Starting phenix.real_space_refine on Sun Mar 24 08:04:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jco_8150/03_2024/5jco_8150_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jco_8150/03_2024/5jco_8150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jco_8150/03_2024/5jco_8150.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jco_8150/03_2024/5jco_8150.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jco_8150/03_2024/5jco_8150_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jco_8150/03_2024/5jco_8150_updated.pdb" } resolution = 4.0 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= 0.004 sd= 0.016 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: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 276 5.16 5 C 25488 2.51 5 N 6912 2.21 5 O 7788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K GLU 3": "OE1" <-> "OE2" Residue "K GLU 27": "OE1" <-> "OE2" Residue "K ASP 41": "OD1" <-> "OD2" Residue "K GLU 53": "OE1" <-> "OE2" Residue "K ASP 74": "OD1" <-> "OD2" Residue "K ARG 77": "NH1" <-> "NH2" Residue "K PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 88": "OD1" <-> "OD2" Residue "K PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 111": "OE1" <-> "OE2" Residue "K ASP 114": "OD1" <-> "OD2" Residue "K ASP 128": "OD1" <-> "OD2" Residue "K GLU 158": "OE1" <-> "OE2" Residue "K TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 197": "OD1" <-> "OD2" Residue "K GLU 198": "OE1" <-> "OE2" Residue "K TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 288": "OE1" <-> "OE2" Residue "K ASP 304": "OD1" <-> "OD2" Residue "K ASP 355": "OD1" <-> "OD2" Residue "K PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H ASP 47": "OD1" <-> "OD2" Residue "H PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 64": "NH1" <-> "NH2" Residue "H TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H GLU 90": "OE1" <-> "OE2" Residue "H ASP 98": "OD1" <-> "OD2" Residue "H TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 168": "OE1" <-> "OE2" Residue "H TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 199": "OD1" <-> "OD2" Residue "H TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 308": "NH1" <-> "NH2" Residue "H ARG 320": "NH1" <-> "NH2" Residue "H ARG 339": "NH1" <-> "NH2" Residue "H PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 373": "NH1" <-> "NH2" Residue "H GLU 386": "OE1" <-> "OE2" Residue "H GLU 414": "OE1" <-> "OE2" Residue "H GLU 429": "OE1" <-> "OE2" Residue "H TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 433": "OE1" <-> "OE2" Residue "H GLU 434": "OE1" <-> "OE2" Residue "I GLU 3": "OE1" <-> "OE2" Residue "I GLU 27": "OE1" <-> "OE2" Residue "I ASP 41": "OD1" <-> "OD2" Residue "I GLU 53": "OE1" <-> "OE2" Residue "I ASP 74": "OD1" <-> "OD2" Residue "I ARG 77": "NH1" <-> "NH2" Residue "I PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 88": "OD1" <-> "OD2" Residue "I PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 111": "OE1" <-> "OE2" Residue "I ASP 114": "OD1" <-> "OD2" Residue "I ASP 128": "OD1" <-> "OD2" Residue "I GLU 158": "OE1" <-> "OE2" Residue "I TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 197": "OD1" <-> "OD2" Residue "I GLU 198": "OE1" <-> "OE2" Residue "I TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 288": "OE1" <-> "OE2" Residue "I ASP 304": "OD1" <-> "OD2" Residue "I ASP 355": "OD1" <-> "OD2" Residue "I PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E ASP 47": "OD1" <-> "OD2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 64": "NH1" <-> "NH2" Residue "E TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E GLU 90": "OE1" <-> "OE2" Residue "E ASP 98": "OD1" <-> "OD2" Residue "E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 168": "OE1" <-> "OE2" Residue "E TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 199": "OD1" <-> "OD2" Residue "E TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 308": "NH1" <-> "NH2" Residue "E ARG 320": "NH1" <-> "NH2" Residue "E ARG 339": "NH1" <-> "NH2" Residue "E PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 373": "NH1" <-> "NH2" Residue "E GLU 386": "OE1" <-> "OE2" Residue "E GLU 414": "OE1" <-> "OE2" Residue "E GLU 429": "OE1" <-> "OE2" Residue "E TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 433": "OE1" <-> "OE2" Residue "E GLU 434": "OE1" <-> "OE2" Residue "J GLU 3": "OE1" <-> "OE2" Residue "J GLU 27": "OE1" <-> "OE2" Residue "J ASP 41": "OD1" <-> "OD2" Residue "J GLU 53": "OE1" <-> "OE2" Residue "J ASP 74": "OD1" <-> "OD2" Residue "J ARG 77": "NH1" <-> "NH2" Residue "J PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 88": "OD1" <-> "OD2" Residue "J PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 111": "OE1" <-> "OE2" Residue "J ASP 114": "OD1" <-> "OD2" Residue "J ASP 128": "OD1" <-> "OD2" Residue "J GLU 158": "OE1" <-> "OE2" Residue "J TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 197": "OD1" <-> "OD2" Residue "J GLU 198": "OE1" <-> "OE2" Residue "J TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 288": "OE1" <-> "OE2" Residue "J ASP 304": "OD1" <-> "OD2" Residue "J ASP 355": "OD1" <-> "OD2" Residue "J PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3": "OE1" <-> "OE2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C ASP 41": "OD1" <-> "OD2" Residue "C GLU 53": "OE1" <-> "OE2" Residue "C ASP 74": "OD1" <-> "OD2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C ASP 114": "OD1" <-> "OD2" Residue "C ASP 128": "OD1" <-> "OD2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 197": "OD1" <-> "OD2" Residue "C GLU 198": "OE1" <-> "OE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 288": "OE1" <-> "OE2" Residue "C ASP 304": "OD1" <-> "OD2" Residue "C ASP 355": "OD1" <-> "OD2" Residue "C PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3": "OE1" <-> "OE2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "D ASP 41": "OD1" <-> "OD2" Residue "D GLU 53": "OE1" <-> "OE2" Residue "D ASP 74": "OD1" <-> "OD2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 88": "OD1" <-> "OD2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 111": "OE1" <-> "OE2" Residue "D ASP 114": "OD1" <-> "OD2" Residue "D ASP 128": "OD1" <-> "OD2" Residue "D GLU 158": "OE1" <-> "OE2" Residue "D TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 197": "OD1" <-> "OD2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 288": "OE1" <-> "OE2" Residue "D ASP 304": "OD1" <-> "OD2" Residue "D ASP 355": "OD1" <-> "OD2" Residue "D PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 27": "OE1" <-> "OE2" Residue "F ASP 47": "OD1" <-> "OD2" Residue "F PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 64": "NH1" <-> "NH2" Residue "F TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 84": "NH1" <-> "NH2" Residue "F GLU 90": "OE1" <-> "OE2" Residue "F ASP 98": "OD1" <-> "OD2" Residue "F TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 168": "OE1" <-> "OE2" Residue "F TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 199": "OD1" <-> "OD2" Residue "F TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 308": "NH1" <-> "NH2" Residue "F ARG 320": "NH1" <-> "NH2" Residue "F ARG 339": "NH1" <-> "NH2" Residue "F PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 373": "NH1" <-> "NH2" Residue "F GLU 386": "OE1" <-> "OE2" Residue "F GLU 414": "OE1" <-> "OE2" Residue "F GLU 429": "OE1" <-> "OE2" Residue "F TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 433": "OE1" <-> "OE2" Residue "F GLU 434": "OE1" <-> "OE2" Residue "A TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ASP 47": "OD1" <-> "OD2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 168": "OE1" <-> "OE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 199": "OD1" <-> "OD2" Residue "A TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A ARG 320": "NH1" <-> "NH2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 373": "NH1" <-> "NH2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "B TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B ASP 47": "OD1" <-> "OD2" Residue "B PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 64": "NH1" <-> "NH2" Residue "B TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B ASP 98": "OD1" <-> "OD2" Residue "B TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 168": "OE1" <-> "OE2" Residue "B TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 199": "OD1" <-> "OD2" Residue "B TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 308": "NH1" <-> "NH2" Residue "B ARG 320": "NH1" <-> "NH2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 373": "NH1" <-> "NH2" Residue "B GLU 386": "OE1" <-> "OE2" Residue "B GLU 414": "OE1" <-> "OE2" Residue "B GLU 429": "OE1" <-> "OE2" Residue "B TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 433": "OE1" <-> "OE2" Residue "B GLU 434": "OE1" <-> "OE2" Residue "L GLU 3": "OE1" <-> "OE2" Residue "L GLU 27": "OE1" <-> "OE2" Residue "L ASP 41": "OD1" <-> "OD2" Residue "L GLU 53": "OE1" <-> "OE2" Residue "L ASP 74": "OD1" <-> "OD2" Residue "L ARG 77": "NH1" <-> "NH2" Residue "L PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 88": "OD1" <-> "OD2" Residue "L PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 111": "OE1" <-> "OE2" Residue "L ASP 114": "OD1" <-> "OD2" Residue "L ASP 128": "OD1" <-> "OD2" Residue "L GLU 158": "OE1" <-> "OE2" Residue "L TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 197": "OD1" <-> "OD2" Residue "L GLU 198": "OE1" <-> "OE2" Residue "L TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 288": "OE1" <-> "OE2" Residue "L ASP 304": "OD1" <-> "OD2" Residue "L ASP 355": "OD1" <-> "OD2" Residue "L PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 27": "OE1" <-> "OE2" Residue "G ASP 47": "OD1" <-> "OD2" Residue "G PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 64": "NH1" <-> "NH2" Residue "G TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 84": "NH1" <-> "NH2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G ASP 98": "OD1" <-> "OD2" Residue "G TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 168": "OE1" <-> "OE2" Residue "G TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 199": "OD1" <-> "OD2" Residue "G TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 308": "NH1" <-> "NH2" Residue "G ARG 320": "NH1" <-> "NH2" Residue "G ARG 339": "NH1" <-> "NH2" Residue "G PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 373": "NH1" <-> "NH2" Residue "G GLU 386": "OE1" <-> "OE2" Residue "G GLU 414": "OE1" <-> "OE2" Residue "G GLU 429": "OE1" <-> "OE2" Residue "G TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 433": "OE1" <-> "OE2" Residue "G GLU 434": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40512 Number of models: 1 Model: "" Number of chains: 24 Chain: "K" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3341 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3345 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3341 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3345 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3341 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3341 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3341 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3345 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3345 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3345 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3341 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3345 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.34, per 1000 atoms: 0.50 Number of scatterers: 40512 At special positions: 0 Unit cell: (174.46, 86.62, 213.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 276 16.00 P 36 15.00 Mg 12 11.99 O 7788 8.00 N 6912 7.00 C 25488 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: 14.95 Conformation dependent library (CDL) restraints added in 6.4 seconds 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9492 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 252 helices and 30 sheets defined 49.3% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.67 Creating SS restraints... Processing helix chain 'K' and resid 10 through 27 Processing helix chain 'K' and resid 41 through 45 Processing helix chain 'K' and resid 47 through 49 No H-bonds generated for 'chain 'K' and resid 47 through 49' Processing helix chain 'K' and resid 55 through 57 No H-bonds generated for 'chain 'K' and resid 55 through 57' Processing helix chain 'K' and resid 70 through 78 Processing helix chain 'K' and resid 82 through 84 No H-bonds generated for 'chain 'K' and resid 82 through 84' Processing helix chain 'K' and resid 87 through 89 No H-bonds generated for 'chain 'K' and resid 87 through 89' Processing helix chain 'K' and resid 101 through 105 Processing helix chain 'K' and resid 109 through 126 removed outlier: 4.451A pdb=" N ASP K 114 " --> pdb=" O ALA K 110 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N SER K 115 " --> pdb=" O GLU K 111 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL K 116 " --> pdb=" O LEU K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 158 removed outlier: 3.717A pdb=" N GLY K 148 " --> pdb=" O GLY K 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 195 removed outlier: 3.836A pdb=" N GLU K 194 " --> pdb=" O HIS K 190 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN K 195 " --> pdb=" O GLN K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 204 through 213 Processing helix chain 'K' and resid 222 through 236 removed outlier: 3.727A pdb=" N LEU K 228 " --> pdb=" O ASP K 224 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL K 229 " --> pdb=" O LEU K 225 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 241 No H-bonds generated for 'chain 'K' and resid 238 through 241' Processing helix chain 'K' and resid 250 through 257 Processing helix chain 'K' and resid 286 through 293 Processing helix chain 'K' and resid 296 through 298 No H-bonds generated for 'chain 'K' and resid 296 through 298' Processing helix chain 'K' and resid 305 through 307 No H-bonds generated for 'chain 'K' and resid 305 through 307' Processing helix chain 'K' and resid 323 through 336 Processing helix chain 'K' and resid 338 through 340 No H-bonds generated for 'chain 'K' and resid 338 through 340' Processing helix chain 'K' and resid 372 through 391 removed outlier: 3.656A pdb=" N ARG K 380 " --> pdb=" O LEU K 377 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG K 390 " --> pdb=" O ALA K 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 395 through 401 removed outlier: 3.545A pdb=" N GLU K 401 " --> pdb=" O TRP K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 425 Processing helix chain 'H' and resid 10 through 27 Processing helix chain 'H' and resid 48 through 51 removed outlier: 3.835A pdb=" N THR H 51 " --> pdb=" O SER H 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 48 through 51' Processing helix chain 'H' and resid 73 through 79 removed outlier: 3.575A pdb=" N GLU H 77 " --> pdb=" O THR H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 91 No H-bonds generated for 'chain 'H' and resid 89 through 91' Processing helix chain 'H' and resid 103 through 107 Processing helix chain 'H' and resid 111 through 128 removed outlier: 5.284A pdb=" N ASP H 116 " --> pdb=" O LYS H 112 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 160 removed outlier: 4.393A pdb=" N THR H 150 " --> pdb=" O GLY H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 177 No H-bonds generated for 'chain 'H' and resid 175 through 177' Processing helix chain 'H' and resid 183 through 197 removed outlier: 4.166A pdb=" N GLU H 196 " --> pdb=" O HIS H 192 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N HIS H 197 " --> pdb=" O THR H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 216 Processing helix chain 'H' and resid 224 through 243 removed outlier: 3.592A pdb=" N ARG H 229 " --> pdb=" O THR H 225 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU H 230 " --> pdb=" O ASN H 226 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N SER H 241 " --> pdb=" O SER H 237 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU H 242 " --> pdb=" O ILE H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 259 removed outlier: 3.574A pdb=" N GLN H 256 " --> pdb=" O LEU H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 283 Processing helix chain 'H' and resid 288 through 296 Processing helix chain 'H' and resid 298 through 300 No H-bonds generated for 'chain 'H' and resid 298 through 300' Processing helix chain 'H' and resid 325 through 337 Processing helix chain 'H' and resid 382 through 401 removed outlier: 3.653A pdb=" N LEU H 397 " --> pdb=" O LYS H 394 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR H 399 " --> pdb=" O ASP H 396 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 411 removed outlier: 3.662A pdb=" N GLU H 411 " --> pdb=" O TRP H 407 " (cutoff:3.500A) Processing helix chain 'H' and resid 415 through 435 removed outlier: 3.826A pdb=" N SER H 419 " --> pdb=" O GLU H 415 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 27 Processing helix chain 'I' and resid 41 through 45 Processing helix chain 'I' and resid 47 through 49 No H-bonds generated for 'chain 'I' and resid 47 through 49' Processing helix chain 'I' and resid 55 through 57 No H-bonds generated for 'chain 'I' and resid 55 through 57' Processing helix chain 'I' and resid 70 through 78 Processing helix chain 'I' and resid 82 through 84 No H-bonds generated for 'chain 'I' and resid 82 through 84' Processing helix chain 'I' and resid 87 through 89 No H-bonds generated for 'chain 'I' and resid 87 through 89' Processing helix chain 'I' and resid 101 through 105 Processing helix chain 'I' and resid 109 through 126 removed outlier: 4.452A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N SER I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL I 116 " --> pdb=" O LEU I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 158 removed outlier: 3.718A pdb=" N GLY I 148 " --> pdb=" O GLY I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 195 removed outlier: 3.834A pdb=" N GLU I 194 " --> pdb=" O HIS I 190 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN I 195 " --> pdb=" O GLN I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 213 Processing helix chain 'I' and resid 222 through 236 removed outlier: 3.728A pdb=" N LEU I 228 " --> pdb=" O ASP I 224 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL I 229 " --> pdb=" O LEU I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 241 No H-bonds generated for 'chain 'I' and resid 238 through 241' Processing helix chain 'I' and resid 250 through 257 Processing helix chain 'I' and resid 286 through 293 Processing helix chain 'I' and resid 296 through 298 No H-bonds generated for 'chain 'I' and resid 296 through 298' Processing helix chain 'I' and resid 305 through 307 No H-bonds generated for 'chain 'I' and resid 305 through 307' Processing helix chain 'I' and resid 323 through 336 Processing helix chain 'I' and resid 338 through 340 No H-bonds generated for 'chain 'I' and resid 338 through 340' Processing helix chain 'I' and resid 372 through 391 removed outlier: 3.656A pdb=" N ARG I 380 " --> pdb=" O LEU I 377 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG I 390 " --> pdb=" O ALA I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 401 removed outlier: 3.545A pdb=" N GLU I 401 " --> pdb=" O TRP I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 425 Processing helix chain 'E' and resid 10 through 27 Processing helix chain 'E' and resid 48 through 51 removed outlier: 3.834A pdb=" N THR E 51 " --> pdb=" O SER E 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 48 through 51' Processing helix chain 'E' and resid 73 through 79 removed outlier: 3.575A pdb=" N GLU E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 111 through 128 removed outlier: 5.284A pdb=" N ASP E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEU E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 160 removed outlier: 4.395A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 183 through 197 removed outlier: 4.168A pdb=" N GLU E 196 " --> pdb=" O HIS E 192 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N HIS E 197 " --> pdb=" O THR E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 216 Processing helix chain 'E' and resid 224 through 243 removed outlier: 3.592A pdb=" N ARG E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU E 230 " --> pdb=" O ASN E 226 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 259 removed outlier: 3.575A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 283 Processing helix chain 'E' and resid 288 through 296 Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' Processing helix chain 'E' and resid 325 through 337 Processing helix chain 'E' and resid 382 through 401 removed outlier: 3.654A pdb=" N LEU E 397 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR E 399 " --> pdb=" O ASP E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 411 removed outlier: 3.661A pdb=" N GLU E 411 " --> pdb=" O TRP E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 435 removed outlier: 3.825A pdb=" N SER E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 27 Processing helix chain 'J' and resid 41 through 45 Processing helix chain 'J' and resid 47 through 49 No H-bonds generated for 'chain 'J' and resid 47 through 49' Processing helix chain 'J' and resid 55 through 57 No H-bonds generated for 'chain 'J' and resid 55 through 57' Processing helix chain 'J' and resid 70 through 78 Processing helix chain 'J' and resid 82 through 84 No H-bonds generated for 'chain 'J' and resid 82 through 84' Processing helix chain 'J' and resid 87 through 89 No H-bonds generated for 'chain 'J' and resid 87 through 89' Processing helix chain 'J' and resid 101 through 105 Processing helix chain 'J' and resid 109 through 126 removed outlier: 4.450A pdb=" N ASP J 114 " --> pdb=" O ALA J 110 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N SER J 115 " --> pdb=" O GLU J 111 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL J 116 " --> pdb=" O LEU J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 158 removed outlier: 3.718A pdb=" N GLY J 148 " --> pdb=" O GLY J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 195 removed outlier: 3.837A pdb=" N GLU J 194 " --> pdb=" O HIS J 190 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN J 195 " --> pdb=" O GLN J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 204 through 213 Processing helix chain 'J' and resid 222 through 236 removed outlier: 3.727A pdb=" N LEU J 228 " --> pdb=" O ASP J 224 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL J 229 " --> pdb=" O LEU J 225 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 241 No H-bonds generated for 'chain 'J' and resid 238 through 241' Processing helix chain 'J' and resid 250 through 257 Processing helix chain 'J' and resid 286 through 293 Processing helix chain 'J' and resid 296 through 298 No H-bonds generated for 'chain 'J' and resid 296 through 298' Processing helix chain 'J' and resid 305 through 307 No H-bonds generated for 'chain 'J' and resid 305 through 307' Processing helix chain 'J' and resid 323 through 336 Processing helix chain 'J' and resid 338 through 340 No H-bonds generated for 'chain 'J' and resid 338 through 340' Processing helix chain 'J' and resid 372 through 391 removed outlier: 3.656A pdb=" N ARG J 380 " --> pdb=" O LEU J 377 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG J 390 " --> pdb=" O ALA J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 395 through 401 removed outlier: 3.547A pdb=" N GLU J 401 " --> pdb=" O TRP J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 425 Processing helix chain 'C' and resid 10 through 27 Processing helix chain 'C' and resid 41 through 45 Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 55 through 57 No H-bonds generated for 'chain 'C' and resid 55 through 57' Processing helix chain 'C' and resid 70 through 78 Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 101 through 105 Processing helix chain 'C' and resid 109 through 126 removed outlier: 4.453A pdb=" N ASP C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N SER C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 158 removed outlier: 3.718A pdb=" N GLY C 148 " --> pdb=" O GLY C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 195 removed outlier: 3.837A pdb=" N GLU C 194 " --> pdb=" O HIS C 190 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN C 195 " --> pdb=" O GLN C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 Processing helix chain 'C' and resid 222 through 236 removed outlier: 3.727A pdb=" N LEU C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL C 229 " --> pdb=" O LEU C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 241 No H-bonds generated for 'chain 'C' and resid 238 through 241' Processing helix chain 'C' and resid 250 through 257 Processing helix chain 'C' and resid 286 through 293 Processing helix chain 'C' and resid 296 through 298 No H-bonds generated for 'chain 'C' and resid 296 through 298' Processing helix chain 'C' and resid 305 through 307 No H-bonds generated for 'chain 'C' and resid 305 through 307' Processing helix chain 'C' and resid 323 through 336 Processing helix chain 'C' and resid 338 through 340 No H-bonds generated for 'chain 'C' and resid 338 through 340' Processing helix chain 'C' and resid 372 through 391 removed outlier: 3.655A pdb=" N ARG C 380 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG C 390 " --> pdb=" O ALA C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 401 removed outlier: 3.545A pdb=" N GLU C 401 " --> pdb=" O TRP C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 425 Processing helix chain 'D' and resid 10 through 27 Processing helix chain 'D' and resid 41 through 45 Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 55 through 57 No H-bonds generated for 'chain 'D' and resid 55 through 57' Processing helix chain 'D' and resid 70 through 78 Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing helix chain 'D' and resid 101 through 105 Processing helix chain 'D' and resid 109 through 126 removed outlier: 4.451A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 158 removed outlier: 3.719A pdb=" N GLY D 148 " --> pdb=" O GLY D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 195 removed outlier: 3.836A pdb=" N GLU D 194 " --> pdb=" O HIS D 190 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN D 195 " --> pdb=" O GLN D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 213 Processing helix chain 'D' and resid 222 through 236 removed outlier: 3.727A pdb=" N LEU D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL D 229 " --> pdb=" O LEU D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 241 No H-bonds generated for 'chain 'D' and resid 238 through 241' Processing helix chain 'D' and resid 250 through 257 Processing helix chain 'D' and resid 286 through 293 Processing helix chain 'D' and resid 296 through 298 No H-bonds generated for 'chain 'D' and resid 296 through 298' Processing helix chain 'D' and resid 305 through 307 No H-bonds generated for 'chain 'D' and resid 305 through 307' Processing helix chain 'D' and resid 323 through 336 Processing helix chain 'D' and resid 338 through 340 No H-bonds generated for 'chain 'D' and resid 338 through 340' Processing helix chain 'D' and resid 372 through 391 removed outlier: 3.655A pdb=" N ARG D 380 " --> pdb=" O LEU D 377 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG D 390 " --> pdb=" O ALA D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 401 removed outlier: 3.547A pdb=" N GLU D 401 " --> pdb=" O TRP D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 425 Processing helix chain 'F' and resid 10 through 27 Processing helix chain 'F' and resid 48 through 51 removed outlier: 3.836A pdb=" N THR F 51 " --> pdb=" O SER F 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 48 through 51' Processing helix chain 'F' and resid 73 through 79 removed outlier: 3.575A pdb=" N GLU F 77 " --> pdb=" O THR F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 103 through 107 Processing helix chain 'F' and resid 111 through 128 removed outlier: 5.286A pdb=" N ASP F 116 " --> pdb=" O LYS F 112 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LEU F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 160 removed outlier: 4.394A pdb=" N THR F 150 " --> pdb=" O GLY F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 183 through 197 removed outlier: 4.166A pdb=" N GLU F 196 " --> pdb=" O HIS F 192 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N HIS F 197 " --> pdb=" O THR F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 216 Processing helix chain 'F' and resid 224 through 243 removed outlier: 3.593A pdb=" N ARG F 229 " --> pdb=" O THR F 225 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU F 230 " --> pdb=" O ASN F 226 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N SER F 241 " --> pdb=" O SER F 237 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LEU F 242 " --> pdb=" O ILE F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 259 removed outlier: 3.574A pdb=" N GLN F 256 " --> pdb=" O LEU F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 283 Processing helix chain 'F' and resid 288 through 296 Processing helix chain 'F' and resid 298 through 300 No H-bonds generated for 'chain 'F' and resid 298 through 300' Processing helix chain 'F' and resid 325 through 337 Processing helix chain 'F' and resid 382 through 401 removed outlier: 3.656A pdb=" N LEU F 397 " --> pdb=" O LYS F 394 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR F 399 " --> pdb=" O ASP F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 411 removed outlier: 3.662A pdb=" N GLU F 411 " --> pdb=" O TRP F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 435 removed outlier: 3.825A pdb=" N SER F 419 " --> pdb=" O GLU F 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 27 Processing helix chain 'A' and resid 48 through 51 removed outlier: 3.835A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 73 through 79 removed outlier: 3.576A pdb=" N GLU A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 111 through 128 removed outlier: 5.285A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 removed outlier: 4.393A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 183 through 197 removed outlier: 4.167A pdb=" N GLU A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N HIS A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 224 through 243 removed outlier: 3.594A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 removed outlier: 3.574A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 288 through 296 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.656A pdb=" N LEU A 397 " --> pdb=" O LYS A 394 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.662A pdb=" N GLU A 411 " --> pdb=" O TRP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 435 removed outlier: 3.826A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 27 Processing helix chain 'B' and resid 48 through 51 removed outlier: 3.836A pdb=" N THR B 51 " --> pdb=" O SER B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 48 through 51' Processing helix chain 'B' and resid 73 through 79 removed outlier: 3.574A pdb=" N GLU B 77 " --> pdb=" O THR B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 111 through 128 removed outlier: 5.285A pdb=" N ASP B 116 " --> pdb=" O LYS B 112 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 160 removed outlier: 4.393A pdb=" N THR B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 183 through 197 removed outlier: 4.167A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N HIS B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 224 through 243 removed outlier: 3.594A pdb=" N ARG B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU B 230 " --> pdb=" O ASN B 226 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N SER B 241 " --> pdb=" O SER B 237 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU B 242 " --> pdb=" O ILE B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 removed outlier: 3.573A pdb=" N GLN B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 288 through 296 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 325 through 337 Processing helix chain 'B' and resid 382 through 401 removed outlier: 3.655A pdb=" N LEU B 397 " --> pdb=" O LYS B 394 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR B 399 " --> pdb=" O ASP B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 3.661A pdb=" N GLU B 411 " --> pdb=" O TRP B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 435 removed outlier: 3.826A pdb=" N SER B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 27 Processing helix chain 'L' and resid 41 through 45 Processing helix chain 'L' and resid 47 through 49 No H-bonds generated for 'chain 'L' and resid 47 through 49' Processing helix chain 'L' and resid 55 through 57 No H-bonds generated for 'chain 'L' and resid 55 through 57' Processing helix chain 'L' and resid 70 through 78 Processing helix chain 'L' and resid 82 through 84 No H-bonds generated for 'chain 'L' and resid 82 through 84' Processing helix chain 'L' and resid 87 through 89 No H-bonds generated for 'chain 'L' and resid 87 through 89' Processing helix chain 'L' and resid 101 through 105 Processing helix chain 'L' and resid 109 through 126 removed outlier: 4.451A pdb=" N ASP L 114 " --> pdb=" O ALA L 110 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N SER L 115 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL L 116 " --> pdb=" O LEU L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 158 removed outlier: 3.719A pdb=" N GLY L 148 " --> pdb=" O GLY L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 195 removed outlier: 3.835A pdb=" N GLU L 194 " --> pdb=" O HIS L 190 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN L 195 " --> pdb=" O GLN L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 204 through 213 Processing helix chain 'L' and resid 222 through 236 removed outlier: 3.727A pdb=" N LEU L 228 " --> pdb=" O ASP L 224 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL L 229 " --> pdb=" O LEU L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 238 through 241 No H-bonds generated for 'chain 'L' and resid 238 through 241' Processing helix chain 'L' and resid 250 through 257 Processing helix chain 'L' and resid 286 through 293 Processing helix chain 'L' and resid 296 through 298 No H-bonds generated for 'chain 'L' and resid 296 through 298' Processing helix chain 'L' and resid 305 through 307 No H-bonds generated for 'chain 'L' and resid 305 through 307' Processing helix chain 'L' and resid 323 through 336 Processing helix chain 'L' and resid 338 through 340 No H-bonds generated for 'chain 'L' and resid 338 through 340' Processing helix chain 'L' and resid 372 through 391 removed outlier: 3.657A pdb=" N ARG L 380 " --> pdb=" O LEU L 377 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG L 390 " --> pdb=" O ALA L 387 " (cutoff:3.500A) Processing helix chain 'L' and resid 395 through 401 removed outlier: 3.544A pdb=" N GLU L 401 " --> pdb=" O TRP L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 425 Processing helix chain 'G' and resid 10 through 27 Processing helix chain 'G' and resid 48 through 51 removed outlier: 3.836A pdb=" N THR G 51 " --> pdb=" O SER G 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 48 through 51' Processing helix chain 'G' and resid 73 through 79 removed outlier: 3.575A pdb=" N GLU G 77 " --> pdb=" O THR G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 91 No H-bonds generated for 'chain 'G' and resid 89 through 91' Processing helix chain 'G' and resid 103 through 107 Processing helix chain 'G' and resid 111 through 128 removed outlier: 5.285A pdb=" N ASP G 116 " --> pdb=" O LYS G 112 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LEU G 117 " --> pdb=" O GLU G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 160 removed outlier: 4.393A pdb=" N THR G 150 " --> pdb=" O GLY G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 177 No H-bonds generated for 'chain 'G' and resid 175 through 177' Processing helix chain 'G' and resid 183 through 197 removed outlier: 4.165A pdb=" N GLU G 196 " --> pdb=" O HIS G 192 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N HIS G 197 " --> pdb=" O THR G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 216 Processing helix chain 'G' and resid 224 through 243 removed outlier: 3.593A pdb=" N ARG G 229 " --> pdb=" O THR G 225 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU G 230 " --> pdb=" O ASN G 226 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER G 241 " --> pdb=" O SER G 237 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LEU G 242 " --> pdb=" O ILE G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 259 removed outlier: 3.574A pdb=" N GLN G 256 " --> pdb=" O LEU G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 283 Processing helix chain 'G' and resid 288 through 296 Processing helix chain 'G' and resid 298 through 300 No H-bonds generated for 'chain 'G' and resid 298 through 300' Processing helix chain 'G' and resid 325 through 337 Processing helix chain 'G' and resid 382 through 401 removed outlier: 3.655A pdb=" N LEU G 397 " --> pdb=" O LYS G 394 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR G 399 " --> pdb=" O ASP G 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 411 removed outlier: 3.662A pdb=" N GLU G 411 " --> pdb=" O TRP G 407 " (cutoff:3.500A) Processing helix chain 'G' and resid 415 through 435 removed outlier: 3.824A pdb=" N SER G 419 " --> pdb=" O GLU G 415 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'K' and resid 90 through 92 removed outlier: 8.177A pdb=" N ILE K 91 " --> pdb=" O ALA K 63 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU K 65 " --> pdb=" O ILE K 91 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ILE K 64 " --> pdb=" O ILE K 4 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N HIS K 6 " --> pdb=" O ILE K 64 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N VAL K 66 " --> pdb=" O HIS K 6 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLN K 8 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL K 5 " --> pdb=" O GLN K 131 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE K 133 " --> pdb=" O VAL K 5 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ILE K 7 " --> pdb=" O PHE K 133 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU K 135 " --> pdb=" O ILE K 7 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ALA K 9 " --> pdb=" O LEU K 135 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N HIS K 137 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE K 163 " --> pdb=" O PHE K 133 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU K 135 " --> pdb=" O ILE K 163 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN K 165 " --> pdb=" O LEU K 135 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N HIS K 137 " --> pdb=" O ASN K 165 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHE K 167 " --> pdb=" O HIS K 137 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLU K 198 " --> pdb=" O THR K 166 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N SER K 168 " --> pdb=" O GLU K 198 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N TYR K 200 " --> pdb=" O SER K 168 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL K 170 " --> pdb=" O TYR K 200 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE K 202 " --> pdb=" O VAL K 170 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 267 through 271 removed outlier: 3.527A pdb=" N THR K 312 " --> pdb=" O ASN K 370 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 65 through 68 removed outlier: 8.713A pdb=" N VAL H 66 " --> pdb=" O CYS H 4 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER H 6 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL H 68 " --> pdb=" O SER H 6 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N HIS H 8 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLY H 134 " --> pdb=" O ILE H 5 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE H 7 " --> pdb=" O GLY H 134 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU H 136 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL H 9 " --> pdb=" O LEU H 136 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N PHE H 138 " --> pdb=" O VAL H 9 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER H 165 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N VAL H 137 " --> pdb=" O SER H 165 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU H 167 " --> pdb=" O VAL H 137 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N HIS H 139 " --> pdb=" O LEU H 167 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHE H 169 " --> pdb=" O HIS H 139 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N CYS H 200 " --> pdb=" O GLU H 168 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N SER H 170 " --> pdb=" O CYS H 200 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N PHE H 202 " --> pdb=" O SER H 170 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TYR H 172 " --> pdb=" O PHE H 202 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL H 204 " --> pdb=" O TYR H 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'H' and resid 53 through 56 removed outlier: 3.791A pdb=" N LYS H 60 " --> pdb=" O THR H 56 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 269 through 273 removed outlier: 3.702A pdb=" N ALA H 314 " --> pdb=" O ASN H 380 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'I' and resid 90 through 92 removed outlier: 8.176A pdb=" N ILE I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU I 65 " --> pdb=" O ILE I 91 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL I 5 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N PHE I 133 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ILE I 7 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU I 135 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ALA I 9 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N HIS I 137 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE I 163 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU I 135 " --> pdb=" O ILE I 163 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN I 165 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N HIS I 137 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N PHE I 167 " --> pdb=" O HIS I 137 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLU I 198 " --> pdb=" O THR I 166 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N SER I 168 " --> pdb=" O GLU I 198 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N TYR I 200 " --> pdb=" O SER I 168 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL I 170 " --> pdb=" O TYR I 200 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE I 202 " --> pdb=" O VAL I 170 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'I' and resid 267 through 271 removed outlier: 3.527A pdb=" N THR I 312 " --> pdb=" O ASN I 370 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 65 through 68 removed outlier: 8.712A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY E 134 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ILE E 7 " --> pdb=" O GLY E 134 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU E 136 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL E 9 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE E 138 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N SER E 165 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N VAL E 137 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU E 167 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N HIS E 139 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N PHE E 169 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N CYS E 200 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N SER E 170 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE E 202 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N TYR E 172 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL E 204 " --> pdb=" O TYR E 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'E' and resid 53 through 56 removed outlier: 3.792A pdb=" N LYS E 60 " --> pdb=" O THR E 56 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 269 through 273 removed outlier: 3.701A pdb=" N ALA E 314 " --> pdb=" O ASN E 380 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'J' and resid 90 through 92 removed outlier: 8.178A pdb=" N ILE J 91 " --> pdb=" O ALA J 63 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU J 65 " --> pdb=" O ILE J 91 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ILE J 64 " --> pdb=" O ILE J 4 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N HIS J 6 " --> pdb=" O ILE J 64 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL J 66 " --> pdb=" O HIS J 6 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN J 8 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL J 5 " --> pdb=" O GLN J 131 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE J 133 " --> pdb=" O VAL J 5 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ILE J 7 " --> pdb=" O PHE J 133 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU J 135 " --> pdb=" O ILE J 7 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ALA J 9 " --> pdb=" O LEU J 135 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N HIS J 137 " --> pdb=" O ALA J 9 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE J 163 " --> pdb=" O PHE J 133 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU J 135 " --> pdb=" O ILE J 163 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN J 165 " --> pdb=" O LEU J 135 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N HIS J 137 " --> pdb=" O ASN J 165 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHE J 167 " --> pdb=" O HIS J 137 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLU J 198 " --> pdb=" O THR J 166 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N SER J 168 " --> pdb=" O GLU J 198 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N TYR J 200 " --> pdb=" O SER J 168 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL J 170 " --> pdb=" O TYR J 200 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE J 202 " --> pdb=" O VAL J 170 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'J' and resid 267 through 271 removed outlier: 3.527A pdb=" N THR J 312 " --> pdb=" O ASN J 370 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 90 through 92 removed outlier: 8.179A pdb=" N ILE C 91 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU C 65 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ILE C 64 " --> pdb=" O ILE C 4 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N HIS C 6 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N VAL C 66 " --> pdb=" O HIS C 6 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLN C 8 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL C 5 " --> pdb=" O GLN C 131 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N PHE C 133 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ILE C 7 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU C 135 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ALA C 9 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N HIS C 137 " --> pdb=" O ALA C 9 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE C 163 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU C 135 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN C 165 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N HIS C 137 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N PHE C 167 " --> pdb=" O HIS C 137 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLU C 198 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N SER C 168 " --> pdb=" O GLU C 198 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR C 200 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL C 170 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE C 202 " --> pdb=" O VAL C 170 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 267 through 271 removed outlier: 3.527A pdb=" N THR C 312 " --> pdb=" O ASN C 370 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 90 through 92 removed outlier: 8.177A pdb=" N ILE D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU D 65 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL D 5 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE D 133 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE D 7 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU D 135 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ALA D 9 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N HIS D 137 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE D 163 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU D 135 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN D 165 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N HIS D 137 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHE D 167 " --> pdb=" O HIS D 137 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLU D 198 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N SER D 168 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N TYR D 200 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL D 170 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE D 202 " --> pdb=" O VAL D 170 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 267 through 271 removed outlier: 3.527A pdb=" N THR D 312 " --> pdb=" O ASN D 370 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 65 through 68 removed outlier: 8.714A pdb=" N VAL F 66 " --> pdb=" O CYS F 4 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER F 6 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL F 68 " --> pdb=" O SER F 6 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N HIS F 8 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLY F 134 " --> pdb=" O ILE F 5 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE F 7 " --> pdb=" O GLY F 134 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU F 136 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL F 9 " --> pdb=" O LEU F 136 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE F 138 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N SER F 165 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL F 137 " --> pdb=" O SER F 165 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU F 167 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N HIS F 139 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHE F 169 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N CYS F 200 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N SER F 170 " --> pdb=" O CYS F 200 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE F 202 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N TYR F 172 " --> pdb=" O PHE F 202 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL F 204 " --> pdb=" O TYR F 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'F' and resid 53 through 56 removed outlier: 3.501A pdb=" N THR F 56 " --> pdb=" O LYS F 60 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS F 60 " --> pdb=" O THR F 56 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 269 through 273 removed outlier: 3.700A pdb=" N ALA F 314 " --> pdb=" O ASN F 380 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 65 through 68 removed outlier: 8.712A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLY A 134 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE A 7 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A 136 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL A 9 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N PHE A 138 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N TYR A 172 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N VAL A 204 " --> pdb=" O TYR A 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'A' and resid 53 through 56 removed outlier: 3.794A pdb=" N LYS A 60 " --> pdb=" O THR A 56 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.697A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 65 through 68 removed outlier: 8.714A pdb=" N VAL B 66 " --> pdb=" O CYS B 4 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER B 6 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL B 68 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N HIS B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLY B 134 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE B 7 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU B 136 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL B 9 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE B 138 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N SER B 165 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N VAL B 137 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU B 167 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N HIS B 139 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHE B 169 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N CYS B 200 " --> pdb=" O GLU B 168 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N SER B 170 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE B 202 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N TYR B 172 " --> pdb=" O PHE B 202 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL B 204 " --> pdb=" O TYR B 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.792A pdb=" N LYS B 60 " --> pdb=" O THR B 56 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 269 through 273 removed outlier: 3.699A pdb=" N ALA B 314 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'L' and resid 90 through 92 removed outlier: 8.177A pdb=" N ILE L 91 " --> pdb=" O ALA L 63 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU L 65 " --> pdb=" O ILE L 91 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N ILE L 64 " --> pdb=" O ILE L 4 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N HIS L 6 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL L 66 " --> pdb=" O HIS L 6 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN L 8 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL L 5 " --> pdb=" O GLN L 131 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE L 133 " --> pdb=" O VAL L 5 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ILE L 7 " --> pdb=" O PHE L 133 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU L 135 " --> pdb=" O ILE L 7 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ALA L 9 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N HIS L 137 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE L 163 " --> pdb=" O PHE L 133 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU L 135 " --> pdb=" O ILE L 163 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN L 165 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N HIS L 137 " --> pdb=" O ASN L 165 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHE L 167 " --> pdb=" O HIS L 137 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLU L 198 " --> pdb=" O THR L 166 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N SER L 168 " --> pdb=" O GLU L 198 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR L 200 " --> pdb=" O SER L 168 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL L 170 " --> pdb=" O TYR L 200 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE L 202 " --> pdb=" O VAL L 170 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'L' and resid 267 through 271 removed outlier: 3.527A pdb=" N THR L 312 " --> pdb=" O ASN L 370 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 65 through 68 removed outlier: 8.714A pdb=" N VAL G 66 " --> pdb=" O CYS G 4 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N SER G 6 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL G 68 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N HIS G 8 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLY G 134 " --> pdb=" O ILE G 5 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE G 7 " --> pdb=" O GLY G 134 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU G 136 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL G 9 " --> pdb=" O LEU G 136 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE G 138 " --> pdb=" O VAL G 9 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N SER G 165 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N VAL G 137 " --> pdb=" O SER G 165 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU G 167 " --> pdb=" O VAL G 137 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N HIS G 139 " --> pdb=" O LEU G 167 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N PHE G 169 " --> pdb=" O HIS G 139 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N CYS G 200 " --> pdb=" O GLU G 168 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N SER G 170 " --> pdb=" O CYS G 200 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE G 202 " --> pdb=" O SER G 170 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N TYR G 172 " --> pdb=" O PHE G 202 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N VAL G 204 " --> pdb=" O TYR G 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'G' and resid 53 through 56 removed outlier: 3.503A pdb=" N THR G 56 " --> pdb=" O LYS G 60 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS G 60 " --> pdb=" O THR G 56 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 269 through 273 removed outlier: 3.702A pdb=" N ALA G 314 " --> pdb=" O ASN G 380 " (cutoff:3.500A) 1684 hydrogen bonds defined for protein. 4440 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: 15.25 Time building geometry restraints manager: 16.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7512 1.32 - 1.45: 10848 1.45 - 1.57: 22572 1.57 - 1.70: 60 1.70 - 1.82: 444 Bond restraints: 41436 Sorted by residual: bond pdb=" CA VAL C 286 " pdb=" CB VAL C 286 " ideal model delta sigma weight residual 1.537 1.569 -0.033 5.00e-03 4.00e+04 4.27e+01 bond pdb=" CA VAL J 286 " pdb=" CB VAL J 286 " ideal model delta sigma weight residual 1.537 1.569 -0.032 5.00e-03 4.00e+04 4.13e+01 bond pdb=" CA VAL D 286 " pdb=" CB VAL D 286 " ideal model delta sigma weight residual 1.537 1.569 -0.032 5.00e-03 4.00e+04 4.08e+01 bond pdb=" CA VAL L 286 " pdb=" CB VAL L 286 " ideal model delta sigma weight residual 1.537 1.568 -0.031 5.00e-03 4.00e+04 3.84e+01 bond pdb=" CA VAL I 286 " pdb=" CB VAL I 286 " ideal model delta sigma weight residual 1.537 1.568 -0.031 5.00e-03 4.00e+04 3.84e+01 ... (remaining 41431 not shown) Histogram of bond angle deviations from ideal: 48.07 - 66.00: 6 66.00 - 83.93: 0 83.93 - 101.86: 135 101.86 - 119.79: 36221 119.79 - 137.73: 19936 Bond angle restraints: 56298 Sorted by residual: angle pdb=" C MET A 36 " pdb=" N PRO A 37 " pdb=" CD PRO A 37 " ideal model delta sigma weight residual 125.00 48.07 76.93 4.10e+00 5.95e-02 3.52e+02 angle pdb=" C MET E 36 " pdb=" N PRO E 37 " pdb=" CD PRO E 37 " ideal model delta sigma weight residual 125.00 52.53 72.47 4.10e+00 5.95e-02 3.12e+02 angle pdb=" C MET H 36 " pdb=" N PRO H 37 " pdb=" CD PRO H 37 " ideal model delta sigma weight residual 125.00 62.33 62.67 4.10e+00 5.95e-02 2.34e+02 angle pdb=" C MET G 36 " pdb=" N PRO G 37 " pdb=" CD PRO G 37 " ideal model delta sigma weight residual 125.00 63.75 61.25 4.10e+00 5.95e-02 2.23e+02 angle pdb=" C MET B 36 " pdb=" N PRO B 37 " pdb=" CD PRO B 37 " ideal model delta sigma weight residual 125.00 65.61 59.39 4.10e+00 5.95e-02 2.10e+02 ... (remaining 56293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.03: 23814 34.03 - 68.07: 809 68.07 - 102.10: 73 102.10 - 136.14: 6 136.14 - 170.17: 12 Dihedral angle restraints: 24714 sinusoidal: 9912 harmonic: 14802 Sorted by residual: dihedral pdb=" O3B GTP B 501 " pdb=" O3A GTP B 501 " pdb=" PB GTP B 501 " pdb=" PA GTP B 501 " ideal model delta sinusoidal sigma weight residual 291.08 120.91 170.17 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O3B GTP H 501 " pdb=" O3A GTP H 501 " pdb=" PB GTP H 501 " pdb=" PA GTP H 501 " ideal model delta sinusoidal sigma weight residual 291.08 122.17 168.91 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O3B GTP F 501 " pdb=" O3A GTP F 501 " pdb=" PB GTP F 501 " pdb=" PA GTP F 501 " ideal model delta sinusoidal sigma weight residual 291.08 122.49 168.59 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 24711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3732 0.071 - 0.142: 1702 0.142 - 0.213: 605 0.213 - 0.283: 111 0.283 - 0.354: 12 Chirality restraints: 6162 Sorted by residual: chirality pdb=" CA MET I 257 " pdb=" N MET I 257 " pdb=" C MET I 257 " pdb=" CB MET I 257 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CA MET C 257 " pdb=" N MET C 257 " pdb=" C MET C 257 " pdb=" CB MET C 257 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA MET K 257 " pdb=" N MET K 257 " pdb=" C MET K 257 " pdb=" CB MET K 257 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 6159 not shown) Planarity restraints: 7308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 36 " 0.251 5.00e-02 4.00e+02 2.78e-01 1.23e+02 pdb=" N PRO A 37 " -0.449 5.00e-02 4.00e+02 pdb=" CA PRO A 37 " 0.209 5.00e-02 4.00e+02 pdb=" CD PRO A 37 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 36 " 0.224 5.00e-02 4.00e+02 2.77e-01 1.23e+02 pdb=" N PRO E 37 " -0.460 5.00e-02 4.00e+02 pdb=" CA PRO E 37 " 0.211 5.00e-02 4.00e+02 pdb=" CD PRO E 37 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET H 36 " -0.186 5.00e-02 4.00e+02 2.69e-01 1.16e+02 pdb=" N PRO H 37 " 0.457 5.00e-02 4.00e+02 pdb=" CA PRO H 37 " -0.202 5.00e-02 4.00e+02 pdb=" CD PRO H 37 " -0.069 5.00e-02 4.00e+02 ... (remaining 7305 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 53 2.45 - 3.07: 26484 3.07 - 3.68: 61867 3.68 - 4.29: 91412 4.29 - 4.90: 151912 Nonbonded interactions: 331728 Sorted by model distance: nonbonded pdb=" O MET A 36 " pdb=" CD PRO A 37 " model vdw 1.843 2.752 nonbonded pdb=" O MET E 36 " pdb=" CD PRO E 37 " model vdw 1.968 2.752 nonbonded pdb=" CA MET A 36 " pdb=" CD PRO A 37 " model vdw 1.993 3.096 nonbonded pdb=" CA MET E 36 " pdb=" CD PRO E 37 " model vdw 2.040 3.096 nonbonded pdb=" O GLY K 141 " pdb=" OG SER K 145 " model vdw 2.069 2.440 ... (remaining 331723 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 2.990 Check model and map are aligned: 0.660 Set scattering table: 0.390 Process input model: 99.920 Find NCS groups from input model: 2.940 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.117 41436 Z= 0.669 Angle : 1.747 76.931 56298 Z= 1.128 Chirality : 0.089 0.354 6162 Planarity : 0.010 0.278 7308 Dihedral : 16.931 170.169 15222 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.13 % Favored : 95.75 % Rotamer: Outliers : 1.73 % Allowed : 10.60 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.01 (0.11), residues: 5088 helix: 1.23 (0.09), residues: 2268 sheet: 0.35 (0.17), residues: 750 loop : -1.54 (0.12), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.005 TRP C 21 HIS 0.013 0.004 HIS I 137 PHE 0.030 0.004 PHE B 343 TYR 0.033 0.004 TYR H 108 ARG 0.007 0.001 ARG G 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1895 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1820 time to evaluate : 4.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 50 TYR cc_start: 0.7853 (m-80) cc_final: 0.7146 (m-10) REVERT: K 51 TYR cc_start: 0.8411 (m-80) cc_final: 0.8193 (m-10) REVERT: K 67 ASP cc_start: 0.7424 (t0) cc_final: 0.7087 (t70) REVERT: K 88 ASP cc_start: 0.8349 (m-30) cc_final: 0.8075 (t0) REVERT: K 114 ASP cc_start: 0.7745 (m-30) cc_final: 0.7403 (t0) REVERT: K 133 PHE cc_start: 0.8669 (m-80) cc_final: 0.8213 (m-80) REVERT: K 167 PHE cc_start: 0.7868 (m-80) cc_final: 0.7549 (m-10) REVERT: K 174 LYS cc_start: 0.8208 (mttt) cc_final: 0.7822 (mmtp) REVERT: K 183 TYR cc_start: 0.7953 (m-80) cc_final: 0.7545 (m-10) REVERT: K 213 ARG cc_start: 0.7858 (ttm110) cc_final: 0.6529 (ttp80) REVERT: K 297 LYS cc_start: 0.8554 (mttt) cc_final: 0.8058 (mmmt) REVERT: K 300 MET cc_start: 0.8043 (mtt) cc_final: 0.7658 (mtt) REVERT: K 303 CYS cc_start: 0.6656 (m) cc_final: 0.5886 (m) REVERT: K 323 MET cc_start: 0.8548 (ttt) cc_final: 0.7883 (ttt) REVERT: K 406 MET cc_start: 0.7920 (ptm) cc_final: 0.5946 (mmm) REVERT: H 6 SER cc_start: 0.9390 (m) cc_final: 0.8996 (t) REVERT: H 85 GLN cc_start: 0.8096 (mt0) cc_final: 0.7690 (mt0) REVERT: H 88 HIS cc_start: 0.8418 (p-80) cc_final: 0.7261 (p90) REVERT: H 90 GLU cc_start: 0.8606 (pt0) cc_final: 0.8268 (pm20) REVERT: H 94 THR cc_start: 0.7780 (p) cc_final: 0.7495 (p) REVERT: H 96 LYS cc_start: 0.6608 (mmtm) cc_final: 0.6184 (tppt) REVERT: H 124 LYS cc_start: 0.8549 (ttpt) cc_final: 0.8031 (tptt) REVERT: H 135 PHE cc_start: 0.8702 (m-80) cc_final: 0.8393 (m-10) REVERT: H 167 LEU cc_start: 0.8908 (mp) cc_final: 0.8497 (tt) REVERT: H 191 THR cc_start: 0.8785 (p) cc_final: 0.8528 (t) REVERT: H 221 ARG cc_start: 0.7984 (ptt-90) cc_final: 0.7490 (ptt-90) REVERT: H 245 ASP cc_start: 0.8104 (m-30) cc_final: 0.7509 (p0) REVERT: H 290 GLU cc_start: 0.7832 (tt0) cc_final: 0.7543 (tp30) REVERT: H 302 MET cc_start: 0.8965 (mmt) cc_final: 0.7976 (mmt) REVERT: H 338 LYS cc_start: 0.8193 (mmtt) cc_final: 0.7805 (mmtp) REVERT: H 356 ASN cc_start: 0.8426 (t0) cc_final: 0.7974 (m-40) REVERT: H 393 HIS cc_start: 0.8470 (t-90) cc_final: 0.8257 (t-90) REVERT: H 413 MET cc_start: 0.8659 (tpt) cc_final: 0.8270 (mmp) REVERT: H 417 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7764 (mm-30) REVERT: H 420 GLU cc_start: 0.8343 (tm-30) cc_final: 0.6266 (tp30) REVERT: I 22 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8131 (mm-30) REVERT: I 26 ASP cc_start: 0.8084 (m-30) cc_final: 0.7877 (m-30) REVERT: I 39 ASP cc_start: 0.6401 (t0) cc_final: 0.5994 (p0) REVERT: I 127 CYS cc_start: 0.6993 (p) cc_final: 0.6646 (p) REVERT: I 130 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8177 (tm) REVERT: I 133 PHE cc_start: 0.8445 (m-80) cc_final: 0.8224 (m-80) REVERT: I 136 THR cc_start: 0.9211 (m) cc_final: 0.8850 (p) REVERT: I 167 PHE cc_start: 0.8093 (m-80) cc_final: 0.7565 (m-10) REVERT: I 174 LYS cc_start: 0.8320 (mttt) cc_final: 0.7975 (mmtm) REVERT: I 183 TYR cc_start: 0.7545 (m-80) cc_final: 0.7245 (m-80) REVERT: I 213 ARG cc_start: 0.7705 (ttm110) cc_final: 0.7168 (ttp80) REVERT: I 217 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6650 (mt) REVERT: I 298 ASN cc_start: 0.7780 (m-40) cc_final: 0.7255 (p0) REVERT: I 338 SER cc_start: 0.8167 (p) cc_final: 0.7846 (t) REVERT: I 379 LYS cc_start: 0.8431 (ttmp) cc_final: 0.8117 (tptp) REVERT: I 425 TYR cc_start: 0.7561 (m-80) cc_final: 0.7153 (m-80) REVERT: E 2 ARG cc_start: 0.7054 (mtm180) cc_final: 0.6302 (mtp-110) REVERT: E 24 TYR cc_start: 0.8320 (m-10) cc_final: 0.7724 (m-80) REVERT: E 83 TYR cc_start: 0.8002 (m-80) cc_final: 0.7367 (m-10) REVERT: E 96 LYS cc_start: 0.6267 (mmtm) cc_final: 0.5894 (tppt) REVERT: E 154 MET cc_start: 0.8281 (tpp) cc_final: 0.7463 (mtm) REVERT: E 192 HIS cc_start: 0.7805 (t70) cc_final: 0.7253 (t70) REVERT: E 193 THR cc_start: 0.8604 (p) cc_final: 0.8320 (p) REVERT: E 202 PHE cc_start: 0.8503 (m-80) cc_final: 0.8163 (m-10) REVERT: E 221 ARG cc_start: 0.8199 (ptt-90) cc_final: 0.7969 (ptt-90) REVERT: E 251 ASP cc_start: 0.8139 (m-30) cc_final: 0.7815 (m-30) REVERT: E 290 GLU cc_start: 0.7996 (tt0) cc_final: 0.7643 (tp30) REVERT: E 302 MET cc_start: 0.9070 (mmt) cc_final: 0.8581 (mmm) REVERT: E 356 ASN cc_start: 0.8282 (t0) cc_final: 0.8003 (m-40) REVERT: E 417 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7527 (mm-30) REVERT: E 425 MET cc_start: 0.8470 (mmm) cc_final: 0.8268 (mmp) REVERT: J 19 LYS cc_start: 0.8813 (tptt) cc_final: 0.8552 (mmmm) REVERT: J 30 ILE cc_start: 0.8312 (mm) cc_final: 0.7530 (mt) REVERT: J 31 ASP cc_start: 0.8456 (m-30) cc_final: 0.8237 (m-30) REVERT: J 50 TYR cc_start: 0.7962 (m-80) cc_final: 0.7489 (m-10) REVERT: J 51 TYR cc_start: 0.8099 (m-80) cc_final: 0.7869 (m-10) REVERT: J 59 TYR cc_start: 0.7496 (m-80) cc_final: 0.6680 (m-80) REVERT: J 67 ASP cc_start: 0.7640 (t0) cc_final: 0.7191 (t70) REVERT: J 69 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7519 (tp30) REVERT: J 114 ASP cc_start: 0.8022 (m-30) cc_final: 0.7790 (p0) REVERT: J 123 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8157 (mm-30) REVERT: J 136 THR cc_start: 0.9176 (m) cc_final: 0.8804 (p) REVERT: J 159 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.7584 (m-80) REVERT: J 167 PHE cc_start: 0.7890 (m-80) cc_final: 0.7322 (m-10) REVERT: J 168 SER cc_start: 0.8168 (m) cc_final: 0.7306 (t) REVERT: J 190 HIS cc_start: 0.7976 (t70) cc_final: 0.7281 (t-170) REVERT: J 213 ARG cc_start: 0.8048 (ttm110) cc_final: 0.7650 (ttp80) REVERT: J 297 LYS cc_start: 0.8697 (mttt) cc_final: 0.8164 (mmmt) REVERT: J 298 ASN cc_start: 0.7992 (m-40) cc_final: 0.7324 (p0) REVERT: J 307 HIS cc_start: 0.7831 (m-70) cc_final: 0.7464 (m90) REVERT: J 313 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.7905 (p) REVERT: J 320 ARG cc_start: 0.8118 (mtm-85) cc_final: 0.7740 (mtm-85) REVERT: J 323 MET cc_start: 0.8559 (ttt) cc_final: 0.7789 (ttt) REVERT: J 379 LYS cc_start: 0.8786 (ttmp) cc_final: 0.8482 (tptp) REVERT: J 391 ARG cc_start: 0.8069 (mmm-85) cc_final: 0.7461 (tmm160) REVERT: J 406 MET cc_start: 0.8127 (ptm) cc_final: 0.5796 (mmm) REVERT: C 8 GLN cc_start: 0.7936 (mt0) cc_final: 0.7337 (mt0) REVERT: C 22 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8186 (mm-30) REVERT: C 83 HIS cc_start: 0.7921 (m-70) cc_final: 0.7715 (m-70) REVERT: C 130 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8180 (tm) REVERT: C 136 THR cc_start: 0.9300 (m) cc_final: 0.9067 (p) REVERT: C 213 ARG cc_start: 0.7833 (ttm110) cc_final: 0.7334 (ttp80) REVERT: C 247 ASN cc_start: 0.8098 (m-40) cc_final: 0.7316 (t0) REVERT: C 279 GLN cc_start: 0.8708 (tt0) cc_final: 0.8022 (mt0) REVERT: C 295 ASP cc_start: 0.8141 (t0) cc_final: 0.7919 (t0) REVERT: C 383 GLU cc_start: 0.8295 (tt0) cc_final: 0.7855 (tp30) REVERT: C 425 TYR cc_start: 0.7414 (m-80) cc_final: 0.7104 (m-80) REVERT: D 8 GLN cc_start: 0.8092 (mt0) cc_final: 0.7882 (mt0) REVERT: D 26 ASP cc_start: 0.8075 (m-30) cc_final: 0.7852 (m-30) REVERT: D 67 ASP cc_start: 0.7320 (t0) cc_final: 0.6908 (t70) REVERT: D 114 ASP cc_start: 0.8038 (m-30) cc_final: 0.7663 (t0) REVERT: D 133 PHE cc_start: 0.8753 (m-80) cc_final: 0.8326 (m-80) REVERT: D 183 TYR cc_start: 0.7913 (m-80) cc_final: 0.7592 (m-10) REVERT: D 189 ILE cc_start: 0.8278 (mt) cc_final: 0.8050 (tp) REVERT: D 208 TYR cc_start: 0.7933 (m-80) cc_final: 0.7726 (m-80) REVERT: D 213 ARG cc_start: 0.7829 (ttm110) cc_final: 0.7308 (ttp80) REVERT: D 247 ASN cc_start: 0.8316 (m-40) cc_final: 0.7630 (t0) REVERT: D 278 SER cc_start: 0.7877 (t) cc_final: 0.7593 (t) REVERT: D 303 CYS cc_start: 0.6573 (m) cc_final: 0.5553 (m) REVERT: D 306 ARG cc_start: 0.8033 (mmt90) cc_final: 0.7618 (mtt-85) REVERT: D 321 MET cc_start: 0.8035 (mtm) cc_final: 0.7723 (mtm) REVERT: D 383 GLU cc_start: 0.8279 (tt0) cc_final: 0.7778 (tm-30) REVERT: D 406 MET cc_start: 0.7891 (ptm) cc_final: 0.5891 (mmm) REVERT: D 412 GLU cc_start: 0.8640 (tt0) cc_final: 0.8377 (tt0) REVERT: D 425 TYR cc_start: 0.7585 (m-80) cc_final: 0.7259 (m-80) REVERT: F 2 ARG cc_start: 0.7954 (mtm180) cc_final: 0.7559 (mtp-110) REVERT: F 94 THR cc_start: 0.7716 (p) cc_final: 0.7332 (p) REVERT: F 96 LYS cc_start: 0.6461 (mmtm) cc_final: 0.6069 (tppt) REVERT: F 108 TYR cc_start: 0.7536 (m-80) cc_final: 0.6620 (m-80) REVERT: F 124 LYS cc_start: 0.8486 (ttpt) cc_final: 0.8207 (tptt) REVERT: F 191 THR cc_start: 0.9076 (p) cc_final: 0.8836 (t) REVERT: F 205 ASP cc_start: 0.7132 (t0) cc_final: 0.6581 (t0) REVERT: F 210 TYR cc_start: 0.7588 (m-10) cc_final: 0.7171 (m-10) REVERT: F 251 ASP cc_start: 0.7669 (m-30) cc_final: 0.7351 (m-30) REVERT: F 269 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7712 (mt) REVERT: F 279 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7198 (tp30) REVERT: F 290 GLU cc_start: 0.8247 (tt0) cc_final: 0.8005 (tp30) REVERT: F 302 MET cc_start: 0.8778 (mmt) cc_final: 0.8320 (mmm) REVERT: F 326 LYS cc_start: 0.8712 (ttmt) cc_final: 0.8450 (tppt) REVERT: F 356 ASN cc_start: 0.8474 (t0) cc_final: 0.8266 (m-40) REVERT: F 399 TYR cc_start: 0.7034 (t80) cc_final: 0.5935 (t80) REVERT: F 413 MET cc_start: 0.8730 (tpt) cc_final: 0.8152 (tpt) REVERT: F 417 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8015 (mm-30) REVERT: F 418 PHE cc_start: 0.8450 (m-80) cc_final: 0.8112 (m-80) REVERT: F 420 GLU cc_start: 0.8199 (tm-30) cc_final: 0.6514 (tp30) REVERT: F 425 MET cc_start: 0.8848 (mmm) cc_final: 0.8506 (mmp) REVERT: F 430 LYS cc_start: 0.8394 (ttpt) cc_final: 0.8185 (ttpp) REVERT: F 431 ASP cc_start: 0.7225 (m-30) cc_final: 0.6667 (t0) REVERT: A 6 SER cc_start: 0.9322 (m) cc_final: 0.8980 (t) REVERT: A 24 TYR cc_start: 0.8332 (m-10) cc_final: 0.7784 (m-80) REVERT: A 83 TYR cc_start: 0.7839 (m-80) cc_final: 0.7184 (m-10) REVERT: A 88 HIS cc_start: 0.8630 (p-80) cc_final: 0.8100 (p90) REVERT: A 124 LYS cc_start: 0.8333 (ttpt) cc_final: 0.7929 (tptt) REVERT: A 251 ASP cc_start: 0.7787 (m-30) cc_final: 0.7560 (m-30) REVERT: A 262 TYR cc_start: 0.8063 (m-80) cc_final: 0.7826 (m-10) REVERT: A 290 GLU cc_start: 0.7992 (tt0) cc_final: 0.7542 (tp30) REVERT: A 302 MET cc_start: 0.8972 (mmt) cc_final: 0.8594 (mmm) REVERT: A 317 LEU cc_start: 0.9277 (mt) cc_final: 0.9059 (mt) REVERT: A 326 LYS cc_start: 0.8728 (ttmt) cc_final: 0.8314 (tppt) REVERT: A 356 ASN cc_start: 0.8536 (t0) cc_final: 0.8169 (m-40) REVERT: A 417 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7868 (mm-30) REVERT: A 429 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6840 (mt-10) REVERT: B 2 ARG cc_start: 0.8060 (mtm180) cc_final: 0.7642 (mtm110) REVERT: B 6 SER cc_start: 0.9281 (m) cc_final: 0.8893 (t) REVERT: B 85 GLN cc_start: 0.8103 (mt0) cc_final: 0.7545 (mp10) REVERT: B 88 HIS cc_start: 0.8510 (p-80) cc_final: 0.8058 (p90) REVERT: B 94 THR cc_start: 0.8038 (p) cc_final: 0.7640 (p) REVERT: B 96 LYS cc_start: 0.6514 (mmtm) cc_final: 0.5750 (tppt) REVERT: B 221 ARG cc_start: 0.8012 (ptt-90) cc_final: 0.7515 (ptt-90) REVERT: B 245 ASP cc_start: 0.7877 (m-30) cc_final: 0.7561 (p0) REVERT: B 250 VAL cc_start: 0.8885 (t) cc_final: 0.8580 (t) REVERT: B 265 ILE cc_start: 0.8171 (mm) cc_final: 0.7946 (tt) REVERT: B 356 ASN cc_start: 0.8222 (t0) cc_final: 0.7921 (t0) REVERT: B 399 TYR cc_start: 0.6920 (t80) cc_final: 0.6634 (t80) REVERT: B 413 MET cc_start: 0.8607 (tpt) cc_final: 0.8102 (mmp) REVERT: B 417 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7895 (mm-30) REVERT: B 420 GLU cc_start: 0.8100 (tm-30) cc_final: 0.6153 (tp30) REVERT: B 429 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6675 (mt-10) REVERT: B 431 ASP cc_start: 0.7359 (m-30) cc_final: 0.6854 (m-30) REVERT: L 8 GLN cc_start: 0.8044 (mt0) cc_final: 0.7838 (mt0) REVERT: L 20 PHE cc_start: 0.8946 (t80) cc_final: 0.8741 (t80) REVERT: L 25 SER cc_start: 0.8475 (m) cc_final: 0.8186 (p) REVERT: L 30 ILE cc_start: 0.8474 (mm) cc_final: 0.8258 (mt) REVERT: L 53 GLU cc_start: 0.8265 (pm20) cc_final: 0.7995 (pm20) REVERT: L 69 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7339 (tt0) REVERT: L 114 ASP cc_start: 0.7755 (m-30) cc_final: 0.7388 (t0) REVERT: L 122 LYS cc_start: 0.7933 (mtpm) cc_final: 0.7720 (mtmm) REVERT: L 167 PHE cc_start: 0.7957 (m-80) cc_final: 0.7638 (m-10) REVERT: L 190 HIS cc_start: 0.7805 (t70) cc_final: 0.7285 (t-170) REVERT: L 213 ARG cc_start: 0.7938 (ttm110) cc_final: 0.7728 (ttp80) REVERT: L 217 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6500 (mt) REVERT: L 225 LEU cc_start: 0.8275 (mp) cc_final: 0.8031 (mp) REVERT: L 233 MET cc_start: 0.8330 (mtp) cc_final: 0.7910 (mtp) REVERT: L 247 ASN cc_start: 0.8216 (m-40) cc_final: 0.7613 (t0) REVERT: L 307 HIS cc_start: 0.7948 (m-70) cc_final: 0.7691 (m-70) REVERT: L 321 MET cc_start: 0.8004 (mtm) cc_final: 0.7789 (mtp) REVERT: L 343 GLU cc_start: 0.7919 (pm20) cc_final: 0.7557 (pm20) REVERT: L 379 LYS cc_start: 0.8669 (ttmp) cc_final: 0.8386 (tptp) REVERT: G 25 CYS cc_start: 0.9099 (m) cc_final: 0.8793 (m) REVERT: G 85 GLN cc_start: 0.8088 (mt0) cc_final: 0.7735 (mp10) REVERT: G 86 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8108 (mm) REVERT: G 94 THR cc_start: 0.7895 (p) cc_final: 0.7326 (p) REVERT: G 96 LYS cc_start: 0.6492 (mmtm) cc_final: 0.6194 (tppt) REVERT: G 108 TYR cc_start: 0.7653 (m-80) cc_final: 0.6874 (m-80) REVERT: G 124 LYS cc_start: 0.8364 (ttpt) cc_final: 0.8087 (tptt) REVERT: G 205 ASP cc_start: 0.6977 (t0) cc_final: 0.6545 (t0) REVERT: G 210 TYR cc_start: 0.7613 (m-10) cc_final: 0.6946 (m-80) REVERT: G 224 TYR cc_start: 0.7607 (OUTLIER) cc_final: 0.7255 (m-10) REVERT: G 302 MET cc_start: 0.8802 (mmt) cc_final: 0.8572 (mmt) REVERT: G 356 ASN cc_start: 0.8471 (t0) cc_final: 0.8240 (m-40) REVERT: G 357 TYR cc_start: 0.8574 (m-80) cc_final: 0.8314 (m-80) REVERT: G 378 LEU cc_start: 0.8119 (mt) cc_final: 0.7700 (mt) REVERT: G 396 ASP cc_start: 0.8595 (t0) cc_final: 0.8140 (m-30) REVERT: G 399 TYR cc_start: 0.7015 (t80) cc_final: 0.6141 (t80) REVERT: G 411 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.7073 (mm-30) REVERT: G 413 MET cc_start: 0.8746 (tpt) cc_final: 0.8112 (mmp) REVERT: G 417 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7924 (mm-30) REVERT: G 420 GLU cc_start: 0.8534 (tm-30) cc_final: 0.6939 (tp30) REVERT: G 425 MET cc_start: 0.8400 (mmm) cc_final: 0.8166 (mmp) REVERT: G 431 ASP cc_start: 0.7064 (m-30) cc_final: 0.6731 (t0) outliers start: 75 outliers final: 22 residues processed: 1852 average time/residue: 0.5722 time to fit residues: 1644.2008 Evaluate side-chains 1230 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1198 time to evaluate : 4.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 313 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain H residue 411 GLU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 159 TYR Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain J residue 159 TYR Chi-restraints excluded: chain J residue 313 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 159 TYR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 159 TYR Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 411 GLU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 224 TYR Chi-restraints excluded: chain G residue 411 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 425 optimal weight: 7.9990 chunk 382 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 257 optimal weight: 3.9990 chunk 204 optimal weight: 6.9990 chunk 395 optimal weight: 0.9990 chunk 152 optimal weight: 9.9990 chunk 240 optimal weight: 6.9990 chunk 294 optimal weight: 5.9990 chunk 457 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 15 GLN K 28 HIS K 57 HIS ** K 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 131 GLN K 279 GLN K 375 GLN K 423 GLN ** H 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 197 HIS H 228 ASN I 6 HIS I 15 GLN I 28 HIS I 131 GLN I 137 HIS ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 396 HIS E 15 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 228 ASN E 258 ASN J 15 GLN ** J 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 227 HIS J 347 ASN C 15 GLN C 28 HIS C 131 GLN ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN D 15 GLN D 28 HIS D 57 HIS ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN D 423 GLN ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 HIS F 228 ASN F 301 GLN F 393 HIS A 197 HIS A 228 ASN ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN L 6 HIS L 15 GLN L 28 HIS L 131 GLN ** L 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 227 HIS L 347 ASN ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 197 HIS G 228 ASN G 258 ASN G 393 HIS Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 41436 Z= 0.264 Angle : 0.723 12.576 56298 Z= 0.366 Chirality : 0.048 0.365 6162 Planarity : 0.006 0.098 7308 Dihedral : 12.126 173.035 5900 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.97 % Allowed : 18.95 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.79 (0.12), residues: 5088 helix: 1.88 (0.11), residues: 2316 sheet: 0.50 (0.18), residues: 828 loop : -1.16 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 346 HIS 0.011 0.002 HIS H 192 PHE 0.033 0.002 PHE D 294 TYR 0.020 0.002 TYR E 103 ARG 0.009 0.001 ARG J 318 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1462 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1290 time to evaluate : 4.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 50 TYR cc_start: 0.7828 (m-80) cc_final: 0.7269 (m-10) REVERT: K 114 ASP cc_start: 0.7813 (m-30) cc_final: 0.7266 (t0) REVERT: K 130 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7997 (tm) REVERT: K 133 PHE cc_start: 0.8542 (m-80) cc_final: 0.7969 (m-80) REVERT: K 167 PHE cc_start: 0.8431 (m-80) cc_final: 0.7494 (m-10) REVERT: K 213 ARG cc_start: 0.7424 (ttm110) cc_final: 0.7149 (ttp80) REVERT: K 222 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.6490 (m-80) REVERT: K 297 LYS cc_start: 0.8684 (mttt) cc_final: 0.8441 (ptmm) REVERT: K 300 MET cc_start: 0.8112 (mtt) cc_final: 0.7853 (mtt) REVERT: K 383 GLU cc_start: 0.8152 (tt0) cc_final: 0.7795 (tm-30) REVERT: H 25 CYS cc_start: 0.8790 (m) cc_final: 0.8572 (m) REVERT: H 88 HIS cc_start: 0.8354 (p-80) cc_final: 0.7438 (p90) REVERT: H 124 LYS cc_start: 0.8635 (ttpt) cc_final: 0.8301 (tptt) REVERT: H 167 LEU cc_start: 0.8563 (mp) cc_final: 0.8328 (tt) REVERT: H 168 GLU cc_start: 0.8298 (pt0) cc_final: 0.7948 (pm20) REVERT: H 239 THR cc_start: 0.7749 (p) cc_final: 0.7369 (p) REVERT: H 245 ASP cc_start: 0.8056 (m-30) cc_final: 0.7546 (p0) REVERT: H 279 GLU cc_start: 0.7509 (tp30) cc_final: 0.7185 (pm20) REVERT: H 290 GLU cc_start: 0.7886 (tt0) cc_final: 0.7342 (tp30) REVERT: H 302 MET cc_start: 0.8945 (mmt) cc_final: 0.8651 (mmm) REVERT: H 356 ASN cc_start: 0.8602 (t0) cc_final: 0.8052 (m-40) REVERT: H 413 MET cc_start: 0.8673 (tpt) cc_final: 0.8397 (mmp) REVERT: H 420 GLU cc_start: 0.8136 (tm-30) cc_final: 0.6186 (tp30) REVERT: H 429 GLU cc_start: 0.6830 (mt-10) cc_final: 0.5966 (pp20) REVERT: I 8 GLN cc_start: 0.8172 (mt0) cc_final: 0.7302 (mt0) REVERT: I 22 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8158 (mm-30) REVERT: I 26 ASP cc_start: 0.8202 (m-30) cc_final: 0.7975 (m-30) REVERT: I 127 CYS cc_start: 0.6943 (p) cc_final: 0.6635 (p) REVERT: I 130 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8046 (tm) REVERT: I 133 PHE cc_start: 0.8352 (m-80) cc_final: 0.7968 (m-10) REVERT: I 136 THR cc_start: 0.9176 (m) cc_final: 0.8832 (p) REVERT: I 157 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8117 (mt-10) REVERT: I 167 PHE cc_start: 0.8233 (m-80) cc_final: 0.7961 (m-10) REVERT: I 222 TYR cc_start: 0.7893 (OUTLIER) cc_final: 0.7495 (m-80) REVERT: I 233 MET cc_start: 0.8273 (mtp) cc_final: 0.7860 (mtp) REVERT: I 257 MET cc_start: 0.7088 (mmp) cc_final: 0.6284 (mmp) REVERT: I 320 ARG cc_start: 0.8068 (mtm-85) cc_final: 0.7793 (mtm-85) REVERT: I 379 LYS cc_start: 0.8475 (ttmp) cc_final: 0.8265 (tptp) REVERT: I 383 GLU cc_start: 0.8389 (tt0) cc_final: 0.8004 (tm-30) REVERT: E 2 ARG cc_start: 0.7198 (mtm180) cc_final: 0.6146 (mtm-85) REVERT: E 24 TYR cc_start: 0.8217 (m-10) cc_final: 0.7889 (m-80) REVERT: E 83 TYR cc_start: 0.7852 (m-80) cc_final: 0.7113 (m-10) REVERT: E 88 HIS cc_start: 0.8616 (p90) cc_final: 0.8403 (p-80) REVERT: E 103 TYR cc_start: 0.8160 (t80) cc_final: 0.7911 (t80) REVERT: E 163 LYS cc_start: 0.8927 (ttpp) cc_final: 0.8510 (tppt) REVERT: E 167 LEU cc_start: 0.8587 (mp) cc_final: 0.8310 (mp) REVERT: E 193 THR cc_start: 0.8523 (p) cc_final: 0.8284 (p) REVERT: E 207 GLU cc_start: 0.8336 (tp30) cc_final: 0.7972 (tp30) REVERT: E 290 GLU cc_start: 0.7782 (tt0) cc_final: 0.7335 (tp30) REVERT: E 302 MET cc_start: 0.9005 (mmt) cc_final: 0.8634 (mmm) REVERT: E 346 TRP cc_start: 0.8299 (p-90) cc_final: 0.7778 (p90) REVERT: E 356 ASN cc_start: 0.8298 (t0) cc_final: 0.7808 (m-40) REVERT: E 417 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7566 (mm-30) REVERT: E 425 MET cc_start: 0.8302 (mmm) cc_final: 0.8024 (mmp) REVERT: E 429 GLU cc_start: 0.6548 (mt-10) cc_final: 0.5788 (tm-30) REVERT: J 27 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7708 (mp0) REVERT: J 50 TYR cc_start: 0.7980 (m-80) cc_final: 0.7444 (m-10) REVERT: J 51 TYR cc_start: 0.8172 (m-80) cc_final: 0.7909 (m-10) REVERT: J 59 TYR cc_start: 0.7470 (m-80) cc_final: 0.6830 (m-80) REVERT: J 114 ASP cc_start: 0.8029 (m-30) cc_final: 0.7674 (p0) REVERT: J 123 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8304 (mm-30) REVERT: J 124 CYS cc_start: 0.8659 (t) cc_final: 0.8431 (m) REVERT: J 127 CYS cc_start: 0.7863 (p) cc_final: 0.7638 (p) REVERT: J 136 THR cc_start: 0.9132 (m) cc_final: 0.8651 (p) REVERT: J 200 TYR cc_start: 0.8413 (m-80) cc_final: 0.7741 (m-80) REVERT: J 213 ARG cc_start: 0.7806 (ttm110) cc_final: 0.7177 (ttp80) REVERT: J 222 TYR cc_start: 0.7940 (OUTLIER) cc_final: 0.6679 (m-80) REVERT: J 297 LYS cc_start: 0.8648 (mttt) cc_final: 0.8263 (mmmt) REVERT: J 298 ASN cc_start: 0.8072 (m-40) cc_final: 0.7441 (p0) REVERT: J 307 HIS cc_start: 0.7958 (m-70) cc_final: 0.7617 (m170) REVERT: J 321 MET cc_start: 0.7918 (mtp) cc_final: 0.7608 (mtm) REVERT: J 383 GLU cc_start: 0.8757 (tt0) cc_final: 0.8187 (tm-30) REVERT: J 391 ARG cc_start: 0.8166 (mmm-85) cc_final: 0.7875 (mmp80) REVERT: J 403 MET cc_start: 0.8470 (mmm) cc_final: 0.7998 (mmm) REVERT: J 406 MET cc_start: 0.7417 (ptm) cc_final: 0.5049 (mmm) REVERT: C 8 GLN cc_start: 0.7949 (mt0) cc_final: 0.7075 (mt0) REVERT: C 22 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8263 (mm-30) REVERT: C 99 ASN cc_start: 0.8148 (m-40) cc_final: 0.7906 (m-40) REVERT: C 105 HIS cc_start: 0.8196 (t-90) cc_final: 0.7857 (t70) REVERT: C 130 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8259 (tm) REVERT: C 136 THR cc_start: 0.9170 (m) cc_final: 0.8804 (p) REVERT: C 164 MET cc_start: 0.7545 (mmt) cc_final: 0.7285 (mmt) REVERT: C 222 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.6428 (m-10) REVERT: C 257 MET cc_start: 0.7934 (mmm) cc_final: 0.7385 (mmm) REVERT: C 312 THR cc_start: 0.8722 (p) cc_final: 0.8370 (t) REVERT: C 383 GLU cc_start: 0.8502 (tt0) cc_final: 0.8055 (tm-30) REVERT: C 388 MET cc_start: 0.6561 (mmp) cc_final: 0.6318 (mmp) REVERT: D 8 GLN cc_start: 0.8067 (mt0) cc_final: 0.7652 (mt0) REVERT: D 92 PHE cc_start: 0.8259 (p90) cc_final: 0.7998 (p90) REVERT: D 99 ASN cc_start: 0.8034 (m-40) cc_final: 0.7609 (m110) REVERT: D 105 HIS cc_start: 0.8127 (t70) cc_final: 0.7900 (t70) REVERT: D 114 ASP cc_start: 0.8066 (m-30) cc_final: 0.7600 (t0) REVERT: D 130 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7922 (tm) REVERT: D 133 PHE cc_start: 0.8728 (m-80) cc_final: 0.8229 (m-80) REVERT: D 213 ARG cc_start: 0.7849 (ttm110) cc_final: 0.7528 (ptm-80) REVERT: D 222 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.7632 (m-80) REVERT: D 267 MET cc_start: 0.8626 (mtm) cc_final: 0.8305 (mtt) REVERT: D 300 MET cc_start: 0.7986 (mtt) cc_final: 0.7621 (mtt) REVERT: D 321 MET cc_start: 0.7990 (mtm) cc_final: 0.7581 (mtm) REVERT: D 383 GLU cc_start: 0.8338 (tt0) cc_final: 0.8096 (tm-30) REVERT: F 2 ARG cc_start: 0.7905 (mtm180) cc_final: 0.7534 (mtp-110) REVERT: F 96 LYS cc_start: 0.6308 (mmtm) cc_final: 0.6086 (tppt) REVERT: F 108 TYR cc_start: 0.7262 (m-80) cc_final: 0.6419 (m-80) REVERT: F 124 LYS cc_start: 0.8692 (ttpt) cc_final: 0.8346 (tptt) REVERT: F 191 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8513 (t) REVERT: F 205 ASP cc_start: 0.7328 (t0) cc_final: 0.7082 (t0) REVERT: F 210 TYR cc_start: 0.7731 (m-10) cc_final: 0.7480 (m-10) REVERT: F 269 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7761 (mp) REVERT: F 276 ILE cc_start: 0.8358 (mt) cc_final: 0.8146 (tt) REVERT: F 290 GLU cc_start: 0.8057 (tt0) cc_final: 0.7688 (tp30) REVERT: F 326 LYS cc_start: 0.8825 (ttmt) cc_final: 0.8425 (tppp) REVERT: F 356 ASN cc_start: 0.8519 (t0) cc_final: 0.8192 (m-40) REVERT: F 413 MET cc_start: 0.8618 (tpt) cc_final: 0.8323 (tpt) REVERT: F 417 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8027 (mp0) REVERT: F 420 GLU cc_start: 0.7933 (tm-30) cc_final: 0.6537 (tp30) REVERT: F 429 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7108 (mt-10) REVERT: F 430 LYS cc_start: 0.8363 (ttpt) cc_final: 0.8136 (ttpp) REVERT: A 24 TYR cc_start: 0.8241 (m-10) cc_final: 0.7292 (m-80) REVERT: A 83 TYR cc_start: 0.7780 (m-80) cc_final: 0.6906 (m-10) REVERT: A 124 LYS cc_start: 0.8458 (ttpt) cc_final: 0.8103 (tptt) REVERT: A 245 ASP cc_start: 0.8085 (m-30) cc_final: 0.7645 (p0) REVERT: A 251 ASP cc_start: 0.7386 (m-30) cc_final: 0.7174 (m-30) REVERT: A 254 GLU cc_start: 0.8225 (mt-10) cc_final: 0.8016 (mt-10) REVERT: A 262 TYR cc_start: 0.8064 (m-80) cc_final: 0.7616 (m-10) REVERT: A 265 ILE cc_start: 0.8326 (mm) cc_final: 0.7960 (tt) REVERT: A 276 ILE cc_start: 0.8623 (mt) cc_final: 0.8122 (tt) REVERT: A 290 GLU cc_start: 0.7892 (tt0) cc_final: 0.7516 (tp30) REVERT: A 302 MET cc_start: 0.8909 (mmt) cc_final: 0.8573 (mmm) REVERT: A 326 LYS cc_start: 0.8766 (ttmt) cc_final: 0.8308 (tppt) REVERT: A 356 ASN cc_start: 0.8388 (t0) cc_final: 0.7947 (m-40) REVERT: A 382 THR cc_start: 0.7339 (p) cc_final: 0.6594 (t) REVERT: A 417 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7809 (mm-30) REVERT: A 429 GLU cc_start: 0.7073 (mt-10) cc_final: 0.5735 (tm-30) REVERT: A 431 ASP cc_start: 0.7016 (t70) cc_final: 0.6766 (t0) REVERT: B 2 ARG cc_start: 0.8045 (mtm180) cc_final: 0.7555 (mtm110) REVERT: B 88 HIS cc_start: 0.8599 (p-80) cc_final: 0.8106 (p-80) REVERT: B 149 PHE cc_start: 0.8434 (t80) cc_final: 0.8193 (t80) REVERT: B 167 LEU cc_start: 0.8604 (mp) cc_final: 0.8379 (tt) REVERT: B 177 VAL cc_start: 0.8251 (t) cc_final: 0.7876 (t) REVERT: B 265 ILE cc_start: 0.7983 (mm) cc_final: 0.7695 (tt) REVERT: B 276 ILE cc_start: 0.8496 (mt) cc_final: 0.8213 (tt) REVERT: B 279 GLU cc_start: 0.7330 (tp30) cc_final: 0.7093 (pm20) REVERT: B 356 ASN cc_start: 0.8462 (t0) cc_final: 0.7971 (m-40) REVERT: B 382 THR cc_start: 0.7806 (p) cc_final: 0.7202 (t) REVERT: B 399 TYR cc_start: 0.6806 (t80) cc_final: 0.6545 (t80) REVERT: B 413 MET cc_start: 0.8533 (tpt) cc_final: 0.8262 (mmp) REVERT: B 415 GLU cc_start: 0.8839 (tt0) cc_final: 0.7126 (tm-30) REVERT: B 420 GLU cc_start: 0.7921 (tm-30) cc_final: 0.6484 (tp30) REVERT: L 30 ILE cc_start: 0.8497 (mm) cc_final: 0.8268 (mt) REVERT: L 122 LYS cc_start: 0.8021 (mtpm) cc_final: 0.7804 (mtmm) REVERT: L 167 PHE cc_start: 0.8255 (m-80) cc_final: 0.7774 (m-10) REVERT: L 213 ARG cc_start: 0.7971 (ttm110) cc_final: 0.7698 (ptt90) REVERT: L 216 LYS cc_start: 0.7377 (mptt) cc_final: 0.6684 (ptmm) REVERT: L 222 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.6184 (m-80) REVERT: L 225 LEU cc_start: 0.8363 (mp) cc_final: 0.7633 (tt) REVERT: L 233 MET cc_start: 0.8551 (mtp) cc_final: 0.8242 (mtp) REVERT: L 257 MET cc_start: 0.7810 (mmm) cc_final: 0.7257 (mmt) REVERT: L 312 THR cc_start: 0.7944 (p) cc_final: 0.7686 (t) REVERT: L 321 MET cc_start: 0.8067 (mtm) cc_final: 0.7538 (mtp) REVERT: L 379 LYS cc_start: 0.8747 (ttmp) cc_final: 0.8513 (tptp) REVERT: L 383 GLU cc_start: 0.8565 (tt0) cc_final: 0.7995 (tm-30) REVERT: G 25 CYS cc_start: 0.8943 (m) cc_final: 0.8453 (m) REVERT: G 85 GLN cc_start: 0.7972 (mt0) cc_final: 0.7667 (mp10) REVERT: G 108 TYR cc_start: 0.7345 (m-80) cc_final: 0.6676 (m-80) REVERT: G 124 LYS cc_start: 0.8480 (ttpt) cc_final: 0.8077 (tptt) REVERT: G 207 GLU cc_start: 0.8583 (tp30) cc_final: 0.8321 (tp30) REVERT: G 210 TYR cc_start: 0.7735 (m-10) cc_final: 0.7354 (m-80) REVERT: G 251 ASP cc_start: 0.7164 (m-30) cc_final: 0.6364 (m-30) REVERT: G 254 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7809 (mt-10) REVERT: G 276 ILE cc_start: 0.8198 (mt) cc_final: 0.7851 (tt) REVERT: G 302 MET cc_start: 0.8721 (mmt) cc_final: 0.8471 (mmm) REVERT: G 356 ASN cc_start: 0.8537 (t0) cc_final: 0.8137 (m-40) REVERT: G 396 ASP cc_start: 0.8712 (t0) cc_final: 0.8294 (m-30) REVERT: G 404 PHE cc_start: 0.7827 (m-80) cc_final: 0.7612 (m-10) REVERT: G 413 MET cc_start: 0.8753 (tpt) cc_final: 0.8331 (mmp) REVERT: G 420 GLU cc_start: 0.8271 (tm-30) cc_final: 0.6889 (tp30) REVERT: G 429 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7277 (mt-10) outliers start: 172 outliers final: 95 residues processed: 1384 average time/residue: 0.5552 time to fit residues: 1218.6945 Evaluate side-chains 1218 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1110 time to evaluate : 4.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 GLN Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 57 HIS Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 222 TYR Chi-restraints excluded: chain K residue 293 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 249 ASN Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 328 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 222 TYR Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 11 GLN Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 222 TYR Chi-restraints excluded: chain J residue 312 THR Chi-restraints excluded: chain J residue 338 SER Chi-restraints excluded: chain J residue 371 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 222 TYR Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain D residue 11 GLN Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain L residue 11 GLN Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 222 TYR Chi-restraints excluded: chain L residue 293 MET Chi-restraints excluded: chain L residue 371 SER Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 224 TYR Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 328 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 254 optimal weight: 10.0000 chunk 142 optimal weight: 8.9990 chunk 380 optimal weight: 3.9990 chunk 311 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 458 optimal weight: 7.9990 chunk 495 optimal weight: 0.0030 chunk 408 optimal weight: 20.0000 chunk 454 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 chunk 367 optimal weight: 7.9990 overall best weight: 5.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 301 GLN H 393 HIS ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN ** J 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 247 ASN ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN D 57 HIS ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN D 423 GLN F 31 GLN F 301 GLN A 31 GLN A 128 GLN A 197 HIS ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS L 57 HIS ** L 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 GLN ** G 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 258 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 41436 Z= 0.262 Angle : 0.676 15.801 56298 Z= 0.338 Chirality : 0.046 0.232 6162 Planarity : 0.005 0.062 7308 Dihedral : 11.121 169.151 5865 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.19 % Allowed : 21.68 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.71 (0.12), residues: 5088 helix: 1.70 (0.11), residues: 2316 sheet: 0.60 (0.18), residues: 822 loop : -1.12 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 344 HIS 0.013 0.001 HIS K 57 PHE 0.021 0.002 PHE A 149 TYR 0.016 0.002 TYR E 103 ARG 0.009 0.001 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1368 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 1143 time to evaluate : 4.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 50 TYR cc_start: 0.7893 (m-80) cc_final: 0.7416 (m-10) REVERT: K 53 GLU cc_start: 0.8155 (pm20) cc_final: 0.7473 (pm20) REVERT: K 73 MET cc_start: 0.9116 (mmm) cc_final: 0.8658 (mmm) REVERT: K 99 ASN cc_start: 0.8425 (m-40) cc_final: 0.7941 (m-40) REVERT: K 114 ASP cc_start: 0.7609 (m-30) cc_final: 0.7090 (t0) REVERT: K 130 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7743 (tm) REVERT: K 133 PHE cc_start: 0.8578 (m-80) cc_final: 0.8354 (m-80) REVERT: K 213 ARG cc_start: 0.7602 (ttm110) cc_final: 0.6724 (ttp80) REVERT: K 222 TYR cc_start: 0.8034 (OUTLIER) cc_final: 0.6577 (m-10) REVERT: K 257 MET cc_start: 0.7989 (mmm) cc_final: 0.7595 (mmm) REVERT: K 297 LYS cc_start: 0.8698 (mttt) cc_final: 0.8267 (mmmt) REVERT: K 355 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.7473 (t70) REVERT: K 383 GLU cc_start: 0.8317 (tt0) cc_final: 0.7761 (tm-30) REVERT: H 47 ASP cc_start: 0.5155 (OUTLIER) cc_final: 0.4809 (m-30) REVERT: H 88 HIS cc_start: 0.8398 (p-80) cc_final: 0.7919 (p90) REVERT: H 124 LYS cc_start: 0.8644 (ttpt) cc_final: 0.8292 (tptt) REVERT: H 154 MET cc_start: 0.8531 (mmp) cc_final: 0.8076 (tpt) REVERT: H 163 LYS cc_start: 0.8794 (ttpp) cc_final: 0.8561 (ptmm) REVERT: H 245 ASP cc_start: 0.7900 (m-30) cc_final: 0.7567 (p0) REVERT: H 279 GLU cc_start: 0.7505 (tp30) cc_final: 0.7199 (pm20) REVERT: H 290 GLU cc_start: 0.7971 (tt0) cc_final: 0.7403 (tp30) REVERT: H 302 MET cc_start: 0.8910 (mmt) cc_final: 0.8403 (mmm) REVERT: H 356 ASN cc_start: 0.8637 (t0) cc_final: 0.8066 (m-40) REVERT: H 413 MET cc_start: 0.8583 (tpt) cc_final: 0.8325 (mmp) REVERT: H 420 GLU cc_start: 0.8067 (tm-30) cc_final: 0.6100 (tp30) REVERT: H 429 GLU cc_start: 0.6969 (mt-10) cc_final: 0.5975 (pp20) REVERT: I 8 GLN cc_start: 0.7961 (mt0) cc_final: 0.7104 (mt0) REVERT: I 22 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8113 (mm-30) REVERT: I 26 ASP cc_start: 0.8300 (m-30) cc_final: 0.8059 (m-30) REVERT: I 133 PHE cc_start: 0.8361 (m-80) cc_final: 0.7782 (m-10) REVERT: I 136 THR cc_start: 0.9173 (m) cc_final: 0.8775 (p) REVERT: I 157 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8082 (mt-10) REVERT: I 167 PHE cc_start: 0.8496 (m-80) cc_final: 0.8153 (m-10) REVERT: I 213 ARG cc_start: 0.8255 (ttp80) cc_final: 0.7996 (ptm-80) REVERT: I 233 MET cc_start: 0.8291 (mtp) cc_final: 0.7951 (mtp) REVERT: I 257 MET cc_start: 0.7178 (mmp) cc_final: 0.6888 (mmm) REVERT: I 298 ASN cc_start: 0.7608 (m110) cc_final: 0.7405 (m-40) REVERT: I 299 MET cc_start: 0.8623 (mmt) cc_final: 0.8283 (mmt) REVERT: I 320 ARG cc_start: 0.8072 (mtm-85) cc_final: 0.7830 (mtm-85) REVERT: I 355 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.7827 (t0) REVERT: I 377 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7222 (mp) REVERT: I 383 GLU cc_start: 0.8401 (tt0) cc_final: 0.7999 (tm-30) REVERT: I 388 MET cc_start: 0.6768 (OUTLIER) cc_final: 0.6537 (mmp) REVERT: E 24 TYR cc_start: 0.8359 (m-10) cc_final: 0.7990 (m-80) REVERT: E 36 MET cc_start: 0.8247 (tmm) cc_final: 0.7930 (tmm) REVERT: E 47 ASP cc_start: 0.5730 (OUTLIER) cc_final: 0.4624 (m-30) REVERT: E 83 TYR cc_start: 0.7866 (m-80) cc_final: 0.7007 (m-10) REVERT: E 88 HIS cc_start: 0.8679 (p90) cc_final: 0.8467 (p-80) REVERT: E 163 LYS cc_start: 0.8981 (ttpp) cc_final: 0.8464 (tppt) REVERT: E 167 LEU cc_start: 0.8579 (mp) cc_final: 0.8321 (mp) REVERT: E 290 GLU cc_start: 0.7923 (tt0) cc_final: 0.7455 (tp30) REVERT: E 302 MET cc_start: 0.9042 (mmt) cc_final: 0.8646 (mmm) REVERT: E 346 TRP cc_start: 0.8279 (p-90) cc_final: 0.7753 (p90) REVERT: E 356 ASN cc_start: 0.8228 (t0) cc_final: 0.7744 (m-40) REVERT: E 388 TRP cc_start: 0.8397 (m-90) cc_final: 0.7766 (m-90) REVERT: E 417 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7629 (mm-30) REVERT: E 425 MET cc_start: 0.8339 (mmm) cc_final: 0.8081 (mmp) REVERT: E 429 GLU cc_start: 0.6713 (mt-10) cc_final: 0.5623 (tm-30) REVERT: J 50 TYR cc_start: 0.7887 (m-80) cc_final: 0.7385 (m-10) REVERT: J 99 ASN cc_start: 0.8043 (m-40) cc_final: 0.7649 (m-40) REVERT: J 114 ASP cc_start: 0.8028 (m-30) cc_final: 0.7733 (p0) REVERT: J 124 CYS cc_start: 0.8650 (t) cc_final: 0.8423 (m) REVERT: J 200 TYR cc_start: 0.8521 (m-80) cc_final: 0.7937 (m-80) REVERT: J 213 ARG cc_start: 0.7735 (ttm110) cc_final: 0.7027 (ttp80) REVERT: J 222 TYR cc_start: 0.7918 (OUTLIER) cc_final: 0.7259 (m-80) REVERT: J 297 LYS cc_start: 0.8697 (mttt) cc_final: 0.8417 (mmmt) REVERT: J 298 ASN cc_start: 0.8032 (m-40) cc_final: 0.7450 (p0) REVERT: J 307 HIS cc_start: 0.7926 (m-70) cc_final: 0.7620 (m170) REVERT: J 321 MET cc_start: 0.8031 (mtp) cc_final: 0.7791 (mtp) REVERT: J 323 MET cc_start: 0.8894 (ttt) cc_final: 0.8681 (ttp) REVERT: J 344 TRP cc_start: 0.6147 (p90) cc_final: 0.5725 (p-90) REVERT: J 383 GLU cc_start: 0.8620 (tt0) cc_final: 0.8279 (tm-30) REVERT: J 403 MET cc_start: 0.8529 (mmm) cc_final: 0.8165 (mmm) REVERT: J 406 MET cc_start: 0.7616 (ptm) cc_final: 0.5191 (mmm) REVERT: C 22 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8131 (mm-30) REVERT: C 73 MET cc_start: 0.8896 (mmm) cc_final: 0.8679 (mmm) REVERT: C 103 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8090 (mtpt) REVERT: C 136 THR cc_start: 0.9144 (m) cc_final: 0.8646 (p) REVERT: C 222 TYR cc_start: 0.8094 (OUTLIER) cc_final: 0.5983 (m-10) REVERT: C 247 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.7510 (p0) REVERT: C 257 MET cc_start: 0.8057 (mmm) cc_final: 0.7646 (mmm) REVERT: C 377 LEU cc_start: 0.7794 (mp) cc_final: 0.7564 (mt) REVERT: C 383 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8123 (tm-30) REVERT: D 8 GLN cc_start: 0.8211 (mt0) cc_final: 0.7611 (mt0) REVERT: D 50 TYR cc_start: 0.8172 (m-80) cc_final: 0.7316 (m-80) REVERT: D 92 PHE cc_start: 0.8276 (p90) cc_final: 0.8052 (p90) REVERT: D 99 ASN cc_start: 0.8001 (m-40) cc_final: 0.7524 (m-40) REVERT: D 105 HIS cc_start: 0.8391 (t70) cc_final: 0.8142 (t70) REVERT: D 114 ASP cc_start: 0.8060 (m-30) cc_final: 0.7590 (t0) REVERT: D 130 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8020 (tm) REVERT: D 133 PHE cc_start: 0.8756 (m-80) cc_final: 0.8261 (m-80) REVERT: D 213 ARG cc_start: 0.7739 (ttm110) cc_final: 0.7319 (ptt90) REVERT: D 217 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6890 (mp) REVERT: D 222 TYR cc_start: 0.8342 (OUTLIER) cc_final: 0.7748 (m-80) REVERT: D 300 MET cc_start: 0.8192 (mtt) cc_final: 0.7830 (mtt) REVERT: D 321 MET cc_start: 0.8021 (mtm) cc_final: 0.7651 (mtm) REVERT: D 355 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8132 (m-30) REVERT: D 383 GLU cc_start: 0.8395 (tt0) cc_final: 0.7944 (tm-30) REVERT: D 391 ARG cc_start: 0.7809 (mmm-85) cc_final: 0.7566 (mmm-85) REVERT: F 2 ARG cc_start: 0.7782 (mtm180) cc_final: 0.7557 (mtm110) REVERT: F 47 ASP cc_start: 0.4756 (OUTLIER) cc_final: 0.3953 (m-30) REVERT: F 124 LYS cc_start: 0.8734 (ttpt) cc_final: 0.8432 (tptt) REVERT: F 205 ASP cc_start: 0.7534 (t0) cc_final: 0.7188 (t0) REVERT: F 210 TYR cc_start: 0.7692 (m-10) cc_final: 0.7442 (m-10) REVERT: F 224 TYR cc_start: 0.7713 (OUTLIER) cc_final: 0.6972 (m-10) REVERT: F 276 ILE cc_start: 0.8429 (mt) cc_final: 0.8116 (tt) REVERT: F 290 GLU cc_start: 0.8236 (tt0) cc_final: 0.7871 (tp30) REVERT: F 326 LYS cc_start: 0.8861 (ttmt) cc_final: 0.8479 (tppt) REVERT: F 356 ASN cc_start: 0.8518 (t0) cc_final: 0.8211 (m-40) REVERT: F 417 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7987 (mp0) REVERT: F 420 GLU cc_start: 0.7794 (tm-30) cc_final: 0.6443 (tp30) REVERT: F 425 MET cc_start: 0.8379 (mmp) cc_final: 0.8127 (mmp) REVERT: A 24 TYR cc_start: 0.8333 (m-80) cc_final: 0.7326 (m-80) REVERT: A 36 MET cc_start: 0.7732 (ttt) cc_final: 0.7313 (tmm) REVERT: A 47 ASP cc_start: 0.5408 (OUTLIER) cc_final: 0.4527 (m-30) REVERT: A 49 PHE cc_start: 0.8076 (p90) cc_final: 0.7860 (p90) REVERT: A 75 ILE cc_start: 0.8303 (mt) cc_final: 0.8059 (mm) REVERT: A 83 TYR cc_start: 0.7849 (m-80) cc_final: 0.6848 (m-10) REVERT: A 88 HIS cc_start: 0.8465 (p-80) cc_final: 0.7961 (p90) REVERT: A 124 LYS cc_start: 0.8568 (ttpt) cc_final: 0.8213 (tptt) REVERT: A 154 MET cc_start: 0.8395 (mmm) cc_final: 0.8045 (tpt) REVERT: A 245 ASP cc_start: 0.8088 (m-30) cc_final: 0.7871 (p0) REVERT: A 251 ASP cc_start: 0.7594 (m-30) cc_final: 0.7257 (m-30) REVERT: A 254 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8063 (mt-10) REVERT: A 262 TYR cc_start: 0.8015 (m-80) cc_final: 0.7702 (m-10) REVERT: A 276 ILE cc_start: 0.8624 (mt) cc_final: 0.8260 (tt) REVERT: A 290 GLU cc_start: 0.8046 (tt0) cc_final: 0.7597 (tp30) REVERT: A 302 MET cc_start: 0.8889 (mmt) cc_final: 0.8632 (mmm) REVERT: A 326 LYS cc_start: 0.8856 (ttmt) cc_final: 0.8340 (tppt) REVERT: A 346 TRP cc_start: 0.6727 (p90) cc_final: 0.6318 (p90) REVERT: A 356 ASN cc_start: 0.8465 (t0) cc_final: 0.7970 (m110) REVERT: A 417 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7900 (mm-30) REVERT: A 429 GLU cc_start: 0.7086 (mt-10) cc_final: 0.5850 (pp20) REVERT: B 2 ARG cc_start: 0.7740 (mtm180) cc_final: 0.7449 (mtm110) REVERT: B 88 HIS cc_start: 0.8323 (p-80) cc_final: 0.8078 (p90) REVERT: B 97 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6602 (tm-30) REVERT: B 167 LEU cc_start: 0.8638 (mp) cc_final: 0.8307 (tt) REVERT: B 202 PHE cc_start: 0.8136 (m-80) cc_final: 0.7881 (m-10) REVERT: B 245 ASP cc_start: 0.7864 (m-30) cc_final: 0.7630 (p0) REVERT: B 356 ASN cc_start: 0.8561 (t0) cc_final: 0.8103 (m-40) REVERT: B 396 ASP cc_start: 0.8224 (t0) cc_final: 0.8019 (m-30) REVERT: B 413 MET cc_start: 0.8514 (tpt) cc_final: 0.8232 (mmp) REVERT: B 420 GLU cc_start: 0.7965 (tm-30) cc_final: 0.6461 (tp30) REVERT: L 122 LYS cc_start: 0.7873 (mtpm) cc_final: 0.7642 (mtmm) REVERT: L 167 PHE cc_start: 0.8318 (m-80) cc_final: 0.7861 (m-10) REVERT: L 222 TYR cc_start: 0.7793 (OUTLIER) cc_final: 0.6739 (m-80) REVERT: L 225 LEU cc_start: 0.8366 (mp) cc_final: 0.7712 (tt) REVERT: L 233 MET cc_start: 0.8539 (mtp) cc_final: 0.8209 (mtp) REVERT: L 257 MET cc_start: 0.7747 (mmm) cc_final: 0.7339 (mmt) REVERT: L 379 LYS cc_start: 0.8768 (ttmp) cc_final: 0.8519 (tptp) REVERT: L 383 GLU cc_start: 0.8615 (tt0) cc_final: 0.8244 (tm-30) REVERT: G 24 TYR cc_start: 0.8258 (m-80) cc_final: 0.8048 (m-80) REVERT: G 47 ASP cc_start: 0.5477 (OUTLIER) cc_final: 0.4745 (m-30) REVERT: G 108 TYR cc_start: 0.7415 (m-80) cc_final: 0.6814 (m-80) REVERT: G 124 LYS cc_start: 0.8527 (ttpt) cc_final: 0.8139 (tptt) REVERT: G 210 TYR cc_start: 0.7675 (m-10) cc_final: 0.6993 (m-80) REVERT: G 251 ASP cc_start: 0.7136 (m-30) cc_final: 0.6385 (m-30) REVERT: G 254 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7869 (mt-10) REVERT: G 326 LYS cc_start: 0.8851 (ttpp) cc_final: 0.8591 (ttpt) REVERT: G 353 VAL cc_start: 0.9351 (OUTLIER) cc_final: 0.9097 (m) REVERT: G 356 ASN cc_start: 0.8568 (t0) cc_final: 0.8118 (m-40) REVERT: G 396 ASP cc_start: 0.8780 (t0) cc_final: 0.8450 (m-30) REVERT: G 413 MET cc_start: 0.8741 (tpt) cc_final: 0.8246 (mmp) REVERT: G 420 GLU cc_start: 0.8362 (tm-30) cc_final: 0.6985 (tp30) outliers start: 225 outliers final: 153 residues processed: 1293 average time/residue: 0.5293 time to fit residues: 1093.3541 Evaluate side-chains 1227 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1049 time to evaluate : 4.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 GLN Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 222 TYR Chi-restraints excluded: chain K residue 247 ASN Chi-restraints excluded: chain K residue 293 MET Chi-restraints excluded: chain K residue 313 VAL Chi-restraints excluded: chain K residue 355 ASP Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 205 ASP Chi-restraints excluded: chain H residue 249 ASN Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 256 GLN Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 287 SER Chi-restraints excluded: chain H residue 328 VAL Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain H residue 377 MET Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 159 TYR Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 355 ASP Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain J residue 11 GLN Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 178 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 222 TYR Chi-restraints excluded: chain J residue 312 THR Chi-restraints excluded: chain J residue 371 SER Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 222 TYR Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 129 CYS Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 57 HIS Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 222 TYR Chi-restraints excluded: chain L residue 347 ASN Chi-restraints excluded: chain L residue 371 SER Chi-restraints excluded: chain L residue 388 MET Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 224 TYR Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 269 LEU Chi-restraints excluded: chain G residue 287 SER Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain G residue 334 THR Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 361 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 453 optimal weight: 6.9990 chunk 344 optimal weight: 10.0000 chunk 237 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 218 optimal weight: 8.9990 chunk 307 optimal weight: 30.0000 chunk 460 optimal weight: 6.9990 chunk 487 optimal weight: 8.9990 chunk 240 optimal weight: 5.9990 chunk 436 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 57 HIS ** K 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 423 GLN H 31 GLN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 285 GLN I 28 HIS I 134 GLN ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 384 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN J 131 GLN ** J 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 HIS ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 HIS ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN D 423 GLN ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 GLN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 134 GLN ** L 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 247 ASN G 31 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 41436 Z= 0.326 Angle : 0.707 16.819 56298 Z= 0.354 Chirality : 0.047 0.254 6162 Planarity : 0.006 0.066 7308 Dihedral : 11.059 169.889 5859 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 7.04 % Allowed : 21.65 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.22 (0.12), residues: 5088 helix: 1.22 (0.11), residues: 2340 sheet: 0.60 (0.18), residues: 810 loop : -1.42 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 388 HIS 0.031 0.002 HIS L 57 PHE 0.033 0.002 PHE J 389 TYR 0.023 0.002 TYR E 103 ARG 0.008 0.001 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1420 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 1115 time to evaluate : 3.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 35 ASN cc_start: 0.7697 (OUTLIER) cc_final: 0.7325 (m110) REVERT: K 50 TYR cc_start: 0.8008 (m-80) cc_final: 0.7526 (m-10) REVERT: K 73 MET cc_start: 0.9165 (mmm) cc_final: 0.8549 (mmm) REVERT: K 113 VAL cc_start: 0.7506 (OUTLIER) cc_final: 0.7295 (p) REVERT: K 114 ASP cc_start: 0.7639 (m-30) cc_final: 0.7139 (t0) REVERT: K 130 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7738 (tm) REVERT: K 213 ARG cc_start: 0.7692 (ttm110) cc_final: 0.7231 (ttp80) REVERT: K 217 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7177 (mt) REVERT: K 222 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.7491 (m-80) REVERT: K 257 MET cc_start: 0.8167 (mmm) cc_final: 0.7932 (mmm) REVERT: K 297 LYS cc_start: 0.8730 (mttt) cc_final: 0.8391 (mmmt) REVERT: K 355 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8107 (m-30) REVERT: K 363 MET cc_start: 0.8410 (mmt) cc_final: 0.7987 (mmt) REVERT: K 383 GLU cc_start: 0.8333 (tt0) cc_final: 0.7779 (tm-30) REVERT: H 88 HIS cc_start: 0.8210 (p-80) cc_final: 0.8002 (p-80) REVERT: H 124 LYS cc_start: 0.8692 (ttpt) cc_final: 0.8299 (tptt) REVERT: H 154 MET cc_start: 0.8571 (mmp) cc_final: 0.8135 (tpt) REVERT: H 163 LYS cc_start: 0.8836 (ttpp) cc_final: 0.8633 (ptmm) REVERT: H 168 GLU cc_start: 0.8557 (pt0) cc_final: 0.8098 (pt0) REVERT: H 221 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7557 (ptm-80) REVERT: H 245 ASP cc_start: 0.7851 (m-30) cc_final: 0.7547 (p0) REVERT: H 251 ASP cc_start: 0.7832 (m-30) cc_final: 0.7591 (m-30) REVERT: H 290 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7437 (tp30) REVERT: H 302 MET cc_start: 0.8999 (mmt) cc_final: 0.8674 (mmm) REVERT: H 356 ASN cc_start: 0.8703 (t0) cc_final: 0.7968 (m-40) REVERT: H 386 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7728 (mp0) REVERT: H 388 TRP cc_start: 0.8419 (m-90) cc_final: 0.8174 (m-90) REVERT: H 407 TRP cc_start: 0.8674 (m100) cc_final: 0.8463 (m100) REVERT: H 420 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.6312 (tp30) REVERT: I 22 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8089 (mm-30) REVERT: I 26 ASP cc_start: 0.8418 (m-30) cc_final: 0.8187 (m-30) REVERT: I 73 MET cc_start: 0.9194 (mmm) cc_final: 0.8804 (mmm) REVERT: I 77 ARG cc_start: 0.7861 (tpt170) cc_final: 0.7643 (tpt170) REVERT: I 81 PHE cc_start: 0.5019 (OUTLIER) cc_final: 0.3756 (t80) REVERT: I 130 LEU cc_start: 0.8335 (tm) cc_final: 0.8026 (tm) REVERT: I 133 PHE cc_start: 0.8424 (m-80) cc_final: 0.8133 (m-10) REVERT: I 136 THR cc_start: 0.9210 (m) cc_final: 0.8838 (p) REVERT: I 167 PHE cc_start: 0.8517 (m-80) cc_final: 0.8134 (m-10) REVERT: I 222 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.7527 (m-80) REVERT: I 233 MET cc_start: 0.8367 (mtp) cc_final: 0.8080 (mtp) REVERT: I 257 MET cc_start: 0.7427 (mmp) cc_final: 0.6544 (mmp) REVERT: I 383 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8025 (tm-30) REVERT: I 397 TRP cc_start: 0.8578 (m100) cc_final: 0.8377 (m100) REVERT: I 425 TYR cc_start: 0.7413 (m-80) cc_final: 0.7133 (m-10) REVERT: E 24 TYR cc_start: 0.8484 (m-10) cc_final: 0.8104 (m-80) REVERT: E 36 MET cc_start: 0.8240 (tmm) cc_final: 0.7909 (tmm) REVERT: E 83 TYR cc_start: 0.8034 (m-80) cc_final: 0.6975 (m-10) REVERT: E 103 TYR cc_start: 0.8292 (t80) cc_final: 0.8064 (t80) REVERT: E 108 TYR cc_start: 0.6970 (m-10) cc_final: 0.6739 (m-10) REVERT: E 163 LYS cc_start: 0.8983 (ttpp) cc_final: 0.8611 (tppt) REVERT: E 167 LEU cc_start: 0.8599 (mp) cc_final: 0.8394 (mp) REVERT: E 251 ASP cc_start: 0.7892 (m-30) cc_final: 0.7631 (m-30) REVERT: E 255 PHE cc_start: 0.8986 (m-10) cc_final: 0.8758 (m-10) REVERT: E 256 GLN cc_start: 0.7785 (mt0) cc_final: 0.7273 (mt0) REVERT: E 257 THR cc_start: 0.9097 (m) cc_final: 0.8817 (p) REVERT: E 262 TYR cc_start: 0.8070 (m-10) cc_final: 0.7855 (m-10) REVERT: E 290 GLU cc_start: 0.8066 (tt0) cc_final: 0.7637 (tp30) REVERT: E 302 MET cc_start: 0.9185 (mmt) cc_final: 0.8902 (mmm) REVERT: E 346 TRP cc_start: 0.8236 (p-90) cc_final: 0.7711 (p90) REVERT: E 356 ASN cc_start: 0.8349 (t0) cc_final: 0.7823 (m-40) REVERT: E 377 MET cc_start: 0.8232 (ttp) cc_final: 0.7928 (ttp) REVERT: E 388 TRP cc_start: 0.8539 (m-90) cc_final: 0.7926 (m-90) REVERT: E 417 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7691 (mm-30) REVERT: E 429 GLU cc_start: 0.6863 (mt-10) cc_final: 0.5671 (tm-30) REVERT: J 50 TYR cc_start: 0.7942 (m-80) cc_final: 0.7246 (m-10) REVERT: J 114 ASP cc_start: 0.8024 (m-30) cc_final: 0.7485 (t0) REVERT: J 124 CYS cc_start: 0.8718 (t) cc_final: 0.8466 (m) REVERT: J 147 MET cc_start: 0.8540 (tmm) cc_final: 0.8231 (tmm) REVERT: J 200 TYR cc_start: 0.8539 (m-80) cc_final: 0.7801 (m-80) REVERT: J 213 ARG cc_start: 0.7804 (ttm110) cc_final: 0.7108 (ttp80) REVERT: J 215 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7829 (mp) REVERT: J 217 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.6755 (mt) REVERT: J 253 LEU cc_start: 0.8456 (mm) cc_final: 0.8253 (mm) REVERT: J 297 LYS cc_start: 0.8684 (mttt) cc_final: 0.8389 (mmmt) REVERT: J 298 ASN cc_start: 0.7928 (m-40) cc_final: 0.7243 (p0) REVERT: J 323 MET cc_start: 0.8982 (ttt) cc_final: 0.8770 (ttp) REVERT: J 344 TRP cc_start: 0.6011 (p90) cc_final: 0.5601 (p-90) REVERT: J 383 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8289 (tm-30) REVERT: J 403 MET cc_start: 0.8549 (mmm) cc_final: 0.8272 (mmm) REVERT: J 406 MET cc_start: 0.7721 (ptm) cc_final: 0.5454 (tpt) REVERT: C 22 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8028 (mm-30) REVERT: C 73 MET cc_start: 0.8987 (mmm) cc_final: 0.8752 (mmm) REVERT: C 136 THR cc_start: 0.9157 (m) cc_final: 0.8662 (p) REVERT: C 222 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.5849 (m-80) REVERT: C 257 MET cc_start: 0.8204 (mmm) cc_final: 0.7853 (mmm) REVERT: C 298 ASN cc_start: 0.7322 (m-40) cc_final: 0.6085 (t0) REVERT: C 383 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8162 (tm-30) REVERT: C 390 ARG cc_start: 0.7996 (ptp-110) cc_final: 0.7602 (tpp-160) REVERT: D 35 ASN cc_start: 0.7498 (OUTLIER) cc_final: 0.7267 (m-40) REVERT: D 50 TYR cc_start: 0.8218 (m-80) cc_final: 0.7400 (m-80) REVERT: D 114 ASP cc_start: 0.8071 (m-30) cc_final: 0.7571 (t0) REVERT: D 130 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7840 (tm) REVERT: D 133 PHE cc_start: 0.8710 (m-80) cc_final: 0.8351 (m-80) REVERT: D 200 TYR cc_start: 0.8758 (m-80) cc_final: 0.8204 (m-80) REVERT: D 217 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7556 (mp) REVERT: D 222 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.7738 (m-80) REVERT: D 300 MET cc_start: 0.8420 (mtt) cc_final: 0.8037 (mtt) REVERT: D 321 MET cc_start: 0.8129 (mtm) cc_final: 0.7859 (mtp) REVERT: D 355 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.7863 (m-30) REVERT: D 383 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7948 (tm-30) REVERT: D 406 MET cc_start: 0.7962 (ptm) cc_final: 0.5766 (mmm) REVERT: F 2 ARG cc_start: 0.7887 (mtm180) cc_final: 0.7427 (mtm110) REVERT: F 47 ASP cc_start: 0.5121 (OUTLIER) cc_final: 0.4183 (m-30) REVERT: F 108 TYR cc_start: 0.7688 (m-80) cc_final: 0.7264 (m-80) REVERT: F 121 ARG cc_start: 0.8250 (tpp-160) cc_final: 0.7778 (mpt180) REVERT: F 124 LYS cc_start: 0.8684 (ttpt) cc_final: 0.8424 (tptt) REVERT: F 157 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8238 (mp) REVERT: F 205 ASP cc_start: 0.7589 (t0) cc_final: 0.7270 (t0) REVERT: F 210 TYR cc_start: 0.7681 (m-10) cc_final: 0.7408 (m-10) REVERT: F 224 TYR cc_start: 0.7684 (OUTLIER) cc_final: 0.7005 (m-10) REVERT: F 276 ILE cc_start: 0.8657 (mt) cc_final: 0.8400 (tt) REVERT: F 290 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7978 (tp30) REVERT: F 326 LYS cc_start: 0.8880 (ttmt) cc_final: 0.8503 (tppt) REVERT: F 332 ILE cc_start: 0.8989 (mm) cc_final: 0.8745 (mm) REVERT: F 356 ASN cc_start: 0.8452 (t0) cc_final: 0.8132 (m-40) REVERT: F 388 TRP cc_start: 0.8069 (m-90) cc_final: 0.7834 (m-90) REVERT: F 417 GLU cc_start: 0.8407 (mm-30) cc_final: 0.7919 (mp0) REVERT: A 24 TYR cc_start: 0.8424 (m-80) cc_final: 0.7418 (m-80) REVERT: A 36 MET cc_start: 0.7429 (ttt) cc_final: 0.7067 (tmm) REVERT: A 83 TYR cc_start: 0.7764 (m-80) cc_final: 0.6748 (m-10) REVERT: A 88 HIS cc_start: 0.8364 (p-80) cc_final: 0.7904 (p90) REVERT: A 124 LYS cc_start: 0.8536 (ttpt) cc_final: 0.8159 (tptt) REVERT: A 128 GLN cc_start: 0.6920 (mt0) cc_final: 0.6718 (mt0) REVERT: A 262 TYR cc_start: 0.8150 (m-80) cc_final: 0.7728 (m-10) REVERT: A 276 ILE cc_start: 0.8705 (mt) cc_final: 0.8411 (tt) REVERT: A 290 GLU cc_start: 0.8253 (tt0) cc_final: 0.7649 (tp30) REVERT: A 302 MET cc_start: 0.8891 (mmt) cc_final: 0.8611 (mmm) REVERT: A 326 LYS cc_start: 0.8771 (ttmt) cc_final: 0.8362 (tppt) REVERT: A 346 TRP cc_start: 0.6572 (p90) cc_final: 0.5955 (p90) REVERT: A 356 ASN cc_start: 0.8494 (t0) cc_final: 0.8052 (m110) REVERT: A 417 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7981 (mm-30) REVERT: B 2 ARG cc_start: 0.7700 (mtm180) cc_final: 0.7474 (mtm110) REVERT: B 167 LEU cc_start: 0.8572 (mp) cc_final: 0.8208 (tt) REVERT: B 202 PHE cc_start: 0.8121 (m-80) cc_final: 0.7821 (m-10) REVERT: B 302 MET cc_start: 0.8710 (mmp) cc_final: 0.8386 (mmp) REVERT: B 316 CYS cc_start: 0.8928 (m) cc_final: 0.8697 (m) REVERT: B 332 ILE cc_start: 0.9043 (mm) cc_final: 0.8796 (mm) REVERT: B 356 ASN cc_start: 0.8530 (t0) cc_final: 0.8077 (m-40) REVERT: B 415 GLU cc_start: 0.8619 (tt0) cc_final: 0.7215 (tm-30) REVERT: B 429 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6991 (mt-10) REVERT: L 45 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8566 (tp30) REVERT: L 122 LYS cc_start: 0.8047 (mtpm) cc_final: 0.7789 (mtmm) REVERT: L 167 PHE cc_start: 0.8309 (m-80) cc_final: 0.7814 (m-10) REVERT: L 215 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7952 (mp) REVERT: L 217 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7575 (mt) REVERT: L 225 LEU cc_start: 0.8219 (mp) cc_final: 0.7590 (tt) REVERT: L 233 MET cc_start: 0.8563 (mtp) cc_final: 0.8270 (mtp) REVERT: L 257 MET cc_start: 0.7914 (mmm) cc_final: 0.7406 (mmt) REVERT: L 379 LYS cc_start: 0.8719 (ttmp) cc_final: 0.8437 (tptp) REVERT: L 383 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8126 (tm-30) REVERT: G 24 TYR cc_start: 0.8413 (m-80) cc_final: 0.8163 (m-80) REVERT: G 47 ASP cc_start: 0.5588 (OUTLIER) cc_final: 0.5148 (t70) REVERT: G 124 LYS cc_start: 0.8584 (ttpt) cc_final: 0.8222 (tptt) REVERT: G 176 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.7161 (pm20) REVERT: G 210 TYR cc_start: 0.7728 (m-10) cc_final: 0.7101 (m-80) REVERT: G 251 ASP cc_start: 0.7384 (m-30) cc_final: 0.6329 (m-30) REVERT: G 254 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7964 (mt-10) REVERT: G 353 VAL cc_start: 0.9394 (OUTLIER) cc_final: 0.9138 (m) REVERT: G 356 ASN cc_start: 0.8573 (t0) cc_final: 0.8099 (m-40) REVERT: G 395 PHE cc_start: 0.8342 (t80) cc_final: 0.8078 (t80) REVERT: G 396 ASP cc_start: 0.8880 (t0) cc_final: 0.8571 (m-30) REVERT: G 413 MET cc_start: 0.8618 (tpt) cc_final: 0.8397 (mmp) outliers start: 305 outliers final: 199 residues processed: 1311 average time/residue: 0.5407 time to fit residues: 1137.1334 Evaluate side-chains 1273 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1040 time to evaluate : 4.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 GLN Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 222 TYR Chi-restraints excluded: chain K residue 293 MET Chi-restraints excluded: chain K residue 313 VAL Chi-restraints excluded: chain K residue 355 ASP Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 172 TYR Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain H residue 205 ASP Chi-restraints excluded: chain H residue 221 ARG Chi-restraints excluded: chain H residue 249 ASN Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 256 GLN Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 287 SER Chi-restraints excluded: chain H residue 290 GLU Chi-restraints excluded: chain H residue 328 VAL Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain H residue 377 MET Chi-restraints excluded: chain H residue 420 GLU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 81 PHE Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 159 TYR Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 194 GLU Chi-restraints excluded: chain I residue 222 TYR Chi-restraints excluded: chain I residue 290 THR Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 355 ASP Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 383 GLU Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 11 GLN Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 263 LEU Chi-restraints excluded: chain J residue 303 CYS Chi-restraints excluded: chain J residue 312 THR Chi-restraints excluded: chain J residue 338 SER Chi-restraints excluded: chain J residue 371 SER Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain J residue 383 GLU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 222 TYR Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 383 GLU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 129 CYS Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 172 TYR Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 81 PHE Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain L residue 172 SER Chi-restraints excluded: chain L residue 215 LEU Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 263 LEU Chi-restraints excluded: chain L residue 347 ASN Chi-restraints excluded: chain L residue 355 ASP Chi-restraints excluded: chain L residue 371 SER Chi-restraints excluded: chain L residue 383 GLU Chi-restraints excluded: chain L residue 388 MET Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 88 HIS Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 224 TYR Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 269 LEU Chi-restraints excluded: chain G residue 287 SER Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain G residue 334 THR Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain G residue 353 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 405 optimal weight: 4.9990 chunk 276 optimal weight: 0.9990 chunk 7 optimal weight: 30.0000 chunk 362 optimal weight: 20.0000 chunk 201 optimal weight: 20.0000 chunk 415 optimal weight: 0.5980 chunk 336 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 248 optimal weight: 5.9990 chunk 437 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 HIS ** K 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 393 HIS ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 307 HIS I 347 ASN E 31 GLN E 101 ASN E 128 GLN ** J 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 423 GLN ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 HIS D 11 GLN D 105 HIS ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 GLN ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 HIS B 266 HIS L 57 HIS ** L 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 247 ASN G 31 GLN ** G 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 406 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 41436 Z= 0.201 Angle : 0.640 15.658 56298 Z= 0.313 Chirality : 0.044 0.318 6162 Planarity : 0.005 0.076 7308 Dihedral : 10.614 165.368 5859 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.40 % Allowed : 23.80 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.35 (0.12), residues: 5088 helix: 1.37 (0.11), residues: 2340 sheet: 0.62 (0.18), residues: 810 loop : -1.38 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 344 HIS 0.019 0.001 HIS D 57 PHE 0.036 0.002 PHE K 294 TYR 0.019 0.001 TYR A 103 ARG 0.011 0.001 ARG D 390 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1380 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1146 time to evaluate : 4.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 3 GLU cc_start: 0.7604 (mp0) cc_final: 0.7377 (mp0) REVERT: K 35 ASN cc_start: 0.7507 (OUTLIER) cc_final: 0.7281 (m110) REVERT: K 50 TYR cc_start: 0.8012 (m-80) cc_final: 0.7543 (m-10) REVERT: K 73 MET cc_start: 0.9300 (mmm) cc_final: 0.8719 (mmm) REVERT: K 99 ASN cc_start: 0.8337 (m-40) cc_final: 0.7863 (m-40) REVERT: K 114 ASP cc_start: 0.7761 (m-30) cc_final: 0.7188 (t0) REVERT: K 133 PHE cc_start: 0.8548 (m-80) cc_final: 0.8156 (m-80) REVERT: K 213 ARG cc_start: 0.7698 (ttm110) cc_final: 0.7360 (ttp80) REVERT: K 217 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7081 (mt) REVERT: K 222 TYR cc_start: 0.8034 (OUTLIER) cc_final: 0.7513 (m-80) REVERT: K 247 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.7600 (p0) REVERT: K 257 MET cc_start: 0.8088 (mmm) cc_final: 0.7722 (mmt) REVERT: K 321 MET cc_start: 0.7761 (mtp) cc_final: 0.7327 (mtm) REVERT: K 363 MET cc_start: 0.8362 (mmt) cc_final: 0.7820 (mmt) REVERT: K 383 GLU cc_start: 0.8305 (tt0) cc_final: 0.7823 (tm-30) REVERT: K 406 MET cc_start: 0.7675 (ptm) cc_final: 0.5840 (mmm) REVERT: H 88 HIS cc_start: 0.8249 (p-80) cc_final: 0.7868 (p-80) REVERT: H 124 LYS cc_start: 0.8618 (ttpt) cc_final: 0.8252 (tptt) REVERT: H 154 MET cc_start: 0.8521 (mmp) cc_final: 0.8099 (tpt) REVERT: H 203 MET cc_start: 0.7175 (mtm) cc_final: 0.6719 (mtm) REVERT: H 221 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7648 (ptm-80) REVERT: H 290 GLU cc_start: 0.7955 (tt0) cc_final: 0.7330 (tp30) REVERT: H 302 MET cc_start: 0.8927 (mmt) cc_final: 0.8513 (mmm) REVERT: H 356 ASN cc_start: 0.8740 (t0) cc_final: 0.8110 (m-40) REVERT: H 388 TRP cc_start: 0.8428 (m-90) cc_final: 0.8204 (m-90) REVERT: H 407 TRP cc_start: 0.8675 (m100) cc_final: 0.8417 (m100) REVERT: H 417 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7948 (mp0) REVERT: H 420 GLU cc_start: 0.8045 (tm-30) cc_final: 0.6111 (tp30) REVERT: I 22 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8041 (mm-30) REVERT: I 26 ASP cc_start: 0.8349 (m-30) cc_final: 0.8114 (m-30) REVERT: I 73 MET cc_start: 0.9162 (mmm) cc_final: 0.8787 (mmm) REVERT: I 77 ARG cc_start: 0.7828 (tpt170) cc_final: 0.7443 (tpm170) REVERT: I 130 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8090 (tm) REVERT: I 133 PHE cc_start: 0.8266 (m-80) cc_final: 0.7964 (m-10) REVERT: I 136 THR cc_start: 0.9113 (m) cc_final: 0.8715 (p) REVERT: I 157 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8132 (mt-10) REVERT: I 167 PHE cc_start: 0.8548 (m-80) cc_final: 0.8093 (m-10) REVERT: I 168 SER cc_start: 0.8268 (m) cc_final: 0.7903 (p) REVERT: I 193 VAL cc_start: 0.8059 (t) cc_final: 0.7820 (t) REVERT: I 233 MET cc_start: 0.8273 (mtp) cc_final: 0.7905 (mtp) REVERT: I 323 MET cc_start: 0.8960 (ttt) cc_final: 0.8758 (ttp) REVERT: I 355 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.7708 (t0) REVERT: I 383 GLU cc_start: 0.8481 (tt0) cc_final: 0.8016 (tm-30) REVERT: I 397 TRP cc_start: 0.8559 (m100) cc_final: 0.7912 (m100) REVERT: I 425 TYR cc_start: 0.7384 (m-80) cc_final: 0.7149 (m-10) REVERT: E 24 TYR cc_start: 0.8393 (m-10) cc_final: 0.8013 (m-80) REVERT: E 36 MET cc_start: 0.8159 (tmm) cc_final: 0.7708 (tmm) REVERT: E 83 TYR cc_start: 0.7894 (m-80) cc_final: 0.6728 (m-10) REVERT: E 103 TYR cc_start: 0.8248 (t80) cc_final: 0.7998 (t80) REVERT: E 121 ARG cc_start: 0.8136 (tpp-160) cc_final: 0.7732 (mmt-90) REVERT: E 163 LYS cc_start: 0.9042 (ttpp) cc_final: 0.8600 (tppt) REVERT: E 251 ASP cc_start: 0.7875 (m-30) cc_final: 0.7563 (m-30) REVERT: E 255 PHE cc_start: 0.8977 (m-10) cc_final: 0.8683 (m-10) REVERT: E 256 GLN cc_start: 0.7678 (mt0) cc_final: 0.7116 (mt0) REVERT: E 257 THR cc_start: 0.9147 (m) cc_final: 0.8760 (p) REVERT: E 282 TYR cc_start: 0.8311 (m-80) cc_final: 0.8017 (m-80) REVERT: E 290 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7420 (tp30) REVERT: E 295 CYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8284 (m) REVERT: E 302 MET cc_start: 0.9132 (mmt) cc_final: 0.8781 (mmm) REVERT: E 319 TYR cc_start: 0.8638 (m-80) cc_final: 0.8036 (m-80) REVERT: E 346 TRP cc_start: 0.8065 (p-90) cc_final: 0.7656 (p90) REVERT: E 356 ASN cc_start: 0.8354 (t0) cc_final: 0.7858 (m-40) REVERT: E 377 MET cc_start: 0.8211 (ttp) cc_final: 0.7992 (ttp) REVERT: E 388 TRP cc_start: 0.8435 (m-90) cc_final: 0.7791 (m-90) REVERT: E 413 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7869 (mmm) REVERT: E 417 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7669 (mm-30) REVERT: E 429 GLU cc_start: 0.6948 (mt-10) cc_final: 0.5656 (tm-30) REVERT: J 19 LYS cc_start: 0.8821 (mmmm) cc_final: 0.8566 (mtpp) REVERT: J 50 TYR cc_start: 0.7948 (m-80) cc_final: 0.7166 (m-10) REVERT: J 77 ARG cc_start: 0.8332 (tpt170) cc_final: 0.7923 (tpt170) REVERT: J 99 ASN cc_start: 0.8062 (m-40) cc_final: 0.7694 (m-40) REVERT: J 114 ASP cc_start: 0.8041 (m-30) cc_final: 0.7610 (t0) REVERT: J 124 CYS cc_start: 0.8700 (t) cc_final: 0.8146 (m) REVERT: J 190 HIS cc_start: 0.7559 (t70) cc_final: 0.7110 (t-170) REVERT: J 200 TYR cc_start: 0.8547 (m-80) cc_final: 0.7932 (m-80) REVERT: J 217 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.6934 (mt) REVERT: J 298 ASN cc_start: 0.7818 (m-40) cc_final: 0.6972 (p0) REVERT: J 307 HIS cc_start: 0.7605 (m170) cc_final: 0.7391 (m170) REVERT: J 323 MET cc_start: 0.8990 (ttt) cc_final: 0.8781 (ttp) REVERT: J 344 TRP cc_start: 0.5977 (p90) cc_final: 0.5577 (p-90) REVERT: J 383 GLU cc_start: 0.8659 (tt0) cc_final: 0.8352 (tm-30) REVERT: J 403 MET cc_start: 0.8517 (mmm) cc_final: 0.8157 (tpt) REVERT: J 406 MET cc_start: 0.7647 (ptm) cc_final: 0.5348 (tpt) REVERT: C 8 GLN cc_start: 0.8057 (mt0) cc_final: 0.7187 (mt0) REVERT: C 22 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8057 (mm-30) REVERT: C 73 MET cc_start: 0.9088 (mmm) cc_final: 0.8560 (mmm) REVERT: C 130 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8423 (tm) REVERT: C 133 PHE cc_start: 0.8360 (m-80) cc_final: 0.8001 (m-10) REVERT: C 136 THR cc_start: 0.9091 (m) cc_final: 0.8709 (p) REVERT: C 158 GLU cc_start: 0.8750 (tp30) cc_final: 0.8340 (tp30) REVERT: C 167 PHE cc_start: 0.8650 (m-80) cc_final: 0.8029 (m-10) REVERT: C 222 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.5681 (m-80) REVERT: C 247 ASN cc_start: 0.8246 (OUTLIER) cc_final: 0.7490 (p0) REVERT: C 257 MET cc_start: 0.8082 (mmm) cc_final: 0.7498 (mmm) REVERT: C 298 ASN cc_start: 0.7179 (m-40) cc_final: 0.5988 (t0) REVERT: C 299 MET cc_start: 0.8556 (mmt) cc_final: 0.8009 (mmm) REVERT: C 306 ARG cc_start: 0.7994 (mpt-90) cc_final: 0.7771 (mtt-85) REVERT: C 312 THR cc_start: 0.8405 (p) cc_final: 0.8067 (t) REVERT: C 383 GLU cc_start: 0.8564 (tt0) cc_final: 0.8207 (tm-30) REVERT: C 390 ARG cc_start: 0.7887 (ptp-110) cc_final: 0.7531 (tpp-160) REVERT: D 8 GLN cc_start: 0.8145 (mt0) cc_final: 0.7564 (mt0) REVERT: D 14 ASN cc_start: 0.8164 (m110) cc_final: 0.7928 (m-40) REVERT: D 50 TYR cc_start: 0.8191 (m-80) cc_final: 0.7454 (m-80) REVERT: D 51 TYR cc_start: 0.8198 (m-80) cc_final: 0.7883 (m-10) REVERT: D 90 PHE cc_start: 0.8247 (m-10) cc_final: 0.7821 (m-80) REVERT: D 99 ASN cc_start: 0.7984 (m-40) cc_final: 0.7298 (m-40) REVERT: D 114 ASP cc_start: 0.7949 (m-30) cc_final: 0.7426 (t0) REVERT: D 130 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7909 (tm) REVERT: D 133 PHE cc_start: 0.8608 (m-80) cc_final: 0.8251 (m-80) REVERT: D 200 TYR cc_start: 0.8729 (m-80) cc_final: 0.8133 (m-80) REVERT: D 222 TYR cc_start: 0.8294 (OUTLIER) cc_final: 0.7770 (m-80) REVERT: D 257 MET cc_start: 0.8079 (mmp) cc_final: 0.7611 (mmp) REVERT: D 300 MET cc_start: 0.8322 (mtt) cc_final: 0.7978 (mtt) REVERT: D 383 GLU cc_start: 0.8471 (tt0) cc_final: 0.8012 (tm-30) REVERT: D 391 ARG cc_start: 0.7836 (mmm-85) cc_final: 0.7603 (mmm-85) REVERT: D 403 MET cc_start: 0.8694 (mmm) cc_final: 0.8477 (mmm) REVERT: D 406 MET cc_start: 0.7859 (ptm) cc_final: 0.5732 (mmm) REVERT: F 2 ARG cc_start: 0.7900 (mtm180) cc_final: 0.7565 (mtm110) REVERT: F 47 ASP cc_start: 0.5124 (OUTLIER) cc_final: 0.4869 (t70) REVERT: F 83 TYR cc_start: 0.7577 (m-80) cc_final: 0.7213 (m-10) REVERT: F 97 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6731 (tm-30) REVERT: F 108 TYR cc_start: 0.7438 (m-80) cc_final: 0.7163 (m-80) REVERT: F 121 ARG cc_start: 0.8178 (tpp-160) cc_final: 0.7676 (mpt180) REVERT: F 124 LYS cc_start: 0.8681 (ttpt) cc_final: 0.8442 (tptp) REVERT: F 157 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8242 (mp) REVERT: F 205 ASP cc_start: 0.7455 (t0) cc_final: 0.7211 (t0) REVERT: F 210 TYR cc_start: 0.7639 (m-10) cc_final: 0.7201 (m-10) REVERT: F 224 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.6805 (m-10) REVERT: F 248 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7220 (tt) REVERT: F 276 ILE cc_start: 0.8760 (mt) cc_final: 0.8510 (tt) REVERT: F 290 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7879 (tp30) REVERT: F 326 LYS cc_start: 0.8853 (ttmt) cc_final: 0.8500 (tppt) REVERT: F 356 ASN cc_start: 0.8473 (t0) cc_final: 0.8042 (m-40) REVERT: F 417 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7825 (mp0) REVERT: F 420 GLU cc_start: 0.7926 (tm-30) cc_final: 0.6617 (tp30) REVERT: F 432 TYR cc_start: 0.7789 (OUTLIER) cc_final: 0.7064 (t80) REVERT: A 24 TYR cc_start: 0.8266 (m-80) cc_final: 0.7279 (m-80) REVERT: A 36 MET cc_start: 0.7375 (ttt) cc_final: 0.6951 (tmm) REVERT: A 83 TYR cc_start: 0.7649 (m-80) cc_final: 0.7151 (m-10) REVERT: A 88 HIS cc_start: 0.8250 (p-80) cc_final: 0.7928 (p-80) REVERT: A 124 LYS cc_start: 0.8543 (ttpt) cc_final: 0.8178 (tptt) REVERT: A 262 TYR cc_start: 0.8167 (m-80) cc_final: 0.7784 (m-10) REVERT: A 276 ILE cc_start: 0.8745 (mt) cc_final: 0.8465 (tt) REVERT: A 290 GLU cc_start: 0.7981 (tt0) cc_final: 0.7548 (tp30) REVERT: A 302 MET cc_start: 0.8860 (mmt) cc_final: 0.8123 (mmm) REVERT: A 326 LYS cc_start: 0.8755 (ttmt) cc_final: 0.8346 (tppt) REVERT: A 346 TRP cc_start: 0.6713 (p90) cc_final: 0.6142 (p90) REVERT: A 356 ASN cc_start: 0.8528 (t0) cc_final: 0.8099 (m110) REVERT: A 417 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7710 (mm-30) REVERT: B 2 ARG cc_start: 0.7602 (mtm180) cc_final: 0.7339 (mtm110) REVERT: B 97 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6443 (tm-30) REVERT: B 155 GLU cc_start: 0.8770 (tt0) cc_final: 0.8405 (tp30) REVERT: B 211 ASP cc_start: 0.6502 (t0) cc_final: 0.5595 (t0) REVERT: B 214 ARG cc_start: 0.8966 (ttp80) cc_final: 0.8669 (ttp80) REVERT: B 302 MET cc_start: 0.8557 (mmp) cc_final: 0.8257 (mmp) REVERT: B 316 CYS cc_start: 0.8903 (m) cc_final: 0.8649 (m) REVERT: B 356 ASN cc_start: 0.8592 (t0) cc_final: 0.8166 (m-40) REVERT: B 413 MET cc_start: 0.8195 (mmp) cc_final: 0.7961 (mmp) REVERT: B 415 GLU cc_start: 0.8554 (tt0) cc_final: 0.7359 (tm-30) REVERT: B 420 GLU cc_start: 0.7945 (tm-30) cc_final: 0.6486 (tp30) REVERT: B 429 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6880 (mt-10) REVERT: L 37 VAL cc_start: 0.7704 (OUTLIER) cc_final: 0.7478 (p) REVERT: L 45 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8580 (tp30) REVERT: L 122 LYS cc_start: 0.7961 (mtpm) cc_final: 0.7706 (mtmm) REVERT: L 167 PHE cc_start: 0.8327 (m-80) cc_final: 0.7837 (m-10) REVERT: L 217 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7601 (mt) REVERT: L 225 LEU cc_start: 0.8179 (mp) cc_final: 0.7547 (tt) REVERT: L 233 MET cc_start: 0.8527 (mtp) cc_final: 0.8192 (mtp) REVERT: L 247 ASN cc_start: 0.8402 (OUTLIER) cc_final: 0.7574 (p0) REVERT: L 257 MET cc_start: 0.7942 (mmm) cc_final: 0.7407 (mmt) REVERT: L 379 LYS cc_start: 0.8702 (ttmp) cc_final: 0.8426 (tptp) REVERT: L 383 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8148 (tm-30) REVERT: G 47 ASP cc_start: 0.5416 (OUTLIER) cc_final: 0.5146 (t70) REVERT: G 123 ARG cc_start: 0.8315 (ttp-110) cc_final: 0.8102 (ttm-80) REVERT: G 124 LYS cc_start: 0.8576 (ttpt) cc_final: 0.8222 (tptt) REVERT: G 210 TYR cc_start: 0.7680 (m-10) cc_final: 0.6768 (m-80) REVERT: G 251 ASP cc_start: 0.7229 (m-30) cc_final: 0.6447 (m-30) REVERT: G 254 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8142 (mt-10) REVERT: G 356 ASN cc_start: 0.8537 (t0) cc_final: 0.8071 (m-40) REVERT: G 395 PHE cc_start: 0.8192 (t80) cc_final: 0.7983 (t80) REVERT: G 396 ASP cc_start: 0.8816 (t0) cc_final: 0.8541 (m-30) REVERT: G 413 MET cc_start: 0.8643 (tpt) cc_final: 0.8439 (mmp) outliers start: 234 outliers final: 156 residues processed: 1297 average time/residue: 0.5447 time to fit residues: 1125.0479 Evaluate side-chains 1242 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1056 time to evaluate : 4.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 GLN Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 222 TYR Chi-restraints excluded: chain K residue 247 ASN Chi-restraints excluded: chain K residue 313 VAL Chi-restraints excluded: chain K residue 338 SER Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 172 TYR Chi-restraints excluded: chain H residue 205 ASP Chi-restraints excluded: chain H residue 221 ARG Chi-restraints excluded: chain H residue 249 ASN Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 328 VAL Chi-restraints excluded: chain H residue 377 MET Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 290 THR Chi-restraints excluded: chain I residue 347 ASN Chi-restraints excluded: chain I residue 355 ASP Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 413 MET Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 11 GLN Chi-restraints excluded: chain J residue 81 PHE Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 178 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 263 LEU Chi-restraints excluded: chain J residue 303 CYS Chi-restraints excluded: chain J residue 312 THR Chi-restraints excluded: chain J residue 371 SER Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 222 TYR Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain D residue 11 GLN Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 172 TYR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 432 TYR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 81 PHE Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 247 ASN Chi-restraints excluded: chain L residue 347 ASN Chi-restraints excluded: chain L residue 383 GLU Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 224 TYR Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain G residue 379 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 163 optimal weight: 0.9980 chunk 438 optimal weight: 10.0000 chunk 96 optimal weight: 0.0770 chunk 286 optimal weight: 0.0980 chunk 120 optimal weight: 6.9990 chunk 487 optimal weight: 6.9990 chunk 404 optimal weight: 9.9990 chunk 225 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 chunk 256 optimal weight: 20.0000 overall best weight: 2.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 99 ASN ** K 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 301 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 307 HIS E 128 GLN E 197 HIS ** J 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 423 GLN ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 HIS ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN D 423 GLN ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 HIS A 128 GLN A 197 HIS ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN ** L 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 41436 Z= 0.185 Angle : 0.620 13.752 56298 Z= 0.305 Chirality : 0.043 0.262 6162 Planarity : 0.005 0.079 7308 Dihedral : 10.377 161.865 5859 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.68 % Allowed : 24.33 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.39 (0.12), residues: 5088 helix: 1.39 (0.11), residues: 2352 sheet: 0.66 (0.18), residues: 816 loop : -1.39 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 344 HIS 0.008 0.001 HIS B 88 PHE 0.024 0.001 PHE A 49 TYR 0.024 0.001 TYR A 103 ARG 0.010 0.001 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1370 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 1124 time to evaluate : 4.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 3 GLU cc_start: 0.7648 (mp0) cc_final: 0.7443 (mp0) REVERT: K 50 TYR cc_start: 0.8061 (m-80) cc_final: 0.7602 (m-10) REVERT: K 73 MET cc_start: 0.9266 (mmm) cc_final: 0.8720 (mmm) REVERT: K 114 ASP cc_start: 0.7616 (m-30) cc_final: 0.7078 (t0) REVERT: K 121 ARG cc_start: 0.8191 (ttm-80) cc_final: 0.7542 (mmt-90) REVERT: K 133 PHE cc_start: 0.8505 (m-80) cc_final: 0.8128 (m-80) REVERT: K 213 ARG cc_start: 0.7653 (ttm110) cc_final: 0.7113 (ttp80) REVERT: K 222 TYR cc_start: 0.7945 (OUTLIER) cc_final: 0.7449 (m-80) REVERT: K 247 ASN cc_start: 0.8021 (OUTLIER) cc_final: 0.7477 (p0) REVERT: K 267 MET cc_start: 0.8654 (ttm) cc_final: 0.8237 (ttm) REVERT: K 297 LYS cc_start: 0.8816 (mttt) cc_final: 0.8487 (mmmt) REVERT: K 300 MET cc_start: 0.7754 (mtt) cc_final: 0.7447 (mtm) REVERT: K 363 MET cc_start: 0.8322 (mmt) cc_final: 0.7905 (mmt) REVERT: K 383 GLU cc_start: 0.8281 (tt0) cc_final: 0.7868 (tm-30) REVERT: H 124 LYS cc_start: 0.8608 (ttpt) cc_final: 0.8242 (tptt) REVERT: H 154 MET cc_start: 0.8520 (mmp) cc_final: 0.8095 (tpt) REVERT: H 203 MET cc_start: 0.7105 (mtm) cc_final: 0.6632 (mtm) REVERT: H 290 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7307 (tp30) REVERT: H 302 MET cc_start: 0.8876 (mmt) cc_final: 0.8444 (mmm) REVERT: H 356 ASN cc_start: 0.8733 (t0) cc_final: 0.8107 (m-40) REVERT: H 388 TRP cc_start: 0.8446 (m-90) cc_final: 0.8148 (m-90) REVERT: H 417 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7954 (mp0) REVERT: H 420 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.6095 (tp30) REVERT: I 22 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8002 (mm-30) REVERT: I 26 ASP cc_start: 0.8344 (m-30) cc_final: 0.8094 (m-30) REVERT: I 73 MET cc_start: 0.9123 (mmm) cc_final: 0.8818 (mmm) REVERT: I 77 ARG cc_start: 0.7889 (tpt170) cc_final: 0.7452 (tpm170) REVERT: I 130 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8080 (tm) REVERT: I 133 PHE cc_start: 0.8202 (m-80) cc_final: 0.7921 (m-10) REVERT: I 136 THR cc_start: 0.9061 (m) cc_final: 0.8694 (p) REVERT: I 167 PHE cc_start: 0.8535 (m-80) cc_final: 0.8117 (m-10) REVERT: I 168 SER cc_start: 0.8256 (m) cc_final: 0.7921 (p) REVERT: I 217 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7278 (mt) REVERT: I 233 MET cc_start: 0.8373 (mtp) cc_final: 0.7957 (mtp) REVERT: I 257 MET cc_start: 0.7162 (mmp) cc_final: 0.6915 (mmp) REVERT: I 323 MET cc_start: 0.8969 (ttt) cc_final: 0.8663 (ttp) REVERT: I 355 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.7638 (t70) REVERT: I 383 GLU cc_start: 0.8476 (tt0) cc_final: 0.8008 (tm-30) REVERT: E 24 TYR cc_start: 0.8365 (m-10) cc_final: 0.7981 (m-80) REVERT: E 36 MET cc_start: 0.8147 (tmm) cc_final: 0.7655 (tmm) REVERT: E 75 ILE cc_start: 0.8093 (mt) cc_final: 0.7858 (mm) REVERT: E 83 TYR cc_start: 0.7776 (m-80) cc_final: 0.6655 (m-10) REVERT: E 121 ARG cc_start: 0.8098 (tpp-160) cc_final: 0.7643 (mmt-90) REVERT: E 163 LYS cc_start: 0.9043 (ttpp) cc_final: 0.8576 (tppt) REVERT: E 257 THR cc_start: 0.9130 (m) cc_final: 0.8877 (p) REVERT: E 285 GLN cc_start: 0.7291 (tt0) cc_final: 0.6544 (mm110) REVERT: E 290 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7405 (tp30) REVERT: E 302 MET cc_start: 0.9123 (mmt) cc_final: 0.8798 (mmm) REVERT: E 319 TYR cc_start: 0.8652 (m-80) cc_final: 0.8080 (m-80) REVERT: E 346 TRP cc_start: 0.8159 (p-90) cc_final: 0.7742 (p90) REVERT: E 356 ASN cc_start: 0.8365 (t0) cc_final: 0.7864 (m-40) REVERT: E 388 TRP cc_start: 0.8415 (m-90) cc_final: 0.7668 (m-90) REVERT: E 417 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7750 (mm-30) REVERT: E 429 GLU cc_start: 0.6942 (mt-10) cc_final: 0.5661 (tm-30) REVERT: J 19 LYS cc_start: 0.8802 (mmmm) cc_final: 0.8546 (mtpp) REVERT: J 50 TYR cc_start: 0.7957 (m-80) cc_final: 0.7113 (m-80) REVERT: J 77 ARG cc_start: 0.8194 (tpt170) cc_final: 0.7738 (tpt170) REVERT: J 99 ASN cc_start: 0.8030 (m-40) cc_final: 0.7697 (m-40) REVERT: J 114 ASP cc_start: 0.7944 (m-30) cc_final: 0.7544 (t0) REVERT: J 121 ARG cc_start: 0.8382 (mmm-85) cc_final: 0.8097 (mmm-85) REVERT: J 190 HIS cc_start: 0.7528 (t70) cc_final: 0.7094 (t-170) REVERT: J 200 TYR cc_start: 0.8516 (m-80) cc_final: 0.7884 (m-80) REVERT: J 217 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7338 (mt) REVERT: J 247 ASN cc_start: 0.8095 (m110) cc_final: 0.7623 (p0) REVERT: J 298 ASN cc_start: 0.7652 (m-40) cc_final: 0.6904 (p0) REVERT: J 306 ARG cc_start: 0.7691 (mpt-90) cc_final: 0.7232 (mtt-85) REVERT: J 323 MET cc_start: 0.8973 (ttt) cc_final: 0.8469 (ttp) REVERT: J 344 TRP cc_start: 0.5969 (p90) cc_final: 0.5549 (p-90) REVERT: J 380 ARG cc_start: 0.7702 (mtm110) cc_final: 0.7434 (mtm110) REVERT: J 383 GLU cc_start: 0.8656 (tt0) cc_final: 0.8268 (tm-30) REVERT: J 406 MET cc_start: 0.7630 (ptm) cc_final: 0.5328 (tpt) REVERT: C 8 GLN cc_start: 0.8040 (mt0) cc_final: 0.7156 (mt0) REVERT: C 11 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7965 (pt0) REVERT: C 22 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8092 (mm-30) REVERT: C 73 MET cc_start: 0.9094 (mmm) cc_final: 0.8483 (mmm) REVERT: C 130 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8449 (tm) REVERT: C 133 PHE cc_start: 0.8290 (m-80) cc_final: 0.7978 (m-10) REVERT: C 136 THR cc_start: 0.9053 (m) cc_final: 0.8723 (p) REVERT: C 167 PHE cc_start: 0.8537 (m-80) cc_final: 0.8184 (m-80) REVERT: C 247 ASN cc_start: 0.8201 (OUTLIER) cc_final: 0.7567 (p0) REVERT: C 257 MET cc_start: 0.7950 (mmm) cc_final: 0.7388 (mmm) REVERT: C 276 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6953 (mtm180) REVERT: C 298 ASN cc_start: 0.7131 (m-40) cc_final: 0.6009 (t0) REVERT: C 299 MET cc_start: 0.8580 (mmt) cc_final: 0.8205 (mmm) REVERT: C 306 ARG cc_start: 0.8012 (mpt-90) cc_final: 0.7787 (mtt-85) REVERT: C 312 THR cc_start: 0.8204 (p) cc_final: 0.7882 (t) REVERT: C 383 GLU cc_start: 0.8551 (tt0) cc_final: 0.8241 (tm-30) REVERT: C 390 ARG cc_start: 0.7790 (ptp-110) cc_final: 0.7540 (tpp-160) REVERT: D 8 GLN cc_start: 0.8137 (mt0) cc_final: 0.7816 (mt0) REVERT: D 35 ASN cc_start: 0.7341 (OUTLIER) cc_final: 0.7122 (m110) REVERT: D 50 TYR cc_start: 0.8165 (m-80) cc_final: 0.7304 (m-80) REVERT: D 77 ARG cc_start: 0.8474 (tpt170) cc_final: 0.7854 (mtm110) REVERT: D 99 ASN cc_start: 0.7941 (m-40) cc_final: 0.7273 (m-40) REVERT: D 114 ASP cc_start: 0.7902 (m-30) cc_final: 0.7425 (t0) REVERT: D 133 PHE cc_start: 0.8610 (m-80) cc_final: 0.8236 (m-80) REVERT: D 157 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8388 (mt-10) REVERT: D 200 TYR cc_start: 0.8633 (m-80) cc_final: 0.8158 (m-80) REVERT: D 217 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7550 (mp) REVERT: D 222 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7812 (m-80) REVERT: D 300 MET cc_start: 0.8337 (mtt) cc_final: 0.8059 (mtt) REVERT: D 306 ARG cc_start: 0.7441 (mmt90) cc_final: 0.7133 (mtt-85) REVERT: D 383 GLU cc_start: 0.8458 (tt0) cc_final: 0.8005 (tm-30) REVERT: D 403 MET cc_start: 0.8732 (mmm) cc_final: 0.8415 (mmm) REVERT: D 406 MET cc_start: 0.7777 (ptm) cc_final: 0.5764 (mmm) REVERT: F 2 ARG cc_start: 0.7886 (mtm180) cc_final: 0.7613 (mtm110) REVERT: F 47 ASP cc_start: 0.5112 (OUTLIER) cc_final: 0.4855 (t70) REVERT: F 83 TYR cc_start: 0.7551 (m-80) cc_final: 0.7138 (m-10) REVERT: F 97 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6686 (tm-30) REVERT: F 108 TYR cc_start: 0.7199 (m-80) cc_final: 0.6982 (m-80) REVERT: F 121 ARG cc_start: 0.8161 (tpp-160) cc_final: 0.7629 (mpt180) REVERT: F 124 LYS cc_start: 0.8670 (ttpt) cc_final: 0.8438 (tptt) REVERT: F 157 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8206 (mp) REVERT: F 210 TYR cc_start: 0.7612 (m-10) cc_final: 0.7289 (m-10) REVERT: F 221 ARG cc_start: 0.8207 (mtp-110) cc_final: 0.7739 (ptm160) REVERT: F 224 TYR cc_start: 0.7711 (OUTLIER) cc_final: 0.6895 (m-10) REVERT: F 248 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7144 (tt) REVERT: F 276 ILE cc_start: 0.8731 (mt) cc_final: 0.8472 (tt) REVERT: F 290 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7872 (tp30) REVERT: F 326 LYS cc_start: 0.8846 (ttmt) cc_final: 0.8497 (tppt) REVERT: F 356 ASN cc_start: 0.8416 (t0) cc_final: 0.8090 (m-40) REVERT: F 417 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7821 (mp0) REVERT: F 420 GLU cc_start: 0.7991 (tm-30) cc_final: 0.6692 (tp30) REVERT: F 432 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.7149 (t80) REVERT: A 24 TYR cc_start: 0.8196 (m-80) cc_final: 0.7190 (m-80) REVERT: A 36 MET cc_start: 0.7693 (ttt) cc_final: 0.7015 (tmm) REVERT: A 83 TYR cc_start: 0.7599 (m-80) cc_final: 0.7184 (m-10) REVERT: A 88 HIS cc_start: 0.8228 (p-80) cc_final: 0.7951 (p-80) REVERT: A 124 LYS cc_start: 0.8532 (ttpt) cc_final: 0.8196 (tptt) REVERT: A 262 TYR cc_start: 0.8161 (m-80) cc_final: 0.7815 (m-10) REVERT: A 276 ILE cc_start: 0.8768 (mt) cc_final: 0.8470 (tt) REVERT: A 287 SER cc_start: 0.8387 (OUTLIER) cc_final: 0.8017 (p) REVERT: A 290 GLU cc_start: 0.7891 (tt0) cc_final: 0.7583 (tp30) REVERT: A 302 MET cc_start: 0.8901 (mmt) cc_final: 0.8242 (mmm) REVERT: A 326 LYS cc_start: 0.8744 (ttmt) cc_final: 0.8409 (tppt) REVERT: A 346 TRP cc_start: 0.6698 (p90) cc_final: 0.6121 (p90) REVERT: A 356 ASN cc_start: 0.8580 (t0) cc_final: 0.8159 (m110) REVERT: A 417 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7618 (mm-30) REVERT: B 2 ARG cc_start: 0.7456 (mtm180) cc_final: 0.7220 (mtm110) REVERT: B 155 GLU cc_start: 0.8733 (tt0) cc_final: 0.8343 (tp30) REVERT: B 214 ARG cc_start: 0.8945 (ttp80) cc_final: 0.8616 (ttp80) REVERT: B 254 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7687 (mt-10) REVERT: B 302 MET cc_start: 0.8625 (mmp) cc_final: 0.8403 (mmp) REVERT: B 356 ASN cc_start: 0.8586 (t0) cc_final: 0.8158 (m-40) REVERT: B 413 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7826 (mmp) REVERT: B 415 GLU cc_start: 0.8644 (tt0) cc_final: 0.7217 (tm-30) REVERT: B 420 GLU cc_start: 0.7905 (tm-30) cc_final: 0.6459 (tp30) REVERT: B 429 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6778 (mt-10) REVERT: L 30 ILE cc_start: 0.8590 (mm) cc_final: 0.8285 (mt) REVERT: L 45 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8624 (tp30) REVERT: L 130 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8152 (tm) REVERT: L 167 PHE cc_start: 0.8335 (m-80) cc_final: 0.7893 (m-10) REVERT: L 215 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7722 (mp) REVERT: L 217 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7497 (mt) REVERT: L 225 LEU cc_start: 0.8164 (mp) cc_final: 0.7506 (tt) REVERT: L 247 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.7885 (p0) REVERT: L 257 MET cc_start: 0.7848 (mmm) cc_final: 0.7302 (mmm) REVERT: L 379 LYS cc_start: 0.8714 (ttmp) cc_final: 0.8428 (tptp) REVERT: L 383 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8106 (tm-30) REVERT: G 47 ASP cc_start: 0.5383 (OUTLIER) cc_final: 0.5121 (t70) REVERT: G 123 ARG cc_start: 0.8289 (ttp-110) cc_final: 0.8074 (ttm-80) REVERT: G 124 LYS cc_start: 0.8573 (ttpt) cc_final: 0.8221 (tptt) REVERT: G 210 TYR cc_start: 0.7631 (m-10) cc_final: 0.7193 (m-80) REVERT: G 245 ASP cc_start: 0.7406 (m-30) cc_final: 0.7173 (p0) REVERT: G 356 ASN cc_start: 0.8602 (t0) cc_final: 0.8211 (m-40) REVERT: G 396 ASP cc_start: 0.8871 (t0) cc_final: 0.8642 (m-30) REVERT: G 413 MET cc_start: 0.8661 (tpt) cc_final: 0.8440 (mmp) REVERT: G 420 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.6832 (tp30) outliers start: 246 outliers final: 164 residues processed: 1273 average time/residue: 0.5370 time to fit residues: 1091.7440 Evaluate side-chains 1260 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1064 time to evaluate : 4.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 222 TYR Chi-restraints excluded: chain K residue 247 ASN Chi-restraints excluded: chain K residue 313 VAL Chi-restraints excluded: chain K residue 338 SER Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 172 TYR Chi-restraints excluded: chain H residue 205 ASP Chi-restraints excluded: chain H residue 249 ASN Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 290 GLU Chi-restraints excluded: chain H residue 328 VAL Chi-restraints excluded: chain H residue 345 ASP Chi-restraints excluded: chain H residue 377 MET Chi-restraints excluded: chain H residue 420 GLU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 290 THR Chi-restraints excluded: chain I residue 347 ASN Chi-restraints excluded: chain I residue 355 ASP Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 81 PHE Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 253 LEU Chi-restraints excluded: chain J residue 263 LEU Chi-restraints excluded: chain J residue 367 PHE Chi-restraints excluded: chain J residue 371 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 11 GLN Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain D residue 11 GLN Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 172 TYR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 432 TYR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 81 PHE Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain L residue 172 SER Chi-restraints excluded: chain L residue 215 LEU Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 247 ASN Chi-restraints excluded: chain L residue 347 ASN Chi-restraints excluded: chain L residue 367 PHE Chi-restraints excluded: chain L residue 383 GLU Chi-restraints excluded: chain L residue 388 MET Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 88 HIS Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain G residue 379 SER Chi-restraints excluded: chain G residue 420 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 470 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 277 optimal weight: 7.9990 chunk 356 optimal weight: 8.9990 chunk 275 optimal weight: 0.4980 chunk 410 optimal weight: 5.9990 chunk 272 optimal weight: 8.9990 chunk 485 optimal weight: 10.0000 chunk 304 optimal weight: 3.9990 chunk 296 optimal weight: 20.0000 chunk 224 optimal weight: 10.0000 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 279 GLN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 301 GLN ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 307 HIS I 347 ASN ** J 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN D 423 GLN ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 GLN A 197 HIS ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN L 57 HIS ** L 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 384 GLN G 256 GLN G 301 GLN G 393 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 41436 Z= 0.249 Angle : 0.654 15.037 56298 Z= 0.321 Chirality : 0.044 0.258 6162 Planarity : 0.005 0.064 7308 Dihedral : 10.450 161.419 5856 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 6.12 % Allowed : 24.17 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.27 (0.12), residues: 5088 helix: 1.24 (0.11), residues: 2352 sheet: 0.73 (0.18), residues: 786 loop : -1.39 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 344 HIS 0.023 0.001 HIS D 57 PHE 0.040 0.002 PHE B 149 TYR 0.030 0.002 TYR A 103 ARG 0.011 0.001 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1369 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 1104 time to evaluate : 4.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 11 GLN cc_start: 0.8032 (pt0) cc_final: 0.7795 (pt0) REVERT: K 50 TYR cc_start: 0.8066 (m-80) cc_final: 0.7567 (m-10) REVERT: K 73 MET cc_start: 0.9307 (mmm) cc_final: 0.8794 (mmm) REVERT: K 77 ARG cc_start: 0.7897 (tpp-160) cc_final: 0.7369 (tpm170) REVERT: K 114 ASP cc_start: 0.7734 (m-30) cc_final: 0.7132 (t0) REVERT: K 133 PHE cc_start: 0.8577 (m-80) cc_final: 0.8274 (m-80) REVERT: K 222 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.7677 (m-80) REVERT: K 247 ASN cc_start: 0.8017 (OUTLIER) cc_final: 0.7498 (p0) REVERT: K 257 MET cc_start: 0.8292 (mmm) cc_final: 0.7956 (mmm) REVERT: K 267 MET cc_start: 0.8665 (ttm) cc_final: 0.8302 (ttm) REVERT: K 300 MET cc_start: 0.7845 (mtt) cc_final: 0.7366 (mtm) REVERT: K 321 MET cc_start: 0.7657 (mtp) cc_final: 0.7282 (mtm) REVERT: K 355 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8027 (m-30) REVERT: K 363 MET cc_start: 0.8375 (mmt) cc_final: 0.7854 (mmt) REVERT: K 383 GLU cc_start: 0.8332 (tt0) cc_final: 0.7857 (tm-30) REVERT: K 388 MET cc_start: 0.6295 (mmp) cc_final: 0.6015 (mmp) REVERT: H 124 LYS cc_start: 0.8648 (ttpt) cc_final: 0.8240 (tptt) REVERT: H 154 MET cc_start: 0.8575 (mmp) cc_final: 0.8122 (tpt) REVERT: H 203 MET cc_start: 0.7232 (mtm) cc_final: 0.6802 (mtm) REVERT: H 290 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7354 (tp30) REVERT: H 302 MET cc_start: 0.8928 (mmt) cc_final: 0.8559 (mmm) REVERT: H 356 ASN cc_start: 0.8761 (t0) cc_final: 0.8127 (m-40) REVERT: H 386 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7756 (mp0) REVERT: H 388 TRP cc_start: 0.8567 (m-90) cc_final: 0.8232 (m-90) REVERT: H 417 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7895 (mp0) REVERT: H 420 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.6160 (tp30) REVERT: I 22 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8006 (mm-30) REVERT: I 73 MET cc_start: 0.9175 (mmm) cc_final: 0.8861 (mmm) REVERT: I 77 ARG cc_start: 0.7908 (tpt170) cc_final: 0.7494 (tpm170) REVERT: I 130 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8107 (tm) REVERT: I 133 PHE cc_start: 0.8267 (m-80) cc_final: 0.7980 (m-10) REVERT: I 136 THR cc_start: 0.9104 (m) cc_final: 0.8749 (p) REVERT: I 167 PHE cc_start: 0.8555 (m-80) cc_final: 0.8163 (m-10) REVERT: I 168 SER cc_start: 0.8272 (m) cc_final: 0.7953 (p) REVERT: I 217 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7390 (mt) REVERT: I 233 MET cc_start: 0.8394 (mtp) cc_final: 0.7958 (mtp) REVERT: I 257 MET cc_start: 0.7411 (mmp) cc_final: 0.7161 (mmp) REVERT: I 323 MET cc_start: 0.8900 (ttt) cc_final: 0.8594 (ttp) REVERT: I 383 GLU cc_start: 0.8513 (tt0) cc_final: 0.8114 (tm-30) REVERT: I 401 GLU cc_start: 0.6106 (mp0) cc_final: 0.5804 (mt-10) REVERT: E 24 TYR cc_start: 0.8480 (m-10) cc_final: 0.8081 (m-80) REVERT: E 36 MET cc_start: 0.8117 (tmm) cc_final: 0.7739 (tmm) REVERT: E 75 ILE cc_start: 0.8104 (mt) cc_final: 0.7898 (mm) REVERT: E 83 TYR cc_start: 0.7653 (m-80) cc_final: 0.6437 (m-10) REVERT: E 163 LYS cc_start: 0.8970 (ttpp) cc_final: 0.8553 (tppt) REVERT: E 167 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8677 (mm) REVERT: E 257 THR cc_start: 0.9166 (m) cc_final: 0.8889 (p) REVERT: E 285 GLN cc_start: 0.7396 (tt0) cc_final: 0.6688 (mm110) REVERT: E 290 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7398 (tp30) REVERT: E 302 MET cc_start: 0.9133 (mmt) cc_final: 0.8862 (mmm) REVERT: E 319 TYR cc_start: 0.8654 (m-80) cc_final: 0.8091 (m-80) REVERT: E 346 TRP cc_start: 0.8173 (p-90) cc_final: 0.7764 (p90) REVERT: E 356 ASN cc_start: 0.8556 (t0) cc_final: 0.8130 (m-40) REVERT: E 388 TRP cc_start: 0.8450 (m-90) cc_final: 0.7687 (m-90) REVERT: E 415 GLU cc_start: 0.7101 (tt0) cc_final: 0.6446 (tm-30) REVERT: E 417 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7758 (mm-30) REVERT: E 429 GLU cc_start: 0.6958 (mt-10) cc_final: 0.5620 (tm-30) REVERT: J 11 GLN cc_start: 0.8213 (pt0) cc_final: 0.7737 (pm20) REVERT: J 99 ASN cc_start: 0.8078 (m-40) cc_final: 0.7733 (m-40) REVERT: J 114 ASP cc_start: 0.7949 (m-30) cc_final: 0.7553 (t0) REVERT: J 121 ARG cc_start: 0.8428 (mmm-85) cc_final: 0.8127 (mmm-85) REVERT: J 190 HIS cc_start: 0.7515 (t70) cc_final: 0.7057 (t-170) REVERT: J 200 TYR cc_start: 0.8515 (m-80) cc_final: 0.7851 (m-80) REVERT: J 217 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7593 (mt) REVERT: J 247 ASN cc_start: 0.8153 (m110) cc_final: 0.7677 (p0) REVERT: J 298 ASN cc_start: 0.7566 (m-40) cc_final: 0.6901 (p0) REVERT: J 306 ARG cc_start: 0.7697 (mpt-90) cc_final: 0.7242 (mtt-85) REVERT: J 344 TRP cc_start: 0.5941 (p90) cc_final: 0.5547 (p-90) REVERT: J 380 ARG cc_start: 0.7614 (mtm110) cc_final: 0.7311 (mtm110) REVERT: J 383 GLU cc_start: 0.8664 (tt0) cc_final: 0.8283 (tm-30) REVERT: J 406 MET cc_start: 0.7627 (ptm) cc_final: 0.5331 (tpt) REVERT: C 22 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8059 (mm-30) REVERT: C 73 MET cc_start: 0.9237 (mmm) cc_final: 0.8863 (mmm) REVERT: C 130 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8507 (tm) REVERT: C 133 PHE cc_start: 0.8362 (m-80) cc_final: 0.7730 (m-80) REVERT: C 136 THR cc_start: 0.9087 (m) cc_final: 0.8698 (p) REVERT: C 167 PHE cc_start: 0.8520 (m-80) cc_final: 0.8285 (m-80) REVERT: C 222 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.5780 (m-80) REVERT: C 247 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7626 (p0) REVERT: C 276 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.7031 (mtm180) REVERT: C 298 ASN cc_start: 0.7305 (m-40) cc_final: 0.6178 (t0) REVERT: C 299 MET cc_start: 0.8729 (mmt) cc_final: 0.8439 (mmt) REVERT: C 306 ARG cc_start: 0.7985 (mpt-90) cc_final: 0.7768 (mtt-85) REVERT: C 379 LYS cc_start: 0.8852 (mttt) cc_final: 0.8400 (mtpp) REVERT: C 383 GLU cc_start: 0.8548 (tt0) cc_final: 0.8260 (tm-30) REVERT: C 390 ARG cc_start: 0.7787 (ptp-110) cc_final: 0.7541 (tpp-160) REVERT: D 8 GLN cc_start: 0.8121 (mt0) cc_final: 0.7743 (mt0) REVERT: D 11 GLN cc_start: 0.8295 (tt0) cc_final: 0.7994 (pt0) REVERT: D 50 TYR cc_start: 0.8195 (m-80) cc_final: 0.7445 (m-80) REVERT: D 99 ASN cc_start: 0.7929 (m-40) cc_final: 0.7381 (m-40) REVERT: D 114 ASP cc_start: 0.7954 (m-30) cc_final: 0.7480 (t0) REVERT: D 133 PHE cc_start: 0.8634 (m-80) cc_final: 0.8221 (m-80) REVERT: D 200 TYR cc_start: 0.8522 (m-80) cc_final: 0.7930 (m-80) REVERT: D 216 LYS cc_start: 0.8418 (mmmm) cc_final: 0.7834 (ptmm) REVERT: D 217 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7506 (mp) REVERT: D 222 TYR cc_start: 0.8353 (OUTLIER) cc_final: 0.7921 (m-80) REVERT: D 355 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7862 (m-30) REVERT: D 383 GLU cc_start: 0.8489 (tt0) cc_final: 0.8014 (tm-30) REVERT: D 403 MET cc_start: 0.8778 (mmm) cc_final: 0.8411 (mmm) REVERT: D 406 MET cc_start: 0.7809 (ptm) cc_final: 0.5773 (mmm) REVERT: F 2 ARG cc_start: 0.7949 (mtm180) cc_final: 0.7677 (mtm110) REVERT: F 47 ASP cc_start: 0.4990 (OUTLIER) cc_final: 0.4730 (t70) REVERT: F 124 LYS cc_start: 0.8629 (ttpt) cc_final: 0.8403 (tptt) REVERT: F 157 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8238 (mp) REVERT: F 168 GLU cc_start: 0.7942 (pt0) cc_final: 0.7539 (pp20) REVERT: F 210 TYR cc_start: 0.7686 (m-10) cc_final: 0.7346 (m-10) REVERT: F 221 ARG cc_start: 0.8220 (mtp-110) cc_final: 0.7753 (ptm160) REVERT: F 224 TYR cc_start: 0.7732 (OUTLIER) cc_final: 0.6936 (m-10) REVERT: F 248 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7224 (tt) REVERT: F 276 ILE cc_start: 0.8749 (mt) cc_final: 0.8496 (tt) REVERT: F 290 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7954 (tp30) REVERT: F 326 LYS cc_start: 0.8851 (ttmt) cc_final: 0.8496 (tppt) REVERT: F 417 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7857 (mp0) REVERT: F 420 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.6590 (tp30) REVERT: F 432 TYR cc_start: 0.7907 (OUTLIER) cc_final: 0.7197 (t80) REVERT: A 24 TYR cc_start: 0.8298 (m-80) cc_final: 0.7313 (m-80) REVERT: A 36 MET cc_start: 0.7713 (ttt) cc_final: 0.7043 (tmm) REVERT: A 83 TYR cc_start: 0.7674 (m-80) cc_final: 0.7307 (m-10) REVERT: A 88 HIS cc_start: 0.8178 (p-80) cc_final: 0.7880 (p-80) REVERT: A 96 LYS cc_start: 0.6438 (tppt) cc_final: 0.6184 (mppt) REVERT: A 122 ILE cc_start: 0.8908 (mt) cc_final: 0.8636 (pt) REVERT: A 124 LYS cc_start: 0.8474 (ttpt) cc_final: 0.8089 (tptt) REVERT: A 262 TYR cc_start: 0.8229 (m-80) cc_final: 0.7877 (m-10) REVERT: A 276 ILE cc_start: 0.8775 (mt) cc_final: 0.8493 (tt) REVERT: A 282 TYR cc_start: 0.8170 (m-80) cc_final: 0.7879 (m-80) REVERT: A 290 GLU cc_start: 0.8247 (tt0) cc_final: 0.7587 (tp30) REVERT: A 302 MET cc_start: 0.8970 (mmt) cc_final: 0.8605 (mmm) REVERT: A 326 LYS cc_start: 0.8900 (ttmt) cc_final: 0.8430 (tppt) REVERT: A 346 TRP cc_start: 0.6715 (p90) cc_final: 0.6089 (p90) REVERT: A 356 ASN cc_start: 0.8554 (t0) cc_final: 0.8120 (m110) REVERT: A 407 TRP cc_start: 0.8755 (m100) cc_final: 0.8442 (m100) REVERT: A 417 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7834 (mm-30) REVERT: B 2 ARG cc_start: 0.7599 (mtm180) cc_final: 0.7320 (mtm110) REVERT: B 155 GLU cc_start: 0.8738 (tt0) cc_final: 0.8318 (mm-30) REVERT: B 168 GLU cc_start: 0.8033 (pt0) cc_final: 0.7634 (pm20) REVERT: B 214 ARG cc_start: 0.8844 (ttp80) cc_final: 0.8589 (ttp80) REVERT: B 254 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7610 (mt-10) REVERT: B 295 CYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8210 (m) REVERT: B 356 ASN cc_start: 0.8589 (t0) cc_final: 0.8172 (m-40) REVERT: B 413 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7811 (mmp) REVERT: B 415 GLU cc_start: 0.8654 (tt0) cc_final: 0.7292 (tm-30) REVERT: B 420 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.6516 (tp30) REVERT: B 429 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6808 (mt-10) REVERT: L 45 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8713 (tp30) REVERT: L 130 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8155 (tm) REVERT: L 167 PHE cc_start: 0.8348 (m-80) cc_final: 0.7909 (m-10) REVERT: L 215 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7653 (mp) REVERT: L 217 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7591 (mt) REVERT: L 225 LEU cc_start: 0.8102 (mp) cc_final: 0.7525 (tt) REVERT: L 257 MET cc_start: 0.7886 (mmm) cc_final: 0.7237 (mmm) REVERT: L 379 LYS cc_start: 0.8669 (ttmp) cc_final: 0.8395 (tptp) REVERT: L 383 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8039 (tm-30) REVERT: G 47 ASP cc_start: 0.5348 (OUTLIER) cc_final: 0.4982 (t70) REVERT: G 123 ARG cc_start: 0.8254 (ttp-110) cc_final: 0.8041 (ttm-80) REVERT: G 124 LYS cc_start: 0.8577 (ttpt) cc_final: 0.8218 (tptt) REVERT: G 210 TYR cc_start: 0.7615 (m-10) cc_final: 0.7264 (m-80) REVERT: G 251 ASP cc_start: 0.7590 (m-30) cc_final: 0.6541 (m-30) REVERT: G 254 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7817 (mt-10) REVERT: G 257 THR cc_start: 0.8923 (m) cc_final: 0.8653 (p) REVERT: G 302 MET cc_start: 0.8647 (mtp) cc_final: 0.8087 (mtp) REVERT: G 353 VAL cc_start: 0.9274 (OUTLIER) cc_final: 0.9043 (m) REVERT: G 356 ASN cc_start: 0.8614 (t0) cc_final: 0.8197 (m-40) REVERT: G 396 ASP cc_start: 0.8872 (t0) cc_final: 0.8643 (m-30) REVERT: G 413 MET cc_start: 0.8629 (tpt) cc_final: 0.8408 (mmp) REVERT: G 420 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.6788 (tp30) outliers start: 265 outliers final: 191 residues processed: 1270 average time/residue: 0.5350 time to fit residues: 1086.5539 Evaluate side-chains 1287 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1061 time to evaluate : 4.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 222 TYR Chi-restraints excluded: chain K residue 247 ASN Chi-restraints excluded: chain K residue 313 VAL Chi-restraints excluded: chain K residue 355 ASP Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 186 ASN Chi-restraints excluded: chain H residue 205 ASP Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 287 SER Chi-restraints excluded: chain H residue 290 GLU Chi-restraints excluded: chain H residue 328 VAL Chi-restraints excluded: chain H residue 345 ASP Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain H residue 377 MET Chi-restraints excluded: chain H residue 420 GLU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 194 GLU Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 290 THR Chi-restraints excluded: chain I residue 303 CYS Chi-restraints excluded: chain I residue 347 ASN Chi-restraints excluded: chain I residue 355 ASP Chi-restraints excluded: chain I residue 363 MET Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 81 PHE Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 222 TYR Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 253 LEU Chi-restraints excluded: chain J residue 263 LEU Chi-restraints excluded: chain J residue 303 CYS Chi-restraints excluded: chain J residue 316 VAL Chi-restraints excluded: chain J residue 337 ASN Chi-restraints excluded: chain J residue 367 PHE Chi-restraints excluded: chain J residue 371 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 222 TYR Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 172 TYR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 420 GLU Chi-restraints excluded: chain F residue 432 TYR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 81 PHE Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain L residue 172 SER Chi-restraints excluded: chain L residue 215 LEU Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 347 ASN Chi-restraints excluded: chain L residue 371 SER Chi-restraints excluded: chain L residue 383 GLU Chi-restraints excluded: chain L residue 388 MET Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 88 HIS Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 269 LEU Chi-restraints excluded: chain G residue 287 SER Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 420 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 300 optimal weight: 4.9990 chunk 193 optimal weight: 0.9990 chunk 290 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 chunk 94 optimal weight: 9.9990 chunk 308 optimal weight: 0.9990 chunk 330 optimal weight: 8.9990 chunk 240 optimal weight: 30.0000 chunk 45 optimal weight: 0.0770 chunk 381 optimal weight: 10.0000 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 279 GLN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 423 GLN E 197 HIS J 134 GLN ** J 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 247 ASN ** J 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 GLN ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 ASN F 393 HIS A 31 GLN A 101 ASN A 128 GLN A 197 HIS ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN B 256 GLN ** L 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 247 ASN G 301 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 41436 Z= 0.174 Angle : 0.616 12.435 56298 Z= 0.302 Chirality : 0.043 0.268 6162 Planarity : 0.005 0.058 7308 Dihedral : 10.109 157.223 5856 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.82 % Allowed : 25.81 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.36 (0.12), residues: 5088 helix: 1.30 (0.11), residues: 2352 sheet: 0.84 (0.18), residues: 786 loop : -1.36 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 346 HIS 0.007 0.001 HIS F 393 PHE 0.031 0.001 PHE B 49 TYR 0.026 0.001 TYR A 103 ARG 0.011 0.001 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1362 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1153 time to evaluate : 4.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 50 TYR cc_start: 0.8026 (m-80) cc_final: 0.7462 (m-10) REVERT: K 73 MET cc_start: 0.9280 (mmm) cc_final: 0.8754 (mmm) REVERT: K 77 ARG cc_start: 0.7799 (tpp-160) cc_final: 0.7293 (tpm170) REVERT: K 99 ASN cc_start: 0.8222 (m110) cc_final: 0.7847 (m-40) REVERT: K 114 ASP cc_start: 0.7731 (m-30) cc_final: 0.7123 (t0) REVERT: K 133 PHE cc_start: 0.8519 (m-80) cc_final: 0.8100 (m-80) REVERT: K 247 ASN cc_start: 0.8156 (OUTLIER) cc_final: 0.7573 (p0) REVERT: K 257 MET cc_start: 0.8147 (mmm) cc_final: 0.7867 (mmm) REVERT: K 267 MET cc_start: 0.8606 (ttm) cc_final: 0.8353 (ttm) REVERT: K 299 MET cc_start: 0.8254 (tpt) cc_final: 0.7983 (mmt) REVERT: K 300 MET cc_start: 0.7606 (mtt) cc_final: 0.7195 (mtm) REVERT: K 321 MET cc_start: 0.7751 (mtp) cc_final: 0.7314 (mtm) REVERT: K 363 MET cc_start: 0.8335 (mmt) cc_final: 0.7824 (mmt) REVERT: K 383 GLU cc_start: 0.8315 (tt0) cc_final: 0.7880 (tm-30) REVERT: K 406 MET cc_start: 0.7631 (ptm) cc_final: 0.5814 (mmm) REVERT: H 124 LYS cc_start: 0.8634 (ttpt) cc_final: 0.8238 (tptt) REVERT: H 154 MET cc_start: 0.8511 (mmp) cc_final: 0.8101 (tpt) REVERT: H 203 MET cc_start: 0.7176 (mtm) cc_final: 0.6693 (mtm) REVERT: H 290 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7188 (tp30) REVERT: H 302 MET cc_start: 0.8884 (mmt) cc_final: 0.8435 (mmm) REVERT: H 356 ASN cc_start: 0.8829 (t0) cc_final: 0.8226 (m-40) REVERT: H 388 TRP cc_start: 0.8516 (m-90) cc_final: 0.8142 (m-90) REVERT: H 413 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7783 (mmp) REVERT: H 420 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.6197 (tp30) REVERT: I 22 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8057 (mm-30) REVERT: I 77 ARG cc_start: 0.8027 (tpt170) cc_final: 0.7540 (tpm170) REVERT: I 130 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8153 (tm) REVERT: I 133 PHE cc_start: 0.8211 (m-80) cc_final: 0.7723 (m-80) REVERT: I 136 THR cc_start: 0.9042 (m) cc_final: 0.8675 (p) REVERT: I 167 PHE cc_start: 0.8525 (m-80) cc_final: 0.8098 (m-10) REVERT: I 168 SER cc_start: 0.8272 (m) cc_final: 0.7980 (p) REVERT: I 217 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7363 (mt) REVERT: I 233 MET cc_start: 0.8358 (mtp) cc_final: 0.7929 (mtp) REVERT: I 257 MET cc_start: 0.7377 (mmp) cc_final: 0.7155 (mmp) REVERT: I 320 ARG cc_start: 0.8165 (mtm-85) cc_final: 0.7857 (mtm-85) REVERT: I 323 MET cc_start: 0.8859 (ttt) cc_final: 0.8583 (ttp) REVERT: I 355 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.7567 (t70) REVERT: I 383 GLU cc_start: 0.8531 (tt0) cc_final: 0.8087 (tm-30) REVERT: E 24 TYR cc_start: 0.8283 (m-10) cc_final: 0.7891 (m-80) REVERT: E 83 TYR cc_start: 0.7855 (m-80) cc_final: 0.6609 (m-10) REVERT: E 163 LYS cc_start: 0.8964 (ttpp) cc_final: 0.8542 (tppt) REVERT: E 167 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8615 (mm) REVERT: E 285 GLN cc_start: 0.7254 (tt0) cc_final: 0.6674 (mm110) REVERT: E 287 SER cc_start: 0.8284 (OUTLIER) cc_final: 0.7929 (p) REVERT: E 290 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7183 (tp30) REVERT: E 302 MET cc_start: 0.9122 (mmt) cc_final: 0.8908 (mmm) REVERT: E 319 TYR cc_start: 0.8590 (m-80) cc_final: 0.8074 (m-80) REVERT: E 346 TRP cc_start: 0.8107 (p-90) cc_final: 0.7764 (p90) REVERT: E 356 ASN cc_start: 0.8558 (t0) cc_final: 0.8146 (m-40) REVERT: E 388 TRP cc_start: 0.8378 (m-90) cc_final: 0.7633 (m-90) REVERT: E 413 MET cc_start: 0.8201 (mmm) cc_final: 0.7910 (mmm) REVERT: E 415 GLU cc_start: 0.6999 (tt0) cc_final: 0.6431 (tm-30) REVERT: E 417 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7793 (mm-30) REVERT: E 429 GLU cc_start: 0.6961 (mt-10) cc_final: 0.5611 (tm-30) REVERT: J 19 LYS cc_start: 0.8766 (mmmm) cc_final: 0.8490 (mtpp) REVERT: J 99 ASN cc_start: 0.8013 (m-40) cc_final: 0.7695 (m-40) REVERT: J 114 ASP cc_start: 0.7888 (m-30) cc_final: 0.7447 (t0) REVERT: J 121 ARG cc_start: 0.8416 (mmm-85) cc_final: 0.8175 (mmm-85) REVERT: J 190 HIS cc_start: 0.7449 (t70) cc_final: 0.7058 (t-170) REVERT: J 200 TYR cc_start: 0.8480 (m-80) cc_final: 0.7876 (m-80) REVERT: J 247 ASN cc_start: 0.8254 (OUTLIER) cc_final: 0.7653 (p0) REVERT: J 298 ASN cc_start: 0.7582 (m-40) cc_final: 0.6960 (p0) REVERT: J 306 ARG cc_start: 0.7705 (mpt-90) cc_final: 0.7247 (mtt-85) REVERT: J 344 TRP cc_start: 0.5949 (p90) cc_final: 0.5540 (p-90) REVERT: J 383 GLU cc_start: 0.8633 (tt0) cc_final: 0.8339 (tm-30) REVERT: J 401 GLU cc_start: 0.5981 (mp0) cc_final: 0.5509 (mt-10) REVERT: J 406 MET cc_start: 0.7599 (ptm) cc_final: 0.5319 (tpt) REVERT: C 8 GLN cc_start: 0.8031 (mt0) cc_final: 0.7146 (mt0) REVERT: C 11 GLN cc_start: 0.8332 (tt0) cc_final: 0.8060 (pt0) REVERT: C 22 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8241 (mm-30) REVERT: C 73 MET cc_start: 0.9167 (mmm) cc_final: 0.8893 (mmm) REVERT: C 130 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8445 (tm) REVERT: C 133 PHE cc_start: 0.8294 (m-80) cc_final: 0.7948 (m-10) REVERT: C 136 THR cc_start: 0.8985 (m) cc_final: 0.8708 (p) REVERT: C 167 PHE cc_start: 0.8499 (m-80) cc_final: 0.8198 (m-80) REVERT: C 222 TYR cc_start: 0.7847 (OUTLIER) cc_final: 0.5714 (m-80) REVERT: C 247 ASN cc_start: 0.8121 (OUTLIER) cc_final: 0.7652 (p0) REVERT: C 276 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6984 (mtm180) REVERT: C 298 ASN cc_start: 0.7152 (m-40) cc_final: 0.6082 (t0) REVERT: C 299 MET cc_start: 0.8656 (mmt) cc_final: 0.8434 (mmt) REVERT: C 306 ARG cc_start: 0.7982 (mpt-90) cc_final: 0.7732 (mtt-85) REVERT: C 379 LYS cc_start: 0.8823 (mttt) cc_final: 0.8315 (mtpp) REVERT: C 383 GLU cc_start: 0.8486 (tt0) cc_final: 0.8282 (tm-30) REVERT: D 8 GLN cc_start: 0.7982 (mt0) cc_final: 0.7758 (mt0) REVERT: D 11 GLN cc_start: 0.8161 (tt0) cc_final: 0.7906 (pt0) REVERT: D 14 ASN cc_start: 0.8152 (m110) cc_final: 0.7916 (m-40) REVERT: D 50 TYR cc_start: 0.8155 (m-80) cc_final: 0.7409 (m-80) REVERT: D 73 MET cc_start: 0.9193 (mmm) cc_final: 0.8678 (mmm) REVERT: D 99 ASN cc_start: 0.7848 (m-40) cc_final: 0.7169 (m-40) REVERT: D 114 ASP cc_start: 0.7858 (m-30) cc_final: 0.7470 (t0) REVERT: D 133 PHE cc_start: 0.8557 (m-80) cc_final: 0.8170 (m-80) REVERT: D 157 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8392 (mt-10) REVERT: D 167 PHE cc_start: 0.8391 (m-80) cc_final: 0.7909 (m-80) REVERT: D 200 TYR cc_start: 0.8647 (m-80) cc_final: 0.8163 (m-80) REVERT: D 222 TYR cc_start: 0.8229 (OUTLIER) cc_final: 0.7789 (m-80) REVERT: D 300 MET cc_start: 0.8289 (mtt) cc_final: 0.8039 (mtt) REVERT: D 306 ARG cc_start: 0.7500 (mmt90) cc_final: 0.7246 (mtt-85) REVERT: D 383 GLU cc_start: 0.8466 (tt0) cc_final: 0.8008 (tm-30) REVERT: D 403 MET cc_start: 0.8729 (mmm) cc_final: 0.8361 (mmm) REVERT: D 406 MET cc_start: 0.7820 (ptm) cc_final: 0.5794 (mmm) REVERT: F 2 ARG cc_start: 0.7988 (mtm180) cc_final: 0.7672 (mtm110) REVERT: F 47 ASP cc_start: 0.5124 (OUTLIER) cc_final: 0.4860 (t70) REVERT: F 97 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6561 (tm-30) REVERT: F 122 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8964 (pt) REVERT: F 124 LYS cc_start: 0.8613 (ttpt) cc_final: 0.8404 (tptt) REVERT: F 157 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8095 (mp) REVERT: F 168 GLU cc_start: 0.7977 (pt0) cc_final: 0.7522 (pp20) REVERT: F 210 TYR cc_start: 0.7613 (m-10) cc_final: 0.7224 (m-10) REVERT: F 221 ARG cc_start: 0.8272 (mtp-110) cc_final: 0.7824 (ptm160) REVERT: F 224 TYR cc_start: 0.7661 (OUTLIER) cc_final: 0.6685 (m-10) REVERT: F 248 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7198 (tt) REVERT: F 290 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7837 (tp30) REVERT: F 326 LYS cc_start: 0.8838 (ttmt) cc_final: 0.8519 (tppt) REVERT: F 415 GLU cc_start: 0.7747 (tt0) cc_final: 0.7004 (tm-30) REVERT: F 420 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.6677 (tp30) REVERT: F 432 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.7230 (t80) REVERT: A 24 TYR cc_start: 0.8101 (m-80) cc_final: 0.7047 (m-80) REVERT: A 36 MET cc_start: 0.7688 (ttt) cc_final: 0.7011 (tmm) REVERT: A 83 TYR cc_start: 0.7549 (m-80) cc_final: 0.6672 (m-10) REVERT: A 88 HIS cc_start: 0.8210 (p-80) cc_final: 0.7753 (p-80) REVERT: A 96 LYS cc_start: 0.6426 (tppt) cc_final: 0.6163 (mppt) REVERT: A 121 ARG cc_start: 0.8372 (mmt-90) cc_final: 0.7975 (mmt180) REVERT: A 124 LYS cc_start: 0.8534 (ttpt) cc_final: 0.8179 (tptt) REVERT: A 276 ILE cc_start: 0.8797 (mt) cc_final: 0.8515 (tt) REVERT: A 282 TYR cc_start: 0.8118 (m-80) cc_final: 0.7893 (m-80) REVERT: A 290 GLU cc_start: 0.7993 (tt0) cc_final: 0.7545 (tp30) REVERT: A 302 MET cc_start: 0.8913 (mmt) cc_final: 0.8539 (mmm) REVERT: A 326 LYS cc_start: 0.8836 (ttmt) cc_final: 0.8406 (tppt) REVERT: A 346 TRP cc_start: 0.6724 (p90) cc_final: 0.6379 (p90) REVERT: A 356 ASN cc_start: 0.8587 (t0) cc_final: 0.8206 (m-40) REVERT: A 395 PHE cc_start: 0.7585 (t80) cc_final: 0.6948 (t80) REVERT: A 407 TRP cc_start: 0.8736 (m100) cc_final: 0.8425 (m100) REVERT: A 417 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7562 (mm-30) REVERT: B 2 ARG cc_start: 0.7743 (mtm180) cc_final: 0.7304 (mtm110) REVERT: B 97 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6385 (tm-30) REVERT: B 254 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7700 (mt-10) REVERT: B 316 CYS cc_start: 0.8643 (m) cc_final: 0.8440 (m) REVERT: B 356 ASN cc_start: 0.8480 (t0) cc_final: 0.8196 (t0) REVERT: B 413 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.8000 (mmp) REVERT: B 415 GLU cc_start: 0.8558 (tt0) cc_final: 0.7206 (tm-30) REVERT: B 420 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.6624 (tp30) REVERT: B 429 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6745 (mt-10) REVERT: L 19 LYS cc_start: 0.8961 (mmmm) cc_final: 0.8672 (mtpp) REVERT: L 45 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8709 (tp30) REVERT: L 130 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8198 (tm) REVERT: L 167 PHE cc_start: 0.8300 (m-80) cc_final: 0.7842 (m-10) REVERT: L 233 MET cc_start: 0.8461 (mtp) cc_final: 0.8144 (mtp) REVERT: L 257 MET cc_start: 0.7712 (mmm) cc_final: 0.7145 (mmm) REVERT: L 327 ASP cc_start: 0.8435 (t0) cc_final: 0.8215 (t0) REVERT: L 379 LYS cc_start: 0.8745 (ttmp) cc_final: 0.8438 (tptp) REVERT: G 47 ASP cc_start: 0.5540 (OUTLIER) cc_final: 0.5130 (t70) REVERT: G 123 ARG cc_start: 0.8293 (ttp-110) cc_final: 0.8071 (ttm-80) REVERT: G 124 LYS cc_start: 0.8558 (ttpt) cc_final: 0.8209 (tptt) REVERT: G 210 TYR cc_start: 0.7561 (m-10) cc_final: 0.7274 (m-80) REVERT: G 250 VAL cc_start: 0.8762 (OUTLIER) cc_final: 0.8135 (t) REVERT: G 251 ASP cc_start: 0.7505 (m-30) cc_final: 0.6524 (m-30) REVERT: G 254 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7719 (mt-10) REVERT: G 257 THR cc_start: 0.8921 (m) cc_final: 0.8643 (p) REVERT: G 302 MET cc_start: 0.8617 (mtp) cc_final: 0.8236 (mtp) REVERT: G 356 ASN cc_start: 0.8627 (t0) cc_final: 0.8315 (m-40) REVERT: G 395 PHE cc_start: 0.7877 (t80) cc_final: 0.7657 (t80) REVERT: G 396 ASP cc_start: 0.8871 (t0) cc_final: 0.8637 (m-30) REVERT: G 413 MET cc_start: 0.8619 (tpt) cc_final: 0.8395 (mmp) REVERT: G 420 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.6849 (tp30) REVERT: G 432 TYR cc_start: 0.7755 (OUTLIER) cc_final: 0.6864 (t80) outliers start: 209 outliers final: 147 residues processed: 1280 average time/residue: 0.5571 time to fit residues: 1129.1797 Evaluate side-chains 1249 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1068 time to evaluate : 4.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 81 PHE Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 247 ASN Chi-restraints excluded: chain K residue 313 VAL Chi-restraints excluded: chain K residue 338 SER Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 205 ASP Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 287 SER Chi-restraints excluded: chain H residue 290 GLU Chi-restraints excluded: chain H residue 328 VAL Chi-restraints excluded: chain H residue 345 ASP Chi-restraints excluded: chain H residue 413 MET Chi-restraints excluded: chain H residue 420 GLU Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 194 GLU Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 290 THR Chi-restraints excluded: chain I residue 355 ASP Chi-restraints excluded: chain I residue 363 MET Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 81 PHE Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 247 ASN Chi-restraints excluded: chain J residue 253 LEU Chi-restraints excluded: chain J residue 263 LEU Chi-restraints excluded: chain J residue 303 CYS Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 316 VAL Chi-restraints excluded: chain J residue 337 ASN Chi-restraints excluded: chain J residue 367 PHE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 222 TYR Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 85 GLN Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 172 TYR Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 420 GLU Chi-restraints excluded: chain F residue 432 TYR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain L residue 172 SER Chi-restraints excluded: chain L residue 247 ASN Chi-restraints excluded: chain L residue 367 PHE Chi-restraints excluded: chain L residue 371 SER Chi-restraints excluded: chain L residue 388 MET Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 256 GLN Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain G residue 420 GLU Chi-restraints excluded: chain G residue 432 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 441 optimal weight: 20.0000 chunk 465 optimal weight: 0.0870 chunk 424 optimal weight: 0.0970 chunk 452 optimal weight: 10.0000 chunk 272 optimal weight: 8.9990 chunk 197 optimal weight: 0.9990 chunk 355 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 409 optimal weight: 20.0000 chunk 428 optimal weight: 9.9990 chunk 451 optimal weight: 6.9990 overall best weight: 2.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 279 GLN ** K 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 ASN I 14 ASN ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 423 GLN ** J 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 HIS ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 HIS ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN A 128 GLN A 197 HIS A 256 GLN ** L 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 301 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 41436 Z= 0.193 Angle : 0.642 12.390 56298 Z= 0.313 Chirality : 0.043 0.266 6162 Planarity : 0.005 0.080 7308 Dihedral : 10.040 154.860 5856 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.69 % Allowed : 26.52 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.42 (0.12), residues: 5088 helix: 1.36 (0.11), residues: 2316 sheet: 0.83 (0.18), residues: 786 loop : -1.26 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 344 HIS 0.006 0.001 HIS E 88 PHE 0.028 0.002 PHE B 169 TYR 0.022 0.001 TYR F 108 ARG 0.013 0.001 ARG D 121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1320 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1117 time to evaluate : 4.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 50 TYR cc_start: 0.8130 (m-80) cc_final: 0.7602 (m-10) REVERT: K 73 MET cc_start: 0.9286 (mmm) cc_final: 0.8758 (mmm) REVERT: K 77 ARG cc_start: 0.7875 (tpp-160) cc_final: 0.7397 (tpm170) REVERT: K 99 ASN cc_start: 0.8230 (m110) cc_final: 0.7865 (m-40) REVERT: K 114 ASP cc_start: 0.7720 (m-30) cc_final: 0.7120 (t0) REVERT: K 133 PHE cc_start: 0.8536 (m-80) cc_final: 0.8098 (m-80) REVERT: K 247 ASN cc_start: 0.8059 (m-40) cc_final: 0.7539 (p0) REVERT: K 257 MET cc_start: 0.8128 (mmm) cc_final: 0.7843 (mmm) REVERT: K 267 MET cc_start: 0.8610 (ttm) cc_final: 0.8356 (ttm) REVERT: K 299 MET cc_start: 0.8246 (tpt) cc_final: 0.7991 (mmt) REVERT: K 300 MET cc_start: 0.7631 (mtt) cc_final: 0.7199 (mtm) REVERT: K 321 MET cc_start: 0.7763 (mtp) cc_final: 0.7350 (mtm) REVERT: K 363 MET cc_start: 0.8345 (mmt) cc_final: 0.7834 (mmt) REVERT: K 383 GLU cc_start: 0.8334 (tt0) cc_final: 0.7899 (tm-30) REVERT: K 406 MET cc_start: 0.7634 (ptm) cc_final: 0.5816 (mmm) REVERT: H 124 LYS cc_start: 0.8676 (ttpt) cc_final: 0.8260 (tptt) REVERT: H 154 MET cc_start: 0.8530 (mmp) cc_final: 0.8078 (tpt) REVERT: H 203 MET cc_start: 0.7079 (mtm) cc_final: 0.6603 (mtm) REVERT: H 290 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7201 (tp30) REVERT: H 302 MET cc_start: 0.8871 (mmt) cc_final: 0.8503 (mmm) REVERT: H 356 ASN cc_start: 0.8860 (t0) cc_final: 0.8266 (m-40) REVERT: H 388 TRP cc_start: 0.8525 (m-90) cc_final: 0.8115 (m-90) REVERT: H 413 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7981 (mmp) REVERT: H 420 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.6206 (tp30) REVERT: I 22 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7990 (mm-30) REVERT: I 77 ARG cc_start: 0.7931 (tpt170) cc_final: 0.7549 (tpm170) REVERT: I 130 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8138 (tm) REVERT: I 133 PHE cc_start: 0.8163 (m-80) cc_final: 0.7696 (m-80) REVERT: I 136 THR cc_start: 0.9082 (m) cc_final: 0.8745 (p) REVERT: I 167 PHE cc_start: 0.8521 (m-80) cc_final: 0.8087 (m-10) REVERT: I 168 SER cc_start: 0.8263 (m) cc_final: 0.8001 (p) REVERT: I 217 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7473 (mt) REVERT: I 233 MET cc_start: 0.8350 (mtp) cc_final: 0.7942 (mtp) REVERT: I 257 MET cc_start: 0.7455 (mmp) cc_final: 0.7208 (mmp) REVERT: I 320 ARG cc_start: 0.8146 (mtm-85) cc_final: 0.7829 (mtm-85) REVERT: I 323 MET cc_start: 0.8767 (ttt) cc_final: 0.8338 (ttp) REVERT: I 355 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7560 (t70) REVERT: I 383 GLU cc_start: 0.8496 (tt0) cc_final: 0.8117 (tm-30) REVERT: I 401 GLU cc_start: 0.6035 (mp0) cc_final: 0.5728 (mt-10) REVERT: E 24 TYR cc_start: 0.8314 (m-10) cc_final: 0.7954 (m-80) REVERT: E 83 TYR cc_start: 0.7846 (m-80) cc_final: 0.6585 (m-10) REVERT: E 163 LYS cc_start: 0.8963 (ttpp) cc_final: 0.8554 (tppt) REVERT: E 167 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8519 (mm) REVERT: E 276 ILE cc_start: 0.8528 (mm) cc_final: 0.8024 (tt) REVERT: E 285 GLN cc_start: 0.7314 (tt0) cc_final: 0.6726 (mm110) REVERT: E 290 GLU cc_start: 0.7835 (tt0) cc_final: 0.7315 (tp30) REVERT: E 319 TYR cc_start: 0.8633 (m-80) cc_final: 0.8137 (m-80) REVERT: E 346 TRP cc_start: 0.8174 (p-90) cc_final: 0.7705 (p90) REVERT: E 356 ASN cc_start: 0.8563 (t0) cc_final: 0.8135 (m-40) REVERT: E 388 TRP cc_start: 0.8314 (m-90) cc_final: 0.7562 (m-90) REVERT: E 417 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7779 (mm-30) REVERT: E 429 GLU cc_start: 0.6851 (mt-10) cc_final: 0.5543 (tm-30) REVERT: J 99 ASN cc_start: 0.8050 (m-40) cc_final: 0.7743 (m-40) REVERT: J 114 ASP cc_start: 0.7874 (m-30) cc_final: 0.7446 (t0) REVERT: J 121 ARG cc_start: 0.8414 (mmm-85) cc_final: 0.8172 (mmm-85) REVERT: J 190 HIS cc_start: 0.7433 (t70) cc_final: 0.7111 (t-170) REVERT: J 200 TYR cc_start: 0.8350 (m-80) cc_final: 0.7820 (m-80) REVERT: J 298 ASN cc_start: 0.7703 (m-40) cc_final: 0.7107 (p0) REVERT: J 300 MET cc_start: 0.7004 (ptt) cc_final: 0.6771 (ptt) REVERT: J 306 ARG cc_start: 0.7725 (mpt-90) cc_final: 0.7246 (mtt-85) REVERT: J 344 TRP cc_start: 0.5964 (p90) cc_final: 0.5571 (p-90) REVERT: J 383 GLU cc_start: 0.8617 (tt0) cc_final: 0.8325 (tm-30) REVERT: J 406 MET cc_start: 0.7535 (ptm) cc_final: 0.5289 (tpt) REVERT: J 423 GLN cc_start: 0.7034 (tp-100) cc_final: 0.5803 (pt0) REVERT: C 8 GLN cc_start: 0.8055 (mt0) cc_final: 0.7178 (mt0) REVERT: C 22 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8124 (mm-30) REVERT: C 73 MET cc_start: 0.9171 (mmm) cc_final: 0.8902 (mmm) REVERT: C 130 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8447 (tm) REVERT: C 133 PHE cc_start: 0.8345 (m-80) cc_final: 0.7994 (m-10) REVERT: C 136 THR cc_start: 0.8998 (m) cc_final: 0.8729 (p) REVERT: C 167 PHE cc_start: 0.8485 (m-80) cc_final: 0.8206 (m-80) REVERT: C 222 TYR cc_start: 0.7844 (OUTLIER) cc_final: 0.5669 (m-80) REVERT: C 247 ASN cc_start: 0.8139 (m-40) cc_final: 0.7691 (p0) REVERT: C 276 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6983 (mtm180) REVERT: C 298 ASN cc_start: 0.7104 (m-40) cc_final: 0.6088 (t0) REVERT: C 299 MET cc_start: 0.8596 (mmt) cc_final: 0.8392 (mmt) REVERT: C 306 ARG cc_start: 0.7964 (mpt-90) cc_final: 0.7710 (mtt-85) REVERT: C 379 LYS cc_start: 0.8810 (mttt) cc_final: 0.8315 (mtpp) REVERT: C 383 GLU cc_start: 0.8466 (tt0) cc_final: 0.8247 (tm-30) REVERT: D 8 GLN cc_start: 0.8052 (mt0) cc_final: 0.7838 (mt0) REVERT: D 11 GLN cc_start: 0.8112 (tt0) cc_final: 0.7835 (pt0) REVERT: D 14 ASN cc_start: 0.8139 (m110) cc_final: 0.7929 (m-40) REVERT: D 50 TYR cc_start: 0.8191 (m-80) cc_final: 0.7447 (m-80) REVERT: D 73 MET cc_start: 0.9197 (mmm) cc_final: 0.8676 (mmm) REVERT: D 77 ARG cc_start: 0.8608 (tpt170) cc_final: 0.7869 (tpm170) REVERT: D 99 ASN cc_start: 0.7911 (m-40) cc_final: 0.7247 (m-40) REVERT: D 114 ASP cc_start: 0.7947 (m-30) cc_final: 0.7539 (t0) REVERT: D 133 PHE cc_start: 0.8573 (m-80) cc_final: 0.8178 (m-80) REVERT: D 157 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8362 (mt-10) REVERT: D 167 PHE cc_start: 0.8173 (m-80) cc_final: 0.7944 (m-80) REVERT: D 200 TYR cc_start: 0.8923 (m-80) cc_final: 0.8451 (m-80) REVERT: D 233 MET cc_start: 0.8080 (mmp) cc_final: 0.7730 (mmt) REVERT: D 300 MET cc_start: 0.8256 (mtt) cc_final: 0.7817 (mtm) REVERT: D 306 ARG cc_start: 0.7501 (mmt90) cc_final: 0.7246 (mtt-85) REVERT: D 355 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7827 (m-30) REVERT: D 383 GLU cc_start: 0.8443 (tt0) cc_final: 0.7994 (tm-30) REVERT: D 403 MET cc_start: 0.8732 (mmm) cc_final: 0.8451 (mmm) REVERT: D 406 MET cc_start: 0.7837 (ptm) cc_final: 0.5799 (mmm) REVERT: F 2 ARG cc_start: 0.8002 (mtm180) cc_final: 0.7684 (mtm110) REVERT: F 47 ASP cc_start: 0.5120 (OUTLIER) cc_final: 0.4866 (t70) REVERT: F 122 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8973 (pt) REVERT: F 124 LYS cc_start: 0.8621 (ttpt) cc_final: 0.8399 (tptt) REVERT: F 157 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8058 (mp) REVERT: F 168 GLU cc_start: 0.7992 (pt0) cc_final: 0.7574 (pp20) REVERT: F 210 TYR cc_start: 0.7604 (m-10) cc_final: 0.7307 (m-10) REVERT: F 224 TYR cc_start: 0.7644 (OUTLIER) cc_final: 0.6660 (m-10) REVERT: F 248 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7185 (tt) REVERT: F 290 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7882 (tp30) REVERT: F 326 LYS cc_start: 0.8795 (ttmt) cc_final: 0.8415 (tppt) REVERT: F 415 GLU cc_start: 0.7785 (tt0) cc_final: 0.7042 (tm-30) REVERT: F 420 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.6585 (tp30) REVERT: F 432 TYR cc_start: 0.7839 (OUTLIER) cc_final: 0.7223 (t80) REVERT: A 24 TYR cc_start: 0.8153 (m-80) cc_final: 0.7061 (m-80) REVERT: A 36 MET cc_start: 0.7706 (ttt) cc_final: 0.7019 (tmm) REVERT: A 83 TYR cc_start: 0.7540 (m-80) cc_final: 0.6680 (m-10) REVERT: A 88 HIS cc_start: 0.8190 (p-80) cc_final: 0.7790 (p-80) REVERT: A 96 LYS cc_start: 0.6429 (tppt) cc_final: 0.6143 (mppt) REVERT: A 124 LYS cc_start: 0.8472 (ttpt) cc_final: 0.8178 (tptt) REVERT: A 154 MET cc_start: 0.7408 (tpt) cc_final: 0.6656 (tmm) REVERT: A 175 PRO cc_start: 0.7547 (Cg_exo) cc_final: 0.7339 (Cg_endo) REVERT: A 262 TYR cc_start: 0.8397 (m-80) cc_final: 0.8004 (m-10) REVERT: A 276 ILE cc_start: 0.8790 (mt) cc_final: 0.8485 (tt) REVERT: A 290 GLU cc_start: 0.8073 (tt0) cc_final: 0.7524 (tp30) REVERT: A 302 MET cc_start: 0.8988 (mmt) cc_final: 0.8437 (mmm) REVERT: A 326 LYS cc_start: 0.8833 (ttmt) cc_final: 0.8408 (tppt) REVERT: A 346 TRP cc_start: 0.6687 (p90) cc_final: 0.5984 (p90) REVERT: A 356 ASN cc_start: 0.8623 (t0) cc_final: 0.8242 (m-40) REVERT: A 395 PHE cc_start: 0.7611 (t80) cc_final: 0.7002 (t80) REVERT: A 407 TRP cc_start: 0.8750 (m100) cc_final: 0.8430 (m100) REVERT: A 417 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7657 (mm-30) REVERT: B 2 ARG cc_start: 0.7733 (mtm180) cc_final: 0.7298 (mtm110) REVERT: B 254 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7609 (mt-10) REVERT: B 356 ASN cc_start: 0.8501 (t0) cc_final: 0.8214 (t0) REVERT: B 413 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7957 (mmp) REVERT: B 415 GLU cc_start: 0.8481 (tt0) cc_final: 0.7231 (tm-30) REVERT: B 420 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.6663 (tp30) REVERT: B 429 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6711 (mt-10) REVERT: L 19 LYS cc_start: 0.8973 (mmmm) cc_final: 0.8704 (mtpp) REVERT: L 45 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8758 (tp30) REVERT: L 121 ARG cc_start: 0.8097 (mmm-85) cc_final: 0.7790 (mmm-85) REVERT: L 130 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8259 (tm) REVERT: L 257 MET cc_start: 0.7792 (mmm) cc_final: 0.7154 (mmm) REVERT: L 327 ASP cc_start: 0.8447 (t0) cc_final: 0.8168 (t0) REVERT: L 379 LYS cc_start: 0.8633 (ttmp) cc_final: 0.8416 (tptp) REVERT: L 383 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8086 (tm-30) REVERT: G 47 ASP cc_start: 0.5558 (OUTLIER) cc_final: 0.5144 (t70) REVERT: G 123 ARG cc_start: 0.8294 (ttp-110) cc_final: 0.8075 (ttm-80) REVERT: G 124 LYS cc_start: 0.8569 (ttpt) cc_final: 0.8213 (tptt) REVERT: G 210 TYR cc_start: 0.7577 (m-10) cc_final: 0.6828 (m-80) REVERT: G 250 VAL cc_start: 0.8783 (OUTLIER) cc_final: 0.8123 (t) REVERT: G 251 ASP cc_start: 0.7511 (m-30) cc_final: 0.6391 (m-30) REVERT: G 254 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7692 (mt-10) REVERT: G 257 THR cc_start: 0.8886 (m) cc_final: 0.8624 (p) REVERT: G 356 ASN cc_start: 0.8627 (t0) cc_final: 0.8306 (m-40) REVERT: G 396 ASP cc_start: 0.8868 (t0) cc_final: 0.8639 (m-30) REVERT: G 413 MET cc_start: 0.8587 (tpt) cc_final: 0.8361 (mmp) REVERT: G 420 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.6851 (tp30) REVERT: G 432 TYR cc_start: 0.7684 (OUTLIER) cc_final: 0.7000 (t80) outliers start: 203 outliers final: 157 residues processed: 1244 average time/residue: 0.5570 time to fit residues: 1100.7508 Evaluate side-chains 1260 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1075 time to evaluate : 4.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 81 PHE Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 313 VAL Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 205 ASP Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 287 SER Chi-restraints excluded: chain H residue 290 GLU Chi-restraints excluded: chain H residue 328 VAL Chi-restraints excluded: chain H residue 345 ASP Chi-restraints excluded: chain H residue 413 MET Chi-restraints excluded: chain H residue 420 GLU Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 194 GLU Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 290 THR Chi-restraints excluded: chain I residue 303 CYS Chi-restraints excluded: chain I residue 355 ASP Chi-restraints excluded: chain I residue 363 MET Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 81 PHE Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 222 TYR Chi-restraints excluded: chain J residue 253 LEU Chi-restraints excluded: chain J residue 263 LEU Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 316 VAL Chi-restraints excluded: chain J residue 337 ASN Chi-restraints excluded: chain J residue 367 PHE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 222 TYR Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 85 GLN Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 420 GLU Chi-restraints excluded: chain F residue 432 TYR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 81 PHE Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain L residue 172 SER Chi-restraints excluded: chain L residue 247 ASN Chi-restraints excluded: chain L residue 347 ASN Chi-restraints excluded: chain L residue 367 PHE Chi-restraints excluded: chain L residue 371 SER Chi-restraints excluded: chain L residue 383 GLU Chi-restraints excluded: chain L residue 388 MET Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 256 GLN Chi-restraints excluded: chain G residue 269 LEU Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain G residue 379 SER Chi-restraints excluded: chain G residue 420 GLU Chi-restraints excluded: chain G residue 432 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 297 optimal weight: 0.8980 chunk 478 optimal weight: 6.9990 chunk 292 optimal weight: 7.9990 chunk 227 optimal weight: 20.0000 chunk 332 optimal weight: 10.0000 chunk 502 optimal weight: 5.9990 chunk 462 optimal weight: 8.9990 chunk 399 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 308 optimal weight: 4.9990 chunk 245 optimal weight: 0.0870 overall best weight: 2.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 HIS ** J 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 HIS ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 HIS A 31 GLN A 128 GLN ** L 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN G 301 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 41436 Z= 0.202 Angle : 0.655 12.771 56298 Z= 0.319 Chirality : 0.043 0.262 6162 Planarity : 0.005 0.087 7308 Dihedral : 9.983 154.041 5856 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.48 % Allowed : 27.10 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.41 (0.12), residues: 5088 helix: 1.33 (0.11), residues: 2316 sheet: 0.82 (0.18), residues: 786 loop : -1.24 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K 101 HIS 0.013 0.001 HIS D 57 PHE 0.028 0.002 PHE L 294 TYR 0.024 0.001 TYR A 103 ARG 0.011 0.001 ARG J 241 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1284 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1090 time to evaluate : 4.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 50 TYR cc_start: 0.8135 (m-80) cc_final: 0.7636 (m-10) REVERT: K 73 MET cc_start: 0.9282 (mmm) cc_final: 0.8751 (mmm) REVERT: K 77 ARG cc_start: 0.7883 (tpp-160) cc_final: 0.7397 (tpm170) REVERT: K 99 ASN cc_start: 0.8262 (m110) cc_final: 0.7887 (m-40) REVERT: K 114 ASP cc_start: 0.7721 (m-30) cc_final: 0.7123 (t0) REVERT: K 133 PHE cc_start: 0.8524 (m-80) cc_final: 0.8089 (m-80) REVERT: K 247 ASN cc_start: 0.8040 (m-40) cc_final: 0.7518 (p0) REVERT: K 267 MET cc_start: 0.8611 (ttm) cc_final: 0.8296 (ttm) REVERT: K 300 MET cc_start: 0.7599 (mtt) cc_final: 0.7196 (mtm) REVERT: K 321 MET cc_start: 0.7770 (mtp) cc_final: 0.7354 (mtm) REVERT: K 363 MET cc_start: 0.8331 (mmt) cc_final: 0.7851 (mmt) REVERT: K 383 GLU cc_start: 0.8303 (tt0) cc_final: 0.7880 (tm-30) REVERT: K 406 MET cc_start: 0.7632 (ptm) cc_final: 0.5808 (mmm) REVERT: H 124 LYS cc_start: 0.8651 (ttpt) cc_final: 0.8249 (tptt) REVERT: H 154 MET cc_start: 0.8535 (mmp) cc_final: 0.8087 (tpt) REVERT: H 203 MET cc_start: 0.7102 (mtm) cc_final: 0.6641 (mtm) REVERT: H 290 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7223 (tp30) REVERT: H 302 MET cc_start: 0.8857 (mmt) cc_final: 0.8486 (mmm) REVERT: H 356 ASN cc_start: 0.8862 (t0) cc_final: 0.8271 (m-40) REVERT: H 388 TRP cc_start: 0.8520 (m-90) cc_final: 0.8029 (m-90) REVERT: H 413 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7642 (mmp) REVERT: H 415 GLU cc_start: 0.8410 (tt0) cc_final: 0.7111 (tm-30) REVERT: H 420 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.6703 (tp30) REVERT: I 8 GLN cc_start: 0.8075 (mt0) cc_final: 0.7610 (mt0) REVERT: I 22 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8029 (mm-30) REVERT: I 73 MET cc_start: 0.8944 (mmm) cc_final: 0.8740 (mmm) REVERT: I 77 ARG cc_start: 0.7883 (tpt170) cc_final: 0.7559 (tpm170) REVERT: I 130 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8155 (tm) REVERT: I 133 PHE cc_start: 0.8163 (m-80) cc_final: 0.7738 (m-80) REVERT: I 136 THR cc_start: 0.9087 (m) cc_final: 0.8823 (p) REVERT: I 167 PHE cc_start: 0.8520 (m-80) cc_final: 0.8015 (m-10) REVERT: I 200 TYR cc_start: 0.8637 (m-80) cc_final: 0.7717 (m-80) REVERT: I 217 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7504 (mt) REVERT: I 233 MET cc_start: 0.8367 (mtp) cc_final: 0.7962 (mtp) REVERT: I 267 MET cc_start: 0.8912 (ttm) cc_final: 0.8308 (ttm) REVERT: I 299 MET cc_start: 0.8369 (mmt) cc_final: 0.7338 (mmt) REVERT: I 320 ARG cc_start: 0.8047 (mtm-85) cc_final: 0.7771 (mtm-85) REVERT: I 355 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7544 (t70) REVERT: I 383 GLU cc_start: 0.8494 (tt0) cc_final: 0.8113 (tm-30) REVERT: I 401 GLU cc_start: 0.6108 (mp0) cc_final: 0.5814 (mt-10) REVERT: E 24 TYR cc_start: 0.8301 (m-10) cc_final: 0.7952 (m-80) REVERT: E 83 TYR cc_start: 0.7848 (m-80) cc_final: 0.6588 (m-10) REVERT: E 163 LYS cc_start: 0.8980 (ttpp) cc_final: 0.8581 (tppt) REVERT: E 167 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8490 (mm) REVERT: E 276 ILE cc_start: 0.8516 (mm) cc_final: 0.8005 (tt) REVERT: E 285 GLN cc_start: 0.7332 (tt0) cc_final: 0.6719 (mm110) REVERT: E 287 SER cc_start: 0.8223 (OUTLIER) cc_final: 0.7886 (p) REVERT: E 290 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7368 (tp30) REVERT: E 319 TYR cc_start: 0.8632 (m-80) cc_final: 0.8143 (m-80) REVERT: E 346 TRP cc_start: 0.8262 (p-90) cc_final: 0.7768 (p90) REVERT: E 356 ASN cc_start: 0.8557 (t0) cc_final: 0.8135 (m-40) REVERT: E 388 TRP cc_start: 0.8326 (m-90) cc_final: 0.7560 (m-90) REVERT: E 415 GLU cc_start: 0.7007 (tt0) cc_final: 0.6422 (tm-30) REVERT: E 417 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7785 (mm-30) REVERT: E 429 GLU cc_start: 0.6854 (mt-10) cc_final: 0.5542 (tm-30) REVERT: J 99 ASN cc_start: 0.8068 (m-40) cc_final: 0.7744 (m-40) REVERT: J 114 ASP cc_start: 0.7863 (m-30) cc_final: 0.7437 (t0) REVERT: J 158 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8068 (tp30) REVERT: J 167 PHE cc_start: 0.7595 (m-80) cc_final: 0.7151 (m-10) REVERT: J 190 HIS cc_start: 0.7410 (t70) cc_final: 0.7083 (t-170) REVERT: J 200 TYR cc_start: 0.8277 (m-80) cc_final: 0.7948 (m-80) REVERT: J 298 ASN cc_start: 0.7832 (m-40) cc_final: 0.7235 (p0) REVERT: J 300 MET cc_start: 0.7151 (ptt) cc_final: 0.6902 (ptt) REVERT: J 306 ARG cc_start: 0.7801 (mpt-90) cc_final: 0.7271 (mtt-85) REVERT: J 344 TRP cc_start: 0.6083 (p90) cc_final: 0.5630 (p-90) REVERT: J 350 LYS cc_start: 0.8362 (tptt) cc_final: 0.8077 (tptm) REVERT: J 383 GLU cc_start: 0.8580 (tt0) cc_final: 0.8328 (tm-30) REVERT: J 401 GLU cc_start: 0.5884 (mp0) cc_final: 0.5517 (mt-10) REVERT: J 406 MET cc_start: 0.7529 (ptm) cc_final: 0.5288 (tpt) REVERT: J 423 GLN cc_start: 0.6961 (tp-100) cc_final: 0.5727 (pt0) REVERT: C 8 GLN cc_start: 0.8054 (mt0) cc_final: 0.7179 (mt0) REVERT: C 22 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8123 (mm-30) REVERT: C 73 MET cc_start: 0.9174 (mmm) cc_final: 0.8897 (mmm) REVERT: C 130 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8431 (tm) REVERT: C 133 PHE cc_start: 0.8361 (m-80) cc_final: 0.7987 (m-10) REVERT: C 136 THR cc_start: 0.9012 (m) cc_final: 0.8735 (p) REVERT: C 167 PHE cc_start: 0.8496 (m-80) cc_final: 0.8205 (m-80) REVERT: C 222 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.5707 (m-80) REVERT: C 247 ASN cc_start: 0.8139 (m-40) cc_final: 0.7681 (p0) REVERT: C 257 MET cc_start: 0.8039 (mmm) cc_final: 0.7182 (mmm) REVERT: C 276 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.7068 (mtm180) REVERT: C 298 ASN cc_start: 0.7261 (m-40) cc_final: 0.6157 (t0) REVERT: C 299 MET cc_start: 0.8479 (mmt) cc_final: 0.8275 (mmt) REVERT: C 306 ARG cc_start: 0.7948 (mpt-90) cc_final: 0.7679 (mtt-85) REVERT: C 379 LYS cc_start: 0.8801 (mttt) cc_final: 0.8301 (mtpp) REVERT: C 383 GLU cc_start: 0.8468 (tt0) cc_final: 0.8260 (tm-30) REVERT: D 8 GLN cc_start: 0.8058 (mt0) cc_final: 0.7836 (mt0) REVERT: D 11 GLN cc_start: 0.8124 (tt0) cc_final: 0.7841 (pt0) REVERT: D 14 ASN cc_start: 0.8154 (m110) cc_final: 0.7942 (m-40) REVERT: D 50 TYR cc_start: 0.8201 (m-80) cc_final: 0.7501 (m-80) REVERT: D 73 MET cc_start: 0.9198 (mmm) cc_final: 0.8719 (mmm) REVERT: D 77 ARG cc_start: 0.8676 (tpt170) cc_final: 0.7928 (tpm170) REVERT: D 99 ASN cc_start: 0.7922 (m-40) cc_final: 0.7286 (m-40) REVERT: D 114 ASP cc_start: 0.7944 (m-30) cc_final: 0.7541 (t0) REVERT: D 133 PHE cc_start: 0.8558 (m-80) cc_final: 0.8159 (m-80) REVERT: D 167 PHE cc_start: 0.8097 (m-80) cc_final: 0.7676 (m-10) REVERT: D 198 GLU cc_start: 0.8507 (pt0) cc_final: 0.8198 (pt0) REVERT: D 200 TYR cc_start: 0.8906 (m-80) cc_final: 0.8473 (m-80) REVERT: D 306 ARG cc_start: 0.7474 (mmt90) cc_final: 0.7224 (mtt-85) REVERT: D 383 GLU cc_start: 0.8436 (tt0) cc_final: 0.8069 (tm-30) REVERT: D 403 MET cc_start: 0.8714 (mmm) cc_final: 0.8497 (mmm) REVERT: D 406 MET cc_start: 0.7783 (ptm) cc_final: 0.5776 (mmm) REVERT: F 2 ARG cc_start: 0.8006 (mtm180) cc_final: 0.7695 (mtm110) REVERT: F 47 ASP cc_start: 0.5107 (OUTLIER) cc_final: 0.4866 (t70) REVERT: F 122 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8978 (pt) REVERT: F 124 LYS cc_start: 0.8590 (ttpt) cc_final: 0.8368 (tptt) REVERT: F 157 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8095 (mp) REVERT: F 168 GLU cc_start: 0.8001 (pt0) cc_final: 0.7607 (pp20) REVERT: F 210 TYR cc_start: 0.7635 (m-10) cc_final: 0.7311 (m-10) REVERT: F 224 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.6625 (m-10) REVERT: F 248 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7224 (tt) REVERT: F 290 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7911 (tp30) REVERT: F 326 LYS cc_start: 0.8766 (ttmt) cc_final: 0.8347 (tppt) REVERT: F 388 TRP cc_start: 0.8365 (m-90) cc_final: 0.8008 (m-90) REVERT: F 420 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.6596 (tp30) REVERT: F 432 TYR cc_start: 0.7840 (OUTLIER) cc_final: 0.7235 (t80) REVERT: A 24 TYR cc_start: 0.8198 (m-80) cc_final: 0.7240 (m-80) REVERT: A 36 MET cc_start: 0.7720 (ttt) cc_final: 0.7031 (tmm) REVERT: A 83 TYR cc_start: 0.7539 (m-80) cc_final: 0.6684 (m-10) REVERT: A 88 HIS cc_start: 0.8175 (p-80) cc_final: 0.7882 (p-80) REVERT: A 96 LYS cc_start: 0.6387 (tppt) cc_final: 0.6084 (mppt) REVERT: A 121 ARG cc_start: 0.8365 (tpp-160) cc_final: 0.8111 (mpt-90) REVERT: A 124 LYS cc_start: 0.8475 (ttpt) cc_final: 0.8147 (tptt) REVERT: A 262 TYR cc_start: 0.8403 (m-80) cc_final: 0.8089 (m-10) REVERT: A 276 ILE cc_start: 0.8925 (mt) cc_final: 0.8620 (tt) REVERT: A 290 GLU cc_start: 0.8140 (tt0) cc_final: 0.7559 (tp30) REVERT: A 302 MET cc_start: 0.9015 (mmt) cc_final: 0.8722 (mmm) REVERT: A 326 LYS cc_start: 0.8834 (ttmt) cc_final: 0.8411 (tppt) REVERT: A 346 TRP cc_start: 0.6704 (p90) cc_final: 0.6028 (p90) REVERT: A 356 ASN cc_start: 0.8596 (t0) cc_final: 0.8207 (m-40) REVERT: A 395 PHE cc_start: 0.7569 (t80) cc_final: 0.6959 (t80) REVERT: A 407 TRP cc_start: 0.8750 (m100) cc_final: 0.8435 (m100) REVERT: A 417 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7782 (mm-30) REVERT: B 2 ARG cc_start: 0.7744 (mtm180) cc_final: 0.7325 (mtm110) REVERT: B 254 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7622 (mt-10) REVERT: B 302 MET cc_start: 0.8555 (mmp) cc_final: 0.8099 (mmm) REVERT: B 356 ASN cc_start: 0.8502 (t0) cc_final: 0.8226 (m-40) REVERT: B 413 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7961 (mmp) REVERT: B 415 GLU cc_start: 0.8469 (tt0) cc_final: 0.7235 (tm-30) REVERT: B 420 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.6611 (tp30) REVERT: B 429 GLU cc_start: 0.6962 (mt-10) cc_final: 0.6717 (mt-10) REVERT: L 19 LYS cc_start: 0.8969 (mmmm) cc_final: 0.8711 (mtpp) REVERT: L 130 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8256 (tm) REVERT: L 257 MET cc_start: 0.7661 (mmm) cc_final: 0.7081 (mmm) REVERT: L 276 ARG cc_start: 0.7642 (mpp80) cc_final: 0.7157 (tpm170) REVERT: L 327 ASP cc_start: 0.8410 (t0) cc_final: 0.8134 (t0) REVERT: G 2 ARG cc_start: 0.7431 (mtm180) cc_final: 0.6573 (mpt-90) REVERT: G 47 ASP cc_start: 0.5424 (OUTLIER) cc_final: 0.5006 (t70) REVERT: G 123 ARG cc_start: 0.8293 (ttp-110) cc_final: 0.8076 (ttm-80) REVERT: G 124 LYS cc_start: 0.8565 (ttpt) cc_final: 0.8212 (tptt) REVERT: G 210 TYR cc_start: 0.7618 (m-10) cc_final: 0.6750 (m-80) REVERT: G 250 VAL cc_start: 0.8752 (OUTLIER) cc_final: 0.8130 (t) REVERT: G 251 ASP cc_start: 0.7430 (m-30) cc_final: 0.6751 (m-30) REVERT: G 254 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7814 (mt-10) REVERT: G 257 THR cc_start: 0.8871 (m) cc_final: 0.8568 (p) REVERT: G 356 ASN cc_start: 0.8631 (t0) cc_final: 0.8299 (m-40) REVERT: G 396 ASP cc_start: 0.8835 (t0) cc_final: 0.8622 (m-30) REVERT: G 413 MET cc_start: 0.8621 (tpt) cc_final: 0.8410 (mmp) REVERT: G 420 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.6858 (tp30) REVERT: G 432 TYR cc_start: 0.7667 (OUTLIER) cc_final: 0.7020 (t80) outliers start: 194 outliers final: 156 residues processed: 1213 average time/residue: 0.5748 time to fit residues: 1113.5439 Evaluate side-chains 1235 residues out of total 4368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1051 time to evaluate : 4.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 81 PHE Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 313 VAL Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 205 ASP Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 287 SER Chi-restraints excluded: chain H residue 290 GLU Chi-restraints excluded: chain H residue 328 VAL Chi-restraints excluded: chain H residue 345 ASP Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain H residue 413 MET Chi-restraints excluded: chain H residue 420 GLU Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 194 GLU Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 290 THR Chi-restraints excluded: chain I residue 303 CYS Chi-restraints excluded: chain I residue 355 ASP Chi-restraints excluded: chain I residue 363 MET Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 222 TYR Chi-restraints excluded: chain J residue 253 LEU Chi-restraints excluded: chain J residue 316 VAL Chi-restraints excluded: chain J residue 337 ASN Chi-restraints excluded: chain J residue 367 PHE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 222 TYR Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 348 ASN Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 85 GLN Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 420 GLU Chi-restraints excluded: chain F residue 432 TYR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 81 PHE Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain L residue 172 SER Chi-restraints excluded: chain L residue 347 ASN Chi-restraints excluded: chain L residue 367 PHE Chi-restraints excluded: chain L residue 388 MET Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 88 HIS Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 256 GLN Chi-restraints excluded: chain G residue 269 LEU Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain G residue 379 SER Chi-restraints excluded: chain G residue 420 GLU Chi-restraints excluded: chain G residue 432 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 317 optimal weight: 10.0000 chunk 425 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 368 optimal weight: 20.0000 chunk 59 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 400 optimal weight: 7.9990 chunk 167 optimal weight: 6.9990 chunk 411 optimal weight: 0.0000 chunk 50 optimal weight: 20.0000 chunk 73 optimal weight: 5.9990 overall best weight: 5.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 11 GLN K 28 HIS K 43 GLN ** K 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 384 GLN H 50 ASN H 301 GLN ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 347 ASN E 197 HIS E 266 HIS ** J 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 HIS ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN A 128 GLN B 101 ASN ** L 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.128366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.118915 restraints weight = 75073.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.121683 restraints weight = 41360.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.123550 restraints weight = 25120.563| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.5728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 41436 Z= 0.283 Angle : 0.707 14.983 56298 Z= 0.346 Chirality : 0.045 0.248 6162 Planarity : 0.005 0.075 7308 Dihedral : 10.251 157.910 5856 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.73 % Allowed : 26.96 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.07 (0.12), residues: 5088 helix: 1.06 (0.11), residues: 2316 sheet: 0.67 (0.19), residues: 750 loop : -1.40 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 344 HIS 0.013 0.001 HIS D 57 PHE 0.051 0.002 PHE B 149 TYR 0.030 0.002 TYR A 103 ARG 0.012 0.001 ARG B 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15038.78 seconds wall clock time: 267 minutes 53.65 seconds (16073.65 seconds total)