OE2" Residue "E TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 191": "OD1" <-> "OD2" Residue "E GLU 235": "OE1" <-> "OE2" Residue "E TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 358": "OE1" <-> "OE2" Residue "E TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 425": "OD1" <-> "OD2" Residue "E PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 437": "OD1" <-> "OD2" Residue "E GLU 438": "OE1" <-> "OE2" Residue "E GLU 450": "OE1" <-> "OE2" Residue "F ASP 24": "OD1" <-> "OD2" Residue "F PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F ASP 71": "OD1" <-> "OD2" Residue "F ASP 78": "OD1" <-> "OD2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F GLU 113": "OE1" <-> "OE2" Residue "F TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 191": "OD1" <-> "OD2" Residue "F GLU 235": "OE1" <-> "OE2" Residue "F TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 358": "OE1" <-> "OE2" Residue "F TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 425": "OD1" <-> "OD2" Residue "F PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 437": "OD1" <-> "OD2" Residue "F GLU 438": "OE1" <-> "OE2" Residue "F GLU 450": "OE1" <-> "OE2" Residue "G ASP 24": "OD1" <-> "OD2" Residue "G PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "G ASP 71": "OD1" <-> "OD2" Residue "G ASP 78": "OD1" <-> "OD2" Residue "G ARG 111": "NH1" <-> "NH2" Residue "G GLU 113": "OE1" <-> "OE2" Residue "G TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 191": "OD1" <-> "OD2" Residue "G GLU 235": "OE1" <-> "OE2" Residue "G TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 358": "OE1" <-> "OE2" Residue "G TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 425": "OD1" <-> "OD2" Residue "G PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 437": "OD1" <-> "OD2" Residue "G GLU 438": "OE1" <-> "OE2" Residue "G GLU 450": "OE1" <-> "OE2" Residue "H ASP 24": "OD1" <-> "OD2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 63": "OE1" <-> "OE2" Residue "H ASP 71": "OD1" <-> "OD2" Residue "H ASP 78": "OD1" <-> "OD2" Residue "H ARG 111": "NH1" <-> "NH2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "H TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 191": "OD1" <-> "OD2" Residue "H GLU 235": "OE1" <-> "OE2" Residue "H TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 358": "OE1" <-> "OE2" Residue "H TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 425": "OD1" <-> "OD2" Residue "H PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 437": "OD1" <-> "OD2" Residue "H GLU 438": "OE1" <-> "OE2" Residue "H GLU 450": "OE1" <-> "OE2" Residue "I ASP 24": "OD1" <-> "OD2" Residue "I PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 63": "OE1" <-> "OE2" Residue "I ASP 71": "OD1" <-> "OD2" Residue "I ASP 78": "OD1" <-> "OD2" Residue "I ARG 111": "NH1" <-> "NH2" Residue "I GLU 113": "OE1" <-> "OE2" Residue "I TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 191": "OD1" <-> "OD2" Residue "I GLU 235": "OE1" <-> "OE2" Residue "I TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 358": "OE1" <-> "OE2" Residue "I TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 425": "OD1" <-> "OD2" Residue "I PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 437": "OD1" <-> "OD2" Residue "I GLU 438": "OE1" <-> "OE2" Residue "I GLU 450": "OE1" <-> "OE2" Residue "J ASP 24": "OD1" <-> "OD2" Residue "J PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 63": "OE1" <-> "OE2" Residue "J ASP 71": "OD1" <-> "OD2" Residue "J ASP 78": "OD1" <-> "OD2" Residue "J ARG 111": "NH1" <-> "NH2" Residue "J GLU 113": "OE1" <-> "OE2" Residue "J TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 191": "OD1" <-> "OD2" Residue "J GLU 235": "OE1" <-> "OE2" Residue "J TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 358": "OE1" <-> "OE2" Residue "J TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 425": "OD1" <-> "OD2" Residue "J PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 437": "OD1" <-> "OD2" Residue "J GLU 438": "OE1" <-> "OE2" Residue "J GLU 450": "OE1" <-> "OE2" Residue "K ASP 24": "OD1" <-> "OD2" Residue "K PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 63": "OE1" <-> "OE2" Residue "K ASP 71": "OD1" <-> "OD2" Residue "K ASP 78": "OD1" <-> "OD2" Residue "K ARG 111": "NH1" <-> "NH2" Residue "K GLU 113": "OE1" <-> "OE2" Residue "K TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 191": "OD1" <-> "OD2" Residue "K GLU 235": "OE1" <-> "OE2" Residue "K TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 358": "OE1" <-> "OE2" Residue "K TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 425": "OD1" <-> "OD2" Residue "K PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 437": "OD1" <-> "OD2" Residue "K GLU 438": "OE1" <-> "OE2" Residue "K GLU 450": "OE1" <-> "OE2" Residue "L ASP 24": "OD1" <-> "OD2" Residue "L PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 63": "OE1" <-> "OE2" Residue "L ASP 71": "OD1" <-> "OD2" Residue "L ASP 78": "OD1" <-> "OD2" Residue "L ARG 111": "NH1" <-> "NH2" Residue "L GLU 113": "OE1" <-> "OE2" Residue "L TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 191": "OD1" <-> "OD2" Residue "L GLU 235": "OE1" <-> "OE2" Residue "L TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 358": "OE1" <-> "OE2" Residue "L TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 425": "OD1" <-> "OD2" Residue "L PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 437": "OD1" <-> "OD2" Residue "L GLU 438": "OE1" <-> "OE2" Residue "L GLU 450": "OE1" <-> "OE2" Residue "M ASP 24": "OD1" <-> "OD2" Residue "M PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 63": "OE1" <-> "OE2" Residue "M ASP 71": "OD1" <-> "OD2" Residue "M ASP 78": "OD1" <-> "OD2" Residue "M ARG 111": "NH1" <-> "NH2" Residue "M GLU 113": "OE1" <-> "OE2" Residue "M TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 191": "OD1" <-> "OD2" Residue "M GLU 235": "OE1" <-> "OE2" Residue "M TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 358": "OE1" <-> "OE2" Residue "M TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 425": "OD1" <-> "OD2" Residue "M PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 437": "OD1" <-> "OD2" Residue "M GLU 438": "OE1" <-> "OE2" Residue "M GLU 450": "OE1" <-> "OE2" Residue "N ASP 24": "OD1" <-> "OD2" Residue "N PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 63": "OE1" <-> "OE2" Residue "N ASP 71": "OD1" <-> "OD2" Residue "N ASP 78": "OD1" <-> "OD2" Residue "N ARG 111": "NH1" <-> "NH2" Residue "N GLU 113": "OE1" <-> "OE2" Residue "N TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 191": "OD1" <-> "OD2" Residue "N GLU 235": "OE1" <-> "OE2" Residue "N TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 358": "OE1" <-> "OE2" Residue "N TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 425": "OD1" <-> "OD2" Residue "N PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 437": "OD1" <-> "OD2" Residue "N GLU 438": "OE1" <-> "OE2" Residue "N GLU 450": "OE1" <-> "OE2" Residue "O ASP 24": "OD1" <-> "OD2" Residue "O PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 63": "OE1" <-> "OE2" Residue "O ASP 71": "OD1" <-> "OD2" Residue "O ASP 78": "OD1" <-> "OD2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "O GLU 113": "OE1" <-> "OE2" Residue "O TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 191": "OD1" <-> "OD2" Residue "O GLU 235": "OE1" <-> "OE2" Residue "O TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 358": "OE1" <-> "OE2" Residue "O TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 425": "OD1" <-> "OD2" Residue "O PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 437": "OD1" <-> "OD2" Residue "O GLU 438": "OE1" <-> "OE2" Residue "O GLU 450": "OE1" <-> "OE2" Residue "P ASP 24": "OD1" <-> "OD2" Residue "P PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 63": "OE1" <-> "OE2" Residue "P ASP 71": "OD1" <-> "OD2" Residue "P ASP 78": "OD1" <-> "OD2" Residue "P ARG 111": "NH1" <-> "NH2" Residue "P GLU 113": "OE1" <-> "OE2" Residue "P TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 191": "OD1" <-> "OD2" Residue "P GLU 235": "OE1" <-> "OE2" Residue "P TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 358": "OE1" <-> "OE2" Residue "P TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 425": "OD1" <-> "OD2" Residue "P PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 437": "OD1" <-> "OD2" Residue "P GLU 438": "OE1" <-> "OE2" Residue "P GLU 450": "OE1" <-> "OE2" Residue "Q ASP 24": "OD1" <-> "OD2" Residue "Q PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 63": "OE1" <-> "OE2" Residue "Q ASP 71": "OD1" <-> "OD2" Residue "Q ASP 78": "OD1" <-> "OD2" Residue "Q ARG 111": "NH1" <-> "NH2" Residue "Q GLU 113": "OE1" <-> "OE2" Residue "Q TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 191": "OD1" <-> "OD2" Residue "Q GLU 235": "OE1" <-> "OE2" Residue "Q TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 358": "OE1" <-> "OE2" Residue "Q TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 425": "OD1" <-> "OD2" Residue "Q PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 437": "OD1" <-> "OD2" Residue "Q GLU 438": "OE1" <-> "OE2" Residue "Q GLU 450": "OE1" <-> "OE2" Residue "R ASP 24": "OD1" <-> "OD2" Residue "R PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 63": "OE1" <-> "OE2" Residue "R ASP 71": "OD1" <-> "OD2" Residue "R ASP 78": "OD1" <-> "OD2" Residue "R ARG 111": "NH1" <-> "NH2" Residue "R GLU 113": "OE1" <-> "OE2" Residue "R TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 191": "OD1" <-> "OD2" Residue "R GLU 235": "OE1" <-> "OE2" Residue "R TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 358": "OE1" <-> "OE2" Residue "R TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 425": "OD1" <-> "OD2" Residue "R PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 437": "OD1" <-> "OD2" Residue "R GLU 438": "OE1" <-> "OE2" Residue "R GLU 450": "OE1" <-> "OE2" Residue "S ASP 24": "OD1" <-> "OD2" Residue "S PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 63": "OE1" <-> "OE2" Residue "S ASP 71": "OD1" <-> "OD2" Residue "S ASP 78": "OD1" <-> "OD2" Residue "S ARG 111": "NH1" <-> "NH2" Residue "S GLU 113": "OE1" <-> "OE2" Residue "S TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 191": "OD1" <-> "OD2" Residue "S GLU 235": "OE1" <-> "OE2" Residue "S TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 358": "OE1" <-> "OE2" Residue "S TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 425": "OD1" <-> "OD2" Residue "S PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 437": "OD1" <-> "OD2" Residue "S GLU 438": "OE1" <-> "OE2" Residue "S GLU 450": "OE1" <-> "OE2" Residue "U ASP 24": "OD1" <-> "OD2" Residue "U PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 63": "OE1" <-> "OE2" Residue "U ASP 71": "OD1" <-> "OD2" Residue "U ASP 78": "OD1" <-> "OD2" Residue "U ARG 111": "NH1" <-> "NH2" Residue "U GLU 113": "OE1" <-> "OE2" Residue "U TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 191": "OD1" <-> "OD2" Residue "U GLU 235": "OE1" <-> "OE2" Residue "U TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 358": "OE1" <-> "OE2" Residue "U TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 425": "OD1" <-> "OD2" Residue "U PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 437": "OD1" <-> "OD2" Residue "U GLU 438": "OE1" <-> "OE2" Residue "U GLU 450": "OE1" <-> "OE2" Residue "V ASP 24": "OD1" <-> "OD2" Residue "V PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 63": "OE1" <-> "OE2" Residue "V ASP 71": "OD1" <-> "OD2" Residue "V ASP 78": "OD1" <-> "OD2" Residue "V ARG 111": "NH1" <-> "NH2" Residue "V GLU 113": "OE1" <-> "OE2" Residue "V TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 191": "OD1" <-> "OD2" Residue "V GLU 235": "OE1" <-> "OE2" Residue "V TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 358": "OE1" <-> "OE2" Residue "V TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 425": "OD1" <-> "OD2" Residue "V PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 437": "OD1" <-> "OD2" Residue "V GLU 438": "OE1" <-> "OE2" Residue "V GLU 450": "OE1" <-> "OE2" Residue "W ASP 24": "OD1" <-> "OD2" Residue "W PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 63": "OE1" <-> "OE2" Residue "W ASP 71": "OD1" <-> "OD2" Residue "W ASP 78": "OD1" <-> "OD2" Residue "W ARG 111": "NH1" <-> "NH2" Residue "W GLU 113": "OE1" <-> "OE2" Residue "W TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 191": "OD1" <-> "OD2" Residue "W GLU 235": "OE1" <-> "OE2" Residue "W TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 358": "OE1" <-> "OE2" Residue "W TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 425": "OD1" <-> "OD2" Residue "W PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 437": "OD1" <-> "OD2" Residue "W GLU 438": "OE1" <-> "OE2" Residue "W GLU 450": "OE1" <-> "OE2" Residue "X ASP 24": "OD1" <-> "OD2" Residue "X PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 63": "OE1" <-> "OE2" Residue "X ASP 71": "OD1" <-> "OD2" Residue "X ASP 78": "OD1" <-> "OD2" Residue "X ARG 111": "NH1" <-> "NH2" Residue "X GLU 113": "OE1" <-> "OE2" Residue "X TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 191": "OD1" <-> "OD2" Residue "X GLU 235": "OE1" <-> "OE2" Residue "X TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 358": "OE1" <-> "OE2" Residue "X TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 425": "OD1" <-> "OD2" Residue "X PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 437": "OD1" <-> "OD2" Residue "X GLU 438": "OE1" <-> "OE2" Residue "X GLU 450": "OE1" <-> "OE2" Residue "Y ASP 24": "OD1" <-> "OD2" Residue "Y PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 63": "OE1" <-> "OE2" Residue "Y ASP 71": "OD1" <-> "OD2" Residue "Y ASP 78": "OD1" <-> "OD2" Residue "Y ARG 111": "NH1" <-> "NH2" Residue "Y GLU 113": "OE1" <-> "OE2" Residue "Y TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 191": "OD1" <-> "OD2" Residue "Y GLU 235": "OE1" <-> "OE2" Residue "Y TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 358": "OE1" <-> "OE2" Residue "Y TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 425": "OD1" <-> "OD2" Residue "Y PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 437": "OD1" <-> "OD2" Residue "Y GLU 438": "OE1" <-> "OE2" Residue "Y GLU 450": "OE1" <-> "OE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 81522 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3395 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "B" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3395 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "C" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3395 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "D" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3395 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "E" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3395 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "F" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3395 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "G" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3395 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "H" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3395 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "I" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3395 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "J" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3395 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "K" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3395 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "L" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3395 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "M" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3395 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "N" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3395 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "O" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3395 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "P" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3395 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "Q" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3395 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "R" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3395 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "S" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3395 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "U" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3395 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "V" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3395 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "W" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3395 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "X" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3395 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "Y" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3395 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NI': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NI': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NI': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NI': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NI': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NI': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 31.74, per 1000 atoms: 0.39 Number of scatterers: 81522 At special positions: 0 Unit cell: (160.29, 160.29, 213.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ni 42 28.00 S 504 16.00 O 15552 8.00 N 13920 7.00 C 51504 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: 24.50 Conformation dependent library (CDL) restraints added in 10.7 seconds 20688 Ramachandran restraints generated. 10344 Oldfield, 0 Emsley, 10344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 19440 Finding SS restraints... Secondary structure from input PDB file: 408 helices and 60 sheets defined 42.1% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.09 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 3.641A pdb=" N VAL A 6 " --> pdb=" O SER A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 42 through 47 Processing helix chain 'A' and resid 72 through 75 removed outlier: 3.595A pdb=" N ALA A 75 " --> pdb=" O ALA A 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 75' Processing helix chain 'A' and resid 104 through 120 removed outlier: 3.661A pdb=" N GLY A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 203 Processing helix chain 'A' and resid 229 through 250 Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 292 through 305 Processing helix chain 'A' and resid 305 through 314 removed outlier: 3.836A pdb=" N LEU A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 321 Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 414 through 425 Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.539A pdb=" N ALA A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 436 through 456 removed outlier: 3.990A pdb=" N GLU A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'B' and resid 2 through 14 removed outlier: 3.640A pdb=" N VAL B 6 " --> pdb=" O SER B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 42 through 47 Processing helix chain 'B' and resid 72 through 75 removed outlier: 3.596A pdb=" N ALA B 75 " --> pdb=" O ALA B 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 72 through 75' Processing helix chain 'B' and resid 104 through 120 removed outlier: 3.660A pdb=" N GLY B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 203 Processing helix chain 'B' and resid 229 through 250 Processing helix chain 'B' and resid 287 through 291 Processing helix chain 'B' and resid 292 through 305 Processing helix chain 'B' and resid 305 through 314 removed outlier: 3.837A pdb=" N LEU B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 321 Processing helix chain 'B' and resid 367 through 385 Processing helix chain 'B' and resid 414 through 425 Processing helix chain 'B' and resid 426 through 431 removed outlier: 3.539A pdb=" N ALA B 431 " --> pdb=" O GLU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'B' and resid 436 through 456 removed outlier: 3.991A pdb=" N GLU B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG B 453 " --> pdb=" O GLU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 467 Processing helix chain 'C' and resid 2 through 14 removed outlier: 3.641A pdb=" N VAL C 6 " --> pdb=" O SER C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'C' and resid 72 through 75 removed outlier: 3.596A pdb=" N ALA C 75 " --> pdb=" O ALA C 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 72 through 75' Processing helix chain 'C' and resid 104 through 120 removed outlier: 3.660A pdb=" N GLY C 120 " --> pdb=" O LEU C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 203 Processing helix chain 'C' and resid 229 through 250 Processing helix chain 'C' and resid 287 through 291 Processing helix chain 'C' and resid 292 through 305 Processing helix chain 'C' and resid 305 through 314 removed outlier: 3.837A pdb=" N LEU C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 367 through 385 Processing helix chain 'C' and resid 414 through 425 Processing helix chain 'C' and resid 426 through 431 removed outlier: 3.539A pdb=" N ALA C 431 " --> pdb=" O GLU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing helix chain 'C' and resid 436 through 456 removed outlier: 3.989A pdb=" N GLU C 450 " --> pdb=" O LEU C 446 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG C 453 " --> pdb=" O GLU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 467 Processing helix chain 'D' and resid 2 through 14 removed outlier: 3.640A pdb=" N VAL D 6 " --> pdb=" O SER D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 42 through 47 Processing helix chain 'D' and resid 72 through 75 removed outlier: 3.595A pdb=" N ALA D 75 " --> pdb=" O ALA D 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 72 through 75' Processing helix chain 'D' and resid 104 through 120 removed outlier: 3.660A pdb=" N GLY D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 203 Processing helix chain 'D' and resid 229 through 250 Processing helix chain 'D' and resid 287 through 291 Processing helix chain 'D' and resid 292 through 305 Processing helix chain 'D' and resid 305 through 314 removed outlier: 3.836A pdb=" N LEU D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 Processing helix chain 'D' and resid 367 through 385 Processing helix chain 'D' and resid 414 through 425 Processing helix chain 'D' and resid 426 through 431 removed outlier: 3.539A pdb=" N ALA D 431 " --> pdb=" O GLU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 434 No H-bonds generated for 'chain 'D' and resid 432 through 434' Processing helix chain 'D' and resid 436 through 456 removed outlier: 3.991A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG D 453 " --> pdb=" O GLU D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 467 Processing helix chain 'E' and resid 2 through 14 removed outlier: 3.641A pdb=" N VAL E 6 " --> pdb=" O SER E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 42 through 47 Processing helix chain 'E' and resid 72 through 75 removed outlier: 3.596A pdb=" N ALA E 75 " --> pdb=" O ALA E 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 72 through 75' Processing helix chain 'E' and resid 104 through 120 removed outlier: 3.660A pdb=" N GLY E 120 " --> pdb=" O LEU E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 203 Processing helix chain 'E' and resid 229 through 250 Processing helix chain 'E' and resid 287 through 291 Processing helix chain 'E' and resid 292 through 305 Processing helix chain 'E' and resid 305 through 314 removed outlier: 3.837A pdb=" N LEU E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 321 Processing helix chain 'E' and resid 367 through 385 Processing helix chain 'E' and resid 414 through 425 Processing helix chain 'E' and resid 426 through 431 removed outlier: 3.540A pdb=" N ALA E 431 " --> pdb=" O GLU E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 434 No H-bonds generated for 'chain 'E' and resid 432 through 434' Processing helix chain 'E' and resid 436 through 456 removed outlier: 3.990A pdb=" N GLU E 450 " --> pdb=" O LEU E 446 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG E 453 " --> pdb=" O GLU E 449 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 467 Processing helix chain 'F' and resid 2 through 14 removed outlier: 3.641A pdb=" N VAL F 6 " --> pdb=" O SER F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 39 No H-bonds generated for 'chain 'F' and resid 37 through 39' Processing helix chain 'F' and resid 42 through 47 Processing helix chain 'F' and resid 72 through 75 removed outlier: 3.595A pdb=" N ALA F 75 " --> pdb=" O ALA F 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 72 through 75' Processing helix chain 'F' and resid 104 through 120 removed outlier: 3.660A pdb=" N GLY F 120 " --> pdb=" O LEU F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 203 Processing helix chain 'F' and resid 229 through 250 Processing helix chain 'F' and resid 287 through 291 Processing helix chain 'F' and resid 292 through 305 Processing helix chain 'F' and resid 305 through 314 removed outlier: 3.836A pdb=" N LEU F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 321 Processing helix chain 'F' and resid 367 through 385 Processing helix chain 'F' and resid 414 through 425 Processing helix chain 'F' and resid 426 through 431 removed outlier: 3.539A pdb=" N ALA F 431 " --> pdb=" O GLU F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 434 No H-bonds generated for 'chain 'F' and resid 432 through 434' Processing helix chain 'F' and resid 436 through 456 removed outlier: 3.990A pdb=" N GLU F 450 " --> pdb=" O LEU F 446 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG F 453 " --> pdb=" O GLU F 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 467 Processing helix chain 'G' and resid 2 through 14 removed outlier: 3.641A pdb=" N VAL G 6 " --> pdb=" O SER G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 42 through 47 Processing helix chain 'G' and resid 72 through 75 removed outlier: 3.596A pdb=" N ALA G 75 " --> pdb=" O ALA G 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 72 through 75' Processing helix chain 'G' and resid 104 through 120 removed outlier: 3.660A pdb=" N GLY G 120 " --> pdb=" O LEU G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 203 Processing helix chain 'G' and resid 229 through 250 Processing helix chain 'G' and resid 287 through 291 Processing helix chain 'G' and resid 292 through 305 Processing helix chain 'G' and resid 305 through 314 removed outlier: 3.837A pdb=" N LEU G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 321 Processing helix chain 'G' and resid 367 through 385 Processing helix chain 'G' and resid 414 through 425 Processing helix chain 'G' and resid 426 through 431 removed outlier: 3.539A pdb=" N ALA G 431 " --> pdb=" O GLU G 427 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 434 No H-bonds generated for 'chain 'G' and resid 432 through 434' Processing helix chain 'G' and resid 436 through 456 removed outlier: 3.991A pdb=" N GLU G 450 " --> pdb=" O LEU G 446 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG G 453 " --> pdb=" O GLU G 449 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 467 Processing helix chain 'H' and resid 2 through 14 removed outlier: 3.641A pdb=" N VAL H 6 " --> pdb=" O SER H 2 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 39 No H-bonds generated for 'chain 'H' and resid 37 through 39' Processing helix chain 'H' and resid 42 through 47 Processing helix chain 'H' and resid 72 through 75 removed outlier: 3.596A pdb=" N ALA H 75 " --> pdb=" O ALA H 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 72 through 75' Processing helix chain 'H' and resid 104 through 120 removed outlier: 3.660A pdb=" N GLY H 120 " --> pdb=" O LEU H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 203 Processing helix chain 'H' and resid 229 through 250 Processing helix chain 'H' and resid 287 through 291 Processing helix chain 'H' and resid 292 through 305 Processing helix chain 'H' and resid 305 through 314 removed outlier: 3.837A pdb=" N LEU H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 317 through 321 Processing helix chain 'H' and resid 367 through 385 Processing helix chain 'H' and resid 414 through 425 Processing helix chain 'H' and resid 426 through 431 removed outlier: 3.539A pdb=" N ALA H 431 " --> pdb=" O GLU H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 432 through 434 No H-bonds generated for 'chain 'H' and resid 432 through 434' Processing helix chain 'H' and resid 436 through 456 removed outlier: 3.990A pdb=" N GLU H 450 " --> pdb=" O LEU H 446 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG H 453 " --> pdb=" O GLU H 449 " (cutoff:3.500A) Processing helix chain 'H' and resid 459 through 467 Processing helix chain 'I' and resid 2 through 14 removed outlier: 3.642A pdb=" N VAL I 6 " --> pdb=" O SER I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 39 No H-bonds generated for 'chain 'I' and resid 37 through 39' Processing helix chain 'I' and resid 42 through 47 Processing helix chain 'I' and resid 72 through 75 removed outlier: 3.596A pdb=" N ALA I 75 " --> pdb=" O ALA I 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 72 through 75' Processing helix chain 'I' and resid 104 through 120 removed outlier: 3.660A pdb=" N GLY I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 190 through 203 Processing helix chain 'I' and resid 229 through 250 Processing helix chain 'I' and resid 287 through 291 Processing helix chain 'I' and resid 292 through 305 Processing helix chain 'I' and resid 305 through 314 removed outlier: 3.837A pdb=" N LEU I 312 " --> pdb=" O ALA I 308 " (cutoff:3.500A) Processing helix chain 'I' and resid 317 through 321 Processing helix chain 'I' and resid 367 through 385 Processing helix chain 'I' and resid 414 through 425 Processing helix chain 'I' and resid 426 through 431 removed outlier: 3.539A pdb=" N ALA I 431 " --> pdb=" O GLU I 427 " (cutoff:3.500A) Processing helix chain 'I' and resid 432 through 434 No H-bonds generated for 'chain 'I' and resid 432 through 434' Processing helix chain 'I' and resid 436 through 456 removed outlier: 3.990A pdb=" N GLU I 450 " --> pdb=" O LEU I 446 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG I 453 " --> pdb=" O GLU I 449 " (cutoff:3.500A) Processing helix chain 'I' and resid 459 through 467 Processing helix chain 'J' and resid 2 through 14 removed outlier: 3.641A pdb=" N VAL J 6 " --> pdb=" O SER J 2 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 39 No H-bonds generated for 'chain 'J' and resid 37 through 39' Processing helix chain 'J' and resid 42 through 47 Processing helix chain 'J' and resid 72 through 75 removed outlier: 3.595A pdb=" N ALA J 75 " --> pdb=" O ALA J 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 72 through 75' Processing helix chain 'J' and resid 104 through 120 removed outlier: 3.660A pdb=" N GLY J 120 " --> pdb=" O LEU J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 190 through 203 Processing helix chain 'J' and resid 229 through 250 Processing helix chain 'J' and resid 287 through 291 Processing helix chain 'J' and resid 292 through 305 Processing helix chain 'J' and resid 305 through 314 removed outlier: 3.836A pdb=" N LEU J 312 " --> pdb=" O ALA J 308 " (cutoff:3.500A) Processing helix chain 'J' and resid 317 through 321 Processing helix chain 'J' and resid 367 through 385 Processing helix chain 'J' and resid 414 through 425 Processing helix chain 'J' and resid 426 through 431 removed outlier: 3.539A pdb=" N ALA J 431 " --> pdb=" O GLU J 427 " (cutoff:3.500A) Processing helix chain 'J' and resid 432 through 434 No H-bonds generated for 'chain 'J' and resid 432 through 434' Processing helix chain 'J' and resid 436 through 456 removed outlier: 3.990A pdb=" N GLU J 450 " --> pdb=" O LEU J 446 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG J 453 " --> pdb=" O GLU J 449 " (cutoff:3.500A) Processing helix chain 'J' and resid 459 through 467 Processing helix chain 'K' and resid 2 through 14 removed outlier: 3.642A pdb=" N VAL K 6 " --> pdb=" O SER K 2 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing helix chain 'K' and resid 42 through 47 Processing helix chain 'K' and resid 72 through 75 removed outlier: 3.595A pdb=" N ALA K 75 " --> pdb=" O ALA K 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 72 through 75' Processing helix chain 'K' and resid 104 through 120 removed outlier: 3.660A pdb=" N GLY K 120 " --> pdb=" O LEU K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 203 Processing helix chain 'K' and resid 229 through 250 Processing helix chain 'K' and resid 287 through 291 Processing helix chain 'K' and resid 292 through 305 Processing helix chain 'K' and resid 305 through 314 removed outlier: 3.837A pdb=" N LEU K 312 " --> pdb=" O ALA K 308 " (cutoff:3.500A) Processing helix chain 'K' and resid 317 through 321 Processing helix chain 'K' and resid 367 through 385 Processing helix chain 'K' and resid 414 through 425 Processing helix chain 'K' and resid 426 through 431 removed outlier: 3.540A pdb=" N ALA K 431 " --> pdb=" O GLU K 427 " (cutoff:3.500A) Processing helix chain 'K' and resid 432 through 434 No H-bonds generated for 'chain 'K' and resid 432 through 434' Processing helix chain 'K' and resid 436 through 456 removed outlier: 3.991A pdb=" N GLU K 450 " --> pdb=" O LEU K 446 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG K 453 " --> pdb=" O GLU K 449 " (cutoff:3.500A) Processing helix chain 'K' and resid 459 through 467 Processing helix chain 'L' and resid 2 through 14 removed outlier: 3.640A pdb=" N VAL L 6 " --> pdb=" O SER L 2 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 39 No H-bonds generated for 'chain 'L' and resid 37 through 39' Processing helix chain 'L' and resid 42 through 47 Processing helix chain 'L' and resid 72 through 75 removed outlier: 3.594A pdb=" N ALA L 75 " --> pdb=" O ALA L 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 72 through 75' Processing helix chain 'L' and resid 104 through 120 removed outlier: 3.660A pdb=" N GLY L 120 " --> pdb=" O LEU L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 190 through 203 Processing helix chain 'L' and resid 229 through 250 Processing helix chain 'L' and resid 287 through 291 Processing helix chain 'L' and resid 292 through 305 Processing helix chain 'L' and resid 305 through 314 removed outlier: 3.836A pdb=" N LEU L 312 " --> pdb=" O ALA L 308 " (cutoff:3.500A) Processing helix chain 'L' and resid 317 through 321 Processing helix chain 'L' and resid 367 through 385 Processing helix chain 'L' and resid 414 through 425 Processing helix chain 'L' and resid 426 through 431 removed outlier: 3.539A pdb=" N ALA L 431 " --> pdb=" O GLU L 427 " (cutoff:3.500A) Processing helix chain 'L' and resid 432 through 434 No H-bonds generated for 'chain 'L' and resid 432 through 434' Processing helix chain 'L' and resid 436 through 456 removed outlier: 3.990A pdb=" N GLU L 450 " --> pdb=" O LEU L 446 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG L 453 " --> pdb=" O GLU L 449 " (cutoff:3.500A) Processing helix chain 'L' and resid 459 through 467 Processing helix chain 'M' and resid 2 through 14 removed outlier: 3.641A pdb=" N VAL M 6 " --> pdb=" O SER M 2 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing helix chain 'M' and resid 42 through 47 Processing helix chain 'M' and resid 72 through 75 removed outlier: 3.596A pdb=" N ALA M 75 " --> pdb=" O ALA M 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 72 through 75' Processing helix chain 'M' and resid 104 through 120 removed outlier: 3.661A pdb=" N GLY M 120 " --> pdb=" O LEU M 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 203 Processing helix chain 'M' and resid 229 through 250 Processing helix chain 'M' and resid 287 through 291 Processing helix chain 'M' and resid 292 through 305 Processing helix chain 'M' and resid 305 through 314 removed outlier: 3.837A pdb=" N LEU M 312 " --> pdb=" O ALA M 308 " (cutoff:3.500A) Processing helix chain 'M' and resid 317 through 321 Processing helix chain 'M' and resid 367 through 385 Processing helix chain 'M' and resid 414 through 425 Processing helix chain 'M' and resid 426 through 431 removed outlier: 3.539A pdb=" N ALA M 431 " --> pdb=" O GLU M 427 " (cutoff:3.500A) Processing helix chain 'M' and resid 432 through 434 No H-bonds generated for 'chain 'M' and resid 432 through 434' Processing helix chain 'M' and resid 436 through 456 removed outlier: 3.990A pdb=" N GLU M 450 " --> pdb=" O LEU M 446 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG M 453 " --> pdb=" O GLU M 449 " (cutoff:3.500A) Processing helix chain 'M' and resid 459 through 467 Processing helix chain 'N' and resid 2 through 14 removed outlier: 3.640A pdb=" N VAL N 6 " --> pdb=" O SER N 2 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 39 No H-bonds generated for 'chain 'N' and resid 37 through 39' Processing helix chain 'N' and resid 42 through 47 Processing helix chain 'N' and resid 72 through 75 removed outlier: 3.595A pdb=" N ALA N 75 " --> pdb=" O ALA N 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 72 through 75' Processing helix chain 'N' and resid 104 through 120 removed outlier: 3.659A pdb=" N GLY N 120 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 190 through 203 Processing helix chain 'N' and resid 229 through 250 Processing helix chain 'N' and resid 287 through 291 Processing helix chain 'N' and resid 292 through 305 Processing helix chain 'N' and resid 305 through 314 removed outlier: 3.837A pdb=" N LEU N 312 " --> pdb=" O ALA N 308 " (cutoff:3.500A) Processing helix chain 'N' and resid 317 through 321 Processing helix chain 'N' and resid 367 through 385 Processing helix chain 'N' and resid 414 through 425 Processing helix chain 'N' and resid 426 through 431 removed outlier: 3.540A pdb=" N ALA N 431 " --> pdb=" O GLU N 427 " (cutoff:3.500A) Processing helix chain 'N' and resid 432 through 434 No H-bonds generated for 'chain 'N' and resid 432 through 434' Processing helix chain 'N' and resid 436 through 456 removed outlier: 3.991A pdb=" N GLU N 450 " --> pdb=" O LEU N 446 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG N 453 " --> pdb=" O GLU N 449 " (cutoff:3.500A) Processing helix chain 'N' and resid 459 through 467 Processing helix chain 'O' and resid 2 through 14 removed outlier: 3.641A pdb=" N VAL O 6 " --> pdb=" O SER O 2 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 39 No H-bonds generated for 'chain 'O' and resid 37 through 39' Processing helix chain 'O' and resid 42 through 47 Processing helix chain 'O' and resid 72 through 75 removed outlier: 3.596A pdb=" N ALA O 75 " --> pdb=" O ALA O 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 72 through 75' Processing helix chain 'O' and resid 104 through 120 removed outlier: 3.660A pdb=" N GLY O 120 " --> pdb=" O LEU O 116 " (cutoff:3.500A) Processing helix chain 'O' and resid 190 through 203 Processing helix chain 'O' and resid 229 through 250 Processing helix chain 'O' and resid 287 through 291 Processing helix chain 'O' and resid 292 through 305 Processing helix chain 'O' and resid 305 through 314 removed outlier: 3.837A pdb=" N LEU O 312 " --> pdb=" O ALA O 308 " (cutoff:3.500A) Processing helix chain 'O' and resid 317 through 321 Processing helix chain 'O' and resid 367 through 385 Processing helix chain 'O' and resid 414 through 425 Processing helix chain 'O' and resid 426 through 431 removed outlier: 3.539A pdb=" N ALA O 431 " --> pdb=" O GLU O 427 " (cutoff:3.500A) Processing helix chain 'O' and resid 432 through 434 No H-bonds generated for 'chain 'O' and resid 432 through 434' Processing helix chain 'O' and resid 436 through 456 removed outlier: 3.989A pdb=" N GLU O 450 " --> pdb=" O LEU O 446 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG O 453 " --> pdb=" O GLU O 449 " (cutoff:3.500A) Processing helix chain 'O' and resid 459 through 467 Processing helix chain 'P' and resid 2 through 14 removed outlier: 3.641A pdb=" N VAL P 6 " --> pdb=" O SER P 2 " (cutoff:3.500A) Processing helix chain 'P' and resid 37 through 39 No H-bonds generated for 'chain 'P' and resid 37 through 39' Processing helix chain 'P' and resid 42 through 47 Processing helix chain 'P' and resid 72 through 75 removed outlier: 3.595A pdb=" N ALA P 75 " --> pdb=" O ALA P 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 72 through 75' Processing helix chain 'P' and resid 104 through 120 removed outlier: 3.660A pdb=" N GLY P 120 " --> pdb=" O LEU P 116 " (cutoff:3.500A) Processing helix chain 'P' and resid 190 through 203 Processing helix chain 'P' and resid 229 through 250 Processing helix chain 'P' and resid 287 through 291 Processing helix chain 'P' and resid 292 through 305 Processing helix chain 'P' and resid 305 through 314 removed outlier: 3.835A pdb=" N LEU P 312 " --> pdb=" O ALA P 308 " (cutoff:3.500A) Processing helix chain 'P' and resid 317 through 321 Processing helix chain 'P' and resid 367 through 385 Processing helix chain 'P' and resid 414 through 425 Processing helix chain 'P' and resid 426 through 431 removed outlier: 3.539A pdb=" N ALA P 431 " --> pdb=" O GLU P 427 " (cutoff:3.500A) Processing helix chain 'P' and resid 432 through 434 No H-bonds generated for 'chain 'P' and resid 432 through 434' Processing helix chain 'P' and resid 436 through 456 removed outlier: 3.990A pdb=" N GLU P 450 " --> pdb=" O LEU P 446 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG P 453 " --> pdb=" O GLU P 449 " (cutoff:3.500A) Processing helix chain 'P' and resid 459 through 467 Processing helix chain 'Q' and resid 2 through 14 removed outlier: 3.642A pdb=" N VAL Q 6 " --> pdb=" O SER Q 2 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 39 No H-bonds generated for 'chain 'Q' and resid 37 through 39' Processing helix chain 'Q' and resid 42 through 47 Processing helix chain 'Q' and resid 72 through 75 removed outlier: 3.596A pdb=" N ALA Q 75 " --> pdb=" O ALA Q 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 72 through 75' Processing helix chain 'Q' and resid 104 through 120 removed outlier: 3.660A pdb=" N GLY Q 120 " --> pdb=" O LEU Q 116 " (cutoff:3.500A) Processing helix chain 'Q' and resid 190 through 203 Processing helix chain 'Q' and resid 229 through 250 Processing helix chain 'Q' and resid 287 through 291 Processing helix chain 'Q' and resid 292 through 305 Processing helix chain 'Q' and resid 305 through 314 removed outlier: 3.836A pdb=" N LEU Q 312 " --> pdb=" O ALA Q 308 " (cutoff:3.500A) Processing helix chain 'Q' and resid 317 through 321 Processing helix chain 'Q' and resid 367 through 385 Processing helix chain 'Q' and resid 414 through 425 Processing helix chain 'Q' and resid 426 through 431 removed outlier: 3.540A pdb=" N ALA Q 431 " --> pdb=" O GLU Q 427 " (cutoff:3.500A) Processing helix chain 'Q' and resid 432 through 434 No H-bonds generated for 'chain 'Q' and resid 432 through 434' Processing helix chain 'Q' and resid 436 through 456 removed outlier: 3.990A pdb=" N GLU Q 450 " --> pdb=" O LEU Q 446 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG Q 453 " --> pdb=" O GLU Q 449 " (cutoff:3.500A) Processing helix chain 'Q' and resid 459 through 467 Processing helix chain 'R' and resid 2 through 14 removed outlier: 3.641A pdb=" N VAL R 6 " --> pdb=" O SER R 2 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 39 No H-bonds generated for 'chain 'R' and resid 37 through 39' Processing helix chain 'R' and resid 42 through 47 Processing helix chain 'R' and resid 72 through 75 removed outlier: 3.595A pdb=" N ALA R 75 " --> pdb=" O ALA R 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 72 through 75' Processing helix chain 'R' and resid 104 through 120 removed outlier: 3.660A pdb=" N GLY R 120 " --> pdb=" O LEU R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 203 Processing helix chain 'R' and resid 229 through 250 Processing helix chain 'R' and resid 287 through 291 Processing helix chain 'R' and resid 292 through 305 Processing helix chain 'R' and resid 305 through 314 removed outlier: 3.836A pdb=" N LEU R 312 " --> pdb=" O ALA R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 321 Processing helix chain 'R' and resid 367 through 385 Processing helix chain 'R' and resid 414 through 425 Processing helix chain 'R' and resid 426 through 431 removed outlier: 3.539A pdb=" N ALA R 431 " --> pdb=" O GLU R 427 " (cutoff:3.500A) Processing helix chain 'R' and resid 432 through 434 No H-bonds generated for 'chain 'R' and resid 432 through 434' Processing helix chain 'R' and resid 436 through 456 removed outlier: 3.990A pdb=" N GLU R 450 " --> pdb=" O LEU R 446 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG R 453 " --> pdb=" O GLU R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 459 through 467 Processing helix chain 'S' and resid 2 through 14 removed outlier: 3.642A pdb=" N VAL S 6 " --> pdb=" O SER S 2 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 39 No H-bonds generated for 'chain 'S' and resid 37 through 39' Processing helix chain 'S' and resid 42 through 47 Processing helix chain 'S' and resid 72 through 75 removed outlier: 3.595A pdb=" N ALA S 75 " --> pdb=" O ALA S 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 72 through 75' Processing helix chain 'S' and resid 104 through 120 removed outlier: 3.660A pdb=" N GLY S 120 " --> pdb=" O LEU S 116 " (cutoff:3.500A) Processing helix chain 'S' and resid 190 through 203 Processing helix chain 'S' and resid 229 through 250 Processing helix chain 'S' and resid 287 through 291 Processing helix chain 'S' and resid 292 through 305 Processing helix chain 'S' and resid 305 through 314 removed outlier: 3.837A pdb=" N LEU S 312 " --> pdb=" O ALA S 308 " (cutoff:3.500A) Processing helix chain 'S' and resid 317 through 321 Processing helix chain 'S' and resid 367 through 385 Processing helix chain 'S' and resid 414 through 425 Processing helix chain 'S' and resid 426 through 431 removed outlier: 3.539A pdb=" N ALA S 431 " --> pdb=" O GLU S 427 " (cutoff:3.500A) Processing helix chain 'S' and resid 432 through 434 No H-bonds generated for 'chain 'S' and resid 432 through 434' Processing helix chain 'S' and resid 436 through 456 removed outlier: 3.990A pdb=" N GLU S 450 " --> pdb=" O LEU S 446 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG S 453 " --> pdb=" O GLU S 449 " (cutoff:3.500A) Processing helix chain 'S' and resid 459 through 467 Processing helix chain 'U' and resid 2 through 14 removed outlier: 3.640A pdb=" N VAL U 6 " --> pdb=" O SER U 2 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 39 No H-bonds generated for 'chain 'U' and resid 37 through 39' Processing helix chain 'U' and resid 42 through 47 Processing helix chain 'U' and resid 72 through 75 removed outlier: 3.596A pdb=" N ALA U 75 " --> pdb=" O ALA U 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 72 through 75' Processing helix chain 'U' and resid 104 through 120 removed outlier: 3.660A pdb=" N GLY U 120 " --> pdb=" O LEU U 116 " (cutoff:3.500A) Processing helix chain 'U' and resid 190 through 203 Processing helix chain 'U' and resid 229 through 250 Processing helix chain 'U' and resid 287 through 291 Processing helix chain 'U' and resid 292 through 305 Processing helix chain 'U' and resid 305 through 314 removed outlier: 3.837A pdb=" N LEU U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) Processing helix chain 'U' and resid 317 through 321 Processing helix chain 'U' and resid 367 through 385 Processing helix chain 'U' and resid 414 through 425 Processing helix chain 'U' and resid 426 through 431 removed outlier: 3.539A pdb=" N ALA U 431 " --> pdb=" O GLU U 427 " (cutoff:3.500A) Processing helix chain 'U' and resid 432 through 434 No H-bonds generated for 'chain 'U' and resid 432 through 434' Processing helix chain 'U' and resid 436 through 456 removed outlier: 3.991A pdb=" N GLU U 450 " --> pdb=" O LEU U 446 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG U 453 " --> pdb=" O GLU U 449 " (cutoff:3.500A) Processing helix chain 'U' and resid 459 through 467 Processing helix chain 'V' and resid 2 through 14 removed outlier: 3.641A pdb=" N VAL V 6 " --> pdb=" O SER V 2 " (cutoff:3.500A) Processing helix chain 'V' and resid 37 through 39 No H-bonds generated for 'chain 'V' and resid 37 through 39' Processing helix chain 'V' and resid 42 through 47 Processing helix chain 'V' and resid 72 through 75 removed outlier: 3.596A pdb=" N ALA V 75 " --> pdb=" O ALA V 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 72 through 75' Processing helix chain 'V' and resid 104 through 120 removed outlier: 3.660A pdb=" N GLY V 120 " --> pdb=" O LEU V 116 " (cutoff:3.500A) Processing helix chain 'V' and resid 190 through 203 Processing helix chain 'V' and resid 229 through 250 Processing helix chain 'V' and resid 287 through 291 Processing helix chain 'V' and resid 292 through 305 Processing helix chain 'V' and resid 305 through 314 removed outlier: 3.837A pdb=" N LEU V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) Processing helix chain 'V' and resid 317 through 321 Processing helix chain 'V' and resid 367 through 385 Processing helix chain 'V' and resid 414 through 425 Processing helix chain 'V' and resid 426 through 431 removed outlier: 3.539A pdb=" N ALA V 431 " --> pdb=" O GLU V 427 " (cutoff:3.500A) Processing helix chain 'V' and resid 432 through 434 No H-bonds generated for 'chain 'V' and resid 432 through 434' Processing helix chain 'V' and resid 436 through 456 removed outlier: 3.991A pdb=" N GLU V 450 " --> pdb=" O LEU V 446 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG V 453 " --> pdb=" O GLU V 449 " (cutoff:3.500A) Processing helix chain 'V' and resid 459 through 467 Processing helix chain 'W' and resid 2 through 14 removed outlier: 3.641A pdb=" N VAL W 6 " --> pdb=" O SER W 2 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 39 No H-bonds generated for 'chain 'W' and resid 37 through 39' Processing helix chain 'W' and resid 42 through 47 Processing helix chain 'W' and resid 72 through 75 removed outlier: 3.595A pdb=" N ALA W 75 " --> pdb=" O ALA W 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 72 through 75' Processing helix chain 'W' and resid 104 through 120 removed outlier: 3.659A pdb=" N GLY W 120 " --> pdb=" O LEU W 116 " (cutoff:3.500A) Processing helix chain 'W' and resid 190 through 203 Processing helix chain 'W' and resid 229 through 250 Processing helix chain 'W' and resid 287 through 291 Processing helix chain 'W' and resid 292 through 305 Processing helix chain 'W' and resid 305 through 314 removed outlier: 3.836A pdb=" N LEU W 312 " --> pdb=" O ALA W 308 " (cutoff:3.500A) Processing helix chain 'W' and resid 317 through 321 Processing helix chain 'W' and resid 367 through 385 Processing helix chain 'W' and resid 414 through 425 Processing helix chain 'W' and resid 426 through 431 removed outlier: 3.539A pdb=" N ALA W 431 " --> pdb=" O GLU W 427 " (cutoff:3.500A) Processing helix chain 'W' and resid 432 through 434 No H-bonds generated for 'chain 'W' and resid 432 through 434' Processing helix chain 'W' and resid 436 through 456 removed outlier: 3.991A pdb=" N GLU W 450 " --> pdb=" O LEU W 446 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG W 453 " --> pdb=" O GLU W 449 " (cutoff:3.500A) Processing helix chain 'W' and resid 459 through 467 Processing helix chain 'X' and resid 2 through 14 removed outlier: 3.641A pdb=" N VAL X 6 " --> pdb=" O SER X 2 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 39 No H-bonds generated for 'chain 'X' and resid 37 through 39' Processing helix chain 'X' and resid 42 through 47 Processing helix chain 'X' and resid 72 through 75 removed outlier: 3.595A pdb=" N ALA X 75 " --> pdb=" O ALA X 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 72 through 75' Processing helix chain 'X' and resid 104 through 120 removed outlier: 3.660A pdb=" N GLY X 120 " --> pdb=" O LEU X 116 " (cutoff:3.500A) Processing helix chain 'X' and resid 190 through 203 Processing helix chain 'X' and resid 229 through 250 Processing helix chain 'X' and resid 287 through 291 Processing helix chain 'X' and resid 292 through 305 Processing helix chain 'X' and resid 305 through 314 removed outlier: 3.837A pdb=" N LEU X 312 " --> pdb=" O ALA X 308 " (cutoff:3.500A) Processing helix chain 'X' and resid 317 through 321 Processing helix chain 'X' and resid 367 through 385 Processing helix chain 'X' and resid 414 through 425 Processing helix chain 'X' and resid 426 through 431 removed outlier: 3.540A pdb=" N ALA X 431 " --> pdb=" O GLU X 427 " (cutoff:3.500A) Processing helix chain 'X' and resid 432 through 434 No H-bonds generated for 'chain 'X' and resid 432 through 434' Processing helix chain 'X' and resid 436 through 456 removed outlier: 3.991A pdb=" N GLU X 450 " --> pdb=" O LEU X 446 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG X 453 " --> pdb=" O GLU X 449 " (cutoff:3.500A) Processing helix chain 'X' and resid 459 through 467 Processing helix chain 'Y' and resid 2 through 14 removed outlier: 3.640A pdb=" N VAL Y 6 " --> pdb=" O SER Y 2 " (cutoff:3.500A) Processing helix chain 'Y' and resid 37 through 39 No H-bonds generated for 'chain 'Y' and resid 37 through 39' Processing helix chain 'Y' and resid 42 through 47 Processing helix chain 'Y' and resid 72 through 75 removed outlier: 3.594A pdb=" N ALA Y 75 " --> pdb=" O ALA Y 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 72 through 75' Processing helix chain 'Y' and resid 104 through 120 removed outlier: 3.661A pdb=" N GLY Y 120 " --> pdb=" O LEU Y 116 " (cutoff:3.500A) Processing helix chain 'Y' and resid 190 through 203 Processing helix chain 'Y' and resid 229 through 250 Processing helix chain 'Y' and resid 287 through 291 Processing helix chain 'Y' and resid 292 through 305 Processing helix chain 'Y' and resid 305 through 314 removed outlier: 3.836A pdb=" N LEU Y 312 " --> pdb=" O ALA Y 308 " (cutoff:3.500A) Processing helix chain 'Y' and resid 317 through 321 Processing helix chain 'Y' and resid 367 through 385 Processing helix chain 'Y' and resid 414 through 425 Processing helix chain 'Y' and resid 426 through 431 removed outlier: 3.539A pdb=" N ALA Y 431 " --> pdb=" O GLU Y 427 " (cutoff:3.500A) Processing helix chain 'Y' and resid 432 through 434 No H-bonds generated for 'chain 'Y' and resid 432 through 434' Processing helix chain 'Y' and resid 436 through 456 removed outlier: 3.991A pdb=" N GLU Y 450 " --> pdb=" O LEU Y 446 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG Y 453 " --> pdb=" O GLU Y 449 " (cutoff:3.500A) Processing helix chain 'Y' and resid 459 through 467 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 29 through 35 current: chain 'A' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 66 through 70 current: chain 'A' and resid 85 through 93 Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 124 through 136 current: chain 'A' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 219 through 224 current: chain 'A' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 280 through 281 current: chain 'A' and resid 342 through 345 Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 144 removed outlier: 3.726A pdb=" N GLY A 147 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY G 147 " --> pdb=" O SER G 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 29 through 35 current: chain 'B' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 66 through 70 current: chain 'B' and resid 85 through 93 Processing sheet with id=AA5, first strand: chain 'B' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 124 through 136 current: chain 'B' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 219 through 224 current: chain 'B' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 280 through 281 current: chain 'B' and resid 342 through 345 Processing sheet with id=AA6, first strand: chain 'B' and resid 138 through 144 removed outlier: 3.726A pdb=" N GLY B 147 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY L 147 " --> pdb=" O SER L 144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 29 through 35 current: chain 'C' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 66 through 70 current: chain 'C' and resid 85 through 93 Processing sheet with id=AA8, first strand: chain 'C' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 124 through 136 current: chain 'C' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 219 through 224 current: chain 'C' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 280 through 281 current: chain 'C' and resid 342 through 345 Processing sheet with id=AA9, first strand: chain 'C' and resid 138 through 144 removed outlier: 3.726A pdb=" N GLY C 147 " --> pdb=" O SER C 144 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY K 147 " --> pdb=" O SER K 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 29 through 35 current: chain 'D' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 66 through 70 current: chain 'D' and resid 85 through 93 Processing sheet with id=AB2, first strand: chain 'D' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 124 through 136 current: chain 'D' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 219 through 224 current: chain 'D' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 280 through 281 current: chain 'D' and resid 342 through 345 Processing sheet with id=AB3, first strand: chain 'D' and resid 138 through 144 removed outlier: 3.726A pdb=" N GLY D 147 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY J 147 " --> pdb=" O SER J 144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 29 through 35 current: chain 'E' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 66 through 70 current: chain 'E' and resid 85 through 93 Processing sheet with id=AB5, first strand: chain 'E' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 124 through 136 current: chain 'E' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 219 through 224 current: chain 'E' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 280 through 281 current: chain 'E' and resid 342 through 345 Processing sheet with id=AB6, first strand: chain 'E' and resid 138 through 144 removed outlier: 3.726A pdb=" N GLY E 147 " --> pdb=" O SER E 144 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY I 147 " --> pdb=" O SER I 144 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 29 through 35 current: chain 'F' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 66 through 70 current: chain 'F' and resid 85 through 93 Processing sheet with id=AB8, first strand: chain 'F' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 124 through 136 current: chain 'F' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 219 through 224 current: chain 'F' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 280 through 281 current: chain 'F' and resid 342 through 345 Processing sheet with id=AB9, first strand: chain 'F' and resid 138 through 144 removed outlier: 3.726A pdb=" N GLY F 147 " --> pdb=" O SER F 144 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY H 147 " --> pdb=" O SER H 144 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 29 through 35 current: chain 'G' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 66 through 70 current: chain 'G' and resid 85 through 93 Processing sheet with id=AC2, first strand: chain 'G' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 124 through 136 current: chain 'G' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 219 through 224 current: chain 'G' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 280 through 281 current: chain 'G' and resid 342 through 345 Processing sheet with id=AC3, first strand: chain 'H' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 29 through 35 current: chain 'H' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 66 through 70 current: chain 'H' and resid 85 through 93 Processing sheet with id=AC4, first strand: chain 'H' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 124 through 136 current: chain 'H' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 219 through 224 current: chain 'H' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 280 through 281 current: chain 'H' and resid 342 through 345 Processing sheet with id=AC5, first strand: chain 'I' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 29 through 35 current: chain 'I' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 66 through 70 current: chain 'I' and resid 85 through 93 Processing sheet with id=AC6, first strand: chain 'I' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 124 through 136 current: chain 'I' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 219 through 224 current: chain 'I' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 280 through 281 current: chain 'I' and resid 342 through 345 Processing sheet with id=AC7, first strand: chain 'J' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 29 through 35 current: chain 'J' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 66 through 70 current: chain 'J' and resid 85 through 93 Processing sheet with id=AC8, first strand: chain 'J' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 124 through 136 current: chain 'J' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 219 through 224 current: chain 'J' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 280 through 281 current: chain 'J' and resid 342 through 345 Processing sheet with id=AC9, first strand: chain 'K' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 29 through 35 current: chain 'K' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 66 through 70 current: chain 'K' and resid 85 through 93 Processing sheet with id=AD1, first strand: chain 'K' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 124 through 136 current: chain 'K' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 219 through 224 current: chain 'K' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 280 through 281 current: chain 'K' and resid 342 through 345 Processing sheet with id=AD2, first strand: chain 'L' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 29 through 35 current: chain 'L' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 66 through 70 current: chain 'L' and resid 85 through 93 Processing sheet with id=AD3, first strand: chain 'L' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 124 through 136 current: chain 'L' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 219 through 224 current: chain 'L' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 280 through 281 current: chain 'L' and resid 342 through 345 Processing sheet with id=AD4, first strand: chain 'M' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 29 through 35 current: chain 'M' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 66 through 70 current: chain 'M' and resid 85 through 93 Processing sheet with id=AD5, first strand: chain 'M' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 124 through 136 current: chain 'M' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 219 through 224 current: chain 'M' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 280 through 281 current: chain 'M' and resid 342 through 345 Processing sheet with id=AD6, first strand: chain 'M' and resid 138 through 144 removed outlier: 3.727A pdb=" N GLY M 147 " --> pdb=" O SER M 144 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY U 147 " --> pdb=" O SER U 144 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 29 through 35 current: chain 'N' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 66 through 70 current: chain 'N' and resid 85 through 93 Processing sheet with id=AD8, first strand: chain 'N' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 124 through 136 current: chain 'N' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 219 through 224 current: chain 'N' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 280 through 281 current: chain 'N' and resid 342 through 345 Processing sheet with id=AD9, first strand: chain 'N' and resid 138 through 144 removed outlier: 3.725A pdb=" N GLY N 147 " --> pdb=" O SER N 144 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY Y 147 " --> pdb=" O SER Y 144 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 29 through 35 current: chain 'O' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 66 through 70 current: chain 'O' and resid 85 through 93 Processing sheet with id=AE2, first strand: chain 'O' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 124 through 136 current: chain 'O' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 219 through 224 current: chain 'O' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 280 through 281 current: chain 'O' and resid 342 through 345 Processing sheet with id=AE3, first strand: chain 'O' and resid 138 through 144 removed outlier: 3.727A pdb=" N GLY O 147 " --> pdb=" O SER O 144 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY X 147 " --> pdb=" O SER X 144 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 29 through 35 current: chain 'P' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 66 through 70 current: chain 'P' and resid 85 through 93 Processing sheet with id=AE5, first strand: chain 'P' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 124 through 136 current: chain 'P' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 219 through 224 current: chain 'P' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 280 through 281 current: chain 'P' and resid 342 through 345 Processing sheet with id=AE6, first strand: chain 'P' and resid 138 through 144 removed outlier: 3.726A pdb=" N GLY P 147 " --> pdb=" O SER P 144 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY S 147 " --> pdb=" O SER S 144 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 29 through 35 current: chain 'Q' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 66 through 70 current: chain 'Q' and resid 85 through 93 Processing sheet with id=AE8, first strand: chain 'Q' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 124 through 136 current: chain 'Q' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 219 through 224 current: chain 'Q' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 280 through 281 current: chain 'Q' and resid 342 through 345 Processing sheet with id=AE9, first strand: chain 'Q' and resid 138 through 144 removed outlier: 3.726A pdb=" N GLY Q 147 " --> pdb=" O SER Q 144 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY W 147 " --> pdb=" O SER W 144 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'R' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 29 through 35 current: chain 'R' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 66 through 70 current: chain 'R' and resid 85 through 93 Processing sheet with id=AF2, first strand: chain 'R' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 124 through 136 current: chain 'R' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 219 through 224 current: chain 'R' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 280 through 281 current: chain 'R' and resid 342 through 345 Processing sheet with id=AF3, first strand: chain 'R' and resid 138 through 144 removed outlier: 3.726A pdb=" N GLY R 147 " --> pdb=" O SER R 144 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY V 147 " --> pdb=" O SER V 144 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 29 through 35 current: chain 'S' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 66 through 70 current: chain 'S' and resid 85 through 93 Processing sheet with id=AF5, first strand: chain 'S' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 124 through 136 current: chain 'S' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 219 through 224 current: chain 'S' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 280 through 281 current: chain 'S' and resid 342 through 345 Processing sheet with id=AF6, first strand: chain 'U' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 29 through 35 current: chain 'U' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 66 through 70 current: chain 'U' and resid 85 through 93 Processing sheet with id=AF7, first strand: chain 'U' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 124 through 136 current: chain 'U' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 219 through 224 current: chain 'U' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 280 through 281 current: chain 'U' and resid 342 through 345 Processing sheet with id=AF8, first strand: chain 'V' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 29 through 35 current: chain 'V' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 66 through 70 current: chain 'V' and resid 85 through 93 Processing sheet with id=AF9, first strand: chain 'V' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 124 through 136 current: chain 'V' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 219 through 224 current: chain 'V' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 280 through 281 current: chain 'V' and resid 342 through 345 Processing sheet with id=AG1, first strand: chain 'W' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 29 through 35 current: chain 'W' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 66 through 70 current: chain 'W' and resid 85 through 93 Processing sheet with id=AG2, first strand: chain 'W' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 124 through 136 current: chain 'W' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 219 through 224 current: chain 'W' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 280 through 281 current: chain 'W' and resid 342 through 345 Processing sheet with id=AG3, first strand: chain 'X' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 29 through 35 current: chain 'X' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 66 through 70 current: chain 'X' and resid 85 through 93 Processing sheet with id=AG4, first strand: chain 'X' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 124 through 136 current: chain 'X' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 219 through 224 current: chain 'X' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 280 through 281 current: chain 'X' and resid 342 through 345 Processing sheet with id=AG5, first strand: chain 'Y' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 29 through 35 current: chain 'Y' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 66 through 70 current: chain 'Y' and resid 85 through 93 Processing sheet with id=AG6, first strand: chain 'Y' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 124 through 136 current: chain 'Y' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 219 through 224 current: chain 'Y' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 280 through 281 current: chain 'Y' and resid 342 through 345 3120 hydrogen bonds defined for protein. 9000 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: 33.30 Time building geometry restraints manager: 27.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 25980 1.33 - 1.45: 10923 1.45 - 1.57: 45465 1.57 - 1.69: 0 1.69 - 1.80: 912 Bond restraints: 83280 Sorted by residual: bond pdb=" C LYS V 259 " pdb=" N PRO V 260 " ideal model delta sigma weight residual 1.332 1.313 0.019 8.90e-03 1.26e+04 4.62e+00 bond pdb=" C LYS Y 259 " pdb=" N PRO Y 260 " ideal model delta sigma weight residual 1.332 1.313 0.019 8.90e-03 1.26e+04 4.61e+00 bond pdb=" C LYS S 259 " pdb=" N PRO S 260 " ideal model delta sigma weight residual 1.332 1.313 0.019 8.90e-03 1.26e+04 4.59e+00 bond pdb=" C LYS N 259 " pdb=" N PRO N 260 " ideal model delta sigma weight residual 1.332 1.313 0.019 8.90e-03 1.26e+04 4.58e+00 bond pdb=" C LYS J 259 " pdb=" N PRO J 260 " ideal model delta sigma weight residual 1.332 1.313 0.019 8.90e-03 1.26e+04 4.53e+00 ... (remaining 83275 not shown) Histogram of bond angle deviations from ideal: 98.58 - 105.65: 2124 105.65 - 112.72: 43524 112.72 - 119.78: 27121 119.78 - 126.85: 38975 126.85 - 133.92: 912 Bond angle restraints: 112656 Sorted by residual: angle pdb=" CA GLU S 293 " pdb=" CB GLU S 293 " pdb=" CG GLU S 293 " ideal model delta sigma weight residual 114.10 119.71 -5.61 2.00e+00 2.50e-01 7.88e+00 angle pdb=" CA GLU P 293 " pdb=" CB GLU P 293 " pdb=" CG GLU P 293 " ideal model delta sigma weight residual 114.10 119.71 -5.61 2.00e+00 2.50e-01 7.87e+00 angle pdb=" CA GLU H 293 " pdb=" CB GLU H 293 " pdb=" CG GLU H 293 " ideal model delta sigma weight residual 114.10 119.71 -5.61 2.00e+00 2.50e-01 7.87e+00 angle pdb=" CA GLU M 293 " pdb=" CB GLU M 293 " pdb=" CG GLU M 293 " ideal model delta sigma weight residual 114.10 119.70 -5.60 2.00e+00 2.50e-01 7.84e+00 angle pdb=" CA GLU D 293 " pdb=" CB GLU D 293 " pdb=" CG GLU D 293 " ideal model delta sigma weight residual 114.10 119.70 -5.60 2.00e+00 2.50e-01 7.83e+00 ... (remaining 112651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 45431 17.27 - 34.54: 4009 34.54 - 51.82: 720 51.82 - 69.09: 120 69.09 - 86.36: 72 Dihedral angle restraints: 50352 sinusoidal: 20160 harmonic: 30192 Sorted by residual: dihedral pdb=" CA ASN Q 62 " pdb=" C ASN Q 62 " pdb=" N GLU Q 63 " pdb=" CA GLU Q 63 " ideal model delta harmonic sigma weight residual -180.00 -149.08 -30.92 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" CA ASN S 62 " pdb=" C ASN S 62 " pdb=" N GLU S 63 " pdb=" CA GLU S 63 " ideal model delta harmonic sigma weight residual 180.00 -149.09 -30.91 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" CA ASN E 62 " pdb=" C ASN E 62 " pdb=" N GLU E 63 " pdb=" CA GLU E 63 " ideal model delta harmonic sigma weight residual -180.00 -149.10 -30.90 0 5.00e+00 4.00e-02 3.82e+01 ... (remaining 50349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 10243 0.067 - 0.135: 1899 0.135 - 0.202: 75 0.202 - 0.270: 23 0.270 - 0.337: 24 Chirality restraints: 12264 Sorted by residual: chirality pdb=" CB ILE W 61 " pdb=" CA ILE W 61 " pdb=" CG1 ILE W 61 " pdb=" CG2 ILE W 61 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CB ILE Y 61 " pdb=" CA ILE Y 61 " pdb=" CG1 ILE Y 61 " pdb=" CG2 ILE Y 61 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CB ILE C 61 " pdb=" CA ILE C 61 " pdb=" CG1 ILE C 61 " pdb=" CG2 ILE C 61 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 12261 not shown) Planarity restraints: 14904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY Y 128 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.32e+00 pdb=" N PRO Y 129 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO Y 129 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO Y 129 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY L 128 " -0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO L 129 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO L 129 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO L 129 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY V 128 " 0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO V 129 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO V 129 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO V 129 " 0.032 5.00e-02 4.00e+02 ... (remaining 14901 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 921 2.64 - 3.20: 74564 3.20 - 3.77: 124717 3.77 - 4.33: 188088 4.33 - 4.90: 308129 Nonbonded interactions: 696419 Sorted by model distance: nonbonded pdb=" O GLY N 57 " pdb=" NH1 ARG N 103 " model vdw 2.070 2.520 nonbonded pdb=" O GLY B 57 " pdb=" NH1 ARG B 103 " model vdw 2.070 2.520 nonbonded pdb=" O GLY R 57 " pdb=" NH1 ARG R 103 " model vdw 2.070 2.520 nonbonded pdb=" O GLY S 57 " pdb=" NH1 ARG S 103 " model vdw 2.070 2.520 nonbonded pdb=" O GLY D 57 " pdb=" NH1 ARG D 103 " model vdw 2.070 2.520 ... (remaining 696414 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' and (resid 1 through 469 or resid 501)) selection = (chain 'B' and (resid 1 through 469 or resid 501)) selection = (chain 'C' and (resid 1 through 469 or resid 501)) selection = (chain 'D' and (resid 1 through 469 or resid 501)) selection = (chain 'E' and (resid 1 through 469 or resid 501)) selection = (chain 'F' and (resid 1 through 469 or resid 501)) selection = (chain 'G' and (resid 1 through 469 or resid 501)) selection = (chain 'H' and (resid 1 through 469 or resid 501)) selection = (chain 'I' and (resid 1 through 469 or resid 501)) selection = (chain 'J' and (resid 1 through 469 or resid 501)) selection = (chain 'K' and (resid 1 through 469 or resid 501)) selection = (chain 'L' and (resid 1 through 469 or resid 501)) selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = (chain 'S' and (resid 1 through 469 or resid 501)) selection = (chain 'U' and (resid 1 through 469 or resid 501)) selection = (chain 'V' and (resid 1 through 469 or resid 501)) selection = (chain 'W' and (resid 1 through 469 or resid 501)) selection = (chain 'X' and (resid 1 through 469 or resid 501)) selection = (chain 'Y' and (resid 1 through 469 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 18.550 Check model and map are aligned: 0.940 Set scattering table: 0.620 Process input model: 167.720 Find NCS groups from input model: 5.330 Set up NCS constraints: 0.960 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:12.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 212.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5996 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 : 0.008 0.055 83280 Z= 0.535 Angle : 0.758 11.136 112656 Z= 0.411 Chirality : 0.052 0.337 12264 Planarity : 0.005 0.058 14904 Dihedral : 13.723 86.361 30912 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.08), residues: 10344 helix: 0.41 (0.08), residues: 3768 sheet: -0.67 (0.11), residues: 2280 loop : -1.18 (0.09), residues: 4296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 58 HIS 0.004 0.001 HIS G 37 PHE 0.021 0.002 PHE I 361 TYR 0.015 0.002 TYR E 239 ARG 0.009 0.001 ARG V 455 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20688 Ramachandran restraints generated. 10344 Oldfield, 0 Emsley, 10344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20688 Ramachandran restraints generated. 10344 Oldfield, 0 Emsley, 10344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1237 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1237 time to evaluate : 6.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 9 MET cc_start: 0.8096 (ttm) cc_final: 0.7635 (ttm) REVERT: E 9 MET cc_start: 0.8038 (ttm) cc_final: 0.7574 (ttm) outliers start: 0 outliers final: 2 residues processed: 1237 average time/residue: 1.8747 time to fit residues: 2978.9142 Evaluate side-chains 701 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 699 time to evaluate : 6.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain F residue 293 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 871 optimal weight: 6.9990 chunk 782 optimal weight: 10.0000 chunk 434 optimal weight: 0.2980 chunk 267 optimal weight: 0.9990 chunk 527 optimal weight: 8.9990 chunk 417 optimal weight: 0.9990 chunk 808 optimal weight: 10.0000 chunk 313 optimal weight: 0.9980 chunk 491 optimal weight: 0.9980 chunk 602 optimal weight: 20.0000 chunk 937 optimal weight: 30.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 GLN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN ** F 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 GLN ** G 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 211 HIS I 30 GLN ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 211 HIS J 30 GLN ** J 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 211 HIS ** K 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 211 HIS L 30 GLN ** L 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 211 HIS M 30 GLN ** M 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 30 GLN ** P 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6015 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 83280 Z= 0.184 Angle : 0.593 9.884 112656 Z= 0.306 Chirality : 0.044 0.215 12264 Planarity : 0.005 0.049 14904 Dihedral : 5.140 106.625 11286 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.66 % Allowed : 9.46 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.08), residues: 10344 helix: 1.46 (0.08), residues: 3528 sheet: -0.39 (0.11), residues: 2400 loop : -0.87 (0.09), residues: 4416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP N 58 HIS 0.014 0.001 HIS P 244 PHE 0.016 0.001 PHE W 134 TYR 0.027 0.002 TYR R 239 ARG 0.008 0.000 ARG C 225 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20688 Ramachandran restraints generated. 10344 Oldfield, 0 Emsley, 10344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20688 Ramachandran restraints generated. 10344 Oldfield, 0 Emsley, 10344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 781 time to evaluate : 6.896 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: B 9 MET cc_start: 0.7840 (ttm) cc_final: 0.7587 (ttm) REVERT: B 231 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8131 (mttt) REVERT: B 391 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7195 (tp30) REVERT: C 103 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7649 (mtt-85) REVERT: C 391 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7253 (tp30) REVERT: F 103 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7931 (mtm-85) REVERT: F 391 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7235 (tp30) REVERT: G 103 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7713 (mtt90) REVERT: H 30 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7554 (mm110) REVERT: H 103 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7745 (mtt90) REVERT: H 449 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7368 (pp20) REVERT: H 455 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.5997 (tpt170) REVERT: I 103 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7706 (mtt90) REVERT: I 231 LYS cc_start: 0.7994 (ttmm) cc_final: 0.7713 (mttt) REVERT: K 30 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7485 (mm110) REVERT: K 103 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7576 (mtp85) REVERT: K 449 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7367 (pp20) REVERT: K 455 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.5979 (tpt170) REVERT: L 103 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7747 (mtt90) REVERT: L 231 LYS cc_start: 0.8039 (ttmm) cc_final: 0.7738 (tttt) REVERT: N 426 ARG cc_start: 0.3244 (OUTLIER) cc_final: 0.2787 (ttp80) REVERT: O 393 MET cc_start: 0.4047 (OUTLIER) cc_final: 0.3496 (pp-130) REVERT: O 404 GLU cc_start: 0.3237 (OUTLIER) cc_final: 0.2695 (tt0) REVERT: P 404 GLU cc_start: 0.3095 (OUTLIER) cc_final: 0.2774 (tt0) REVERT: Q 426 ARG cc_start: 0.3166 (OUTLIER) cc_final: 0.2770 (tpp80) REVERT: R 393 MET cc_start: 0.4098 (OUTLIER) cc_final: 0.3636 (pp-130) REVERT: R 426 ARG cc_start: 0.3329 (OUTLIER) cc_final: 0.2914 (tpp80) REVERT: W 456 MET cc_start: 0.4532 (OUTLIER) cc_final: 0.4313 (ttp) outliers start: 144 outliers final: 42 residues processed: 872 average time/residue: 1.8234 time to fit residues: 2055.3072 Evaluate side-chains 734 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 667 time to evaluate : 6.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 391 GLU Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain E residue 391 GLU Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 391 GLU Chi-restraints excluded: chain F residue 424 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 103 ARG Chi-restraints excluded: chain G residue 449 GLU Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 103 ARG Chi-restraints excluded: chain H residue 449 GLU Chi-restraints excluded: chain H residue 455 ARG Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain I residue 449 GLU Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 449 GLU Chi-restraints excluded: chain K residue 30 GLN Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 103 ARG Chi-restraints excluded: chain K residue 449 GLU Chi-restraints excluded: chain K residue 455 ARG Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 103 ARG Chi-restraints excluded: chain L residue 449 GLU Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 153 ASP Chi-restraints excluded: chain M residue 469 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 153 ASP Chi-restraints excluded: chain N residue 426 ARG Chi-restraints excluded: chain N residue 469 VAL Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 153 ASP Chi-restraints excluded: chain O residue 393 MET Chi-restraints excluded: chain O residue 404 GLU Chi-restraints excluded: chain O residue 469 VAL Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 153 ASP Chi-restraints excluded: chain P residue 404 GLU Chi-restraints excluded: chain P residue 469 VAL Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 153 ASP Chi-restraints excluded: chain Q residue 426 ARG Chi-restraints excluded: chain Q residue 469 VAL Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 393 MET Chi-restraints excluded: chain R residue 426 ARG Chi-restraints excluded: chain R residue 469 VAL Chi-restraints excluded: chain S residue 293 GLU Chi-restraints excluded: chain U residue 293 GLU Chi-restraints excluded: chain W residue 293 GLU Chi-restraints excluded: chain W residue 456 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 520 optimal weight: 0.3980 chunk 290 optimal weight: 0.1980 chunk 779 optimal weight: 0.1980 chunk 638 optimal weight: 0.9980 chunk 258 optimal weight: 10.0000 chunk 938 optimal weight: 3.9990 chunk 1014 optimal weight: 50.0000 chunk 836 optimal weight: 50.0000 chunk 931 optimal weight: 20.0000 chunk 320 optimal weight: 0.7980 chunk 753 optimal weight: 20.0000 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 HIS ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 HIS ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 HIS ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 211 HIS G 30 GLN ** G 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 211 HIS ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 211 HIS ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 212 HIS J 30 GLN ** J 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6002 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 83280 Z= 0.159 Angle : 0.541 8.870 112656 Z= 0.277 Chirality : 0.043 0.184 12264 Planarity : 0.004 0.044 14904 Dihedral : 4.619 29.381 11280 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.97 % Allowed : 11.28 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.08), residues: 10344 helix: 1.65 (0.09), residues: 3672 sheet: -0.29 (0.11), residues: 2160 loop : -0.83 (0.09), residues: 4512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP P 58 HIS 0.007 0.000 HIS V 5 PHE 0.025 0.001 PHE P 50 TYR 0.028 0.002 TYR N 239 ARG 0.009 0.000 ARG D 249 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20688 Ramachandran restraints generated. 10344 Oldfield, 0 Emsley, 10344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20688 Ramachandran restraints generated. 10344 Oldfield, 0 Emsley, 10344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 711 time to evaluate : 7.122 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 1 MET cc_start: 0.6256 (tpp) cc_final: 0.5807 (ttt) REVERT: A 456 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.7005 (mtt) REVERT: B 9 MET cc_start: 0.7803 (ttm) cc_final: 0.7583 (ttm) REVERT: B 231 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8108 (mttt) REVERT: C 103 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7585 (mtt-85) REVERT: C 391 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7233 (tp30) REVERT: D 49 MET cc_start: 0.8260 (tpp) cc_final: 0.7663 (mmt) REVERT: D 456 MET cc_start: 0.7184 (OUTLIER) cc_final: 0.6980 (mtt) REVERT: F 45 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: F 103 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7914 (mtm-85) REVERT: F 391 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7209 (tp30) REVERT: F 455 ARG cc_start: 0.6769 (ttt90) cc_final: 0.6533 (mtm110) REVERT: G 66 MET cc_start: 0.7736 (mmm) cc_final: 0.7507 (mmt) REVERT: G 103 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7711 (mtt90) REVERT: H 103 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7755 (mtt90) REVERT: H 249 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7726 (ptp-170) REVERT: H 449 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7317 (pp20) REVERT: H 455 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.5963 (tpt170) REVERT: I 103 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7702 (mtt90) REVERT: I 231 LYS cc_start: 0.7954 (ttmm) cc_final: 0.7675 (mttt) REVERT: I 249 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7387 (ptp-170) REVERT: K 1 MET cc_start: 0.6789 (OUTLIER) cc_final: 0.5233 (tmm) REVERT: K 103 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7582 (mtp85) REVERT: K 249 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7754 (ptp-170) REVERT: K 449 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7321 (pp20) REVERT: K 455 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.5925 (tpt170) REVERT: L 231 LYS cc_start: 0.7978 (ttmm) cc_final: 0.7695 (mttt) REVERT: L 384 LYS cc_start: 0.7964 (ttmm) cc_final: 0.7750 (tppp) REVERT: M 426 ARG cc_start: 0.3235 (OUTLIER) cc_final: 0.2941 (tpp80) REVERT: N 426 ARG cc_start: 0.3232 (OUTLIER) cc_final: 0.2790 (ttp80) REVERT: O 42 GLU cc_start: 0.4463 (OUTLIER) cc_final: 0.4018 (pt0) REVERT: O 393 MET cc_start: 0.3968 (OUTLIER) cc_final: 0.3695 (pp-130) REVERT: P 404 GLU cc_start: 0.3029 (OUTLIER) cc_final: 0.2699 (tt0) REVERT: Q 426 ARG cc_start: 0.3207 (OUTLIER) cc_final: 0.2811 (ttp80) REVERT: R 393 MET cc_start: 0.4004 (OUTLIER) cc_final: 0.3647 (pp-130) REVERT: R 426 ARG cc_start: 0.3272 (OUTLIER) cc_final: 0.2862 (tpp80) outliers start: 171 outliers final: 38 residues processed: 811 average time/residue: 1.7568 time to fit residues: 1856.3822 Evaluate side-chains 727 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 661 time to evaluate : 6.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 391 GLU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 391 GLU Chi-restraints excluded: chain F residue 424 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 103 ARG Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 103 ARG Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain H residue 449 GLU Chi-restraints excluded: chain H residue 455 ARG Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain I residue 249 ARG Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 103 ARG Chi-restraints excluded: chain K residue 249 ARG Chi-restraints excluded: chain K residue 449 GLU Chi-restraints excluded: chain K residue 455 ARG Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 153 ASP Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 426 ARG Chi-restraints excluded: chain M residue 469 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 426 ARG Chi-restraints excluded: chain O residue 42 GLU Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 153 ASP Chi-restraints excluded: chain O residue 154 ASP Chi-restraints excluded: chain O residue 393 MET Chi-restraints excluded: chain O residue 469 VAL Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 153 ASP Chi-restraints excluded: chain P residue 257 MET Chi-restraints excluded: chain P residue 404 GLU Chi-restraints excluded: chain P residue 469 VAL Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 426 ARG Chi-restraints excluded: chain Q residue 469 VAL Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 154 ASP Chi-restraints excluded: chain R residue 393 MET Chi-restraints excluded: chain R residue 426 ARG Chi-restraints excluded: chain R residue 469 VAL Chi-restraints excluded: chain S residue 293 GLU Chi-restraints excluded: chain U residue 293 GLU Chi-restraints excluded: chain W residue 293 GLU Chi-restraints excluded: chain Y residue 293 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 927 optimal weight: 40.0000 chunk 705 optimal weight: 50.0000 chunk 487 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 448 optimal weight: 8.9990 chunk 630 optimal weight: 40.0000 chunk 942 optimal weight: 7.9990 chunk 997 optimal weight: 50.0000 chunk 492 optimal weight: 6.9990 chunk 892 optimal weight: 6.9990 chunk 268 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 HIS A 220 ASN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 HIS B 220 ASN ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN C 305 HIS ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 HIS D 220 ASN ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 HIS E 220 ASN ** F 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 HIS F 220 ASN F 305 HIS ** G 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 281 ASN G 310 ASN ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 212 HIS H 310 ASN I 30 GLN ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 212 HIS I 281 ASN I 310 ASN ** J 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 281 ASN J 310 ASN ** K 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 212 HIS K 281 ASN K 310 ASN L 30 GLN ** L 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 212 HIS L 281 ASN L 310 ASN ** M 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 211 HIS ** N 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 211 HIS S 270 HIS ** S 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 385 ASN ** U 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 211 HIS ** U 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 385 ASN U 459 HIS ** V 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 211 HIS V 270 HIS ** V 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 294 GLN ** W 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 211 HIS W 270 HIS ** W 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 385 ASN ** X 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 211 HIS X 385 ASN ** Y 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 211 HIS Y 270 HIS ** Y 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 385 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6190 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.079 83280 Z= 0.579 Angle : 0.703 10.428 112656 Z= 0.363 Chirality : 0.052 0.248 12264 Planarity : 0.006 0.050 14904 Dihedral : 5.182 30.081 11280 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.04 % Allowed : 12.62 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.08), residues: 10344 helix: 1.47 (0.08), residues: 3528 sheet: -0.29 (0.12), residues: 2016 loop : -1.24 (0.09), residues: 4800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP N 58 HIS 0.009 0.002 HIS L 212 PHE 0.030 0.003 PHE K 43 TYR 0.027 0.003 TYR Q 239 ARG 0.012 0.001 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20688 Ramachandran restraints generated. 10344 Oldfield, 0 Emsley, 10344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20688 Ramachandran restraints generated. 10344 Oldfield, 0 Emsley, 10344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 976 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 712 time to evaluate : 7.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 456 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.7079 (mtt) REVERT: B 45 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7013 (mp0) REVERT: C 103 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7418 (mtm-85) REVERT: D 49 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7711 (mmt) REVERT: E 45 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.6985 (mp0) REVERT: F 103 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7432 (mtm-85) REVERT: G 4 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7232 (mt-10) REVERT: G 103 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7684 (mtt90) REVERT: H 103 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7893 (mtt90) REVERT: H 229 MET cc_start: 0.8504 (ttm) cc_final: 0.8269 (ttp) REVERT: H 384 LYS cc_start: 0.8191 (ttmm) cc_final: 0.7748 (ttmm) REVERT: I 103 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7848 (mtt90) REVERT: I 231 LYS cc_start: 0.8324 (ttmm) cc_final: 0.7971 (tttt) REVERT: J 4 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7195 (mt-10) REVERT: K 1 MET cc_start: 0.6766 (OUTLIER) cc_final: 0.5228 (tmm) REVERT: K 4 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7221 (mt-10) REVERT: K 103 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7871 (mtt90) REVERT: K 229 MET cc_start: 0.8522 (ttm) cc_final: 0.8298 (ttp) REVERT: K 249 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7979 (ptp-170) REVERT: K 384 LYS cc_start: 0.8216 (ttmm) cc_final: 0.7797 (ttmm) REVERT: M 404 GLU cc_start: 0.3439 (OUTLIER) cc_final: 0.2960 (tt0) REVERT: M 426 ARG cc_start: 0.3348 (OUTLIER) cc_final: 0.3068 (tpp80) REVERT: N 426 ARG cc_start: 0.3543 (OUTLIER) cc_final: 0.3264 (tpp80) REVERT: O 393 MET cc_start: 0.3983 (ttp) cc_final: 0.3680 (pp-130) REVERT: O 404 GLU cc_start: 0.3484 (OUTLIER) cc_final: 0.3121 (tt0) REVERT: P 404 GLU cc_start: 0.3251 (OUTLIER) cc_final: 0.2725 (tt0) REVERT: Q 426 ARG cc_start: 0.3484 (OUTLIER) cc_final: 0.3212 (tpp80) REVERT: R 393 MET cc_start: 0.4090 (OUTLIER) cc_final: 0.3685 (pp-130) REVERT: R 404 GLU cc_start: 0.3662 (OUTLIER) cc_final: 0.3304 (tt0) REVERT: S 403 GLU cc_start: 0.4153 (pm20) cc_final: 0.3940 (pm20) REVERT: S 453 ARG cc_start: 0.5813 (OUTLIER) cc_final: 0.4343 (ttm-80) REVERT: U 403 GLU cc_start: 0.4136 (pm20) cc_final: 0.3859 (pm20) REVERT: Y 403 GLU cc_start: 0.4192 (pm20) cc_final: 0.3827 (pm20) outliers start: 264 outliers final: 85 residues processed: 880 average time/residue: 1.8078 time to fit residues: 2061.6735 Evaluate side-chains 774 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 665 time to evaluate : 7.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 391 GLU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 391 GLU Chi-restraints excluded: chain F residue 49 MET Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 391 GLU Chi-restraints excluded: chain F residue 424 LEU Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 103 ARG Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 211 HIS Chi-restraints excluded: chain G residue 212 HIS Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain G residue 393 MET Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 103 ARG Chi-restraints excluded: chain H residue 211 HIS Chi-restraints excluded: chain H residue 212 HIS Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 211 HIS Chi-restraints excluded: chain J residue 212 HIS Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 331 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 4 GLU Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 103 ARG Chi-restraints excluded: chain K residue 211 HIS Chi-restraints excluded: chain K residue 212 HIS Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 249 ARG Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain L residue 331 VAL Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 153 ASP Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 404 GLU Chi-restraints excluded: chain M residue 426 ARG Chi-restraints excluded: chain M residue 469 VAL Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 153 ASP Chi-restraints excluded: chain N residue 222 VAL Chi-restraints excluded: chain N residue 257 MET Chi-restraints excluded: chain N residue 426 ARG Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 153 ASP Chi-restraints excluded: chain O residue 154 ASP Chi-restraints excluded: chain O residue 198 LEU Chi-restraints excluded: chain O residue 200 MET Chi-restraints excluded: chain O residue 203 MET Chi-restraints excluded: chain O residue 404 GLU Chi-restraints excluded: chain O residue 469 VAL Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 153 ASP Chi-restraints excluded: chain P residue 257 MET Chi-restraints excluded: chain P residue 404 GLU Chi-restraints excluded: chain P residue 469 VAL Chi-restraints excluded: chain Q residue 62 ASN Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 153 ASP Chi-restraints excluded: chain Q residue 222 VAL Chi-restraints excluded: chain Q residue 426 ARG Chi-restraints excluded: chain Q residue 469 VAL Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 154 ASP Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 393 MET Chi-restraints excluded: chain R residue 404 GLU Chi-restraints excluded: chain R residue 469 VAL Chi-restraints excluded: chain S residue 453 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 830 optimal weight: 20.0000 chunk 566 optimal weight: 30.0000 chunk 14 optimal weight: 2.9990 chunk 742 optimal weight: 0.9990 chunk 411 optimal weight: 0.9990 chunk 851 optimal weight: 9.9990 chunk 689 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 509 optimal weight: 0.0010 chunk 895 optimal weight: 40.0000 chunk 251 optimal weight: 0.1980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 HIS ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 211 HIS ** F 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 HIS ** G 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 281 ASN ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 281 ASN I 30 GLN ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 281 ASN ** K 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 211 HIS L 30 GLN ** L 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 294 GLN ** W 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 248 HIS ** W 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 248 HIS ** Y 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6077 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 83280 Z= 0.160 Angle : 0.555 15.938 112656 Z= 0.278 Chirality : 0.042 0.209 12264 Planarity : 0.004 0.061 14904 Dihedral : 4.614 30.662 11280 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.11 % Allowed : 14.64 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.08), residues: 10344 helix: 1.74 (0.09), residues: 3696 sheet: -0.60 (0.11), residues: 2328 loop : -0.86 (0.09), residues: 4320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP U 58 HIS 0.006 0.001 HIS E 212 PHE 0.015 0.001 PHE M 134 TYR 0.023 0.002 TYR A 297 ARG 0.009 0.000 ARG G 340 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20688 Ramachandran restraints generated. 10344 Oldfield, 0 Emsley, 10344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20688 Ramachandran restraints generated. 10344 Oldfield, 0 Emsley, 10344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 712 time to evaluate : 6.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 MET cc_start: 0.8893 (ttm) cc_final: 0.8684 (ttp) REVERT: A 456 MET cc_start: 0.7241 (OUTLIER) cc_final: 0.6922 (mtt) REVERT: B 45 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: B 424 LEU cc_start: 0.8646 (mt) cc_final: 0.8339 (mt) REVERT: C 103 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7738 (mtt-85) REVERT: D 49 MET cc_start: 0.8268 (tpp) cc_final: 0.7763 (mmt) REVERT: E 45 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: F 103 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7735 (mtt-85) REVERT: G 103 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8231 (mtt180) REVERT: G 249 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7757 (ptp-170) REVERT: H 103 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7684 (mtp85) REVERT: H 249 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7788 (ptp-170) REVERT: H 384 LYS cc_start: 0.8013 (ttmm) cc_final: 0.7642 (ttmm) REVERT: I 103 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7796 (mtt90) REVERT: I 231 LYS cc_start: 0.8125 (ttmm) cc_final: 0.7787 (tttt) REVERT: J 249 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7982 (ptp-170) REVERT: K 1 MET cc_start: 0.6847 (OUTLIER) cc_final: 0.5282 (tmm) REVERT: K 103 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7670 (mtp85) REVERT: K 296 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8397 (mm) REVERT: K 384 LYS cc_start: 0.8033 (ttmm) cc_final: 0.7681 (ttmm) REVERT: L 231 LYS cc_start: 0.8111 (ttmm) cc_final: 0.7768 (tttt) REVERT: M 404 GLU cc_start: 0.3185 (OUTLIER) cc_final: 0.2804 (tt0) REVERT: M 426 ARG cc_start: 0.3404 (OUTLIER) cc_final: 0.3141 (tpp80) REVERT: N 288 TYR cc_start: 0.3282 (OUTLIER) cc_final: 0.2930 (t80) REVERT: N 426 ARG cc_start: 0.3450 (OUTLIER) cc_final: 0.3062 (tpp80) REVERT: O 288 TYR cc_start: 0.3448 (OUTLIER) cc_final: 0.3120 (t80) REVERT: O 395 LYS cc_start: 0.4988 (OUTLIER) cc_final: 0.4036 (tptp) REVERT: O 404 GLU cc_start: 0.3176 (OUTLIER) cc_final: 0.2943 (tt0) REVERT: P 404 GLU cc_start: 0.3026 (OUTLIER) cc_final: 0.2568 (tt0) REVERT: Q 288 TYR cc_start: 0.3258 (OUTLIER) cc_final: 0.2931 (t80) REVERT: Q 426 ARG cc_start: 0.3495 (OUTLIER) cc_final: 0.3104 (tpp80) REVERT: R 288 TYR cc_start: 0.3340 (OUTLIER) cc_final: 0.3088 (t80) REVERT: R 297 TYR cc_start: 0.4424 (m-10) cc_final: 0.4182 (m-10) REVERT: V 30 GLN cc_start: 0.1084 (mm110) cc_final: 0.0814 (mp10) REVERT: V 69 MET cc_start: 0.4554 (ppp) cc_final: 0.4349 (pp-130) REVERT: X 30 GLN cc_start: 0.1129 (mm110) cc_final: 0.0845 (mp10) outliers start: 183 outliers final: 51 residues processed: 835 average time/residue: 1.7827 time to fit residues: 1938.0383 Evaluate side-chains 733 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 657 time to evaluate : 6.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 391 GLU Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 391 GLU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 103 ARG Chi-restraints excluded: chain G residue 212 HIS Chi-restraints excluded: chain G residue 249 ARG Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain G residue 393 MET Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 103 ARG Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain H residue 449 GLU Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 154 ASP Chi-restraints excluded: chain J residue 249 ARG Chi-restraints excluded: chain J residue 331 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 103 ARG Chi-restraints excluded: chain K residue 296 LEU Chi-restraints excluded: chain K residue 449 GLU Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 331 VAL Chi-restraints excluded: chain L residue 449 GLU Chi-restraints excluded: chain M residue 62 ASN Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 153 ASP Chi-restraints excluded: chain M residue 202 GLN Chi-restraints excluded: chain M residue 404 GLU Chi-restraints excluded: chain M residue 426 ARG Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 153 ASP Chi-restraints excluded: chain N residue 257 MET Chi-restraints excluded: chain N residue 288 TYR Chi-restraints excluded: chain N residue 426 ARG Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 153 ASP Chi-restraints excluded: chain O residue 154 ASP Chi-restraints excluded: chain O residue 198 LEU Chi-restraints excluded: chain O residue 200 MET Chi-restraints excluded: chain O residue 288 TYR Chi-restraints excluded: chain O residue 395 LYS Chi-restraints excluded: chain O residue 404 GLU Chi-restraints excluded: chain O residue 469 VAL Chi-restraints excluded: chain P residue 62 ASN Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 153 ASP Chi-restraints excluded: chain P residue 404 GLU Chi-restraints excluded: chain Q residue 59 LYS Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 153 ASP Chi-restraints excluded: chain Q residue 288 TYR Chi-restraints excluded: chain Q residue 426 ARG Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 154 ASP Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 288 TYR Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain Y residue 1 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 335 optimal weight: 10.0000 chunk 898 optimal weight: 50.0000 chunk 197 optimal weight: 9.9990 chunk 585 optimal weight: 8.9990 chunk 246 optimal weight: 1.9990 chunk 998 optimal weight: 30.0000 chunk 828 optimal weight: 20.0000 chunk 462 optimal weight: 0.4980 chunk 83 optimal weight: 1.9990 chunk 330 optimal weight: 0.2980 chunk 524 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 ASN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 ASN ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 ASN ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 HIS ** G 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 211 HIS ** K 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 281 ASN ** L 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 219 GLN ** V 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 294 GLN ** W 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6080 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 83280 Z= 0.177 Angle : 0.552 15.180 112656 Z= 0.272 Chirality : 0.043 0.192 12264 Planarity : 0.004 0.047 14904 Dihedral : 4.375 29.987 11280 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.18 % Allowed : 15.56 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.08), residues: 10344 helix: 1.95 (0.09), residues: 3696 sheet: -0.58 (0.11), residues: 2328 loop : -0.83 (0.09), residues: 4320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Q 58 HIS 0.009 0.001 HIS B 212 PHE 0.020 0.001 PHE H 43 TYR 0.026 0.001 TYR B 297 ARG 0.008 0.000 ARG I 225 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20688 Ramachandran restraints generated. 10344 Oldfield, 0 Emsley, 10344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20688 Ramachandran restraints generated. 10344 Oldfield, 0 Emsley, 10344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 681 time to evaluate : 7.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 MET cc_start: 0.8898 (ttm) cc_final: 0.8679 (ttp) REVERT: A 427 GLU cc_start: 0.6600 (mp0) cc_final: 0.6334 (mp0) REVERT: A 456 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.6952 (mtt) REVERT: B 231 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8135 (mttt) REVERT: B 424 LEU cc_start: 0.8631 (mt) cc_final: 0.8335 (mt) REVERT: C 103 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7834 (mtt-85) REVERT: C 456 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.6838 (mtt) REVERT: D 49 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7707 (mmt) REVERT: D 269 MET cc_start: 0.8910 (ttm) cc_final: 0.8689 (ttp) REVERT: E 273 MET cc_start: 0.8186 (mtm) cc_final: 0.7977 (mtm) REVERT: E 424 LEU cc_start: 0.8635 (mt) cc_final: 0.8351 (mt) REVERT: F 103 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7855 (mtm-85) REVERT: F 456 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.6850 (mtt) REVERT: G 249 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7812 (ptp-170) REVERT: H 42 GLU cc_start: 0.7039 (tp30) cc_final: 0.6807 (tp30) REVERT: H 103 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7686 (mtp85) REVERT: H 249 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7811 (ptp-170) REVERT: H 384 LYS cc_start: 0.8022 (ttmm) cc_final: 0.7724 (ttmm) REVERT: I 103 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7834 (mtt90) REVERT: I 212 HIS cc_start: 0.7290 (t-90) cc_final: 0.6680 (t70) REVERT: I 231 LYS cc_start: 0.8149 (ttmm) cc_final: 0.7809 (tttt) REVERT: J 400 LEU cc_start: 0.2039 (OUTLIER) cc_final: 0.1631 (tt) REVERT: K 1 MET cc_start: 0.6808 (OUTLIER) cc_final: 0.5336 (tmm) REVERT: K 103 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7810 (mtt90) REVERT: K 249 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7832 (ptp-170) REVERT: K 296 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8433 (mm) REVERT: K 384 LYS cc_start: 0.8045 (ttmm) cc_final: 0.7736 (ttmm) REVERT: L 231 LYS cc_start: 0.8142 (ttmm) cc_final: 0.7822 (tttt) REVERT: M 404 GLU cc_start: 0.3201 (OUTLIER) cc_final: 0.2812 (tt0) REVERT: M 426 ARG cc_start: 0.3426 (OUTLIER) cc_final: 0.3189 (tpp80) REVERT: N 288 TYR cc_start: 0.3355 (OUTLIER) cc_final: 0.2983 (t80) REVERT: N 426 ARG cc_start: 0.3408 (OUTLIER) cc_final: 0.3001 (ttp80) REVERT: O 288 TYR cc_start: 0.3358 (OUTLIER) cc_final: 0.3016 (t80) REVERT: O 395 LYS cc_start: 0.4956 (OUTLIER) cc_final: 0.4035 (tptp) REVERT: O 404 GLU cc_start: 0.3201 (OUTLIER) cc_final: 0.2960 (tt0) REVERT: P 404 GLU cc_start: 0.2972 (OUTLIER) cc_final: 0.2583 (tt0) REVERT: Q 288 TYR cc_start: 0.3257 (OUTLIER) cc_final: 0.2898 (t80) REVERT: Q 426 ARG cc_start: 0.3446 (OUTLIER) cc_final: 0.3041 (ttp80) REVERT: R 288 TYR cc_start: 0.3295 (OUTLIER) cc_final: 0.2972 (t80) REVERT: R 393 MET cc_start: 0.4180 (ttm) cc_final: 0.3898 (ttp) REVERT: S 66 MET cc_start: 0.2191 (OUTLIER) cc_final: 0.1939 (mmt) REVERT: S 453 ARG cc_start: 0.5644 (OUTLIER) cc_final: 0.3895 (ttm-80) REVERT: V 400 LEU cc_start: 0.3169 (OUTLIER) cc_final: 0.2964 (pt) outliers start: 189 outliers final: 63 residues processed: 803 average time/residue: 1.7484 time to fit residues: 1832.4499 Evaluate side-chains 737 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 644 time to evaluate : 7.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 391 GLU Chi-restraints excluded: chain F residue 49 MET Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 391 GLU Chi-restraints excluded: chain F residue 456 MET Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 212 HIS Chi-restraints excluded: chain G residue 249 ARG Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain G residue 393 MET Chi-restraints excluded: chain G residue 449 GLU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 103 ARG Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 212 HIS Chi-restraints excluded: chain J residue 331 VAL Chi-restraints excluded: chain J residue 400 LEU Chi-restraints excluded: chain J residue 449 GLU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 103 ARG Chi-restraints excluded: chain K residue 249 ARG Chi-restraints excluded: chain K residue 296 LEU Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 331 VAL Chi-restraints excluded: chain L residue 449 GLU Chi-restraints excluded: chain M residue 49 MET Chi-restraints excluded: chain M residue 62 ASN Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 153 ASP Chi-restraints excluded: chain M residue 202 GLN Chi-restraints excluded: chain M residue 404 GLU Chi-restraints excluded: chain M residue 426 ARG Chi-restraints excluded: chain N residue 9 MET Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 153 ASP Chi-restraints excluded: chain N residue 257 MET Chi-restraints excluded: chain N residue 288 TYR Chi-restraints excluded: chain N residue 426 ARG Chi-restraints excluded: chain O residue 9 MET Chi-restraints excluded: chain O residue 62 ASN Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 153 ASP Chi-restraints excluded: chain O residue 198 LEU Chi-restraints excluded: chain O residue 288 TYR Chi-restraints excluded: chain O residue 395 LYS Chi-restraints excluded: chain O residue 404 GLU Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain P residue 62 ASN Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 153 ASP Chi-restraints excluded: chain P residue 202 GLN Chi-restraints excluded: chain P residue 404 GLU Chi-restraints excluded: chain Q residue 9 MET Chi-restraints excluded: chain Q residue 59 LYS Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 153 ASP Chi-restraints excluded: chain Q residue 288 TYR Chi-restraints excluded: chain Q residue 426 ARG Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 288 TYR Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 453 ARG Chi-restraints excluded: chain U residue 456 MET Chi-restraints excluded: chain V residue 214 VAL Chi-restraints excluded: chain V residue 400 LEU Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain X residue 214 VAL Chi-restraints excluded: chain Y residue 1 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 962 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 568 optimal weight: 9.9990 chunk 729 optimal weight: 50.0000 chunk 564 optimal weight: 8.9990 chunk 840 optimal weight: 50.0000 chunk 557 optimal weight: 50.0000 chunk 994 optimal weight: 0.0030 chunk 622 optimal weight: 30.0000 chunk 606 optimal weight: 9.9990 chunk 459 optimal weight: 0.0980 overall best weight: 5.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 HIS B 305 HIS ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 HIS ** F 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 HIS ** G 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 212 HIS ** J 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 212 HIS ** L 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 212 HIS ** M 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 11 ASN ** O 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 HIS ** R 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 459 HIS ** U 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 270 HIS ** U 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 385 ASN V 459 HIS ** W 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 459 HIS ** X 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 219 GLN ** X 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 459 HIS ** Y 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 459 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6189 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 83280 Z= 0.467 Angle : 0.665 13.318 112656 Z= 0.336 Chirality : 0.048 0.251 12264 Planarity : 0.005 0.052 14904 Dihedral : 4.823 30.204 11280 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.54 % Allowed : 16.28 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.08), residues: 10344 helix: 1.58 (0.08), residues: 3672 sheet: -0.49 (0.12), residues: 1944 loop : -1.26 (0.09), residues: 4728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP O 58 HIS 0.011 0.001 HIS B 212 PHE 0.034 0.002 PHE K 43 TYR 0.030 0.002 TYR B 297 ARG 0.008 0.001 ARG E 455 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20688 Ramachandran restraints generated. 10344 Oldfield, 0 Emsley, 10344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20688 Ramachandran restraints generated. 10344 Oldfield, 0 Emsley, 10344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 934 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 713 time to evaluate : 6.969 Fit side-chains REVERT: A 456 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.7013 (mtt) REVERT: B 438 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6936 (mt-10) REVERT: C 103 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7708 (mtt-85) REVERT: C 456 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6890 (mtt) REVERT: D 49 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7801 (mmt) REVERT: D 269 MET cc_start: 0.8984 (ttm) cc_final: 0.8757 (ttp) REVERT: E 45 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: E 438 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6929 (mt-10) REVERT: F 103 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7684 (mtt-85) REVERT: F 456 MET cc_start: 0.7171 (OUTLIER) cc_final: 0.6907 (mtt) REVERT: G 249 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7853 (ptp-170) REVERT: H 30 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7554 (mm-40) REVERT: H 103 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7862 (mtt90) REVERT: H 249 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7785 (ptp-170) REVERT: I 1 MET cc_start: 0.6501 (tpp) cc_final: 0.6294 (ttt) REVERT: I 103 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7855 (mtt90) REVERT: J 249 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8110 (ptp-170) REVERT: J 400 LEU cc_start: 0.2155 (OUTLIER) cc_final: 0.1667 (tt) REVERT: K 1 MET cc_start: 0.6769 (OUTLIER) cc_final: 0.5291 (tmm) REVERT: K 30 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7564 (mm-40) REVERT: K 103 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7838 (mtt90) REVERT: K 249 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7856 (ptp-170) REVERT: K 296 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8569 (mm) REVERT: L 231 LYS cc_start: 0.8318 (ttmm) cc_final: 0.7980 (tttt) REVERT: M 404 GLU cc_start: 0.3301 (OUTLIER) cc_final: 0.2781 (tt0) REVERT: N 38 GLN cc_start: 0.6280 (OUTLIER) cc_final: 0.5930 (tp40) REVERT: N 49 MET cc_start: 0.4801 (OUTLIER) cc_final: 0.4583 (pmm) REVERT: N 288 TYR cc_start: 0.3462 (OUTLIER) cc_final: 0.3112 (t80) REVERT: N 426 ARG cc_start: 0.3581 (OUTLIER) cc_final: 0.3379 (tpp80) REVERT: O 49 MET cc_start: 0.4137 (OUTLIER) cc_final: 0.3917 (pmm) REVERT: O 273 MET cc_start: 0.4927 (mmm) cc_final: 0.4631 (mpm) REVERT: O 288 TYR cc_start: 0.3606 (OUTLIER) cc_final: 0.3179 (t80) REVERT: O 404 GLU cc_start: 0.3289 (OUTLIER) cc_final: 0.3085 (tt0) REVERT: P 404 GLU cc_start: 0.3278 (OUTLIER) cc_final: 0.2710 (tt0) REVERT: Q 288 TYR cc_start: 0.3451 (OUTLIER) cc_final: 0.3095 (t80) REVERT: Q 426 ARG cc_start: 0.3519 (OUTLIER) cc_final: 0.3312 (tpp80) REVERT: R 49 MET cc_start: 0.4074 (OUTLIER) cc_final: 0.3848 (pmm) REVERT: R 273 MET cc_start: 0.4894 (mmm) cc_final: 0.4597 (mpm) REVERT: R 288 TYR cc_start: 0.3517 (OUTLIER) cc_final: 0.3143 (t80) REVERT: R 395 LYS cc_start: 0.4645 (OUTLIER) cc_final: 0.3400 (tmtt) REVERT: S 453 ARG cc_start: 0.5899 (OUTLIER) cc_final: 0.4338 (ttm-80) REVERT: U 403 GLU cc_start: 0.4044 (pm20) cc_final: 0.3748 (pm20) REVERT: W 453 ARG cc_start: 0.5776 (OUTLIER) cc_final: 0.4407 (ttm-80) REVERT: X 388 HIS cc_start: 0.3400 (OUTLIER) cc_final: 0.3188 (t-90) REVERT: Y 453 ARG cc_start: 0.5878 (OUTLIER) cc_final: 0.4370 (ttm-80) outliers start: 221 outliers final: 86 residues processed: 850 average time/residue: 1.7933 time to fit residues: 1985.3292 Evaluate side-chains 801 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 676 time to evaluate : 6.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 212 HIS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 391 GLU Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 424 LEU Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 391 GLU Chi-restraints excluded: chain F residue 424 LEU Chi-restraints excluded: chain F residue 456 MET Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 211 HIS Chi-restraints excluded: chain G residue 212 HIS Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 249 ARG Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 103 ARG Chi-restraints excluded: chain H residue 212 HIS Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 154 ASP Chi-restraints excluded: chain J residue 211 HIS Chi-restraints excluded: chain J residue 212 HIS Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 249 ARG Chi-restraints excluded: chain J residue 261 MET Chi-restraints excluded: chain J residue 331 VAL Chi-restraints excluded: chain J residue 400 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 30 GLN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 103 ARG Chi-restraints excluded: chain K residue 212 HIS Chi-restraints excluded: chain K residue 249 ARG Chi-restraints excluded: chain K residue 296 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 331 VAL Chi-restraints excluded: chain M residue 9 MET Chi-restraints excluded: chain M residue 49 MET Chi-restraints excluded: chain M residue 62 ASN Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 153 ASP Chi-restraints excluded: chain M residue 202 GLN Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 404 GLU Chi-restraints excluded: chain N residue 9 MET Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 153 ASP Chi-restraints excluded: chain N residue 257 MET Chi-restraints excluded: chain N residue 288 TYR Chi-restraints excluded: chain N residue 426 ARG Chi-restraints excluded: chain O residue 9 MET Chi-restraints excluded: chain O residue 49 MET Chi-restraints excluded: chain O residue 62 ASN Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 153 ASP Chi-restraints excluded: chain O residue 196 MET Chi-restraints excluded: chain O residue 198 LEU Chi-restraints excluded: chain O residue 222 VAL Chi-restraints excluded: chain O residue 288 TYR Chi-restraints excluded: chain O residue 404 GLU Chi-restraints excluded: chain P residue 9 MET Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain P residue 62 ASN Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 153 ASP Chi-restraints excluded: chain P residue 202 GLN Chi-restraints excluded: chain P residue 222 VAL Chi-restraints excluded: chain P residue 404 GLU Chi-restraints excluded: chain Q residue 9 MET Chi-restraints excluded: chain Q residue 62 ASN Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 153 ASP Chi-restraints excluded: chain Q residue 277 LYS Chi-restraints excluded: chain Q residue 288 TYR Chi-restraints excluded: chain Q residue 426 ARG Chi-restraints excluded: chain R residue 9 MET Chi-restraints excluded: chain R residue 49 MET Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain R residue 288 TYR Chi-restraints excluded: chain R residue 395 LYS Chi-restraints excluded: chain S residue 453 ARG Chi-restraints excluded: chain V residue 214 VAL Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 453 ARG Chi-restraints excluded: chain X residue 214 VAL Chi-restraints excluded: chain X residue 388 HIS Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 453 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 615 optimal weight: 20.0000 chunk 397 optimal weight: 0.8980 chunk 594 optimal weight: 7.9990 chunk 299 optimal weight: 0.7980 chunk 195 optimal weight: 7.9990 chunk 192 optimal weight: 0.6980 chunk 632 optimal weight: 20.0000 chunk 677 optimal weight: 40.0000 chunk 491 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 781 optimal weight: 9.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 ASN ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 ASN ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 ASN E 385 ASN ** F 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 HIS F 281 ASN F 385 ASN ** G 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 ASN ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 211 HIS H 227 ASN ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 211 HIS ** J 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 227 ASN J 294 GLN K 5 HIS ** K 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 227 ASN ** L 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 459 HIS ** O 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 459 HIS ** Q 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 83280 Z= 0.171 Angle : 0.573 13.378 112656 Z= 0.280 Chirality : 0.042 0.191 12264 Planarity : 0.004 0.055 14904 Dihedral : 4.390 28.136 11280 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.63 % Allowed : 17.31 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.08), residues: 10344 helix: 1.92 (0.09), residues: 3672 sheet: -0.64 (0.11), residues: 2328 loop : -0.89 (0.09), residues: 4344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP O 58 HIS 0.007 0.001 HIS B 212 PHE 0.015 0.001 PHE P 134 TYR 0.026 0.001 TYR B 297 ARG 0.009 0.000 ARG L 225 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20688 Ramachandran restraints generated. 10344 Oldfield, 0 Emsley, 10344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20688 Ramachandran restraints generated. 10344 Oldfield, 0 Emsley, 10344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 718 time to evaluate : 6.941 Fit side-chains REVERT: A 269 MET cc_start: 0.8894 (ttm) cc_final: 0.8673 (ttp) REVERT: A 427 GLU cc_start: 0.6519 (mp0) cc_final: 0.6263 (mp0) REVERT: A 456 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.6925 (mtt) REVERT: B 231 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8160 (mttt) REVERT: C 103 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7758 (mtt-85) REVERT: D 269 MET cc_start: 0.8893 (ttm) cc_final: 0.8674 (ttp) REVERT: E 273 MET cc_start: 0.8215 (mtm) cc_final: 0.8011 (mtm) REVERT: F 103 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7757 (mtt-85) REVERT: G 4 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.7043 (mt-10) REVERT: G 249 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7754 (ptp-170) REVERT: H 103 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7696 (mtp85) REVERT: H 249 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7733 (ptp-170) REVERT: I 103 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7822 (mtt90) REVERT: I 231 LYS cc_start: 0.8196 (ttmm) cc_final: 0.7795 (tttt) REVERT: J 4 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.7077 (mt-10) REVERT: J 46 GLU cc_start: 0.7260 (pt0) cc_final: 0.7047 (pt0) REVERT: J 249 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.8004 (ptp-170) REVERT: J 400 LEU cc_start: 0.2320 (OUTLIER) cc_final: 0.1898 (tt) REVERT: K 1 MET cc_start: 0.6787 (OUTLIER) cc_final: 0.5343 (tmm) REVERT: K 103 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7672 (mtp85) REVERT: K 249 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7724 (ptp-170) REVERT: K 296 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8403 (mm) REVERT: K 384 LYS cc_start: 0.8087 (ttmm) cc_final: 0.7697 (ttmm) REVERT: L 231 LYS cc_start: 0.8159 (ttmm) cc_final: 0.7826 (tttt) REVERT: M 49 MET cc_start: 0.4947 (OUTLIER) cc_final: 0.4580 (pmm) REVERT: M 404 GLU cc_start: 0.3256 (OUTLIER) cc_final: 0.2832 (tt0) REVERT: N 9 MET cc_start: 0.4507 (OUTLIER) cc_final: 0.3039 (mtp) REVERT: N 288 TYR cc_start: 0.3433 (OUTLIER) cc_final: 0.3139 (t80) REVERT: N 426 ARG cc_start: 0.3574 (OUTLIER) cc_final: 0.3287 (tpp80) REVERT: O 273 MET cc_start: 0.4987 (mmm) cc_final: 0.4647 (mpm) REVERT: O 288 TYR cc_start: 0.3609 (OUTLIER) cc_final: 0.3149 (t80) REVERT: P 49 MET cc_start: 0.4965 (OUTLIER) cc_final: 0.4458 (pmm) REVERT: P 404 GLU cc_start: 0.3121 (OUTLIER) cc_final: 0.2590 (tt0) REVERT: Q 9 MET cc_start: 0.4503 (OUTLIER) cc_final: 0.3089 (mtp) REVERT: Q 288 TYR cc_start: 0.3317 (OUTLIER) cc_final: 0.3081 (t80) REVERT: Q 426 ARG cc_start: 0.3538 (OUTLIER) cc_final: 0.3244 (tpp80) REVERT: R 273 MET cc_start: 0.4969 (mmm) cc_final: 0.4632 (mpm) REVERT: R 288 TYR cc_start: 0.3609 (OUTLIER) cc_final: 0.3198 (t80) REVERT: S 273 MET cc_start: 0.2790 (OUTLIER) cc_final: 0.2554 (mtp) REVERT: S 453 ARG cc_start: 0.5702 (OUTLIER) cc_final: 0.3940 (ttm-80) outliers start: 142 outliers final: 55 residues processed: 821 average time/residue: 1.7524 time to fit residues: 1883.0126 Evaluate side-chains 759 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 674 time to evaluate : 6.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 391 GLU Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 391 GLU Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 212 HIS Chi-restraints excluded: chain G residue 227 ASN Chi-restraints excluded: chain G residue 249 ARG Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 103 ARG Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain H residue 449 GLU Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 154 ASP Chi-restraints excluded: chain J residue 227 ASN Chi-restraints excluded: chain J residue 249 ARG Chi-restraints excluded: chain J residue 331 VAL Chi-restraints excluded: chain J residue 400 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 103 ARG Chi-restraints excluded: chain K residue 249 ARG Chi-restraints excluded: chain K residue 296 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 331 VAL Chi-restraints excluded: chain M residue 9 MET Chi-restraints excluded: chain M residue 49 MET Chi-restraints excluded: chain M residue 62 ASN Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 153 ASP Chi-restraints excluded: chain M residue 202 GLN Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 404 GLU Chi-restraints excluded: chain N residue 9 MET Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 153 ASP Chi-restraints excluded: chain N residue 288 TYR Chi-restraints excluded: chain N residue 426 ARG Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 153 ASP Chi-restraints excluded: chain O residue 198 LEU Chi-restraints excluded: chain O residue 288 TYR Chi-restraints excluded: chain P residue 9 MET Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain P residue 62 ASN Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 153 ASP Chi-restraints excluded: chain P residue 222 VAL Chi-restraints excluded: chain P residue 404 GLU Chi-restraints excluded: chain Q residue 9 MET Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 153 ASP Chi-restraints excluded: chain Q residue 288 TYR Chi-restraints excluded: chain Q residue 426 ARG Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 288 TYR Chi-restraints excluded: chain S residue 273 MET Chi-restraints excluded: chain S residue 453 ARG Chi-restraints excluded: chain V residue 214 VAL Chi-restraints excluded: chain X residue 214 VAL Chi-restraints excluded: chain Y residue 1 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 904 optimal weight: 0.0970 chunk 952 optimal weight: 50.0000 chunk 869 optimal weight: 0.7980 chunk 926 optimal weight: 40.0000 chunk 557 optimal weight: 40.0000 chunk 403 optimal weight: 0.9990 chunk 727 optimal weight: 0.2980 chunk 284 optimal weight: 0.7980 chunk 837 optimal weight: 40.0000 chunk 876 optimal weight: 6.9990 chunk 923 optimal weight: 8.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 HIS ** G 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 ASN ** H 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 GLN ** K 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 227 ASN ** K 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 GLN ** L 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 278 ASN ** M 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 459 HIS ** P 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 83280 Z= 0.155 Angle : 0.568 13.671 112656 Z= 0.276 Chirality : 0.042 0.219 12264 Planarity : 0.004 0.051 14904 Dihedral : 4.168 26.540 11280 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.34 % Allowed : 18.06 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.08), residues: 10344 helix: 2.10 (0.09), residues: 3672 sheet: -0.58 (0.10), residues: 2328 loop : -0.82 (0.09), residues: 4344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP R 58 HIS 0.007 0.001 HIS B 212 PHE 0.058 0.001 PHE X 428 TYR 0.022 0.001 TYR A 297 ARG 0.009 0.000 ARG J 225 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20688 Ramachandran restraints generated. 10344 Oldfield, 0 Emsley, 10344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20688 Ramachandran restraints generated. 10344 Oldfield, 0 Emsley, 10344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 716 time to evaluate : 7.023 Fit side-chains revert: symmetry clash REVERT: A 269 MET cc_start: 0.8843 (ttm) cc_final: 0.8623 (ttp) REVERT: A 427 GLU cc_start: 0.6458 (mp0) cc_final: 0.6243 (mp0) REVERT: A 456 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6921 (mtt) REVERT: B 231 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8123 (mttt) REVERT: B 385 ASN cc_start: 0.8083 (m-40) cc_final: 0.7858 (m-40) REVERT: C 103 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7733 (mtt-85) REVERT: D 269 MET cc_start: 0.8839 (ttm) cc_final: 0.8621 (ttp) REVERT: F 103 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7733 (mtt-85) REVERT: G 42 GLU cc_start: 0.7055 (tp30) cc_final: 0.6725 (tp30) REVERT: G 46 GLU cc_start: 0.7178 (pt0) cc_final: 0.6955 (pt0) REVERT: G 249 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7797 (ptp-170) REVERT: H 103 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7840 (mtt90) REVERT: H 249 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7733 (ptp-170) REVERT: I 103 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7798 (mtt90) REVERT: I 231 LYS cc_start: 0.8145 (ttmm) cc_final: 0.7742 (tttt) REVERT: J 249 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7960 (ptp-170) REVERT: J 261 MET cc_start: 0.7486 (mtm) cc_final: 0.7285 (mtp) REVERT: J 400 LEU cc_start: 0.2275 (OUTLIER) cc_final: 0.1858 (tt) REVERT: K 1 MET cc_start: 0.6692 (OUTLIER) cc_final: 0.5377 (tmm) REVERT: K 249 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7766 (ptp-170) REVERT: K 296 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8314 (mm) REVERT: K 384 LYS cc_start: 0.8053 (ttmm) cc_final: 0.7710 (ttmm) REVERT: L 24 ASP cc_start: 0.7211 (m-30) cc_final: 0.6499 (m-30) REVERT: L 66 MET cc_start: 0.7565 (mtp) cc_final: 0.7350 (mmm) REVERT: L 231 LYS cc_start: 0.8129 (ttmm) cc_final: 0.7797 (tttt) REVERT: M 9 MET cc_start: 0.3145 (OUTLIER) cc_final: 0.2165 (mtp) REVERT: M 49 MET cc_start: 0.4848 (OUTLIER) cc_final: 0.4510 (pmm) REVERT: M 404 GLU cc_start: 0.3245 (OUTLIER) cc_final: 0.2842 (tt0) REVERT: N 9 MET cc_start: 0.4181 (OUTLIER) cc_final: 0.2881 (mtp) REVERT: N 288 TYR cc_start: 0.3199 (OUTLIER) cc_final: 0.2893 (t80) REVERT: O 273 MET cc_start: 0.4887 (mmm) cc_final: 0.4543 (mpm) REVERT: O 288 TYR cc_start: 0.3585 (OUTLIER) cc_final: 0.3079 (t80) REVERT: P 9 MET cc_start: 0.3274 (OUTLIER) cc_final: 0.2265 (mtp) REVERT: P 49 MET cc_start: 0.4769 (OUTLIER) cc_final: 0.4396 (pmm) REVERT: P 332 MET cc_start: 0.2496 (ptt) cc_final: 0.2283 (ptt) REVERT: P 404 GLU cc_start: 0.3159 (OUTLIER) cc_final: 0.2729 (tt0) REVERT: Q 9 MET cc_start: 0.3827 (OUTLIER) cc_final: 0.2563 (mtp) REVERT: Q 288 TYR cc_start: 0.3186 (OUTLIER) cc_final: 0.2885 (t80) REVERT: R 9 MET cc_start: 0.3466 (OUTLIER) cc_final: 0.2339 (mtp) REVERT: R 273 MET cc_start: 0.4860 (mmm) cc_final: 0.4517 (mpm) REVERT: R 288 TYR cc_start: 0.3701 (OUTLIER) cc_final: 0.3189 (t80) REVERT: S 273 MET cc_start: 0.2750 (OUTLIER) cc_final: 0.2519 (mtp) REVERT: S 453 ARG cc_start: 0.5698 (OUTLIER) cc_final: 0.3896 (ttm-80) REVERT: V 332 MET cc_start: 0.4835 (pmm) cc_final: 0.4558 (pmm) REVERT: W 453 ARG cc_start: 0.5763 (OUTLIER) cc_final: 0.4145 (ttm-80) REVERT: Y 453 ARG cc_start: 0.5798 (OUTLIER) cc_final: 0.4209 (ttm-80) outliers start: 116 outliers final: 51 residues processed: 802 average time/residue: 1.7079 time to fit residues: 1803.2086 Evaluate side-chains 756 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 675 time to evaluate : 6.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 391 GLU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 249 ARG Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 103 ARG Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain H residue 449 GLU Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 154 ASP Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 249 ARG Chi-restraints excluded: chain J residue 331 VAL Chi-restraints excluded: chain J residue 400 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 249 ARG Chi-restraints excluded: chain K residue 296 LEU Chi-restraints excluded: chain K residue 449 GLU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 331 VAL Chi-restraints excluded: chain M residue 9 MET Chi-restraints excluded: chain M residue 49 MET Chi-restraints excluded: chain M residue 62 ASN Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 153 ASP Chi-restraints excluded: chain M residue 202 GLN Chi-restraints excluded: chain M residue 404 GLU Chi-restraints excluded: chain N residue 9 MET Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 153 ASP Chi-restraints excluded: chain N residue 288 TYR Chi-restraints excluded: chain O residue 9 MET Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 153 ASP Chi-restraints excluded: chain O residue 198 LEU Chi-restraints excluded: chain O residue 288 TYR Chi-restraints excluded: chain P residue 9 MET Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain P residue 62 ASN Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 153 ASP Chi-restraints excluded: chain P residue 222 VAL Chi-restraints excluded: chain P residue 404 GLU Chi-restraints excluded: chain Q residue 9 MET Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 153 ASP Chi-restraints excluded: chain Q residue 288 TYR Chi-restraints excluded: chain R residue 9 MET Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 288 TYR Chi-restraints excluded: chain S residue 273 MET Chi-restraints excluded: chain S residue 453 ARG Chi-restraints excluded: chain V residue 214 VAL Chi-restraints excluded: chain W residue 453 ARG Chi-restraints excluded: chain X residue 214 VAL Chi-restraints excluded: chain Y residue 453 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 608 optimal weight: 1.9990 chunk 980 optimal weight: 50.0000 chunk 598 optimal weight: 7.9990 chunk 464 optimal weight: 8.9990 chunk 681 optimal weight: 10.0000 chunk 1028 optimal weight: 4.9990 chunk 946 optimal weight: 50.0000 chunk 818 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 632 optimal weight: 50.0000 chunk 502 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 HIS G 30 GLN ** G 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 ASN ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 GLN ** K 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 227 ASN ** L 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 HIS ** N 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 149 HIS ** O 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 5 HIS ** P 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 149 HIS ** Q 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6169 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 83280 Z= 0.386 Angle : 0.651 14.415 112656 Z= 0.321 Chirality : 0.047 0.300 12264 Planarity : 0.005 0.050 14904 Dihedral : 4.484 26.254 11280 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.38 % Allowed : 18.28 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.08), residues: 10344 helix: 1.82 (0.09), residues: 3672 sheet: -0.66 (0.11), residues: 2328 loop : -0.94 (0.09), residues: 4344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 58 HIS 0.009 0.001 HIS O 149 PHE 0.050 0.002 PHE X 428 TYR 0.029 0.002 TYR A 297 ARG 0.008 0.001 ARG I 225 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20688 Ramachandran restraints generated. 10344 Oldfield, 0 Emsley, 10344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20688 Ramachandran restraints generated. 10344 Oldfield, 0 Emsley, 10344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 697 time to evaluate : 7.037 Fit side-chains revert: symmetry clash REVERT: A 138 ASP cc_start: 0.7015 (OUTLIER) cc_final: 0.6497 (t0) REVERT: A 427 GLU cc_start: 0.6590 (mp0) cc_final: 0.6344 (mp0) REVERT: A 456 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.7009 (mtt) REVERT: C 103 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7715 (mtt-85) REVERT: D 269 MET cc_start: 0.8957 (ttm) cc_final: 0.8728 (ttp) REVERT: F 103 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7697 (mtt-85) REVERT: G 249 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7827 (ptp-170) REVERT: H 42 GLU cc_start: 0.6965 (tp30) cc_final: 0.6653 (tp30) REVERT: H 249 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7700 (ptp-170) REVERT: H 384 LYS cc_start: 0.8106 (ttmm) cc_final: 0.7751 (ttmm) REVERT: I 103 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7862 (mtt90) REVERT: I 231 LYS cc_start: 0.8330 (ttmm) cc_final: 0.7933 (tttt) REVERT: J 249 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8091 (ptp-170) REVERT: J 400 LEU cc_start: 0.2426 (OUTLIER) cc_final: 0.1950 (tt) REVERT: K 1 MET cc_start: 0.6825 (OUTLIER) cc_final: 0.5462 (tmm) REVERT: K 249 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7825 (ptp-170) REVERT: K 296 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8463 (mm) REVERT: K 297 TYR cc_start: 0.7152 (m-10) cc_final: 0.6948 (m-10) REVERT: K 384 LYS cc_start: 0.8045 (ttmm) cc_final: 0.7720 (ttmm) REVERT: L 231 LYS cc_start: 0.8304 (ttmm) cc_final: 0.7932 (tttt) REVERT: M 9 MET cc_start: 0.3157 (OUTLIER) cc_final: 0.2153 (mtp) REVERT: M 49 MET cc_start: 0.5139 (OUTLIER) cc_final: 0.4688 (pmm) REVERT: M 66 MET cc_start: 0.5455 (tpp) cc_final: 0.3732 (tpp) REVERT: M 404 GLU cc_start: 0.3263 (OUTLIER) cc_final: 0.2826 (tt0) REVERT: N 9 MET cc_start: 0.4323 (OUTLIER) cc_final: 0.3012 (mtp) REVERT: N 288 TYR cc_start: 0.3243 (OUTLIER) cc_final: 0.2942 (t80) REVERT: O 9 MET cc_start: 0.3877 (OUTLIER) cc_final: 0.2763 (mtp) REVERT: O 288 TYR cc_start: 0.3668 (OUTLIER) cc_final: 0.3122 (t80) REVERT: P 9 MET cc_start: 0.3278 (OUTLIER) cc_final: 0.2305 (mtp) REVERT: P 49 MET cc_start: 0.5087 (OUTLIER) cc_final: 0.4647 (pmm) REVERT: P 404 GLU cc_start: 0.3365 (OUTLIER) cc_final: 0.2803 (tt0) REVERT: Q 9 MET cc_start: 0.3920 (OUTLIER) cc_final: 0.2676 (mtp) REVERT: Q 49 MET cc_start: 0.4392 (OUTLIER) cc_final: 0.4165 (pmm) REVERT: Q 288 TYR cc_start: 0.3231 (OUTLIER) cc_final: 0.2958 (t80) REVERT: R 9 MET cc_start: 0.3281 (OUTLIER) cc_final: 0.2197 (mtp) REVERT: R 288 TYR cc_start: 0.3702 (OUTLIER) cc_final: 0.3162 (t80) REVERT: S 273 MET cc_start: 0.2768 (OUTLIER) cc_final: 0.2472 (mtp) REVERT: S 453 ARG cc_start: 0.5741 (OUTLIER) cc_final: 0.4177 (ttm-80) REVERT: U 273 MET cc_start: 0.2774 (OUTLIER) cc_final: 0.2512 (mtp) REVERT: V 332 MET cc_start: 0.4854 (pmm) cc_final: 0.4578 (pmm) REVERT: W 453 ARG cc_start: 0.5829 (OUTLIER) cc_final: 0.4418 (ttm-80) REVERT: X 388 HIS cc_start: 0.3405 (OUTLIER) cc_final: 0.3173 (t-90) REVERT: Y 453 ARG cc_start: 0.5868 (OUTLIER) cc_final: 0.4380 (ttm-80) outliers start: 120 outliers final: 56 residues processed: 785 average time/residue: 1.7381 time to fit residues: 1785.0936 Evaluate side-chains 771 residues out of total 8688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 682 time to evaluate : 6.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 391 GLU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 212 HIS Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 249 ARG Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 154 ASP Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 249 ARG Chi-restraints excluded: chain J residue 331 VAL Chi-restraints excluded: chain J residue 400 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 249 ARG Chi-restraints excluded: chain K residue 296 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 331 VAL Chi-restraints excluded: chain M residue 9 MET Chi-restraints excluded: chain M residue 49 MET Chi-restraints excluded: chain M residue 62 ASN Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 153 ASP Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 404 GLU Chi-restraints excluded: chain N residue 9 MET Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 153 ASP Chi-restraints excluded: chain N residue 288 TYR Chi-restraints excluded: chain O residue 9 MET Chi-restraints excluded: chain O residue 62 ASN Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 153 ASP Chi-restraints excluded: chain O residue 198 LEU Chi-restraints excluded: chain O residue 222 VAL Chi-restraints excluded: chain O residue 288 TYR Chi-restraints excluded: chain P residue 9 MET Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain P residue 62 ASN Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 153 ASP Chi-restraints excluded: chain P residue 222 VAL Chi-restraints excluded: chain P residue 404 GLU Chi-restraints excluded: chain Q residue 9 MET Chi-restraints excluded: chain Q residue 49 MET Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 153 ASP Chi-restraints excluded: chain Q residue 288 TYR Chi-restraints excluded: chain R residue 9 MET Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 288 TYR Chi-restraints excluded: chain S residue 273 MET Chi-restraints excluded: chain S residue 453 ARG Chi-restraints excluded: chain U residue 273 MET Chi-restraints excluded: chain V residue 214 VAL Chi-restraints excluded: chain W residue 400 LEU Chi-restraints excluded: chain W residue 453 ARG Chi-restraints excluded: chain X residue 214 VAL Chi-restraints excluded: chain X residue 388 HIS Chi-restraints excluded: chain Y residue 453 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 650 optimal weight: 10.0000 chunk 872 optimal weight: 50.0000 chunk 250 optimal weight: 2.9990 chunk 754 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 227 optimal weight: 0.9980 chunk 820 optimal weight: 20.0000 chunk 343 optimal weight: 0.8980 chunk 842 optimal weight: 20.0000 chunk 103 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 HIS ** G 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 ASN ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 227 ASN ** J 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 GLN ** K 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 211 HIS K 227 ASN ** L 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 211 HIS L 227 ASN ** M 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 272 HIS ** M 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 272 HIS ** P 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 272 HIS ** P 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 219 GLN ** X 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.229722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.144414 restraints weight = 96019.880| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 3.31 r_work: 0.3358 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 83280 Z= 0.203 Angle : 0.609 13.690 112656 Z= 0.295 Chirality : 0.044 0.301 12264 Planarity : 0.004 0.052 14904 Dihedral : 4.273 27.614 11280 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.13 % Allowed : 18.78 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.08), residues: 10344 helix: 1.96 (0.09), residues: 3672 sheet: -0.61 (0.10), residues: 2328 loop : -0.88 (0.09), residues: 4344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP V 58 HIS 0.007 0.001 HIS E 212 PHE 0.047 0.001 PHE X 428 TYR 0.017 0.001 TYR P 239 ARG 0.008 0.000 ARG I 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29324.57 seconds wall clock time: 510 minutes 38.60 seconds (30638.60 seconds total)