Starting phenix.real_space_refine on Fri Feb 23 17:22:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilm_35536/02_2024/8ilm_35536_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilm_35536/02_2024/8ilm_35536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilm_35536/02_2024/8ilm_35536.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilm_35536/02_2024/8ilm_35536.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilm_35536/02_2024/8ilm_35536_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilm_35536/02_2024/8ilm_35536_neut.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1296 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 217 5.16 5 C 24041 2.51 5 N 6628 2.21 5 O 7022 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 25": "OD1" <-> "OD2" Residue "A ASP 32": "OD1" <-> "OD2" Residue "A PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "A TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 200": "OD1" <-> "OD2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "A GLU 430": "OE1" <-> "OE2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "B ASP 16": "OD1" <-> "OD2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B ASP 69": "OD1" <-> "OD2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 200": "OD1" <-> "OD2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B GLU 389": "OE1" <-> "OE2" Residue "B PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 422": "OE1" <-> "OE2" Residue "B GLU 430": "OE1" <-> "OE2" Residue "B ASP 433": "OD1" <-> "OD2" Residue "B GLU 461": "OE1" <-> "OE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D ASP 51": "OD1" <-> "OD2" Residue "D ASP 96": "OD1" <-> "OD2" Residue "D PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 154": "OD1" <-> "OD2" Residue "D TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 178": "OD1" <-> "OD2" Residue "D GLU 194": "OE1" <-> "OE2" Residue "D TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 40": "OE1" <-> "OE2" Residue "E ASP 51": "OD1" <-> "OD2" Residue "E ASP 96": "OD1" <-> "OD2" Residue "E PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 154": "OD1" <-> "OD2" Residue "E TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 178": "OD1" <-> "OD2" Residue "E GLU 194": "OE1" <-> "OE2" Residue "E TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 25": "OD1" <-> "OD2" Residue "F ASP 30": "OD1" <-> "OD2" Residue "F PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 48": "OD1" <-> "OD2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F ASP 69": "OD1" <-> "OD2" Residue "F ASP 73": "OD1" <-> "OD2" Residue "F ASP 75": "OD1" <-> "OD2" Residue "F TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 90": "OE1" <-> "OE2" Residue "F PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 157": "OD1" <-> "OD2" Residue "F TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 252": "OE1" <-> "OE2" Residue "F PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 283": "OD1" <-> "OD2" Residue "F ASP 299": "OD1" <-> "OD2" Residue "F GLU 333": "OE1" <-> "OE2" Residue "F PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 344": "OD1" <-> "OD2" Residue "F GLU 348": "OE1" <-> "OE2" Residue "F GLU 389": "OE1" <-> "OE2" Residue "F PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 25": "OD1" <-> "OD2" Residue "G ASP 32": "OD1" <-> "OD2" Residue "G PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 73": "OD1" <-> "OD2" Residue "G TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 106": "OE1" <-> "OE2" Residue "G PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 200": "OD1" <-> "OD2" Residue "G PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 364": "OD1" <-> "OD2" Residue "G ASP 393": "OD1" <-> "OD2" Residue "G PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 422": "OE1" <-> "OE2" Residue "G GLU 430": "OE1" <-> "OE2" Residue "G GLU 437": "OE1" <-> "OE2" Residue "G GLU 465": "OE1" <-> "OE2" Residue "H ASP 32": "OD1" <-> "OD2" Residue "H PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 48": "OD1" <-> "OD2" Residue "H ASP 73": "OD1" <-> "OD2" Residue "H TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 90": "OE1" <-> "OE2" Residue "H GLU 91": "OE1" <-> "OE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 106": "OE1" <-> "OE2" Residue "H PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 155": "OE1" <-> "OE2" Residue "H TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 246": "OE1" <-> "OE2" Residue "H ASP 265": "OD1" <-> "OD2" Residue "H PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 283": "OD1" <-> "OD2" Residue "H ASP 299": "OD1" <-> "OD2" Residue "H GLU 333": "OE1" <-> "OE2" Residue "H PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 389": "OE1" <-> "OE2" Residue "H ASP 394": "OD1" <-> "OD2" Residue "H PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 422": "OE1" <-> "OE2" Residue "H TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 465": "OE1" <-> "OE2" Residue "H PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 467": "OE1" <-> "OE2" Residue "I TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 25": "OD1" <-> "OD2" Residue "I PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 48": "OD1" <-> "OD2" Residue "I GLU 57": "OE1" <-> "OE2" Residue "I TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 90": "OE1" <-> "OE2" Residue "I GLU 91": "OE1" <-> "OE2" Residue "I PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 188": "OE1" <-> "OE2" Residue "I PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 200": "OD1" <-> "OD2" Residue "I GLU 201": "OE1" <-> "OE2" Residue "I PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 246": "OE1" <-> "OE2" Residue "I GLU 252": "OE1" <-> "OE2" Residue "I GLU 256": "OE1" <-> "OE2" Residue "I PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 349": "OD1" <-> "OD2" Residue "I ASP 354": "OD1" <-> "OD2" Residue "I ASP 364": "OD1" <-> "OD2" Residue "I GLU 389": "OE1" <-> "OE2" Residue "I PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 457": "OD1" <-> "OD2" Residue "J ASP 16": "OD1" <-> "OD2" Residue "J TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 57": "OE1" <-> "OE2" Residue "J ASP 69": "OD1" <-> "OD2" Residue "J TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 200": "OD1" <-> "OD2" Residue "J PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 364": "OD1" <-> "OD2" Residue "J PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 422": "OE1" <-> "OE2" Residue "J GLU 430": "OE1" <-> "OE2" Residue "J ASP 433": "OD1" <-> "OD2" Residue "J GLU 437": "OE1" <-> "OE2" Residue "J GLU 444": "OE1" <-> "OE2" Residue "J GLU 461": "OE1" <-> "OE2" Residue "J PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 16": "OD1" <-> "OD2" Residue "K PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 48": "OD1" <-> "OD2" Residue "K GLU 57": "OE1" <-> "OE2" Residue "K ASP 69": "OD1" <-> "OD2" Residue "K TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 90": "OE1" <-> "OE2" Residue "K TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 200": "OD1" <-> "OD2" Residue "K PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 245": "OE1" <-> "OE2" Residue "K ASP 265": "OD1" <-> "OD2" Residue "K PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 283": "OD1" <-> "OD2" Residue "K PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 389": "OE1" <-> "OE2" Residue "K PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 422": "OE1" <-> "OE2" Residue "K GLU 430": "OE1" <-> "OE2" Residue "K ASP 433": "OD1" <-> "OD2" Residue "K GLU 444": "OE1" <-> "OE2" Residue "K GLU 461": "OE1" <-> "OE2" Residue "K GLU 465": "OE1" <-> "OE2" Residue "K PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 64": "OD1" <-> "OD2" Residue "L PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 80": "OE1" <-> "OE2" Residue "M GLU 22": "OE1" <-> "OE2" Residue "M PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 64": "OD1" <-> "OD2" Residue "M PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 79": "OD1" <-> "OD2" Residue "M GLU 80": "OE1" <-> "OE2" Residue "N GLU 22": "OE1" <-> "OE2" Residue "N ASP 39": "OD1" <-> "OD2" Residue "N PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 79": "OD1" <-> "OD2" Residue "O PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 64": "OD1" <-> "OD2" Residue "O PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 80": "OE1" <-> "OE2" Residue "P PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 79": "OD1" <-> "OD2" Residue "P GLU 80": "OE1" <-> "OE2" Residue "Q GLU 22": "OE1" <-> "OE2" Residue "Q ASP 39": "OD1" <-> "OD2" Residue "Q PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 79": "OD1" <-> "OD2" Residue "R GLU 325": "OE1" <-> "OE2" Residue "R ASP 331": "OD1" <-> "OD2" Residue "R PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 367": "OD1" <-> "OD2" Residue "R ASP 375": "OD1" <-> "OD2" Residue "R GLU 379": "OE1" <-> "OE2" Residue "R ARG 387": "NH1" <-> "NH2" Residue "R GLU 393": "OE1" <-> "OE2" Residue "R ASP 395": "OD1" <-> "OD2" Residue "R ASP 396": "OD1" <-> "OD2" Residue "R TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 414": "OD1" <-> "OD2" Residue "R GLU 419": "OE1" <-> "OE2" Residue "R GLU 422": "OE1" <-> "OE2" Residue "R ASP 437": "OD1" <-> "OD2" Residue "S GLU 297": "OE1" <-> "OE2" Residue "S GLU 313": "OE1" <-> "OE2" Residue "S GLU 314": "OE1" <-> "OE2" Residue "S ASP 331": "OD1" <-> "OD2" Residue "S PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 336": "OE1" <-> "OE2" Residue "S ARG 343": "NH1" <-> "NH2" Residue "S ARG 366": "NH1" <-> "NH2" Residue "S ASP 375": "OD1" <-> "OD2" Residue "S GLU 378": "OE1" <-> "OE2" Residue "S ARG 387": "NH1" <-> "NH2" Residue "S TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 435": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 37908 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3581 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 21, 'TRANS': 434} Chain: "B" Number of atoms: 3557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3557 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 21, 'TRANS': 431} Chain: "C" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 515 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "D" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1640 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 12, 'TRANS': 194} Chain: "E" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1640 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 12, 'TRANS': 194} Chain: "F" Number of atoms: 3581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3581 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 21, 'TRANS': 434} Chain: "G" Number of atoms: 3581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3581 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 21, 'TRANS': 434} Chain: "H" Number of atoms: 3581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3581 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 21, 'TRANS': 434} Chain: "I" Number of atoms: 3557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3557 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 21, 'TRANS': 431} Chain: "J" Number of atoms: 3557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3557 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 21, 'TRANS': 431} Chain: "K" Number of atoms: 3557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3557 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 21, 'TRANS': 431} Chain: "L" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 564 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "M" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 564 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "N" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 519 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "O" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 569 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "P" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 569 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "Q" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 519 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "R" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1133 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 138} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "S" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1124 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 140} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 19.46, per 1000 atoms: 0.51 Number of scatterers: 37908 At special positions: 0 Unit cell: (189.376, 147.412, 150.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 217 16.00 O 7022 8.00 N 6628 7.00 C 24041 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 244 " - pdb=" SG CYS B 244 " distance=2.29 Simple disulfide: pdb=" SG CYS F 244 " - pdb=" SG CYS I 244 " distance=2.05 Simple disulfide: pdb=" SG CYS G 244 " - pdb=" SG CYS J 244 " distance=2.04 Simple disulfide: pdb=" SG CYS H 244 " - pdb=" SG CYS K 244 " distance=2.05 Simple disulfide: pdb=" SG CYS L 16 " - pdb=" SG CYS L 65 " distance=2.04 Simple disulfide: pdb=" SG CYS M 16 " - pdb=" SG CYS M 65 " distance=2.04 Simple disulfide: pdb=" SG CYS O 19 " - pdb=" SG CYS O 65 " distance=2.02 Simple disulfide: pdb=" SG CYS P 19 " - pdb=" SG CYS P 65 " distance=2.03 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: 13.07 Conformation dependent library (CDL) restraints added in 7.4 seconds 9692 Ramachandran restraints generated. 4846 Oldfield, 0 Emsley, 4846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8784 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 36 sheets defined 40.6% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.36 Creating SS restraints... Processing helix chain 'A' and resid 47 through 58 Processing helix chain 'A' and resid 109 through 118 removed outlier: 3.908A pdb=" N ILE A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 152 through 160 removed outlier: 3.854A pdb=" N LEU A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.819A pdb=" N GLY A 193 " --> pdb=" O CYS A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 230 removed outlier: 3.611A pdb=" N ARG A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 257 Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.721A pdb=" N ASN A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 319 removed outlier: 4.045A pdb=" N LEU A 311 " --> pdb=" O HIS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 391 removed outlier: 3.727A pdb=" N GLU A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 removed outlier: 4.214A pdb=" N LEU A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 400 through 405' Processing helix chain 'A' and resid 410 through 430 removed outlier: 3.799A pdb=" N GLU A 430 " --> pdb=" O GLN A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 446 removed outlier: 3.623A pdb=" N ILE A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 459 removed outlier: 3.595A pdb=" N LEU A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 58 Processing helix chain 'B' and resid 101 through 105 removed outlier: 4.086A pdb=" N LEU B 104 " --> pdb=" O PRO B 101 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE B 105 " --> pdb=" O LEU B 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 101 through 105' Processing helix chain 'B' and resid 109 through 118 removed outlier: 3.961A pdb=" N ILE B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 152 through 160 Processing helix chain 'B' and resid 178 through 192 Processing helix chain 'B' and resid 211 through 230 removed outlier: 4.095A pdb=" N PHE B 217 " --> pdb=" O ASP B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 258 removed outlier: 3.676A pdb=" N GLY B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 284 removed outlier: 3.647A pdb=" N ASN B 274 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 319 removed outlier: 3.905A pdb=" N LEU B 311 " --> pdb=" O HIS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 348 removed outlier: 3.935A pdb=" N THR B 339 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 345 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 348 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 380 through 382 No H-bonds generated for 'chain 'B' and resid 380 through 382' Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 400 through 405 removed outlier: 3.724A pdb=" N LEU B 404 " --> pdb=" O GLY B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 430 removed outlier: 3.506A pdb=" N GLU B 430 " --> pdb=" O GLN B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 447 removed outlier: 3.685A pdb=" N GLU B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLY B 439 " --> pdb=" O TYR B 435 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ASP B 440 " --> pdb=" O ARG B 436 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS B 447 " --> pdb=" O ARG B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 459 Processing helix chain 'D' and resid 23 through 33 Processing helix chain 'D' and resid 37 through 49 Proline residue: D 43 - end of helix Processing helix chain 'D' and resid 50 through 52 No H-bonds generated for 'chain 'D' and resid 50 through 52' Processing helix chain 'D' and resid 54 through 62 Processing helix chain 'D' and resid 65 through 84 Processing helix chain 'D' and resid 88 through 93 removed outlier: 4.607A pdb=" N ILE D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 104 Processing helix chain 'D' and resid 105 through 109 removed outlier: 4.211A pdb=" N LEU D 108 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 124 removed outlier: 4.138A pdb=" N VAL D 115 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA D 116 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR D 119 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE D 120 " --> pdb=" O ALA D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 141 Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 157 through 172 Processing helix chain 'D' and resid 179 through 189 removed outlier: 3.929A pdb=" N MET D 183 " --> pdb=" O GLN D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 205 Processing helix chain 'E' and resid 23 through 33 Processing helix chain 'E' and resid 37 through 49 Proline residue: E 43 - end of helix Processing helix chain 'E' and resid 50 through 52 No H-bonds generated for 'chain 'E' and resid 50 through 52' Processing helix chain 'E' and resid 54 through 62 Processing helix chain 'E' and resid 65 through 84 Processing helix chain 'E' and resid 88 through 93 removed outlier: 4.608A pdb=" N ILE E 92 " --> pdb=" O GLU E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 104 Processing helix chain 'E' and resid 105 through 109 removed outlier: 4.210A pdb=" N LEU E 108 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 124 removed outlier: 4.137A pdb=" N VAL E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA E 116 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR E 119 " --> pdb=" O VAL E 115 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE E 120 " --> pdb=" O ALA E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 141 Processing helix chain 'E' and resid 142 through 144 No H-bonds generated for 'chain 'E' and resid 142 through 144' Processing helix chain 'E' and resid 157 through 172 Processing helix chain 'E' and resid 179 through 189 removed outlier: 3.928A pdb=" N MET E 183 " --> pdb=" O GLN E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 205 Processing helix chain 'F' and resid 17 through 21 removed outlier: 3.547A pdb=" N THR F 20 " --> pdb=" O TYR F 17 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TYR F 21 " --> pdb=" O LYS F 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 17 through 21' Processing helix chain 'F' and resid 46 through 58 removed outlier: 3.536A pdb=" N SER F 58 " --> pdb=" O ILE F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 78 removed outlier: 4.277A pdb=" N LYS F 78 " --> pdb=" O ASP F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 119 removed outlier: 3.837A pdb=" N ILE F 113 " --> pdb=" O SER F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 124 removed outlier: 3.651A pdb=" N GLY F 123 " --> pdb=" O ASN F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 143 Processing helix chain 'F' and resid 152 through 160 Processing helix chain 'F' and resid 180 through 193 removed outlier: 3.842A pdb=" N GLY F 193 " --> pdb=" O CYS F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 230 removed outlier: 3.618A pdb=" N ARG F 214 " --> pdb=" O ARG F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 257 Processing helix chain 'F' and resid 270 through 285 removed outlier: 3.690A pdb=" N ASN F 274 " --> pdb=" O GLY F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 319 removed outlier: 3.997A pdb=" N LEU F 311 " --> pdb=" O HIS F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 345 removed outlier: 3.834A pdb=" N SER F 338 " --> pdb=" O GLY F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 382 No H-bonds generated for 'chain 'F' and resid 380 through 382' Processing helix chain 'F' and resid 383 through 391 Processing helix chain 'F' and resid 400 through 405 removed outlier: 3.865A pdb=" N LEU F 404 " --> pdb=" O GLY F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 429 Processing helix chain 'F' and resid 437 through 446 Processing helix chain 'F' and resid 449 through 459 Processing helix chain 'G' and resid 46 through 58 removed outlier: 3.868A pdb=" N ALA G 50 " --> pdb=" O PRO G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 118 removed outlier: 3.908A pdb=" N ILE G 113 " --> pdb=" O SER G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 143 Processing helix chain 'G' and resid 152 through 160 removed outlier: 3.855A pdb=" N LEU G 159 " --> pdb=" O GLU G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 193 removed outlier: 3.679A pdb=" N GLY G 193 " --> pdb=" O CYS G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 230 removed outlier: 3.611A pdb=" N ARG G 214 " --> pdb=" O ARG G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 257 Processing helix chain 'G' and resid 270 through 285 removed outlier: 3.721A pdb=" N ASN G 274 " --> pdb=" O GLY G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 319 removed outlier: 4.044A pdb=" N LEU G 311 " --> pdb=" O HIS G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 345 Processing helix chain 'G' and resid 354 through 358 Processing helix chain 'G' and resid 380 through 382 No H-bonds generated for 'chain 'G' and resid 380 through 382' Processing helix chain 'G' and resid 383 through 392 removed outlier: 3.803A pdb=" N GLU G 389 " --> pdb=" O PRO G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 400 through 405 removed outlier: 4.213A pdb=" N LEU G 404 " --> pdb=" O GLY G 400 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY G 405 " --> pdb=" O GLY G 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 400 through 405' Processing helix chain 'G' and resid 410 through 430 removed outlier: 3.764A pdb=" N GLU G 430 " --> pdb=" O GLN G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 446 removed outlier: 3.623A pdb=" N ILE G 441 " --> pdb=" O GLU G 437 " (cutoff:3.500A) Processing helix chain 'G' and resid 449 through 459 Processing helix chain 'H' and resid 47 through 58 removed outlier: 3.537A pdb=" N SER H 58 " --> pdb=" O ILE H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 118 removed outlier: 3.853A pdb=" N ILE H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 143 Processing helix chain 'H' and resid 152 through 160 Processing helix chain 'H' and resid 178 through 193 removed outlier: 3.705A pdb=" N GLY H 193 " --> pdb=" O CYS H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 230 removed outlier: 3.655A pdb=" N ARG H 214 " --> pdb=" O ARG H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 257 Processing helix chain 'H' and resid 270 through 285 removed outlier: 3.731A pdb=" N ASN H 274 " --> pdb=" O GLY H 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 319 removed outlier: 4.046A pdb=" N LEU H 311 " --> pdb=" O HIS H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 345 removed outlier: 3.588A pdb=" N ALA H 337 " --> pdb=" O GLU H 333 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER H 338 " --> pdb=" O GLY H 334 " (cutoff:3.500A) Processing helix chain 'H' and resid 354 through 358 Processing helix chain 'H' and resid 380 through 382 No H-bonds generated for 'chain 'H' and resid 380 through 382' Processing helix chain 'H' and resid 383 through 391 Processing helix chain 'H' and resid 400 through 405 removed outlier: 4.303A pdb=" N LEU H 404 " --> pdb=" O GLY H 400 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY H 405 " --> pdb=" O GLY H 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 400 through 405' Processing helix chain 'H' and resid 410 through 430 removed outlier: 3.576A pdb=" N GLU H 430 " --> pdb=" O GLN H 426 " (cutoff:3.500A) Processing helix chain 'H' and resid 437 through 446 Processing helix chain 'H' and resid 449 through 459 Processing helix chain 'I' and resid 47 through 59 Processing helix chain 'I' and resid 101 through 105 removed outlier: 3.959A pdb=" N LEU I 104 " --> pdb=" O PRO I 101 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE I 105 " --> pdb=" O LEU I 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 101 through 105' Processing helix chain 'I' and resid 109 through 118 removed outlier: 3.910A pdb=" N ILE I 113 " --> pdb=" O SER I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 124 Processing helix chain 'I' and resid 138 through 143 Processing helix chain 'I' and resid 152 through 160 removed outlier: 3.784A pdb=" N LEU I 159 " --> pdb=" O GLU I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 193 removed outlier: 3.824A pdb=" N GLY I 193 " --> pdb=" O CYS I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 230 removed outlier: 3.626A pdb=" N ARG I 214 " --> pdb=" O ARG I 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 243 through 257 Processing helix chain 'I' and resid 270 through 285 removed outlier: 3.632A pdb=" N ASN I 274 " --> pdb=" O GLY I 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 300 removed outlier: 3.623A pdb=" N ARG I 300 " --> pdb=" O ALA I 296 " (cutoff:3.500A) Processing helix chain 'I' and resid 307 through 319 removed outlier: 3.848A pdb=" N LEU I 311 " --> pdb=" O HIS I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 334 through 346 removed outlier: 3.969A pdb=" N SER I 338 " --> pdb=" O GLY I 334 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 358 Processing helix chain 'I' and resid 380 through 382 No H-bonds generated for 'chain 'I' and resid 380 through 382' Processing helix chain 'I' and resid 383 through 391 Processing helix chain 'I' and resid 400 through 405 removed outlier: 3.756A pdb=" N LEU I 404 " --> pdb=" O GLY I 400 " (cutoff:3.500A) Processing helix chain 'I' and resid 410 through 430 removed outlier: 3.572A pdb=" N GLU I 430 " --> pdb=" O GLN I 426 " (cutoff:3.500A) Processing helix chain 'I' and resid 437 through 447 Processing helix chain 'I' and resid 449 through 459 removed outlier: 3.612A pdb=" N TRP I 459 " --> pdb=" O ALA I 455 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 58 Processing helix chain 'J' and resid 101 through 105 removed outlier: 4.087A pdb=" N LEU J 104 " --> pdb=" O PRO J 101 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE J 105 " --> pdb=" O LEU J 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 101 through 105' Processing helix chain 'J' and resid 109 through 118 removed outlier: 3.962A pdb=" N ILE J 113 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 120 through 124 Processing helix chain 'J' and resid 138 through 143 Processing helix chain 'J' and resid 152 through 160 Processing helix chain 'J' and resid 178 through 193 removed outlier: 3.788A pdb=" N GLY J 193 " --> pdb=" O CYS J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 230 removed outlier: 4.095A pdb=" N PHE J 217 " --> pdb=" O ASP J 213 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA J 227 " --> pdb=" O HIS J 223 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU J 228 " --> pdb=" O LYS J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 243 through 258 removed outlier: 3.676A pdb=" N GLY J 258 " --> pdb=" O ALA J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 270 through 284 removed outlier: 3.647A pdb=" N ASN J 274 " --> pdb=" O GLY J 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 307 through 319 removed outlier: 3.905A pdb=" N LEU J 311 " --> pdb=" O HIS J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 334 through 348 removed outlier: 3.935A pdb=" N THR J 339 " --> pdb=" O ASP J 335 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU J 345 " --> pdb=" O GLY J 341 " (cutoff:3.500A) Processing helix chain 'J' and resid 354 through 358 Processing helix chain 'J' and resid 380 through 382 No H-bonds generated for 'chain 'J' and resid 380 through 382' Processing helix chain 'J' and resid 383 through 391 Processing helix chain 'J' and resid 400 through 405 removed outlier: 3.736A pdb=" N LEU J 404 " --> pdb=" O GLY J 400 " (cutoff:3.500A) Processing helix chain 'J' and resid 410 through 431 Processing helix chain 'J' and resid 433 through 446 removed outlier: 5.418A pdb=" N GLY J 439 " --> pdb=" O TYR J 435 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ASP J 440 " --> pdb=" O ARG J 436 " (cutoff:3.500A) Processing helix chain 'J' and resid 449 through 459 Processing helix chain 'K' and resid 46 through 58 removed outlier: 3.807A pdb=" N ALA K 50 " --> pdb=" O PRO K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 105 removed outlier: 4.079A pdb=" N LEU K 104 " --> pdb=" O PRO K 101 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE K 105 " --> pdb=" O LEU K 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 101 through 105' Processing helix chain 'K' and resid 109 through 118 removed outlier: 3.955A pdb=" N ILE K 113 " --> pdb=" O SER K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 120 through 124 Processing helix chain 'K' and resid 138 through 143 Processing helix chain 'K' and resid 152 through 160 Processing helix chain 'K' and resid 178 through 193 removed outlier: 3.843A pdb=" N GLY K 193 " --> pdb=" O CYS K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 230 removed outlier: 4.296A pdb=" N PHE K 217 " --> pdb=" O ASP K 213 " (cutoff:3.500A) Processing helix chain 'K' and resid 243 through 258 removed outlier: 3.682A pdb=" N GLY K 258 " --> pdb=" O ALA K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 270 through 285 removed outlier: 3.665A pdb=" N ASN K 274 " --> pdb=" O GLY K 270 " (cutoff:3.500A) Processing helix chain 'K' and resid 295 through 300 removed outlier: 3.547A pdb=" N ARG K 300 " --> pdb=" O ALA K 296 " (cutoff:3.500A) Processing helix chain 'K' and resid 307 through 319 removed outlier: 3.876A pdb=" N LEU K 311 " --> pdb=" O HIS K 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 348 Processing helix chain 'K' and resid 354 through 358 Processing helix chain 'K' and resid 380 through 382 No H-bonds generated for 'chain 'K' and resid 380 through 382' Processing helix chain 'K' and resid 383 through 391 Processing helix chain 'K' and resid 400 through 405 removed outlier: 3.692A pdb=" N LEU K 404 " --> pdb=" O GLY K 400 " (cutoff:3.500A) Processing helix chain 'K' and resid 410 through 430 removed outlier: 3.524A pdb=" N GLU K 430 " --> pdb=" O GLN K 426 " (cutoff:3.500A) Processing helix chain 'K' and resid 437 through 446 Processing helix chain 'K' and resid 449 through 459 Processing helix chain 'R' and resid 315 through 322 removed outlier: 3.653A pdb=" N ILE R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) Processing helix chain 'R' and resid 350 through 357 removed outlier: 4.218A pdb=" N GLY R 357 " --> pdb=" O VAL R 353 " (cutoff:3.500A) Processing helix chain 'R' and resid 412 through 418 Processing helix chain 'S' and resid 315 through 322 removed outlier: 3.604A pdb=" N ILE S 319 " --> pdb=" O GLY S 315 " (cutoff:3.500A) Processing helix chain 'S' and resid 350 through 357 removed outlier: 3.552A pdb=" N ILE S 356 " --> pdb=" O PRO S 352 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY S 357 " --> pdb=" O VAL S 353 " (cutoff:3.500A) Processing helix chain 'S' and resid 367 through 372 removed outlier: 4.262A pdb=" N VAL S 371 " --> pdb=" O ASP S 367 " (cutoff:3.500A) Processing helix chain 'S' and resid 388 through 390 No H-bonds generated for 'chain 'S' and resid 388 through 390' Processing helix chain 'S' and resid 412 through 418 Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 86 removed outlier: 5.670A pdb=" N CYS A 81 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA A 99 " --> pdb=" O CYS A 81 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A 34 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE A 135 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA A 36 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N GLY A 305 " --> pdb=" O ARG A 128 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU A 130 " --> pdb=" O GLY A 305 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 196 through 198 removed outlier: 6.966A pdb=" N LEU A 167 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LYS A 198 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N CYS A 169 " --> pdb=" O LYS A 198 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N MET A 166 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS A 324 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE A 262 " --> pdb=" O HIS A 289 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N HIS A 291 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N HIS A 264 " --> pdb=" O HIS A 291 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU A 237 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N ASP A 265 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 83 removed outlier: 6.040A pdb=" N CYS B 81 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA B 99 " --> pdb=" O CYS B 81 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS B 83 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 34 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ILE B 135 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ALA B 36 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N GLY B 305 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU B 130 " --> pdb=" O GLY B 305 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 166 through 170 removed outlier: 6.580A pdb=" N LEU B 167 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LYS B 198 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N CYS B 169 " --> pdb=" O LYS B 198 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N THR B 197 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N ASN B 238 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS B 235 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N MET B 263 " --> pdb=" O HIS B 235 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU B 237 " --> pdb=" O MET B 263 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N ASP B 265 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE B 262 " --> pdb=" O HIS B 289 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N HIS B 291 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N HIS B 264 " --> pdb=" O HIS B 291 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS B 324 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLN B 398 " --> pdb=" O PRO B 373 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA B 375 " --> pdb=" O GLN B 398 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 350 through 351 Processing sheet with id=AA7, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AA8, first strand: chain 'F' and resid 80 through 86 removed outlier: 5.991A pdb=" N CYS F 81 " --> pdb=" O ALA F 99 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA F 99 " --> pdb=" O CYS F 81 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS F 83 " --> pdb=" O PHE F 97 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU F 34 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE F 135 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA F 36 " --> pdb=" O GLU F 133 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N GLY F 305 " --> pdb=" O ARG F 128 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU F 130 " --> pdb=" O GLY F 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 166 through 170 removed outlier: 6.683A pdb=" N LEU F 167 " --> pdb=" O PHE F 196 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LYS F 198 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N CYS F 169 " --> pdb=" O LYS F 198 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N THR F 197 " --> pdb=" O TYR F 236 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ASN F 238 " --> pdb=" O THR F 197 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N HIS F 235 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N MET F 263 " --> pdb=" O HIS F 235 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU F 237 " --> pdb=" O MET F 263 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ASP F 265 " --> pdb=" O LEU F 237 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE F 262 " --> pdb=" O HIS F 289 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N HIS F 291 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N HIS F 264 " --> pdb=" O HIS F 291 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS F 324 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N GLN F 398 " --> pdb=" O PRO F 373 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA F 375 " --> pdb=" O GLN F 398 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 350 through 351 Processing sheet with id=AB2, first strand: chain 'G' and resid 81 through 86 removed outlier: 5.670A pdb=" N CYS G 81 " --> pdb=" O ALA G 99 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA G 99 " --> pdb=" O CYS G 81 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU G 34 " --> pdb=" O ILE G 135 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE G 135 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA G 36 " --> pdb=" O GLU G 133 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N GLY G 305 " --> pdb=" O ARG G 128 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU G 130 " --> pdb=" O GLY G 305 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 196 through 198 removed outlier: 6.965A pdb=" N LEU G 167 " --> pdb=" O PHE G 196 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N LYS G 198 " --> pdb=" O LEU G 167 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N CYS G 169 " --> pdb=" O LYS G 198 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N MET G 166 " --> pdb=" O LEU G 397 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS G 324 " --> pdb=" O ILE G 290 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE G 262 " --> pdb=" O HIS G 289 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N HIS G 291 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N HIS G 264 " --> pdb=" O HIS G 291 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU G 237 " --> pdb=" O MET G 263 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N ASP G 265 " --> pdb=" O LEU G 237 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 350 through 351 Processing sheet with id=AB5, first strand: chain 'H' and resid 81 through 86 removed outlier: 5.575A pdb=" N CYS H 81 " --> pdb=" O ALA H 99 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA H 99 " --> pdb=" O CYS H 81 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU H 34 " --> pdb=" O ILE H 135 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE H 135 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ALA H 36 " --> pdb=" O GLU H 133 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N GLY H 305 " --> pdb=" O ARG H 128 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU H 130 " --> pdb=" O GLY H 305 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 196 through 198 removed outlier: 6.968A pdb=" N LEU H 167 " --> pdb=" O PHE H 196 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N LYS H 198 " --> pdb=" O LEU H 167 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N CYS H 169 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N MET H 166 " --> pdb=" O LEU H 397 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS H 324 " --> pdb=" O ILE H 290 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU H 237 " --> pdb=" O MET H 263 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 350 through 351 Processing sheet with id=AB8, first strand: chain 'I' and resid 80 through 83 removed outlier: 6.017A pdb=" N CYS I 81 " --> pdb=" O ALA I 99 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ALA I 99 " --> pdb=" O CYS I 81 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N HIS I 83 " --> pdb=" O PHE I 97 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU I 34 " --> pdb=" O ILE I 135 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE I 135 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA I 36 " --> pdb=" O GLU I 133 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 166 through 170 removed outlier: 7.207A pdb=" N THR I 197 " --> pdb=" O TYR I 236 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ASN I 238 " --> pdb=" O THR I 197 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N HIS I 235 " --> pdb=" O ILE I 261 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N MET I 263 " --> pdb=" O HIS I 235 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LEU I 237 " --> pdb=" O MET I 263 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N ASP I 265 " --> pdb=" O LEU I 237 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N GLN I 398 " --> pdb=" O PRO I 373 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA I 375 " --> pdb=" O GLN I 398 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 350 through 351 Processing sheet with id=AC2, first strand: chain 'J' and resid 80 through 83 removed outlier: 6.040A pdb=" N CYS J 81 " --> pdb=" O ALA J 99 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA J 99 " --> pdb=" O CYS J 81 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS J 83 " --> pdb=" O PHE J 97 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU J 34 " --> pdb=" O ILE J 135 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ILE J 135 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ALA J 36 " --> pdb=" O GLU J 133 " (cutoff:3.500A) removed outlier: 9.134A pdb=" N GLY J 305 " --> pdb=" O ARG J 128 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU J 130 " --> pdb=" O GLY J 305 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 166 through 170 removed outlier: 6.580A pdb=" N LEU J 167 " --> pdb=" O PHE J 196 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N LYS J 198 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N CYS J 169 " --> pdb=" O LYS J 198 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N THR J 197 " --> pdb=" O TYR J 236 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N ASN J 238 " --> pdb=" O THR J 197 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS J 235 " --> pdb=" O ILE J 261 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N MET J 263 " --> pdb=" O HIS J 235 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU J 237 " --> pdb=" O MET J 263 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N ASP J 265 " --> pdb=" O LEU J 237 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE J 262 " --> pdb=" O HIS J 289 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N HIS J 291 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N HIS J 264 " --> pdb=" O HIS J 291 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS J 324 " --> pdb=" O ILE J 290 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLN J 398 " --> pdb=" O PRO J 373 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA J 375 " --> pdb=" O GLN J 398 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 350 through 351 Processing sheet with id=AC5, first strand: chain 'K' and resid 80 through 83 removed outlier: 6.071A pdb=" N CYS K 81 " --> pdb=" O ALA K 99 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA K 99 " --> pdb=" O CYS K 81 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS K 83 " --> pdb=" O PHE K 97 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU K 34 " --> pdb=" O ILE K 135 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE K 135 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA K 36 " --> pdb=" O GLU K 133 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N GLY K 305 " --> pdb=" O ARG K 128 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU K 130 " --> pdb=" O GLY K 305 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 166 through 170 removed outlier: 6.546A pdb=" N LEU K 167 " --> pdb=" O PHE K 196 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LYS K 198 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N CYS K 169 " --> pdb=" O LYS K 198 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR K 197 " --> pdb=" O TYR K 236 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N ASN K 238 " --> pdb=" O THR K 197 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N HIS K 235 " --> pdb=" O ILE K 261 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N MET K 263 " --> pdb=" O HIS K 235 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU K 237 " --> pdb=" O MET K 263 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ASP K 265 " --> pdb=" O LEU K 237 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE K 262 " --> pdb=" O HIS K 289 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N HIS K 291 " --> pdb=" O ILE K 262 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N HIS K 264 " --> pdb=" O HIS K 291 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS K 324 " --> pdb=" O ILE K 290 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N GLN K 398 " --> pdb=" O PRO K 373 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA K 375 " --> pdb=" O GLN K 398 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 350 through 351 Processing sheet with id=AC8, first strand: chain 'L' and resid 24 through 26 Processing sheet with id=AC9, first strand: chain 'M' and resid 24 through 26 Processing sheet with id=AD1, first strand: chain 'N' and resid 24 through 26 Processing sheet with id=AD2, first strand: chain 'O' and resid 24 through 26 Processing sheet with id=AD3, first strand: chain 'P' and resid 24 through 26 Processing sheet with id=AD4, first strand: chain 'Q' and resid 24 through 26 Processing sheet with id=AD5, first strand: chain 'R' and resid 344 through 345 removed outlier: 3.721A pdb=" N GLY R 425 " --> pdb=" O LEU R 400 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N TYR R 398 " --> pdb=" O VAL R 427 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 326 through 328 Processing sheet with id=AD7, first strand: chain 'S' and resid 290 through 292 removed outlier: 3.686A pdb=" N ARG S 432 " --> pdb=" O VAL S 291 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL S 427 " --> pdb=" O ASP S 386 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP S 386 " --> pdb=" O VAL S 427 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU S 429 " --> pdb=" O VAL S 384 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLY S 360 " --> pdb=" O VAL S 306 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'S' and resid 290 through 292 removed outlier: 3.686A pdb=" N ARG S 432 " --> pdb=" O VAL S 291 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY S 425 " --> pdb=" O LEU S 400 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N TYR S 398 " --> pdb=" O VAL S 427 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 326 through 328 1426 hydrogen bonds defined for protein. 4080 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.17 Time building geometry restraints manager: 14.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.52: 29014 1.52 - 1.85: 9786 1.85 - 2.18: 3 2.18 - 2.51: 0 2.51 - 2.85: 1 Bond restraints: 38804 Sorted by residual: bond pdb=" C ASP R 367 " pdb=" N ARG R 369 " ideal model delta sigma weight residual 1.329 2.848 -1.519 1.40e-02 5.10e+03 1.18e+04 bond pdb=" N TRP B 459 " pdb=" CA TRP B 459 " ideal model delta sigma weight residual 1.463 1.382 0.081 1.31e-02 5.83e+03 3.81e+01 bond pdb=" CA PRO R 433 " pdb=" C PRO R 433 " ideal model delta sigma weight residual 1.517 1.574 -0.057 9.30e-03 1.16e+04 3.80e+01 bond pdb=" N VAL R 430 " pdb=" CA VAL R 430 " ideal model delta sigma weight residual 1.456 1.511 -0.055 1.11e-02 8.12e+03 2.49e+01 bond pdb=" CB SER N 28 " pdb=" OG SER N 28 " ideal model delta sigma weight residual 1.417 1.505 -0.088 2.00e-02 2.50e+03 1.92e+01 ... (remaining 38799 not shown) Histogram of bond angle deviations from ideal: 91.47 - 100.93: 77 100.93 - 110.39: 10475 110.39 - 119.85: 23849 119.85 - 129.31: 17779 129.31 - 138.77: 359 Bond angle restraints: 52539 Sorted by residual: angle pdb=" N VAL R 431 " pdb=" CA VAL R 431 " pdb=" C VAL R 431 " ideal model delta sigma weight residual 110.74 138.77 -28.03 9.10e-01 1.21e+00 9.49e+02 angle pdb=" N VAL C 15 " pdb=" CA VAL C 15 " pdb=" C VAL C 15 " ideal model delta sigma weight residual 109.30 91.47 17.83 1.25e+00 6.40e-01 2.04e+02 angle pdb=" N TYR B 17 " pdb=" CA TYR B 17 " pdb=" C TYR B 17 " ideal model delta sigma weight residual 112.89 99.06 13.83 1.24e+00 6.50e-01 1.24e+02 angle pdb=" O ASP R 367 " pdb=" C ASP R 367 " pdb=" N ARG R 369 " ideal model delta sigma weight residual 121.74 107.25 14.49 1.31e+00 5.83e-01 1.22e+02 angle pdb=" N PRO R 433 " pdb=" CA PRO R 433 " pdb=" C PRO R 433 " ideal model delta sigma weight residual 110.70 123.72 -13.02 1.22e+00 6.72e-01 1.14e+02 ... (remaining 52534 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 20239 17.98 - 35.96: 2005 35.96 - 53.94: 464 53.94 - 71.92: 125 71.92 - 89.90: 44 Dihedral angle restraints: 22877 sinusoidal: 9100 harmonic: 13777 Sorted by residual: dihedral pdb=" N ALA R 301 " pdb=" C ALA R 301 " pdb=" CA ALA R 301 " pdb=" CB ALA R 301 " ideal model delta harmonic sigma weight residual 122.90 154.13 -31.23 0 2.50e+00 1.60e-01 1.56e+02 dihedral pdb=" C ALA R 301 " pdb=" N ALA R 301 " pdb=" CA ALA R 301 " pdb=" CB ALA R 301 " ideal model delta harmonic sigma weight residual -122.60 -153.73 31.13 0 2.50e+00 1.60e-01 1.55e+02 dihedral pdb=" CB CYS O 19 " pdb=" SG CYS O 19 " pdb=" SG CYS O 65 " pdb=" CB CYS O 65 " ideal model delta sinusoidal sigma weight residual -86.00 -175.75 89.75 1 1.00e+01 1.00e-02 9.56e+01 ... (remaining 22874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.281: 5615 0.281 - 0.561: 22 0.561 - 0.842: 4 0.842 - 1.122: 0 1.122 - 1.403: 1 Chirality restraints: 5642 Sorted by residual: chirality pdb=" CA ALA R 301 " pdb=" N ALA R 301 " pdb=" C ALA R 301 " pdb=" CB ALA R 301 " both_signs ideal model delta sigma weight residual False 2.48 1.08 1.40 2.00e-01 2.50e+01 4.92e+01 chirality pdb=" CA LYS Q 10 " pdb=" N LYS Q 10 " pdb=" C LYS Q 10 " pdb=" CB LYS Q 10 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.84 2.00e-01 2.50e+01 1.75e+01 chirality pdb=" CA LYS N 10 " pdb=" N LYS N 10 " pdb=" C LYS N 10 " pdb=" CB LYS N 10 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.84 2.00e-01 2.50e+01 1.75e+01 ... (remaining 5639 not shown) Planarity restraints: 6889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP R 367 " -0.116 2.00e-02 2.50e+03 1.80e-01 3.25e+02 pdb=" C ASP R 367 " 0.306 2.00e-02 2.50e+03 pdb=" O ASP R 367 " -0.144 2.00e-02 2.50e+03 pdb=" N ARG R 369 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 169 " 0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C CYS B 169 " -0.067 2.00e-02 2.50e+03 pdb=" O CYS B 169 " 0.025 2.00e-02 2.50e+03 pdb=" N THR B 170 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE S 326 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C ILE S 326 " -0.058 2.00e-02 2.50e+03 pdb=" O ILE S 326 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE S 327 " 0.019 2.00e-02 2.50e+03 ... (remaining 6886 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 12 2.16 - 2.85: 13281 2.85 - 3.53: 48190 3.53 - 4.22: 86022 4.22 - 4.90: 157363 Nonbonded interactions: 304868 Sorted by model distance: nonbonded pdb=" NZ LYS B 172 " pdb=" N GLY B 401 " model vdw 1.476 3.200 nonbonded pdb=" NH1 ARG A 191 " pdb=" CB TYR E 5 " model vdw 1.500 3.520 nonbonded pdb=" NZ LYS B 460 " pdb=" OD1 ASP Q 64 " model vdw 1.655 2.520 nonbonded pdb=" CZ3 TRP J 459 " pdb=" OD1 ASN N 66 " model vdw 1.790 3.340 nonbonded pdb=" CE LYS B 172 " pdb=" N GLY B 401 " model vdw 1.856 3.520 ... (remaining 304863 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 14 through 466) selection = chain 'B' selection = (chain 'F' and resid 14 through 466) selection = (chain 'G' and resid 14 through 466) selection = (chain 'H' and resid 14 through 466) selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = (chain 'C' and resid 7 through 77) selection = (chain 'L' and resid 7 through 77) selection = (chain 'M' and resid 7 through 77) selection = (chain 'N' and resid 7 through 77) selection = (chain 'O' and resid 7 through 77) selection = (chain 'P' and resid 7 through 77) selection = (chain 'Q' and resid 7 through 77) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = (chain 'R' and (resid 288 through 293 or (resid 294 and (name N or name CA or na \ me C or name O or name CB )) or resid 295 through 357 or (resid 358 and (name N \ or name CA or name C or name O or name CB )) or resid 359 through 369 or (resid \ 370 and (name N or name CA or name C or name O or name CB )) or resid 371 throug \ h 407 or (resid 408 and (name N or name CA or name C or name O or name CB )) or \ resid 409 through 418 or (resid 419 and (name N or name CA or name C or name O o \ r name CB )) or resid 420 through 435 or (resid 436 and (name N or name CA or na \ me C or name O or name CB )))) selection = (chain 'S' and (resid 288 through 316 or (resid 317 and (name N or name CA or na \ me C or name O or name CB )) or resid 318 through 367 or (resid 369 through 370 \ and (name N or name CA or name C or name O or name CB )) or resid 371 through 43 \ 6)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.240 Construct map_model_manager: 0.040 Extract box with map and model: 9.050 Check model and map are aligned: 0.560 Set scattering table: 0.350 Process input model: 94.510 Find NCS groups from input model: 3.040 Set up NCS constraints: 0.190 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 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 : 0.013 1.519 38804 Z= 0.698 Angle : 0.990 28.031 52539 Z= 0.602 Chirality : 0.070 1.403 5642 Planarity : 0.006 0.180 6889 Dihedral : 15.765 89.895 14069 Min Nonbonded Distance : 1.476 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.77 % Favored : 91.00 % Rotamer: Outliers : 4.66 % Allowed : 7.16 % Favored : 88.18 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.10), residues: 4846 helix: -1.15 (0.11), residues: 1715 sheet: -0.88 (0.22), residues: 455 loop : -2.90 (0.10), residues: 2676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP G 408 HIS 0.007 0.002 HIS A 307 PHE 0.029 0.002 PHE G 342 TYR 0.012 0.002 TYR E 167 ARG 0.006 0.001 ARG H 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9692 Ramachandran restraints generated. 4846 Oldfield, 0 Emsley, 4846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9692 Ramachandran restraints generated. 4846 Oldfield, 0 Emsley, 4846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 3965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 856 time to evaluate : 4.349 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: A 65 THR cc_start: 0.7485 (p) cc_final: 0.7282 (t) REVERT: A 174 LYS cc_start: 0.4779 (mppt) cc_final: 0.4549 (mttt) REVERT: A 393 ASP cc_start: 0.8155 (p0) cc_final: 0.7525 (m-30) REVERT: A 457 ASP cc_start: 0.5845 (m-30) cc_final: 0.5604 (m-30) REVERT: B 17 TYR cc_start: 0.3165 (OUTLIER) cc_final: 0.2875 (p90) REVERT: B 25 ASP cc_start: 0.7181 (p0) cc_final: 0.6949 (p0) REVERT: B 249 LYS cc_start: 0.8017 (mtpt) cc_final: 0.7789 (mtmt) REVERT: B 336 LYS cc_start: 0.7040 (OUTLIER) cc_final: 0.6771 (tmmt) REVERT: B 389 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7082 (tt0) REVERT: B 437 GLU cc_start: 0.5837 (OUTLIER) cc_final: 0.5269 (pt0) REVERT: C 16 CYS cc_start: 0.6480 (OUTLIER) cc_final: 0.5402 (p) REVERT: C 58 LYS cc_start: 0.7678 (mttt) cc_final: 0.6767 (tptt) REVERT: C 66 ASN cc_start: 0.5965 (m-40) cc_final: 0.5354 (t0) REVERT: C 71 ILE cc_start: 0.7061 (OUTLIER) cc_final: 0.6552 (mm) REVERT: D 9 ARG cc_start: 0.6368 (tpp-160) cc_final: 0.5524 (mmm-85) REVERT: D 19 PHE cc_start: 0.5852 (m-80) cc_final: 0.5551 (m-80) REVERT: D 35 MET cc_start: 0.7303 (mtm) cc_final: 0.6700 (mmm) REVERT: D 59 GLU cc_start: 0.6941 (tm-30) cc_final: 0.6638 (tm-30) REVERT: D 202 THR cc_start: 0.7264 (m) cc_final: 0.6938 (p) REVERT: E 1 MET cc_start: 0.1775 (ttp) cc_final: 0.0925 (ppp) REVERT: E 132 GLN cc_start: 0.5804 (mt0) cc_final: 0.5305 (mt0) REVERT: F 25 ASP cc_start: 0.6666 (p0) cc_final: 0.6087 (m-30) REVERT: F 77 TYR cc_start: 0.8195 (m-80) cc_final: 0.7758 (m-80) REVERT: F 125 LYS cc_start: 0.7979 (mmmt) cc_final: 0.7653 (ttmt) REVERT: F 222 ILE cc_start: 0.8855 (mt) cc_final: 0.8492 (mt) REVERT: F 315 LEU cc_start: 0.8503 (tp) cc_final: 0.8289 (tp) REVERT: F 426 GLN cc_start: 0.7434 (tp40) cc_final: 0.7124 (tp-100) REVERT: F 469 MET cc_start: 0.2807 (mmt) cc_final: 0.2407 (mpp) REVERT: G 73 ASP cc_start: 0.3560 (OUTLIER) cc_final: 0.3164 (p0) REVERT: G 109 SER cc_start: 0.8754 (t) cc_final: 0.8491 (p) REVERT: G 125 LYS cc_start: 0.7971 (mmmt) cc_final: 0.7545 (mttp) REVERT: G 128 ARG cc_start: 0.7536 (ttp80) cc_final: 0.7165 (ttp-170) REVERT: G 191 ARG cc_start: 0.7683 (tpt90) cc_final: 0.7471 (tpt90) REVERT: G 444 GLU cc_start: 0.7132 (tm-30) cc_final: 0.6910 (tm-30) REVERT: H 80 LYS cc_start: 0.8106 (mtmm) cc_final: 0.7813 (mptt) REVERT: H 92 ASN cc_start: 0.7601 (t0) cc_final: 0.7105 (t0) REVERT: H 125 LYS cc_start: 0.8215 (mmmt) cc_final: 0.7771 (mttt) REVERT: H 301 GLN cc_start: 0.7697 (mm-40) cc_final: 0.7427 (mt0) REVERT: I 23 THR cc_start: 0.8015 (p) cc_final: 0.7803 (t) REVERT: I 76 ARG cc_start: 0.6909 (ptm-80) cc_final: 0.6689 (ptt90) REVERT: I 94 TYR cc_start: 0.8268 (m-80) cc_final: 0.7881 (m-80) REVERT: I 118 VAL cc_start: 0.8464 (t) cc_final: 0.8242 (m) REVERT: I 169 CYS cc_start: 0.8152 (p) cc_final: 0.7929 (t) REVERT: I 340 LEU cc_start: 0.7568 (mt) cc_final: 0.7281 (mt) REVERT: I 384 MET cc_start: 0.7757 (tpp) cc_final: 0.7553 (tpp) REVERT: I 426 GLN cc_start: 0.7387 (tp40) cc_final: 0.7019 (pt0) REVERT: I 448 TRP cc_start: 0.6212 (p-90) cc_final: 0.5513 (p90) REVERT: I 460 LYS cc_start: 0.7901 (mtpt) cc_final: 0.7393 (mmtt) REVERT: J 74 MET cc_start: 0.6735 (tmm) cc_final: 0.6125 (ptt) REVERT: J 175 LEU cc_start: 0.6516 (OUTLIER) cc_final: 0.6296 (mt) REVERT: J 200 ASP cc_start: 0.6551 (t0) cc_final: 0.6211 (t70) REVERT: K 32 ASP cc_start: 0.7158 (m-30) cc_final: 0.6924 (m-30) REVERT: K 74 MET cc_start: 0.3513 (tpt) cc_final: 0.3176 (mtp) REVERT: K 231 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6841 (tt0) REVERT: K 299 ASP cc_start: 0.7004 (p0) cc_final: 0.6696 (p0) REVERT: K 422 GLU cc_start: 0.6556 (mt-10) cc_final: 0.6317 (mm-30) REVERT: L 58 LYS cc_start: 0.7850 (mttp) cc_final: 0.7644 (mtmt) REVERT: M 22 GLU cc_start: 0.7017 (tt0) cc_final: 0.6254 (tp30) REVERT: M 53 LEU cc_start: 0.8281 (tp) cc_final: 0.8028 (tp) REVERT: M 57 LYS cc_start: 0.7581 (mmmm) cc_final: 0.7124 (mmmm) REVERT: O 18 ASN cc_start: 0.7383 (t0) cc_final: 0.7167 (t0) REVERT: Q 12 ASN cc_start: 0.6242 (OUTLIER) cc_final: 0.5870 (p0) REVERT: R 342 LYS cc_start: 0.0550 (OUTLIER) cc_final: -0.0122 (mmtm) REVERT: R 346 VAL cc_start: 0.2693 (m) cc_final: 0.2056 (m) REVERT: R 347 LEU cc_start: 0.3705 (OUTLIER) cc_final: 0.3431 (mm) REVERT: R 431 VAL cc_start: 0.2214 (OUTLIER) cc_final: 0.1749 (p) REVERT: S 336 GLU cc_start: 0.1890 (OUTLIER) cc_final: 0.1208 (tt0) REVERT: S 347 LEU cc_start: -0.0053 (OUTLIER) cc_final: -0.0387 (tt) REVERT: S 363 VAL cc_start: 0.0223 (OUTLIER) cc_final: -0.0217 (t) REVERT: S 369 ARG cc_start: 0.1852 (OUTLIER) cc_final: 0.1232 (ppt170) REVERT: S 393 GLU cc_start: 0.0519 (OUTLIER) cc_final: 0.0158 (pp20) outliers start: 184 outliers final: 35 residues processed: 1007 average time/residue: 0.5592 time to fit residues: 873.9923 Evaluate side-chains 589 residues out of total 3965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 537 time to evaluate : 4.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 174 LYS Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain J residue 379 ILE Chi-restraints excluded: chain N residue 12 ASN Chi-restraints excluded: chain N residue 70 PHE Chi-restraints excluded: chain Q residue 12 ASN Chi-restraints excluded: chain Q residue 62 CYS Chi-restraints excluded: chain Q residue 70 PHE Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 303 SER Chi-restraints excluded: chain R residue 313 GLU Chi-restraints excluded: chain R residue 316 GLU Chi-restraints excluded: chain R residue 342 LYS Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 363 VAL Chi-restraints excluded: chain R residue 366 ARG Chi-restraints excluded: chain R residue 370 LYS Chi-restraints excluded: chain R residue 371 VAL Chi-restraints excluded: chain R residue 379 GLU Chi-restraints excluded: chain R residue 405 ASN Chi-restraints excluded: chain R residue 408 LYS Chi-restraints excluded: chain R residue 413 SER Chi-restraints excluded: chain R residue 418 ARG Chi-restraints excluded: chain R residue 431 VAL Chi-restraints excluded: chain R residue 435 ARG Chi-restraints excluded: chain S residue 288 ILE Chi-restraints excluded: chain S residue 317 LYS Chi-restraints excluded: chain S residue 335 VAL Chi-restraints excluded: chain S residue 336 GLU Chi-restraints excluded: chain S residue 343 ARG Chi-restraints excluded: chain S residue 347 LEU Chi-restraints excluded: chain S residue 363 VAL Chi-restraints excluded: chain S residue 369 ARG Chi-restraints excluded: chain S residue 389 ARG Chi-restraints excluded: chain S residue 393 GLU Chi-restraints excluded: chain S residue 401 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 405 optimal weight: 0.9980 chunk 363 optimal weight: 0.9980 chunk 201 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 245 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 376 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 228 optimal weight: 4.9990 chunk 280 optimal weight: 0.9990 chunk 435 optimal weight: 0.0050 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 92 ASN A 112 ASN A 160 ASN A 209 GLN A 322 HIS A 417 ASN A 429 ASN B 146 GLN B 181 ASN C 7 GLN D 6 GLN D 70 ASN D 77 GLN D 84 GLN E 70 ASN E 84 GLN ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 ASN F 417 ASN G 112 ASN G 209 GLN G 301 GLN G 322 HIS G 350 HIS G 383 HIS G 417 ASN G 426 GLN H 112 ASN H 181 ASN H 307 HIS I 304 HIS J 92 ASN J 181 ASN ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 291 HIS K 146 GLN K 181 ASN L 5 ASN L 29 GLN M 5 ASN M 7 GLN M 12 ASN M 18 ASN P 5 ASN P 12 ASN P 44 GLN Q 36 ASN Q 66 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 38804 Z= 0.183 Angle : 0.615 14.778 52539 Z= 0.323 Chirality : 0.044 0.245 5642 Planarity : 0.005 0.069 6889 Dihedral : 6.947 83.415 5389 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.80 % Favored : 94.06 % Rotamer: Outliers : 2.73 % Allowed : 12.68 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.80 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.12), residues: 4848 helix: 0.56 (0.13), residues: 1738 sheet: -0.53 (0.20), residues: 512 loop : -2.14 (0.11), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 408 HIS 0.009 0.001 HIS D 87 PHE 0.040 0.001 PHE S 332 TYR 0.019 0.001 TYR E 41 ARG 0.006 0.000 ARG R 366 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 3965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 576 time to evaluate : 4.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.4981 (mppt) cc_final: 0.4682 (mttm) REVERT: A 302 ARG cc_start: 0.7645 (ttp80) cc_final: 0.7402 (ttt180) REVERT: A 456 LEU cc_start: 0.8288 (mt) cc_final: 0.8042 (mt) REVERT: B 25 ASP cc_start: 0.7241 (p0) cc_final: 0.6979 (p0) REVERT: B 74 MET cc_start: 0.5784 (tpp) cc_final: 0.4975 (mmt) REVERT: B 245 GLU cc_start: 0.6699 (mp0) cc_final: 0.6413 (mp0) REVERT: B 302 ARG cc_start: 0.7940 (tmm-80) cc_final: 0.7611 (ttt-90) REVERT: C 58 LYS cc_start: 0.7420 (mttt) cc_final: 0.6597 (tptt) REVERT: C 66 ASN cc_start: 0.6726 (m-40) cc_final: 0.6260 (t0) REVERT: C 74 PHE cc_start: 0.1645 (OUTLIER) cc_final: 0.0867 (m-80) REVERT: D 35 MET cc_start: 0.7199 (mtm) cc_final: 0.6620 (mmm) REVERT: D 96 ASP cc_start: 0.6794 (t0) cc_final: 0.6071 (p0) REVERT: D 178 ASP cc_start: 0.7009 (t70) cc_final: 0.6689 (t0) REVERT: D 202 THR cc_start: 0.7244 (m) cc_final: 0.7025 (p) REVERT: E 1 MET cc_start: 0.1769 (ttp) cc_final: 0.0953 (ppp) REVERT: E 35 MET cc_start: 0.5260 (tmm) cc_final: 0.5041 (ptp) REVERT: E 83 LEU cc_start: 0.4998 (OUTLIER) cc_final: 0.4715 (mp) REVERT: E 107 ARG cc_start: 0.5717 (ptt-90) cc_final: 0.5504 (ptt-90) REVERT: E 132 GLN cc_start: 0.6386 (mt0) cc_final: 0.5966 (mt0) REVERT: E 136 ARG cc_start: 0.5591 (ttm110) cc_final: 0.4713 (mmt180) REVERT: F 25 ASP cc_start: 0.6642 (p0) cc_final: 0.6069 (m-30) REVERT: F 222 ILE cc_start: 0.8843 (mt) cc_final: 0.8386 (mm) REVERT: F 247 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.8053 (ttp) REVERT: F 259 MET cc_start: 0.8342 (mmp) cc_final: 0.8099 (mmp) REVERT: F 382 TRP cc_start: 0.8266 (m100) cc_final: 0.7961 (m100) REVERT: F 469 MET cc_start: 0.2807 (mmt) cc_final: 0.2419 (mpp) REVERT: G 73 ASP cc_start: 0.2859 (OUTLIER) cc_final: 0.2226 (p0) REVERT: G 109 SER cc_start: 0.8667 (t) cc_final: 0.8380 (p) REVERT: G 128 ARG cc_start: 0.7632 (ttp80) cc_final: 0.7258 (ttp-170) REVERT: G 166 MET cc_start: 0.7801 (mtm) cc_final: 0.7554 (mtt) REVERT: G 191 ARG cc_start: 0.7508 (tpt90) cc_final: 0.7082 (tpt90) REVERT: G 228 GLU cc_start: 0.6612 (pt0) cc_final: 0.6211 (tp30) REVERT: G 346 MET cc_start: 0.8390 (ptt) cc_final: 0.8067 (ptt) REVERT: G 426 GLN cc_start: 0.7194 (tp40) cc_final: 0.6746 (tp-100) REVERT: G 432 ARG cc_start: 0.7361 (mtm180) cc_final: 0.6769 (ttt180) REVERT: H 76 ARG cc_start: 0.7747 (mtm180) cc_final: 0.7504 (mtm180) REVERT: H 80 LYS cc_start: 0.7989 (mtmm) cc_final: 0.7741 (mptt) REVERT: H 92 ASN cc_start: 0.7406 (t0) cc_final: 0.6988 (t0) REVERT: H 220 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7537 (t0) REVERT: H 301 GLN cc_start: 0.7491 (mm-40) cc_final: 0.7290 (mt0) REVERT: I 48 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7457 (p0) REVERT: I 74 MET cc_start: 0.5902 (ptm) cc_final: 0.5422 (ptm) REVERT: I 76 ARG cc_start: 0.6898 (ptm-80) cc_final: 0.6668 (ptt90) REVERT: I 422 GLU cc_start: 0.6752 (mm-30) cc_final: 0.6513 (mm-30) REVERT: I 426 GLN cc_start: 0.7445 (tp40) cc_final: 0.7013 (pt0) REVERT: I 448 TRP cc_start: 0.6259 (p-90) cc_final: 0.5475 (p90) REVERT: I 460 LYS cc_start: 0.7998 (mtpt) cc_final: 0.7337 (mmtt) REVERT: J 74 MET cc_start: 0.6759 (tmm) cc_final: 0.5939 (ptt) REVERT: J 75 ASP cc_start: 0.7188 (m-30) cc_final: 0.6718 (m-30) REVERT: J 175 LEU cc_start: 0.6431 (OUTLIER) cc_final: 0.6184 (mt) REVERT: J 436 ARG cc_start: 0.6307 (tpp80) cc_final: 0.6020 (tpp80) REVERT: K 32 ASP cc_start: 0.7300 (m-30) cc_final: 0.7014 (m-30) REVERT: K 67 TRP cc_start: 0.6248 (t-100) cc_final: 0.6029 (t-100) REVERT: K 231 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7106 (tt0) REVERT: K 348 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6743 (mt-10) REVERT: K 422 GLU cc_start: 0.6496 (mt-10) cc_final: 0.6184 (mm-30) REVERT: K 435 TYR cc_start: 0.7590 (m-10) cc_final: 0.7376 (m-80) REVERT: L 58 LYS cc_start: 0.7976 (mttp) cc_final: 0.7666 (mtmt) REVERT: M 22 GLU cc_start: 0.6879 (tt0) cc_final: 0.6100 (tp30) REVERT: M 57 LYS cc_start: 0.7566 (mmmm) cc_final: 0.7212 (mmmm) REVERT: Q 12 ASN cc_start: 0.7025 (OUTLIER) cc_final: 0.6172 (p0) REVERT: R 342 LYS cc_start: 0.0833 (OUTLIER) cc_final: 0.0264 (mmtp) REVERT: S 393 GLU cc_start: 0.0003 (OUTLIER) cc_final: -0.0356 (pp20) REVERT: S 426 MET cc_start: 0.1779 (ptm) cc_final: 0.0581 (ttp) outliers start: 108 outliers final: 53 residues processed: 661 average time/residue: 0.5414 time to fit residues: 563.0997 Evaluate side-chains 564 residues out of total 3965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 501 time to evaluate : 4.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 247 MET Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 265 ASP Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 189 CYS Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 389 GLU Chi-restraints excluded: chain H residue 220 ASP Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 342 PHE Chi-restraints excluded: chain I residue 48 ASP Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 91 GLU Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain J residue 174 LYS Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 379 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 169 CYS Chi-restraints excluded: chain N residue 12 ASN Chi-restraints excluded: chain N residue 57 LYS Chi-restraints excluded: chain N residue 62 CYS Chi-restraints excluded: chain N residue 70 PHE Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 62 CYS Chi-restraints excluded: chain Q residue 12 ASN Chi-restraints excluded: chain Q residue 70 PHE Chi-restraints excluded: chain R residue 342 LYS Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 370 LYS Chi-restraints excluded: chain R residue 371 VAL Chi-restraints excluded: chain R residue 379 GLU Chi-restraints excluded: chain R residue 405 ASN Chi-restraints excluded: chain R residue 418 ARG Chi-restraints excluded: chain S residue 303 SER Chi-restraints excluded: chain S residue 317 LYS Chi-restraints excluded: chain S residue 335 VAL Chi-restraints excluded: chain S residue 369 ARG Chi-restraints excluded: chain S residue 393 GLU Chi-restraints excluded: chain S residue 401 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 362 optimal weight: 8.9990 chunk 296 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 436 optimal weight: 0.0870 chunk 471 optimal weight: 0.0000 chunk 388 optimal weight: 1.9990 chunk 433 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 350 optimal weight: 5.9990 overall best weight: 2.0168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS A 383 HIS E 84 GLN F 289 HIS G 209 GLN H 146 GLN H 209 GLN H 350 HIS H 383 HIS H 417 ASN ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 181 ASN M 66 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 38804 Z= 0.305 Angle : 0.667 10.717 52539 Z= 0.348 Chirality : 0.047 0.272 5642 Planarity : 0.005 0.068 6889 Dihedral : 6.099 59.420 5324 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.28 % Favored : 92.59 % Rotamer: Outliers : 3.49 % Allowed : 15.11 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.80 % Twisted General : 0.04 % 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: -0.88 (0.12), residues: 4848 helix: 0.92 (0.13), residues: 1771 sheet: -0.37 (0.20), residues: 548 loop : -1.81 (0.12), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 408 HIS 0.009 0.002 HIS E 87 PHE 0.044 0.002 PHE S 332 TYR 0.017 0.002 TYR E 41 ARG 0.010 0.001 ARG R 387 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 3965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 521 time to evaluate : 4.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLN cc_start: 0.7409 (mm110) cc_final: 0.7158 (mm110) REVERT: A 120 ASN cc_start: 0.8726 (p0) cc_final: 0.8502 (p0) REVERT: A 174 LYS cc_start: 0.5185 (mppt) cc_final: 0.4666 (mttm) REVERT: A 294 MET cc_start: 0.8626 (ttp) cc_final: 0.8284 (ttt) REVERT: A 444 GLU cc_start: 0.7644 (pp20) cc_final: 0.6784 (mp0) REVERT: C 22 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6707 (tp30) REVERT: C 58 LYS cc_start: 0.7529 (mttt) cc_final: 0.6719 (tptt) REVERT: C 66 ASN cc_start: 0.7912 (m-40) cc_final: 0.7376 (t0) REVERT: C 70 PHE cc_start: 0.8655 (p90) cc_final: 0.8339 (p90) REVERT: C 74 PHE cc_start: 0.1700 (OUTLIER) cc_final: 0.0417 (m-10) REVERT: D 35 MET cc_start: 0.7393 (mtm) cc_final: 0.6870 (mmm) REVERT: D 95 PHE cc_start: 0.6425 (m-10) cc_final: 0.6163 (m-10) REVERT: D 96 ASP cc_start: 0.7137 (t0) cc_final: 0.6143 (p0) REVERT: D 139 LYS cc_start: 0.7069 (mmtm) cc_final: 0.6663 (mmtp) REVERT: D 178 ASP cc_start: 0.7170 (t70) cc_final: 0.6845 (t0) REVERT: E 1 MET cc_start: 0.2454 (ttp) cc_final: 0.1507 (ppp) REVERT: E 35 MET cc_start: 0.5164 (tmm) cc_final: 0.4714 (ptp) REVERT: E 83 LEU cc_start: 0.4887 (OUTLIER) cc_final: 0.4389 (mp) REVERT: E 132 GLN cc_start: 0.6602 (mt0) cc_final: 0.6223 (mt0) REVERT: E 136 ARG cc_start: 0.5678 (ttm110) cc_final: 0.4783 (mmt180) REVERT: F 25 ASP cc_start: 0.6715 (p0) cc_final: 0.6110 (m-30) REVERT: F 222 ILE cc_start: 0.8891 (mt) cc_final: 0.8553 (mt) REVERT: F 382 TRP cc_start: 0.8281 (m100) cc_final: 0.8045 (m100) REVERT: F 384 MET cc_start: 0.7272 (tpp) cc_final: 0.6909 (mmm) REVERT: F 469 MET cc_start: 0.3117 (mmt) cc_final: 0.2513 (mpp) REVERT: G 73 ASP cc_start: 0.3172 (OUTLIER) cc_final: 0.2442 (p0) REVERT: G 103 ASP cc_start: 0.6881 (m-30) cc_final: 0.6568 (m-30) REVERT: G 109 SER cc_start: 0.8691 (t) cc_final: 0.8444 (p) REVERT: G 128 ARG cc_start: 0.7632 (ttp80) cc_final: 0.7241 (ttp-170) REVERT: G 426 GLN cc_start: 0.7123 (tp40) cc_final: 0.6606 (tp-100) REVERT: G 444 GLU cc_start: 0.6829 (tm-30) cc_final: 0.6559 (tm-30) REVERT: G 469 MET cc_start: 0.4352 (pmm) cc_final: 0.4122 (pmm) REVERT: H 74 MET cc_start: 0.5837 (ptm) cc_final: 0.5593 (mtm) REVERT: H 76 ARG cc_start: 0.7891 (mtm180) cc_final: 0.7689 (mtm180) REVERT: H 80 LYS cc_start: 0.8242 (mtmm) cc_final: 0.7914 (mttt) REVERT: H 92 ASN cc_start: 0.7832 (t0) cc_final: 0.7211 (t0) REVERT: H 201 GLU cc_start: 0.7294 (pm20) cc_final: 0.6807 (pm20) REVERT: H 220 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7670 (t0) REVERT: H 283 ASP cc_start: 0.7139 (m-30) cc_final: 0.6736 (m-30) REVERT: H 301 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7315 (mt0) REVERT: H 469 MET cc_start: 0.1660 (tpp) cc_final: 0.1372 (tpp) REVERT: I 76 ARG cc_start: 0.6978 (ptm-80) cc_final: 0.6682 (ptt90) REVERT: I 267 LEU cc_start: 0.8594 (mt) cc_final: 0.8344 (mt) REVERT: I 426 GLN cc_start: 0.7439 (tp40) cc_final: 0.6970 (pt0) REVERT: I 448 TRP cc_start: 0.6438 (p-90) cc_final: 0.5649 (p90) REVERT: I 460 LYS cc_start: 0.7790 (mtpt) cc_final: 0.7149 (mmtt) REVERT: J 23 THR cc_start: 0.7399 (m) cc_final: 0.6944 (p) REVERT: J 49 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7556 (mt-10) REVERT: J 74 MET cc_start: 0.6675 (tmm) cc_final: 0.6321 (tpp) REVERT: J 91 GLU cc_start: 0.5690 (OUTLIER) cc_final: 0.5463 (pm20) REVERT: K 279 LYS cc_start: 0.8355 (mttt) cc_final: 0.7977 (mmtp) REVERT: L 10 LYS cc_start: 0.5834 (mtmt) cc_final: 0.5593 (mtmt) REVERT: L 58 LYS cc_start: 0.8039 (mttp) cc_final: 0.7702 (mtmt) REVERT: M 57 LYS cc_start: 0.7932 (mmmm) cc_final: 0.7598 (mmmm) REVERT: R 324 MET cc_start: -0.2313 (mmm) cc_final: -0.2962 (ptp) REVERT: R 342 LYS cc_start: 0.1195 (OUTLIER) cc_final: 0.0493 (mmtt) REVERT: S 393 GLU cc_start: 0.0329 (OUTLIER) cc_final: -0.0159 (pp20) REVERT: S 426 MET cc_start: 0.2168 (ptm) cc_final: 0.1009 (ttp) outliers start: 138 outliers final: 87 residues processed: 627 average time/residue: 0.5488 time to fit residues: 546.0437 Evaluate side-chains 574 residues out of total 3965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 478 time to evaluate : 4.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 265 ASP Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 189 CYS Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 342 PHE Chi-restraints excluded: chain G residue 389 GLU Chi-restraints excluded: chain G residue 424 CYS Chi-restraints excluded: chain H residue 209 GLN Chi-restraints excluded: chain H residue 220 ASP Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 342 PHE Chi-restraints excluded: chain H residue 462 ILE Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 189 CYS Chi-restraints excluded: chain I residue 195 ASP Chi-restraints excluded: chain I residue 327 THR Chi-restraints excluded: chain I residue 424 CYS Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 91 GLU Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain J residue 376 SER Chi-restraints excluded: chain J residue 379 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 169 CYS Chi-restraints excluded: chain K residue 424 CYS Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain N residue 12 ASN Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 57 LYS Chi-restraints excluded: chain N residue 62 CYS Chi-restraints excluded: chain N residue 70 PHE Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 62 CYS Chi-restraints excluded: chain P residue 5 ASN Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain Q residue 12 ASN Chi-restraints excluded: chain Q residue 70 PHE Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 342 LYS Chi-restraints excluded: chain R residue 370 LYS Chi-restraints excluded: chain R residue 371 VAL Chi-restraints excluded: chain R residue 405 ASN Chi-restraints excluded: chain R residue 418 ARG Chi-restraints excluded: chain S residue 317 LYS Chi-restraints excluded: chain S residue 335 VAL Chi-restraints excluded: chain S residue 369 ARG Chi-restraints excluded: chain S residue 393 GLU Chi-restraints excluded: chain S residue 401 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 9.9990 chunk 328 optimal weight: 4.9990 chunk 226 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 208 optimal weight: 0.8980 chunk 293 optimal weight: 2.9990 chunk 438 optimal weight: 8.9990 chunk 463 optimal weight: 4.9990 chunk 228 optimal weight: 0.8980 chunk 415 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 289 HIS E 6 GLN E 84 GLN F 120 ASN ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 ASN M 29 GLN M 66 ASN ** N 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 38804 Z= 0.354 Angle : 0.680 10.647 52539 Z= 0.355 Chirality : 0.048 0.225 5642 Planarity : 0.006 0.065 6889 Dihedral : 6.014 58.922 5311 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.67 % Favored : 92.22 % Rotamer: Outliers : 4.18 % Allowed : 16.24 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.80 % Twisted General : 0.04 % 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: -0.85 (0.12), residues: 4848 helix: 0.96 (0.13), residues: 1766 sheet: -0.49 (0.20), residues: 551 loop : -1.77 (0.12), residues: 2531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 408 HIS 0.009 0.002 HIS J 150 PHE 0.035 0.002 PHE S 332 TYR 0.015 0.002 TYR I 21 ARG 0.005 0.001 ARG R 343 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 507 time to evaluate : 4.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASN cc_start: 0.8681 (p0) cc_final: 0.8468 (p0) REVERT: A 174 LYS cc_start: 0.5396 (mppt) cc_final: 0.4708 (mttm) REVERT: A 226 GLN cc_start: 0.8384 (tt0) cc_final: 0.8088 (tt0) REVERT: A 381 VAL cc_start: 0.8228 (m) cc_final: 0.7688 (p) REVERT: A 444 GLU cc_start: 0.7634 (pp20) cc_final: 0.6792 (mp0) REVERT: B 32 ASP cc_start: 0.7928 (m-30) cc_final: 0.7726 (m-30) REVERT: C 22 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6720 (tp30) REVERT: C 58 LYS cc_start: 0.7726 (mttt) cc_final: 0.6843 (tptt) REVERT: C 66 ASN cc_start: 0.8090 (m-40) cc_final: 0.7639 (t0) REVERT: C 74 PHE cc_start: 0.1729 (OUTLIER) cc_final: 0.0514 (m-10) REVERT: D 35 MET cc_start: 0.7527 (mtm) cc_final: 0.7000 (mmm) REVERT: D 139 LYS cc_start: 0.7098 (mmtm) cc_final: 0.6719 (mmtp) REVERT: D 178 ASP cc_start: 0.7006 (t70) cc_final: 0.6659 (t0) REVERT: E 18 GLN cc_start: 0.4652 (tt0) cc_final: 0.4401 (mp10) REVERT: E 35 MET cc_start: 0.5448 (tmm) cc_final: 0.4992 (tmm) REVERT: E 132 GLN cc_start: 0.6350 (mt0) cc_final: 0.5718 (mt0) REVERT: E 136 ARG cc_start: 0.5788 (ttm110) cc_final: 0.4834 (mmt180) REVERT: F 25 ASP cc_start: 0.6577 (p0) cc_final: 0.6185 (m-30) REVERT: F 222 ILE cc_start: 0.8863 (mt) cc_final: 0.8658 (mm) REVERT: F 382 TRP cc_start: 0.8328 (m100) cc_final: 0.8041 (m100) REVERT: F 440 ASP cc_start: 0.6830 (t0) cc_final: 0.6308 (t0) REVERT: F 469 MET cc_start: 0.2977 (mmt) cc_final: 0.2232 (mpp) REVERT: G 73 ASP cc_start: 0.3590 (OUTLIER) cc_final: 0.2754 (p0) REVERT: G 109 SER cc_start: 0.8691 (t) cc_final: 0.8487 (p) REVERT: G 128 ARG cc_start: 0.7749 (ttp80) cc_final: 0.7318 (ttp-170) REVERT: G 426 GLN cc_start: 0.7238 (tp40) cc_final: 0.6863 (tp40) REVERT: G 444 GLU cc_start: 0.6738 (tm-30) cc_final: 0.6449 (tm-30) REVERT: H 57 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7664 (mm-30) REVERT: H 80 LYS cc_start: 0.8281 (mtmm) cc_final: 0.7927 (mptt) REVERT: H 125 LYS cc_start: 0.8675 (mmmt) cc_final: 0.7957 (mttm) REVERT: H 220 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7646 (t0) REVERT: H 283 ASP cc_start: 0.7151 (m-30) cc_final: 0.6710 (m-30) REVERT: H 301 GLN cc_start: 0.7919 (mm-40) cc_final: 0.7534 (mt0) REVERT: H 469 MET cc_start: 0.0787 (tpp) cc_final: 0.0520 (tpp) REVERT: I 263 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8649 (ptp) REVERT: I 267 LEU cc_start: 0.8704 (mt) cc_final: 0.8454 (mt) REVERT: I 426 GLN cc_start: 0.7440 (tp40) cc_final: 0.6992 (pt0) REVERT: I 448 TRP cc_start: 0.6617 (p-90) cc_final: 0.6064 (p-90) REVERT: I 460 LYS cc_start: 0.7855 (mtpt) cc_final: 0.7190 (mmtt) REVERT: J 23 THR cc_start: 0.7559 (m) cc_final: 0.7080 (p) REVERT: J 57 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7093 (mm-30) REVERT: J 74 MET cc_start: 0.6718 (tmm) cc_final: 0.6383 (tpp) REVERT: J 91 GLU cc_start: 0.5748 (OUTLIER) cc_final: 0.5411 (pm20) REVERT: J 294 MET cc_start: 0.8285 (ttt) cc_final: 0.8020 (ttt) REVERT: J 357 ARG cc_start: 0.7365 (mtp85) cc_final: 0.6948 (mtm180) REVERT: K 279 LYS cc_start: 0.8365 (mttt) cc_final: 0.8022 (mmtp) REVERT: L 10 LYS cc_start: 0.5735 (mtmt) cc_final: 0.5446 (mtmt) REVERT: L 41 PHE cc_start: 0.5797 (m-80) cc_final: 0.5596 (m-80) REVERT: L 58 LYS cc_start: 0.8075 (mttp) cc_final: 0.7696 (mtmt) REVERT: M 57 LYS cc_start: 0.7959 (mmmm) cc_final: 0.7608 (mmmt) REVERT: R 324 MET cc_start: -0.1246 (mmm) cc_final: -0.3060 (ptm) REVERT: R 342 LYS cc_start: 0.1315 (OUTLIER) cc_final: 0.0590 (mmtt) REVERT: S 369 ARG cc_start: 0.1511 (OUTLIER) cc_final: 0.1017 (mmt180) REVERT: S 393 GLU cc_start: 0.0456 (OUTLIER) cc_final: -0.0123 (pp20) outliers start: 165 outliers final: 113 residues processed: 630 average time/residue: 0.5451 time to fit residues: 543.5819 Evaluate side-chains 589 residues out of total 3965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 467 time to evaluate : 4.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 265 ASP Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 294 MET Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 342 PHE Chi-restraints excluded: chain G residue 389 GLU Chi-restraints excluded: chain G residue 424 CYS Chi-restraints excluded: chain H residue 220 ASP Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 342 PHE Chi-restraints excluded: chain H residue 425 VAL Chi-restraints excluded: chain H residue 462 ILE Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 120 ASN Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 195 ASP Chi-restraints excluded: chain I residue 249 LYS Chi-restraints excluded: chain I residue 263 MET Chi-restraints excluded: chain I residue 325 SER Chi-restraints excluded: chain I residue 327 THR Chi-restraints excluded: chain I residue 424 CYS Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 91 GLU Chi-restraints excluded: chain J residue 120 ASN Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain J residue 376 SER Chi-restraints excluded: chain J residue 379 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 146 GLN Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 169 CYS Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 424 CYS Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 42 ASN Chi-restraints excluded: chain N residue 57 LYS Chi-restraints excluded: chain N residue 62 CYS Chi-restraints excluded: chain N residue 70 PHE Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 62 CYS Chi-restraints excluded: chain O residue 64 ASP Chi-restraints excluded: chain P residue 5 ASN Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain Q residue 70 PHE Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 342 LYS Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 370 LYS Chi-restraints excluded: chain R residue 383 VAL Chi-restraints excluded: chain R residue 405 ASN Chi-restraints excluded: chain R residue 418 ARG Chi-restraints excluded: chain S residue 317 LYS Chi-restraints excluded: chain S residue 327 ILE Chi-restraints excluded: chain S residue 335 VAL Chi-restraints excluded: chain S residue 369 ARG Chi-restraints excluded: chain S residue 393 GLU Chi-restraints excluded: chain S residue 401 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 0.9990 chunk 263 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 345 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 395 optimal weight: 1.9990 chunk 320 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 236 optimal weight: 0.9980 chunk 416 optimal weight: 0.0470 chunk 117 optimal weight: 0.8980 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN E 84 GLN F 426 GLN H 209 GLN ** I 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 223 HIS M 12 ASN M 66 ASN N 12 ASN N 40 HIS ** Q 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 38804 Z= 0.183 Angle : 0.565 10.650 52539 Z= 0.294 Chirality : 0.043 0.276 5642 Planarity : 0.004 0.066 6889 Dihedral : 5.483 59.063 5306 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.70 % Favored : 93.21 % Rotamer: Outliers : 3.09 % Allowed : 17.79 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.80 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.12), residues: 4848 helix: 1.46 (0.13), residues: 1760 sheet: -0.10 (0.20), residues: 559 loop : -1.59 (0.12), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 408 HIS 0.006 0.001 HIS E 87 PHE 0.023 0.001 PHE S 332 TYR 0.016 0.001 TYR D 41 ARG 0.003 0.000 ARG H 191 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 503 time to evaluate : 4.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASN cc_start: 0.8698 (p0) cc_final: 0.8453 (p0) REVERT: A 174 LYS cc_start: 0.5353 (mppt) cc_final: 0.4722 (mttm) REVERT: A 226 GLN cc_start: 0.8222 (tt0) cc_final: 0.7908 (tt0) REVERT: A 299 ASP cc_start: 0.8462 (p0) cc_final: 0.8220 (p0) REVERT: A 381 VAL cc_start: 0.8195 (m) cc_final: 0.7752 (p) REVERT: A 444 GLU cc_start: 0.7547 (pp20) cc_final: 0.6777 (mp0) REVERT: B 32 ASP cc_start: 0.7896 (m-30) cc_final: 0.7668 (m-30) REVERT: B 74 MET cc_start: 0.5485 (tpp) cc_final: 0.5066 (mmm) REVERT: C 22 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6794 (tp30) REVERT: C 58 LYS cc_start: 0.7642 (mttt) cc_final: 0.6756 (tptt) REVERT: C 66 ASN cc_start: 0.8099 (m-40) cc_final: 0.7665 (t0) REVERT: C 74 PHE cc_start: 0.1785 (OUTLIER) cc_final: 0.0585 (m-10) REVERT: D 35 MET cc_start: 0.7483 (mtm) cc_final: 0.6964 (mmm) REVERT: D 139 LYS cc_start: 0.6926 (mmtm) cc_final: 0.6559 (mmtp) REVERT: D 178 ASP cc_start: 0.6802 (t70) cc_final: 0.6540 (t0) REVERT: E 35 MET cc_start: 0.5547 (tmm) cc_final: 0.5056 (tmm) REVERT: E 132 GLN cc_start: 0.6309 (mt0) cc_final: 0.5643 (mt0) REVERT: E 136 ARG cc_start: 0.5844 (ttm110) cc_final: 0.4842 (mmt180) REVERT: F 25 ASP cc_start: 0.6589 (p0) cc_final: 0.6162 (m-30) REVERT: F 222 ILE cc_start: 0.8880 (mt) cc_final: 0.8510 (mt) REVERT: F 384 MET cc_start: 0.7208 (tpp) cc_final: 0.6946 (mmp) REVERT: F 469 MET cc_start: 0.2793 (mmt) cc_final: 0.2056 (mpp) REVERT: G 25 ASP cc_start: 0.6601 (t0) cc_final: 0.6308 (p0) REVERT: G 73 ASP cc_start: 0.3358 (OUTLIER) cc_final: 0.2717 (p0) REVERT: G 109 SER cc_start: 0.8674 (t) cc_final: 0.8453 (p) REVERT: G 128 ARG cc_start: 0.7746 (ttp80) cc_final: 0.7310 (ttp-170) REVERT: G 298 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7675 (mt) REVERT: G 426 GLN cc_start: 0.7183 (tp40) cc_final: 0.6662 (tp-100) REVERT: G 437 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6274 (mp0) REVERT: G 444 GLU cc_start: 0.6623 (tm-30) cc_final: 0.6319 (tm-30) REVERT: H 57 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7633 (mm-30) REVERT: H 80 LYS cc_start: 0.8096 (mtmm) cc_final: 0.7644 (mptt) REVERT: H 125 LYS cc_start: 0.8700 (mmmt) cc_final: 0.7956 (mttm) REVERT: H 220 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7603 (t0) REVERT: H 283 ASP cc_start: 0.7083 (m-30) cc_final: 0.6644 (m-30) REVERT: H 301 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7568 (mt0) REVERT: H 444 GLU cc_start: 0.6306 (mt-10) cc_final: 0.6020 (tt0) REVERT: I 48 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.6915 (m-30) REVERT: I 166 MET cc_start: 0.8301 (mtm) cc_final: 0.7713 (mpp) REVERT: I 426 GLN cc_start: 0.7384 (tp40) cc_final: 0.6899 (pt0) REVERT: I 448 TRP cc_start: 0.6560 (p-90) cc_final: 0.5990 (p-90) REVERT: I 460 LYS cc_start: 0.7967 (mtpt) cc_final: 0.7223 (mmtt) REVERT: J 23 THR cc_start: 0.7374 (m) cc_final: 0.6914 (p) REVERT: J 49 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7611 (mt-10) REVERT: J 57 GLU cc_start: 0.7304 (mm-30) cc_final: 0.7099 (mm-30) REVERT: J 294 MET cc_start: 0.8282 (ttt) cc_final: 0.7961 (ttt) REVERT: J 357 ARG cc_start: 0.7291 (mtp85) cc_final: 0.7063 (mtm180) REVERT: J 436 ARG cc_start: 0.6691 (tpp80) cc_final: 0.6266 (mtp85) REVERT: K 279 LYS cc_start: 0.8294 (mttt) cc_final: 0.7954 (mmtp) REVERT: L 41 PHE cc_start: 0.5727 (m-80) cc_final: 0.5514 (m-80) REVERT: L 58 LYS cc_start: 0.8075 (mttp) cc_final: 0.7699 (mtmt) REVERT: M 57 LYS cc_start: 0.7847 (mmmm) cc_final: 0.7580 (mmmt) REVERT: R 324 MET cc_start: -0.1487 (mmm) cc_final: -0.3262 (ptm) REVERT: S 295 PHE cc_start: 0.0841 (OUTLIER) cc_final: 0.0216 (m-80) REVERT: S 333 LYS cc_start: 0.0676 (OUTLIER) cc_final: 0.0206 (mmmt) REVERT: S 393 GLU cc_start: 0.0289 (OUTLIER) cc_final: -0.0088 (pp20) outliers start: 122 outliers final: 79 residues processed: 593 average time/residue: 0.5335 time to fit residues: 503.0647 Evaluate side-chains 567 residues out of total 3965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 478 time to evaluate : 4.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 265 ASP Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain F residue 444 GLU Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain G residue 248 MET Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 342 PHE Chi-restraints excluded: chain G residue 389 GLU Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain H residue 220 ASP Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 342 PHE Chi-restraints excluded: chain H residue 462 ILE Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 48 ASP Chi-restraints excluded: chain I residue 120 ASN Chi-restraints excluded: chain I residue 189 CYS Chi-restraints excluded: chain I residue 299 ASP Chi-restraints excluded: chain I residue 342 PHE Chi-restraints excluded: chain I residue 424 CYS Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain J residue 379 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 146 GLN Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 169 CYS Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 342 PHE Chi-restraints excluded: chain K residue 424 CYS Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain N residue 62 CYS Chi-restraints excluded: chain N residue 70 PHE Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 62 CYS Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain Q residue 12 ASN Chi-restraints excluded: chain Q residue 70 PHE Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 371 VAL Chi-restraints excluded: chain R residue 405 ASN Chi-restraints excluded: chain R residue 418 ARG Chi-restraints excluded: chain S residue 295 PHE Chi-restraints excluded: chain S residue 305 VAL Chi-restraints excluded: chain S residue 317 LYS Chi-restraints excluded: chain S residue 324 MET Chi-restraints excluded: chain S residue 333 LYS Chi-restraints excluded: chain S residue 335 VAL Chi-restraints excluded: chain S residue 393 GLU Chi-restraints excluded: chain S residue 401 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 0.7980 chunk 417 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 272 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 464 optimal weight: 10.0000 chunk 385 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 38 optimal weight: 0.4980 chunk 153 optimal weight: 3.9990 chunk 243 optimal weight: 3.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS C 18 ASN E 6 GLN E 84 GLN ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 274 ASN ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 ASN N 12 ASN Q 29 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 38804 Z= 0.343 Angle : 0.668 14.291 52539 Z= 0.346 Chirality : 0.048 0.245 5642 Planarity : 0.005 0.064 6889 Dihedral : 5.570 57.082 5292 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.00 % Favored : 91.91 % Rotamer: Outliers : 4.05 % Allowed : 17.66 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.80 % Twisted General : 0.02 % 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: -0.58 (0.12), residues: 4848 helix: 1.21 (0.13), residues: 1766 sheet: -0.21 (0.20), residues: 551 loop : -1.65 (0.12), residues: 2531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 408 HIS 0.009 0.002 HIS I 150 PHE 0.025 0.002 PHE B 342 TYR 0.017 0.002 TYR B 26 ARG 0.008 0.001 ARG S 369 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 3965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 472 time to evaluate : 4.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.5112 (tpp) cc_final: 0.4907 (tmm) REVERT: A 75 ASP cc_start: 0.6389 (p0) cc_final: 0.6022 (p0) REVERT: A 92 ASN cc_start: 0.7705 (t0) cc_final: 0.7285 (t0) REVERT: A 120 ASN cc_start: 0.8689 (p0) cc_final: 0.8403 (p0) REVERT: A 174 LYS cc_start: 0.5548 (mppt) cc_final: 0.4913 (mttm) REVERT: A 226 GLN cc_start: 0.8449 (tt0) cc_final: 0.8137 (tt0) REVERT: A 349 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7973 (t0) REVERT: A 444 GLU cc_start: 0.7544 (pp20) cc_final: 0.6745 (mp0) REVERT: B 74 MET cc_start: 0.5729 (tpp) cc_final: 0.5224 (mmm) REVERT: B 265 ASP cc_start: 0.7525 (m-30) cc_final: 0.7325 (m-30) REVERT: C 22 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6821 (tp30) REVERT: C 58 LYS cc_start: 0.7679 (mttt) cc_final: 0.6751 (tptt) REVERT: C 66 ASN cc_start: 0.8170 (m-40) cc_final: 0.7674 (t0) REVERT: C 74 PHE cc_start: 0.2016 (OUTLIER) cc_final: 0.0797 (m-10) REVERT: D 35 MET cc_start: 0.7477 (mtm) cc_final: 0.6967 (mmm) REVERT: D 139 LYS cc_start: 0.7106 (mmtm) cc_final: 0.6732 (mmtp) REVERT: D 178 ASP cc_start: 0.6669 (t70) cc_final: 0.6445 (t0) REVERT: E 35 MET cc_start: 0.5473 (tmm) cc_final: 0.5094 (tmm) REVERT: E 105 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.5615 (mp0) REVERT: E 132 GLN cc_start: 0.6227 (mt0) cc_final: 0.5690 (mt0) REVERT: E 136 ARG cc_start: 0.5892 (ttm110) cc_final: 0.4888 (mmt180) REVERT: F 16 ASP cc_start: 0.3522 (OUTLIER) cc_final: 0.3288 (t0) REVERT: F 222 ILE cc_start: 0.8928 (mt) cc_final: 0.8634 (mt) REVERT: F 469 MET cc_start: 0.3029 (mmt) cc_final: 0.1484 (mtp) REVERT: G 25 ASP cc_start: 0.6563 (t0) cc_final: 0.6235 (p0) REVERT: G 73 ASP cc_start: 0.3507 (OUTLIER) cc_final: 0.2857 (p0) REVERT: G 109 SER cc_start: 0.8722 (t) cc_final: 0.8482 (p) REVERT: G 298 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7618 (mt) REVERT: G 444 GLU cc_start: 0.6660 (tm-30) cc_final: 0.6379 (tm-30) REVERT: H 57 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7688 (mm-30) REVERT: H 80 LYS cc_start: 0.8291 (mtmm) cc_final: 0.7943 (mptt) REVERT: H 125 LYS cc_start: 0.8691 (mmmt) cc_final: 0.7962 (mttm) REVERT: H 220 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7669 (t0) REVERT: H 283 ASP cc_start: 0.7168 (m-30) cc_final: 0.6693 (m-30) REVERT: H 301 GLN cc_start: 0.7980 (mm-40) cc_final: 0.7535 (mt0) REVERT: I 48 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.6973 (m-30) REVERT: I 426 GLN cc_start: 0.7399 (tp40) cc_final: 0.6922 (pt0) REVERT: I 448 TRP cc_start: 0.6499 (p-90) cc_final: 0.6036 (p-90) REVERT: I 460 LYS cc_start: 0.7905 (mtpt) cc_final: 0.7240 (mmtt) REVERT: J 49 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7611 (mt-10) REVERT: J 294 MET cc_start: 0.8254 (ttt) cc_final: 0.7939 (ttt) REVERT: J 357 ARG cc_start: 0.7338 (mtp85) cc_final: 0.7137 (mtm180) REVERT: J 436 ARG cc_start: 0.6631 (tpp80) cc_final: 0.6264 (mtp85) REVERT: K 120 ASN cc_start: 0.7811 (OUTLIER) cc_final: 0.7492 (p0) REVERT: K 206 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.7527 (mt0) REVERT: K 279 LYS cc_start: 0.8368 (mttt) cc_final: 0.8034 (mmtp) REVERT: K 441 ILE cc_start: 0.7592 (OUTLIER) cc_final: 0.7376 (mp) REVERT: K 463 LYS cc_start: 0.6198 (tmtt) cc_final: 0.5312 (tttm) REVERT: L 10 LYS cc_start: 0.5716 (mtmt) cc_final: 0.5380 (mtmt) REVERT: L 41 PHE cc_start: 0.5725 (m-80) cc_final: 0.5524 (m-80) REVERT: L 58 LYS cc_start: 0.8090 (mttp) cc_final: 0.7814 (mtpt) REVERT: M 57 LYS cc_start: 0.7986 (mmmm) cc_final: 0.7683 (mmmt) REVERT: Q 28 SER cc_start: 0.7813 (t) cc_final: 0.7495 (p) REVERT: R 324 MET cc_start: -0.0787 (mmm) cc_final: -0.3172 (ptm) REVERT: S 295 PHE cc_start: 0.1325 (OUTLIER) cc_final: 0.0467 (m-80) REVERT: S 333 LYS cc_start: 0.0202 (OUTLIER) cc_final: -0.0009 (mmmt) REVERT: S 393 GLU cc_start: 0.0447 (OUTLIER) cc_final: -0.0222 (pp20) outliers start: 160 outliers final: 109 residues processed: 597 average time/residue: 0.5383 time to fit residues: 514.8529 Evaluate side-chains 579 residues out of total 3965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 454 time to evaluate : 4.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 265 ASP Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 444 GLU Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 189 CYS Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 223 HIS Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 294 MET Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 342 PHE Chi-restraints excluded: chain G residue 389 GLU Chi-restraints excluded: chain G residue 435 TYR Chi-restraints excluded: chain G residue 469 MET Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain H residue 220 ASP Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 342 PHE Chi-restraints excluded: chain H residue 424 CYS Chi-restraints excluded: chain H residue 462 ILE Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 48 ASP Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 120 ASN Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 189 CYS Chi-restraints excluded: chain I residue 249 LYS Chi-restraints excluded: chain I residue 325 SER Chi-restraints excluded: chain I residue 342 PHE Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain J residue 376 SER Chi-restraints excluded: chain J residue 379 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 120 ASN Chi-restraints excluded: chain K residue 146 GLN Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 169 CYS Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 206 GLN Chi-restraints excluded: chain K residue 342 PHE Chi-restraints excluded: chain K residue 424 CYS Chi-restraints excluded: chain K residue 429 ASN Chi-restraints excluded: chain K residue 441 ILE Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain N residue 12 ASN Chi-restraints excluded: chain N residue 42 ASN Chi-restraints excluded: chain N residue 62 CYS Chi-restraints excluded: chain N residue 70 PHE Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 62 CYS Chi-restraints excluded: chain O residue 64 ASP Chi-restraints excluded: chain P residue 5 ASN Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain Q residue 12 ASN Chi-restraints excluded: chain Q residue 70 PHE Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain S residue 295 PHE Chi-restraints excluded: chain S residue 305 VAL Chi-restraints excluded: chain S residue 317 LYS Chi-restraints excluded: chain S residue 324 MET Chi-restraints excluded: chain S residue 333 LYS Chi-restraints excluded: chain S residue 393 GLU Chi-restraints excluded: chain S residue 401 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 264 optimal weight: 2.9990 chunk 339 optimal weight: 4.9990 chunk 262 optimal weight: 2.9990 chunk 390 optimal weight: 4.9990 chunk 259 optimal weight: 0.9990 chunk 462 optimal weight: 10.0000 chunk 289 optimal weight: 3.9990 chunk 282 optimal weight: 0.6980 chunk 213 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN E 84 GLN ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 291 HIS M 12 ASN N 12 ASN Q 29 GLN R 405 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 38804 Z= 0.216 Angle : 0.589 10.839 52539 Z= 0.304 Chirality : 0.044 0.239 5642 Planarity : 0.005 0.064 6889 Dihedral : 5.190 58.258 5285 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.01 % Favored : 92.90 % Rotamer: Outliers : 3.57 % Allowed : 18.60 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.35 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.12), residues: 4848 helix: 1.53 (0.13), residues: 1758 sheet: 0.08 (0.21), residues: 535 loop : -1.56 (0.12), residues: 2555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 408 HIS 0.006 0.001 HIS E 87 PHE 0.018 0.001 PHE B 342 TYR 0.017 0.001 TYR B 26 ARG 0.004 0.000 ARG M 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 483 time to evaluate : 4.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.7689 (t0) cc_final: 0.7277 (t0) REVERT: A 120 ASN cc_start: 0.8682 (p0) cc_final: 0.8371 (p0) REVERT: A 174 LYS cc_start: 0.5413 (mppt) cc_final: 0.4777 (mttm) REVERT: A 226 GLN cc_start: 0.8348 (tt0) cc_final: 0.8011 (tt0) REVERT: A 349 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7933 (t0) REVERT: A 444 GLU cc_start: 0.7519 (pp20) cc_final: 0.6766 (mp0) REVERT: B 74 MET cc_start: 0.5570 (tpp) cc_final: 0.5172 (mmm) REVERT: C 22 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6778 (tp30) REVERT: C 58 LYS cc_start: 0.7848 (mttt) cc_final: 0.6828 (tptt) REVERT: C 66 ASN cc_start: 0.8183 (m-40) cc_final: 0.7698 (t0) REVERT: C 74 PHE cc_start: 0.1941 (OUTLIER) cc_final: 0.0891 (m-10) REVERT: D 35 MET cc_start: 0.7474 (mtm) cc_final: 0.6967 (mmm) REVERT: D 139 LYS cc_start: 0.6960 (mmtm) cc_final: 0.6598 (mmtp) REVERT: D 178 ASP cc_start: 0.6737 (t70) cc_final: 0.6492 (t0) REVERT: E 105 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.5632 (mp0) REVERT: E 136 ARG cc_start: 0.5727 (ttm110) cc_final: 0.4835 (mmt180) REVERT: F 222 ILE cc_start: 0.8905 (mt) cc_final: 0.8612 (mt) REVERT: F 384 MET cc_start: 0.7228 (tpp) cc_final: 0.7017 (mmp) REVERT: F 451 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7180 (mp0) REVERT: F 469 MET cc_start: 0.2812 (mmt) cc_final: 0.1349 (mtp) REVERT: G 25 ASP cc_start: 0.6608 (t0) cc_final: 0.6288 (p0) REVERT: G 73 ASP cc_start: 0.3496 (OUTLIER) cc_final: 0.2946 (p0) REVERT: G 109 SER cc_start: 0.8713 (t) cc_final: 0.8450 (p) REVERT: G 292 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8138 (ptt180) REVERT: G 298 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7570 (mt) REVERT: G 437 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6261 (mp0) REVERT: G 444 GLU cc_start: 0.6711 (tm-30) cc_final: 0.6442 (tm-30) REVERT: H 57 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7618 (mm-30) REVERT: H 80 LYS cc_start: 0.8134 (mtmm) cc_final: 0.7768 (mptt) REVERT: H 125 LYS cc_start: 0.8714 (mmmt) cc_final: 0.8006 (mttm) REVERT: H 220 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7646 (t0) REVERT: H 283 ASP cc_start: 0.7133 (m-30) cc_final: 0.6674 (m-30) REVERT: H 301 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7496 (mt0) REVERT: I 48 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.6884 (m-30) REVERT: I 166 MET cc_start: 0.8343 (mtm) cc_final: 0.7762 (mpp) REVERT: I 426 GLN cc_start: 0.7401 (tp40) cc_final: 0.6909 (pt0) REVERT: I 448 TRP cc_start: 0.6468 (p-90) cc_final: 0.6019 (p-90) REVERT: I 460 LYS cc_start: 0.7846 (mtpt) cc_final: 0.7157 (mmtt) REVERT: J 49 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7617 (mt-10) REVERT: J 57 GLU cc_start: 0.7340 (mm-30) cc_final: 0.6933 (mm-30) REVERT: J 294 MET cc_start: 0.8271 (ttt) cc_final: 0.7933 (ttt) REVERT: J 357 ARG cc_start: 0.7294 (mtp85) cc_final: 0.7087 (mtm180) REVERT: J 436 ARG cc_start: 0.6801 (tpp80) cc_final: 0.6328 (mtp85) REVERT: K 120 ASN cc_start: 0.7442 (OUTLIER) cc_final: 0.7142 (p0) REVERT: K 279 LYS cc_start: 0.8325 (mttt) cc_final: 0.7998 (mmtp) REVERT: L 41 PHE cc_start: 0.5676 (m-80) cc_final: 0.5471 (m-80) REVERT: L 58 LYS cc_start: 0.7967 (mttp) cc_final: 0.7678 (mtpt) REVERT: M 57 LYS cc_start: 0.7979 (mmmm) cc_final: 0.7688 (mmmt) REVERT: O 65 CYS cc_start: 0.5111 (OUTLIER) cc_final: 0.4681 (p) REVERT: Q 57 LYS cc_start: 0.8338 (ptmt) cc_final: 0.8041 (mtpt) REVERT: R 324 MET cc_start: -0.0958 (mmm) cc_final: -0.3264 (ptm) REVERT: R 342 LYS cc_start: 0.1171 (OUTLIER) cc_final: 0.0509 (mmtt) REVERT: S 295 PHE cc_start: 0.0811 (OUTLIER) cc_final: 0.0109 (m-80) REVERT: S 318 LYS cc_start: 0.1364 (OUTLIER) cc_final: 0.0512 (ptmm) outliers start: 141 outliers final: 98 residues processed: 587 average time/residue: 0.5284 time to fit residues: 494.6612 Evaluate side-chains 583 residues out of total 3965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 469 time to evaluate : 4.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 265 ASP Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 444 GLU Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain G residue 223 HIS Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 292 ARG Chi-restraints excluded: chain G residue 294 MET Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 342 PHE Chi-restraints excluded: chain G residue 389 GLU Chi-restraints excluded: chain G residue 435 TYR Chi-restraints excluded: chain G residue 469 MET Chi-restraints excluded: chain H residue 220 ASP Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 342 PHE Chi-restraints excluded: chain H residue 462 ILE Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 48 ASP Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 120 ASN Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 249 LYS Chi-restraints excluded: chain I residue 299 ASP Chi-restraints excluded: chain I residue 325 SER Chi-restraints excluded: chain I residue 342 PHE Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 120 ASN Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain J residue 376 SER Chi-restraints excluded: chain J residue 379 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 120 ASN Chi-restraints excluded: chain K residue 146 GLN Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 169 CYS Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 339 THR Chi-restraints excluded: chain K residue 342 PHE Chi-restraints excluded: chain K residue 379 ILE Chi-restraints excluded: chain K residue 424 CYS Chi-restraints excluded: chain K residue 429 ASN Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 38 ILE Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain N residue 12 ASN Chi-restraints excluded: chain N residue 62 CYS Chi-restraints excluded: chain N residue 70 PHE Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 62 CYS Chi-restraints excluded: chain O residue 65 CYS Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain Q residue 12 ASN Chi-restraints excluded: chain Q residue 70 PHE Chi-restraints excluded: chain R residue 342 LYS Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain S residue 295 PHE Chi-restraints excluded: chain S residue 305 VAL Chi-restraints excluded: chain S residue 317 LYS Chi-restraints excluded: chain S residue 318 LYS Chi-restraints excluded: chain S residue 324 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 chunk 276 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 89 optimal weight: 0.3980 chunk 294 optimal weight: 4.9990 chunk 315 optimal weight: 0.8980 chunk 228 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 363 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN E 84 GLN E 113 GLN ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN M 12 ASN Q 29 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 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 : 0.003 0.042 38804 Z= 0.183 Angle : 0.573 11.167 52539 Z= 0.293 Chirality : 0.043 0.274 5642 Planarity : 0.004 0.065 6889 Dihedral : 4.993 59.969 5281 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.77 % Favored : 93.15 % Rotamer: Outliers : 3.29 % Allowed : 18.80 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.35 % 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: -0.08 (0.12), residues: 4848 helix: 1.70 (0.13), residues: 1767 sheet: 0.17 (0.21), residues: 539 loop : -1.45 (0.12), residues: 2542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 408 HIS 0.009 0.001 HIS C 40 PHE 0.017 0.001 PHE H 466 TYR 0.016 0.001 TYR B 26 ARG 0.004 0.000 ARG M 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 3965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 486 time to evaluate : 4.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.5319 (tpp) cc_final: 0.4925 (tpt) REVERT: A 92 ASN cc_start: 0.7682 (t0) cc_final: 0.7273 (t0) REVERT: A 120 ASN cc_start: 0.8678 (p0) cc_final: 0.8376 (p0) REVERT: A 174 LYS cc_start: 0.5478 (mppt) cc_final: 0.4843 (mttm) REVERT: A 444 GLU cc_start: 0.7512 (pp20) cc_final: 0.6763 (mp0) REVERT: A 456 LEU cc_start: 0.8426 (mt) cc_final: 0.8194 (mt) REVERT: B 74 MET cc_start: 0.5495 (tpp) cc_final: 0.5087 (mmm) REVERT: C 22 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6777 (tp30) REVERT: C 58 LYS cc_start: 0.7839 (mttt) cc_final: 0.6820 (tptt) REVERT: C 66 ASN cc_start: 0.8158 (m-40) cc_final: 0.7697 (t0) REVERT: C 74 PHE cc_start: 0.1998 (OUTLIER) cc_final: 0.0953 (m-10) REVERT: D 35 MET cc_start: 0.7442 (mtm) cc_final: 0.6939 (mmm) REVERT: D 139 LYS cc_start: 0.6961 (mmtm) cc_final: 0.6592 (mmtp) REVERT: D 172 GLU cc_start: 0.6643 (tm-30) cc_final: 0.6409 (tm-30) REVERT: D 178 ASP cc_start: 0.6719 (t70) cc_final: 0.6488 (t0) REVERT: E 35 MET cc_start: 0.5433 (tmm) cc_final: 0.5185 (tmm) REVERT: E 105 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.5596 (mp0) REVERT: E 136 ARG cc_start: 0.5804 (ttm110) cc_final: 0.4980 (mmt180) REVERT: F 222 ILE cc_start: 0.8894 (mt) cc_final: 0.8573 (mt) REVERT: F 384 MET cc_start: 0.7230 (tpp) cc_final: 0.6993 (mmp) REVERT: F 451 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: F 469 MET cc_start: 0.2879 (mmt) cc_final: 0.1500 (mtp) REVERT: G 25 ASP cc_start: 0.6603 (t0) cc_final: 0.6352 (p0) REVERT: G 73 ASP cc_start: 0.3531 (OUTLIER) cc_final: 0.3025 (p0) REVERT: G 109 SER cc_start: 0.8732 (t) cc_final: 0.8452 (p) REVERT: G 292 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8109 (ptt180) REVERT: G 298 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7524 (mt) REVERT: G 437 GLU cc_start: 0.6943 (mt-10) cc_final: 0.6182 (mp0) REVERT: G 444 GLU cc_start: 0.6740 (tm-30) cc_final: 0.6471 (tm-30) REVERT: H 57 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7604 (mm-30) REVERT: H 80 LYS cc_start: 0.8053 (mtmm) cc_final: 0.7602 (mptt) REVERT: H 220 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7627 (t0) REVERT: H 283 ASP cc_start: 0.7095 (m-30) cc_final: 0.6634 (m-30) REVERT: H 301 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7391 (mt0) REVERT: I 48 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7441 (p0) REVERT: I 166 MET cc_start: 0.8334 (mtm) cc_final: 0.7777 (mpp) REVERT: I 426 GLN cc_start: 0.7400 (tp40) cc_final: 0.6888 (pt0) REVERT: I 460 LYS cc_start: 0.7873 (mtpt) cc_final: 0.7156 (mmtt) REVERT: J 49 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7602 (mt-10) REVERT: J 57 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7101 (mm-30) REVERT: J 74 MET cc_start: 0.5601 (tpp) cc_final: 0.5302 (tpp) REVERT: J 294 MET cc_start: 0.8267 (ttt) cc_final: 0.7933 (ttt) REVERT: J 357 ARG cc_start: 0.7275 (mtp85) cc_final: 0.7056 (mtm180) REVERT: J 436 ARG cc_start: 0.6809 (tpp80) cc_final: 0.6348 (mtp85) REVERT: K 120 ASN cc_start: 0.7421 (OUTLIER) cc_final: 0.7111 (p0) REVERT: K 279 LYS cc_start: 0.8329 (mttt) cc_final: 0.8019 (mmtp) REVERT: L 41 PHE cc_start: 0.5693 (m-80) cc_final: 0.5456 (m-80) REVERT: L 58 LYS cc_start: 0.7930 (mttp) cc_final: 0.7640 (mtpt) REVERT: M 57 LYS cc_start: 0.7963 (mmmm) cc_final: 0.7661 (mmmt) REVERT: O 65 CYS cc_start: 0.4959 (OUTLIER) cc_final: 0.4506 (p) REVERT: Q 57 LYS cc_start: 0.8172 (ptmt) cc_final: 0.7910 (mtpt) REVERT: R 324 MET cc_start: -0.0920 (mmm) cc_final: -0.3247 (ptm) REVERT: R 342 LYS cc_start: 0.1244 (OUTLIER) cc_final: 0.0592 (mmtt) REVERT: S 295 PHE cc_start: 0.0769 (OUTLIER) cc_final: 0.0063 (m-80) REVERT: S 318 LYS cc_start: 0.1420 (OUTLIER) cc_final: 0.0538 (ptmm) outliers start: 130 outliers final: 100 residues processed: 580 average time/residue: 0.5242 time to fit residues: 485.3156 Evaluate side-chains 585 residues out of total 3965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 470 time to evaluate : 4.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 466 PHE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 265 ASP Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 444 GLU Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain G residue 223 HIS Chi-restraints excluded: chain G residue 248 MET Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 292 ARG Chi-restraints excluded: chain G residue 294 MET Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 342 PHE Chi-restraints excluded: chain G residue 469 MET Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain H residue 220 ASP Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 342 PHE Chi-restraints excluded: chain H residue 462 ILE Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 48 ASP Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 120 ASN Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 189 CYS Chi-restraints excluded: chain I residue 249 LYS Chi-restraints excluded: chain I residue 299 ASP Chi-restraints excluded: chain I residue 324 HIS Chi-restraints excluded: chain I residue 325 SER Chi-restraints excluded: chain I residue 342 PHE Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 120 ASN Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain J residue 376 SER Chi-restraints excluded: chain J residue 379 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 120 ASN Chi-restraints excluded: chain K residue 146 GLN Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 169 CYS Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 339 THR Chi-restraints excluded: chain K residue 342 PHE Chi-restraints excluded: chain K residue 379 ILE Chi-restraints excluded: chain K residue 424 CYS Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain N residue 62 CYS Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 62 CYS Chi-restraints excluded: chain O residue 65 CYS Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain Q residue 12 ASN Chi-restraints excluded: chain Q residue 70 PHE Chi-restraints excluded: chain R residue 342 LYS Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain S residue 290 VAL Chi-restraints excluded: chain S residue 295 PHE Chi-restraints excluded: chain S residue 318 LYS Chi-restraints excluded: chain S residue 324 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 1.9990 chunk 443 optimal weight: 7.9990 chunk 404 optimal weight: 0.9990 chunk 431 optimal weight: 8.9990 chunk 259 optimal weight: 0.8980 chunk 187 optimal weight: 0.0040 chunk 338 optimal weight: 0.0770 chunk 132 optimal weight: 1.9990 chunk 389 optimal weight: 3.9990 chunk 407 optimal weight: 8.9990 chunk 429 optimal weight: 0.7980 overall best weight: 0.5552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN C 40 HIS E 6 GLN E 84 GLN ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 204 ASN I 209 GLN ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN M 12 ASN Q 29 GLN Q 36 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 38804 Z= 0.150 Angle : 0.547 11.075 52539 Z= 0.279 Chirality : 0.042 0.258 5642 Planarity : 0.004 0.066 6889 Dihedral : 4.677 58.409 5275 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.13 % Favored : 93.81 % Rotamer: Outliers : 2.63 % Allowed : 19.74 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.35 % 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: 0.16 (0.12), residues: 4848 helix: 2.05 (0.13), residues: 1743 sheet: 0.11 (0.21), residues: 571 loop : -1.38 (0.12), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 408 HIS 0.009 0.001 HIS C 40 PHE 0.016 0.001 PHE H 466 TYR 0.017 0.001 TYR D 41 ARG 0.003 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 505 time to evaluate : 4.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.7648 (t0) cc_final: 0.7002 (t0) REVERT: A 120 ASN cc_start: 0.8643 (p0) cc_final: 0.8331 (p0) REVERT: A 174 LYS cc_start: 0.5507 (mppt) cc_final: 0.4819 (mttm) REVERT: A 226 GLN cc_start: 0.8108 (tt0) cc_final: 0.7702 (tt0) REVERT: A 444 GLU cc_start: 0.7504 (pp20) cc_final: 0.6775 (mp0) REVERT: A 456 LEU cc_start: 0.8359 (mt) cc_final: 0.8119 (mt) REVERT: B 74 MET cc_start: 0.5449 (tpp) cc_final: 0.5067 (mmm) REVERT: B 228 GLU cc_start: 0.6291 (mt-10) cc_final: 0.5996 (mm-30) REVERT: C 58 LYS cc_start: 0.7619 (mttt) cc_final: 0.6699 (tptt) REVERT: C 66 ASN cc_start: 0.8121 (m-40) cc_final: 0.7695 (t0) REVERT: C 74 PHE cc_start: 0.1815 (OUTLIER) cc_final: 0.0666 (m-10) REVERT: D 35 MET cc_start: 0.7420 (mtm) cc_final: 0.6963 (mmm) REVERT: D 139 LYS cc_start: 0.6681 (mmtm) cc_final: 0.6324 (mmtp) REVERT: D 178 ASP cc_start: 0.6702 (t70) cc_final: 0.6478 (t0) REVERT: E 35 MET cc_start: 0.5328 (tmm) cc_final: 0.4946 (tmm) REVERT: E 105 GLU cc_start: 0.6501 (OUTLIER) cc_final: 0.5608 (mp0) REVERT: E 136 ARG cc_start: 0.5751 (ttm110) cc_final: 0.4975 (mmt180) REVERT: F 77 TYR cc_start: 0.8007 (m-80) cc_final: 0.6643 (m-80) REVERT: F 222 ILE cc_start: 0.8872 (mt) cc_final: 0.8536 (mt) REVERT: F 384 MET cc_start: 0.7273 (tpp) cc_final: 0.7034 (mmp) REVERT: F 426 GLN cc_start: 0.7233 (tp40) cc_final: 0.6981 (tp-100) REVERT: F 469 MET cc_start: 0.2786 (mmt) cc_final: 0.1421 (mtp) REVERT: G 25 ASP cc_start: 0.6602 (t0) cc_final: 0.6380 (p0) REVERT: G 109 SER cc_start: 0.8708 (t) cc_final: 0.8423 (p) REVERT: G 292 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8084 (ptt180) REVERT: G 437 GLU cc_start: 0.6786 (mt-10) cc_final: 0.6197 (mp0) REVERT: G 444 GLU cc_start: 0.6812 (tm-30) cc_final: 0.6535 (tm-30) REVERT: H 57 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7538 (mm-30) REVERT: H 80 LYS cc_start: 0.7934 (mtmm) cc_final: 0.7694 (mtmm) REVERT: H 220 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7418 (t0) REVERT: H 301 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7333 (mt0) REVERT: I 166 MET cc_start: 0.8254 (mtm) cc_final: 0.7729 (mpp) REVERT: I 426 GLN cc_start: 0.7369 (tp40) cc_final: 0.6859 (pt0) REVERT: I 460 LYS cc_start: 0.7872 (mtpt) cc_final: 0.7181 (mmtt) REVERT: J 49 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7483 (mt-10) REVERT: J 57 GLU cc_start: 0.7287 (mm-30) cc_final: 0.7048 (mm-30) REVERT: J 74 MET cc_start: 0.5539 (tpp) cc_final: 0.4902 (tpp) REVERT: J 76 ARG cc_start: 0.7558 (mtt90) cc_final: 0.7345 (mpp-170) REVERT: J 294 MET cc_start: 0.8245 (ttt) cc_final: 0.7912 (ttt) REVERT: J 357 ARG cc_start: 0.7198 (mtp85) cc_final: 0.6920 (mtm180) REVERT: J 436 ARG cc_start: 0.6810 (tpp80) cc_final: 0.6356 (mtp85) REVERT: K 206 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7132 (mt0) REVERT: K 279 LYS cc_start: 0.8287 (mttt) cc_final: 0.7975 (mmtp) REVERT: L 41 PHE cc_start: 0.6009 (m-80) cc_final: 0.5724 (m-80) REVERT: L 58 LYS cc_start: 0.7924 (mttp) cc_final: 0.7497 (mtmt) REVERT: M 57 LYS cc_start: 0.7908 (mmmm) cc_final: 0.7634 (mmmt) REVERT: N 57 LYS cc_start: 0.6876 (mmtm) cc_final: 0.6554 (tttm) REVERT: O 65 CYS cc_start: 0.4830 (OUTLIER) cc_final: 0.4121 (p) REVERT: Q 57 LYS cc_start: 0.8084 (ptmt) cc_final: 0.7826 (mtpt) REVERT: R 324 MET cc_start: -0.0975 (mmm) cc_final: -0.3242 (ptm) REVERT: R 342 LYS cc_start: 0.1201 (OUTLIER) cc_final: 0.0597 (mmtt) REVERT: S 295 PHE cc_start: 0.0814 (OUTLIER) cc_final: 0.0023 (m-80) REVERT: S 318 LYS cc_start: 0.0997 (OUTLIER) cc_final: 0.0495 (ptmm) REVERT: S 393 GLU cc_start: 0.0281 (OUTLIER) cc_final: -0.0467 (pp20) outliers start: 104 outliers final: 73 residues processed: 579 average time/residue: 0.5361 time to fit residues: 492.0597 Evaluate side-chains 566 residues out of total 3965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 482 time to evaluate : 4.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 265 ASP Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 292 ARG Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 342 PHE Chi-restraints excluded: chain G residue 469 MET Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain H residue 220 ASP Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 342 PHE Chi-restraints excluded: chain H residue 462 ILE Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 120 ASN Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 189 CYS Chi-restraints excluded: chain I residue 249 LYS Chi-restraints excluded: chain I residue 299 ASP Chi-restraints excluded: chain I residue 324 HIS Chi-restraints excluded: chain I residue 325 SER Chi-restraints excluded: chain I residue 342 PHE Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 120 ASN Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain J residue 379 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 146 GLN Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 169 CYS Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 206 GLN Chi-restraints excluded: chain K residue 342 PHE Chi-restraints excluded: chain K residue 379 ILE Chi-restraints excluded: chain K residue 424 CYS Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 62 CYS Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 65 CYS Chi-restraints excluded: chain Q residue 70 PHE Chi-restraints excluded: chain R residue 342 LYS Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain S residue 290 VAL Chi-restraints excluded: chain S residue 295 PHE Chi-restraints excluded: chain S residue 318 LYS Chi-restraints excluded: chain S residue 324 MET Chi-restraints excluded: chain S residue 393 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 5.9990 chunk 455 optimal weight: 8.9990 chunk 278 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 chunk 316 optimal weight: 5.9990 chunk 478 optimal weight: 0.9990 chunk 440 optimal weight: 10.0000 chunk 380 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 294 optimal weight: 4.9990 chunk 233 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN D 175 ASN E 6 GLN E 84 GLN ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 ASN ** I 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 307 HIS M 12 ASN ** M 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 ASN Q 29 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 38804 Z= 0.453 Angle : 0.736 11.558 52539 Z= 0.381 Chirality : 0.050 0.295 5642 Planarity : 0.006 0.064 6889 Dihedral : 5.395 58.732 5273 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.33 % Favored : 91.58 % Rotamer: Outliers : 2.51 % Allowed : 19.99 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.35 % 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: -0.45 (0.12), residues: 4848 helix: 1.35 (0.13), residues: 1739 sheet: 0.08 (0.21), residues: 523 loop : -1.62 (0.12), residues: 2586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 408 HIS 0.009 0.002 HIS E 87 PHE 0.031 0.003 PHE G 464 TYR 0.016 0.002 TYR A 21 ARG 0.007 0.001 ARG F 282 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 479 time to evaluate : 4.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.5423 (tpt) cc_final: 0.5115 (pmm) REVERT: A 92 ASN cc_start: 0.7805 (t0) cc_final: 0.7345 (t0) REVERT: A 120 ASN cc_start: 0.8678 (p0) cc_final: 0.8346 (p0) REVERT: A 174 LYS cc_start: 0.5591 (mppt) cc_final: 0.4990 (mttm) REVERT: A 226 GLN cc_start: 0.8467 (tt0) cc_final: 0.8165 (tt0) REVERT: A 444 GLU cc_start: 0.7566 (pp20) cc_final: 0.6817 (mp0) REVERT: C 58 LYS cc_start: 0.7770 (mttt) cc_final: 0.6782 (tptt) REVERT: C 66 ASN cc_start: 0.8272 (m-40) cc_final: 0.7693 (t0) REVERT: C 74 PHE cc_start: 0.2112 (OUTLIER) cc_final: 0.1192 (m-10) REVERT: D 35 MET cc_start: 0.7499 (mtm) cc_final: 0.7031 (mmm) REVERT: D 139 LYS cc_start: 0.7144 (mmtm) cc_final: 0.6769 (mmtp) REVERT: D 178 ASP cc_start: 0.6778 (t70) cc_final: 0.6563 (t0) REVERT: E 35 MET cc_start: 0.5355 (tmm) cc_final: 0.5042 (tmm) REVERT: E 105 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.5626 (mp0) REVERT: E 132 GLN cc_start: 0.5988 (mt0) cc_final: 0.5512 (mt0) REVERT: E 136 ARG cc_start: 0.5679 (ttm110) cc_final: 0.4863 (mmt180) REVERT: G 25 ASP cc_start: 0.6576 (t0) cc_final: 0.6251 (p0) REVERT: G 73 ASP cc_start: 0.3655 (OUTLIER) cc_final: 0.3197 (p0) REVERT: G 109 SER cc_start: 0.8795 (t) cc_final: 0.8533 (p) REVERT: G 292 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8227 (ptt180) REVERT: G 444 GLU cc_start: 0.6696 (tm-30) cc_final: 0.6408 (tm-30) REVERT: H 57 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7755 (mm-30) REVERT: H 80 LYS cc_start: 0.8311 (mtmm) cc_final: 0.7958 (mptt) REVERT: H 220 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7722 (t0) REVERT: H 283 ASP cc_start: 0.7137 (m-30) cc_final: 0.6620 (m-30) REVERT: H 301 GLN cc_start: 0.7785 (mm-40) cc_final: 0.7408 (mt0) REVERT: I 166 MET cc_start: 0.8385 (mtm) cc_final: 0.7899 (mpp) REVERT: I 426 GLN cc_start: 0.7375 (tp40) cc_final: 0.6913 (pt0) REVERT: I 460 LYS cc_start: 0.7770 (mtpt) cc_final: 0.7073 (ptmm) REVERT: J 49 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7605 (mt-10) REVERT: J 74 MET cc_start: 0.5804 (tpp) cc_final: 0.5568 (tpp) REVERT: J 294 MET cc_start: 0.8255 (ttt) cc_final: 0.7929 (ttt) REVERT: J 357 ARG cc_start: 0.7287 (mtp85) cc_final: 0.6902 (mtm180) REVERT: J 436 ARG cc_start: 0.6776 (tpp80) cc_final: 0.6212 (mtp85) REVERT: K 120 ASN cc_start: 0.7859 (OUTLIER) cc_final: 0.7557 (p0) REVERT: K 206 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.7544 (mt0) REVERT: K 279 LYS cc_start: 0.8331 (mttt) cc_final: 0.7994 (mmtp) REVERT: L 41 PHE cc_start: 0.5713 (m-80) cc_final: 0.5500 (m-80) REVERT: L 58 LYS cc_start: 0.7959 (mttp) cc_final: 0.7633 (mtpt) REVERT: M 57 LYS cc_start: 0.7933 (mmmm) cc_final: 0.7532 (mtpp) REVERT: N 57 LYS cc_start: 0.6777 (mmtm) cc_final: 0.6384 (tttm) REVERT: Q 57 LYS cc_start: 0.8361 (ptmt) cc_final: 0.8091 (mtpt) REVERT: R 324 MET cc_start: -0.0538 (mmm) cc_final: -0.3043 (ptm) REVERT: R 342 LYS cc_start: 0.1092 (OUTLIER) cc_final: 0.0532 (mmtt) REVERT: S 295 PHE cc_start: 0.0922 (OUTLIER) cc_final: 0.0261 (m-80) outliers start: 99 outliers final: 78 residues processed: 556 average time/residue: 0.5567 time to fit residues: 491.7457 Evaluate side-chains 553 residues out of total 3965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 465 time to evaluate : 4.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 466 PHE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 265 ASP Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 292 ARG Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 342 PHE Chi-restraints excluded: chain G residue 465 GLU Chi-restraints excluded: chain G residue 469 MET Chi-restraints excluded: chain H residue 220 ASP Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 342 PHE Chi-restraints excluded: chain H residue 462 ILE Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 189 CYS Chi-restraints excluded: chain I residue 249 LYS Chi-restraints excluded: chain I residue 299 ASP Chi-restraints excluded: chain I residue 324 HIS Chi-restraints excluded: chain I residue 325 SER Chi-restraints excluded: chain I residue 342 PHE Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 120 ASN Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain J residue 379 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 120 ASN Chi-restraints excluded: chain K residue 146 GLN Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 169 CYS Chi-restraints excluded: chain K residue 206 GLN Chi-restraints excluded: chain K residue 339 THR Chi-restraints excluded: chain K residue 342 PHE Chi-restraints excluded: chain K residue 424 CYS Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain N residue 12 ASN Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 62 CYS Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 64 ASP Chi-restraints excluded: chain Q residue 12 ASN Chi-restraints excluded: chain Q residue 70 PHE Chi-restraints excluded: chain R residue 342 LYS Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain S residue 295 PHE Chi-restraints excluded: chain S residue 324 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 0.7980 chunk 405 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 351 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 381 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 391 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 ASN E 6 GLN E 84 GLN ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 223 HIS M 12 ASN Q 29 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.168769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.135711 restraints weight = 45348.320| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.58 r_work: 0.3229 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 38804 Z= 0.177 Angle : 0.578 12.216 52539 Z= 0.297 Chirality : 0.043 0.269 5642 Planarity : 0.004 0.063 6889 Dihedral : 4.897 57.805 5273 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.35 % Favored : 93.58 % Rotamer: Outliers : 2.00 % Allowed : 20.65 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.35 % 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: -0.03 (0.12), residues: 4848 helix: 1.81 (0.13), residues: 1739 sheet: 0.34 (0.21), residues: 522 loop : -1.47 (0.12), residues: 2587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 408 HIS 0.005 0.001 HIS K 223 PHE 0.017 0.001 PHE H 466 TYR 0.017 0.001 TYR D 41 ARG 0.006 0.000 ARG G 302 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9874.10 seconds wall clock time: 180 minutes 35.64 seconds (10835.64 seconds total)