Starting phenix.real_space_refine on Mon Mar 25 21:34:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pew_20334/03_2024/6pew_20334.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pew_20334/03_2024/6pew_20334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pew_20334/03_2024/6pew_20334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pew_20334/03_2024/6pew_20334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pew_20334/03_2024/6pew_20334.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pew_20334/03_2024/6pew_20334.pdb" } resolution = 3.2 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= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 288 5.16 5 C 33084 2.51 5 N 8244 2.21 5 O 9732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ASP 18": "OD1" <-> "OD2" Residue "D ASP 22": "OD1" <-> "OD2" Residue "D PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 53": "OE1" <-> "OE2" Residue "D ASP 59": "OD1" <-> "OD2" Residue "D GLU 70": "OE1" <-> "OE2" Residue "D PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 79": "OD1" <-> "OD2" Residue "D TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 121": "OE1" <-> "OE2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "D PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 144": "OD1" <-> "OD2" Residue "D TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 259": "OD1" <-> "OD2" Residue "D PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "D GLU 389": "OE1" <-> "OE2" Residue "D GLU 393": "OE1" <-> "OE2" Residue "D ASP 416": "OD1" <-> "OD2" Residue "D GLU 429": "OE1" <-> "OE2" Residue "D PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 462": "OE1" <-> "OE2" Residue "D GLU 469": "OE1" <-> "OE2" Residue "D PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 481": "OE1" <-> "OE2" Residue "D ASP 494": "OD1" <-> "OD2" Residue "D PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 511": "OE1" <-> "OE2" Residue "D GLU 512": "OE1" <-> "OE2" Residue "D GLU 523": "OE1" <-> "OE2" Residue "D TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 18": "OD1" <-> "OD2" Residue "G ASP 22": "OD1" <-> "OD2" Residue "G PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 53": "OE1" <-> "OE2" Residue "G ASP 59": "OD1" <-> "OD2" Residue "G GLU 70": "OE1" <-> "OE2" Residue "G PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 79": "OD1" <-> "OD2" Residue "G TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 121": "OE1" <-> "OE2" Residue "G GLU 126": "OE1" <-> "OE2" Residue "G PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 144": "OD1" <-> "OD2" Residue "G TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 259": "OD1" <-> "OD2" Residue "G PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 361": "OE1" <-> "OE2" Residue "G GLU 389": "OE1" <-> "OE2" Residue "G GLU 393": "OE1" <-> "OE2" Residue "G ASP 416": "OD1" <-> "OD2" Residue "G GLU 429": "OE1" <-> "OE2" Residue "G PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 462": "OE1" <-> "OE2" Residue "G GLU 469": "OE1" <-> "OE2" Residue "G PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 481": "OE1" <-> "OE2" Residue "G ASP 494": "OD1" <-> "OD2" Residue "G PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 511": "OE1" <-> "OE2" Residue "G GLU 512": "OE1" <-> "OE2" Residue "G GLU 523": "OE1" <-> "OE2" Residue "G TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 18": "OD1" <-> "OD2" Residue "H ASP 22": "OD1" <-> "OD2" Residue "H PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 53": "OE1" <-> "OE2" Residue "H ASP 59": "OD1" <-> "OD2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 79": "OD1" <-> "OD2" Residue "H TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 121": "OE1" <-> "OE2" Residue "H GLU 126": "OE1" <-> "OE2" Residue "H PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 144": "OD1" <-> "OD2" Residue "H TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 259": "OD1" <-> "OD2" Residue "H PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 361": "OE1" <-> "OE2" Residue "H GLU 389": "OE1" <-> "OE2" Residue "H GLU 393": "OE1" <-> "OE2" Residue "H ASP 416": "OD1" <-> "OD2" Residue "H GLU 429": "OE1" <-> "OE2" Residue "H PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 462": "OE1" <-> "OE2" Residue "H GLU 469": "OE1" <-> "OE2" Residue "H PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 481": "OE1" <-> "OE2" Residue "H ASP 494": "OD1" <-> "OD2" Residue "H PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 511": "OE1" <-> "OE2" Residue "H GLU 512": "OE1" <-> "OE2" Residue "H GLU 523": "OE1" <-> "OE2" Residue "H TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 18": "OD1" <-> "OD2" Residue "I ASP 22": "OD1" <-> "OD2" Residue "I PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 53": "OE1" <-> "OE2" Residue "I ASP 59": "OD1" <-> "OD2" Residue "I GLU 70": "OE1" <-> "OE2" Residue "I PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 79": "OD1" <-> "OD2" Residue "I TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 121": "OE1" <-> "OE2" Residue "I GLU 126": "OE1" <-> "OE2" Residue "I PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 144": "OD1" <-> "OD2" Residue "I TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 259": "OD1" <-> "OD2" Residue "I PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 361": "OE1" <-> "OE2" Residue "I GLU 389": "OE1" <-> "OE2" Residue "I GLU 393": "OE1" <-> "OE2" Residue "I ASP 416": "OD1" <-> "OD2" Residue "I GLU 429": "OE1" <-> "OE2" Residue "I PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 462": "OE1" <-> "OE2" Residue "I GLU 469": "OE1" <-> "OE2" Residue "I PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 481": "OE1" <-> "OE2" Residue "I ASP 494": "OD1" <-> "OD2" Residue "I PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 511": "OE1" <-> "OE2" Residue "I GLU 512": "OE1" <-> "OE2" Residue "I GLU 523": "OE1" <-> "OE2" Residue "I TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 18": "OD1" <-> "OD2" Residue "J ASP 22": "OD1" <-> "OD2" Residue "J PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 53": "OE1" <-> "OE2" Residue "J ASP 59": "OD1" <-> "OD2" Residue "J GLU 70": "OE1" <-> "OE2" Residue "J PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 79": "OD1" <-> "OD2" Residue "J TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "J GLU 126": "OE1" <-> "OE2" Residue "J PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 144": "OD1" <-> "OD2" Residue "J TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 259": "OD1" <-> "OD2" Residue "J PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 361": "OE1" <-> "OE2" Residue "J GLU 389": "OE1" <-> "OE2" Residue "J GLU 393": "OE1" <-> "OE2" Residue "J ASP 416": "OD1" <-> "OD2" Residue "J GLU 429": "OE1" <-> "OE2" Residue "J PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 462": "OE1" <-> "OE2" Residue "J GLU 469": "OE1" <-> "OE2" Residue "J PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 481": "OE1" <-> "OE2" Residue "J ASP 494": "OD1" <-> "OD2" Residue "J PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 511": "OE1" <-> "OE2" Residue "J GLU 512": "OE1" <-> "OE2" Residue "J GLU 523": "OE1" <-> "OE2" Residue "J TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 18": "OD1" <-> "OD2" Residue "K ASP 22": "OD1" <-> "OD2" Residue "K PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 53": "OE1" <-> "OE2" Residue "K ASP 59": "OD1" <-> "OD2" Residue "K GLU 70": "OE1" <-> "OE2" Residue "K PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 79": "OD1" <-> "OD2" Residue "K TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 121": "OE1" <-> "OE2" Residue "K GLU 126": "OE1" <-> "OE2" Residue "K PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 144": "OD1" <-> "OD2" Residue "K TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 259": "OD1" <-> "OD2" Residue "K PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 361": "OE1" <-> "OE2" Residue "K GLU 389": "OE1" <-> "OE2" Residue "K GLU 393": "OE1" <-> "OE2" Residue "K ASP 416": "OD1" <-> "OD2" Residue "K GLU 429": "OE1" <-> "OE2" Residue "K PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 462": "OE1" <-> "OE2" Residue "K GLU 469": "OE1" <-> "OE2" Residue "K PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 481": "OE1" <-> "OE2" Residue "K ASP 494": "OD1" <-> "OD2" Residue "K PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 511": "OE1" <-> "OE2" Residue "K GLU 512": "OE1" <-> "OE2" Residue "K GLU 523": "OE1" <-> "OE2" Residue "K TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 18": "OD1" <-> "OD2" Residue "L ASP 22": "OD1" <-> "OD2" Residue "L PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 53": "OE1" <-> "OE2" Residue "L ASP 59": "OD1" <-> "OD2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 79": "OD1" <-> "OD2" Residue "L TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "L GLU 126": "OE1" <-> "OE2" Residue "L PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 144": "OD1" <-> "OD2" Residue "L TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 259": "OD1" <-> "OD2" Residue "L PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 361": "OE1" <-> "OE2" Residue "L GLU 389": "OE1" <-> "OE2" Residue "L GLU 393": "OE1" <-> "OE2" Residue "L ASP 416": "OD1" <-> "OD2" Residue "L GLU 429": "OE1" <-> "OE2" Residue "L PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 462": "OE1" <-> "OE2" Residue "L GLU 469": "OE1" <-> "OE2" Residue "L PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 481": "OE1" <-> "OE2" Residue "L ASP 494": "OD1" <-> "OD2" Residue "L PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 511": "OE1" <-> "OE2" Residue "L GLU 512": "OE1" <-> "OE2" Residue "L GLU 523": "OE1" <-> "OE2" Residue "L TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 18": "OD1" <-> "OD2" Residue "A ASP 22": "OD1" <-> "OD2" Residue "A PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 53": "OE1" <-> "OE2" Residue "A ASP 59": "OD1" <-> "OD2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 79": "OD1" <-> "OD2" Residue "A TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 144": "OD1" <-> "OD2" Residue "A TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 259": "OD1" <-> "OD2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 361": "OE1" <-> "OE2" Residue "A GLU 389": "OE1" <-> "OE2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A ASP 416": "OD1" <-> "OD2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 462": "OE1" <-> "OE2" Residue "A GLU 469": "OE1" <-> "OE2" Residue "A PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 481": "OE1" <-> "OE2" Residue "A ASP 494": "OD1" <-> "OD2" Residue "A PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 511": "OE1" <-> "OE2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "A TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 18": "OD1" <-> "OD2" Residue "B ASP 22": "OD1" <-> "OD2" Residue "B PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B ASP 59": "OD1" <-> "OD2" Residue "B GLU 70": "OE1" <-> "OE2" Residue "B PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 79": "OD1" <-> "OD2" Residue "B TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 121": "OE1" <-> "OE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 144": "OD1" <-> "OD2" Residue "B TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 259": "OD1" <-> "OD2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "B GLU 389": "OE1" <-> "OE2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B ASP 416": "OD1" <-> "OD2" Residue "B GLU 429": "OE1" <-> "OE2" Residue "B PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 462": "OE1" <-> "OE2" Residue "B GLU 469": "OE1" <-> "OE2" Residue "B PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 481": "OE1" <-> "OE2" Residue "B ASP 494": "OD1" <-> "OD2" Residue "B PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 511": "OE1" <-> "OE2" Residue "B GLU 512": "OE1" <-> "OE2" Residue "B GLU 523": "OE1" <-> "OE2" Residue "B TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 18": "OD1" <-> "OD2" Residue "C ASP 22": "OD1" <-> "OD2" Residue "C PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 53": "OE1" <-> "OE2" Residue "C ASP 59": "OD1" <-> "OD2" Residue "C GLU 70": "OE1" <-> "OE2" Residue "C PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 79": "OD1" <-> "OD2" Residue "C TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 144": "OD1" <-> "OD2" Residue "C TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 259": "OD1" <-> "OD2" Residue "C PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 361": "OE1" <-> "OE2" Residue "C GLU 389": "OE1" <-> "OE2" Residue "C GLU 393": "OE1" <-> "OE2" Residue "C ASP 416": "OD1" <-> "OD2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "C PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 462": "OE1" <-> "OE2" Residue "C GLU 469": "OE1" <-> "OE2" Residue "C PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 481": "OE1" <-> "OE2" Residue "C ASP 494": "OD1" <-> "OD2" Residue "C PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 511": "OE1" <-> "OE2" Residue "C GLU 512": "OE1" <-> "OE2" Residue "C GLU 523": "OE1" <-> "OE2" Residue "C TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 18": "OD1" <-> "OD2" Residue "E ASP 22": "OD1" <-> "OD2" Residue "E PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 53": "OE1" <-> "OE2" Residue "E ASP 59": "OD1" <-> "OD2" Residue "E GLU 70": "OE1" <-> "OE2" Residue "E PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 79": "OD1" <-> "OD2" Residue "E TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "E PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 144": "OD1" <-> "OD2" Residue "E TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 259": "OD1" <-> "OD2" Residue "E PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 361": "OE1" <-> "OE2" Residue "E GLU 389": "OE1" <-> "OE2" Residue "E GLU 393": "OE1" <-> "OE2" Residue "E ASP 416": "OD1" <-> "OD2" Residue "E GLU 429": "OE1" <-> "OE2" Residue "E PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 462": "OE1" <-> "OE2" Residue "E GLU 469": "OE1" <-> "OE2" Residue "E PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 481": "OE1" <-> "OE2" Residue "E ASP 494": "OD1" <-> "OD2" Residue "E PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 511": "OE1" <-> "OE2" Residue "E GLU 512": "OE1" <-> "OE2" Residue "E GLU 523": "OE1" <-> "OE2" Residue "E TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 18": "OD1" <-> "OD2" Residue "F ASP 22": "OD1" <-> "OD2" Residue "F PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F ASP 59": "OD1" <-> "OD2" Residue "F GLU 70": "OE1" <-> "OE2" Residue "F PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 79": "OD1" <-> "OD2" Residue "F TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 121": "OE1" <-> "OE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "F PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 144": "OD1" <-> "OD2" Residue "F TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 259": "OD1" <-> "OD2" Residue "F PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 361": "OE1" <-> "OE2" Residue "F GLU 389": "OE1" <-> "OE2" Residue "F GLU 393": "OE1" <-> "OE2" Residue "F ASP 416": "OD1" <-> "OD2" Residue "F GLU 429": "OE1" <-> "OE2" Residue "F PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 462": "OE1" <-> "OE2" Residue "F GLU 469": "OE1" <-> "OE2" Residue "F PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 481": "OE1" <-> "OE2" Residue "F ASP 494": "OD1" <-> "OD2" Residue "F PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 511": "OE1" <-> "OE2" Residue "F GLU 512": "OE1" <-> "OE2" Residue "F GLU 523": "OE1" <-> "OE2" Residue "F TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 51348 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 4279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4279 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 14, 'TRANS': 506} Chain breaks: 1 Chain: "G" Number of atoms: 4279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4279 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 14, 'TRANS': 506} Chain breaks: 1 Chain: "H" Number of atoms: 4279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4279 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 14, 'TRANS': 506} Chain breaks: 1 Chain: "I" Number of atoms: 4279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4279 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 14, 'TRANS': 506} Chain breaks: 1 Chain: "J" Number of atoms: 4279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4279 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 14, 'TRANS': 506} Chain breaks: 1 Chain: "K" Number of atoms: 4279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4279 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 14, 'TRANS': 506} Chain breaks: 1 Chain: "L" Number of atoms: 4279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4279 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 14, 'TRANS': 506} Chain breaks: 1 Chain: "A" Number of atoms: 4279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4279 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 14, 'TRANS': 506} Chain breaks: 1 Chain: "B" Number of atoms: 4279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4279 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 14, 'TRANS': 506} Chain breaks: 1 Chain: "C" Number of atoms: 4279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4279 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 14, 'TRANS': 506} Chain breaks: 1 Chain: "E" Number of atoms: 4279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4279 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 14, 'TRANS': 506} Chain breaks: 1 Chain: "F" Number of atoms: 4279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4279 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 14, 'TRANS': 506} Chain breaks: 1 Time building chain proxies: 25.86, per 1000 atoms: 0.50 Number of scatterers: 51348 At special positions: 0 Unit cell: (178.69, 178.69, 127.33, 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 288 16.00 O 9732 8.00 N 8244 7.00 C 33084 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.53 Conformation dependent library (CDL) restraints added in 9.7 seconds 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12120 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 60 sheets defined 33.6% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.44 Creating SS restraints... Processing helix chain 'D' and resid 8 through 18 removed outlier: 3.787A pdb=" N LEU D 12 " --> pdb=" O ASN D 8 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR D 13 " --> pdb=" O ASN D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'D' and resid 49 through 54 removed outlier: 4.004A pdb=" N GLU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 124 removed outlier: 3.522A pdb=" N GLU D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 127 No H-bonds generated for 'chain 'D' and resid 125 through 127' Processing helix chain 'D' and resid 201 through 205 removed outlier: 3.838A pdb=" N LYS D 204 " --> pdb=" O ASP D 201 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS D 205 " --> pdb=" O ASP D 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 201 through 205' Processing helix chain 'D' and resid 222 through 234 removed outlier: 3.554A pdb=" N LEU D 226 " --> pdb=" O ASN D 222 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 280 removed outlier: 3.695A pdb=" N ALA D 264 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 268 " --> pdb=" O ALA D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 338 removed outlier: 3.711A pdb=" N PHE D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE D 331 " --> pdb=" O GLU D 327 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE D 335 " --> pdb=" O PHE D 331 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS D 338 " --> pdb=" O GLY D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 347 removed outlier: 4.218A pdb=" N ALA D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE D 345 " --> pdb=" O ALA D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'D' and resid 402 through 420 removed outlier: 3.556A pdb=" N ILE D 411 " --> pdb=" O MET D 407 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE D 418 " --> pdb=" O GLY D 414 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER D 420 " --> pdb=" O ASP D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.772A pdb=" N LYS D 443 " --> pdb=" O SER D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 499 removed outlier: 3.765A pdb=" N ASP D 494 " --> pdb=" O VAL D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 508 Processing helix chain 'D' and resid 510 through 530 removed outlier: 3.738A pdb=" N ASP D 526 " --> pdb=" O ARG D 522 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS D 530 " --> pdb=" O ASP D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 540 removed outlier: 3.531A pdb=" N HIS D 538 " --> pdb=" O ALA D 534 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 18 removed outlier: 3.787A pdb=" N LEU G 12 " --> pdb=" O ASN G 8 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR G 13 " --> pdb=" O ASN G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'G' and resid 49 through 54 removed outlier: 4.003A pdb=" N GLU G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 124 removed outlier: 3.521A pdb=" N GLU G 121 " --> pdb=" O LYS G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 127 No H-bonds generated for 'chain 'G' and resid 125 through 127' Processing helix chain 'G' and resid 201 through 205 removed outlier: 3.838A pdb=" N LYS G 204 " --> pdb=" O ASP G 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS G 205 " --> pdb=" O ASP G 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 201 through 205' Processing helix chain 'G' and resid 222 through 234 removed outlier: 3.554A pdb=" N LEU G 226 " --> pdb=" O ASN G 222 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA G 231 " --> pdb=" O ARG G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 280 removed outlier: 3.695A pdb=" N ALA G 264 " --> pdb=" O ALA G 260 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU G 268 " --> pdb=" O ALA G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 338 removed outlier: 3.710A pdb=" N PHE G 329 " --> pdb=" O SER G 325 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE G 331 " --> pdb=" O GLU G 327 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE G 335 " --> pdb=" O PHE G 331 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS G 338 " --> pdb=" O GLY G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 347 removed outlier: 4.218A pdb=" N ALA G 344 " --> pdb=" O LYS G 340 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE G 345 " --> pdb=" O ALA G 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 355 Processing helix chain 'G' and resid 402 through 420 removed outlier: 3.556A pdb=" N ILE G 411 " --> pdb=" O MET G 407 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP G 416 " --> pdb=" O LEU G 412 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE G 418 " --> pdb=" O GLY G 414 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER G 420 " --> pdb=" O ASP G 416 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 443 removed outlier: 3.772A pdb=" N LYS G 443 " --> pdb=" O SER G 439 " (cutoff:3.500A) Processing helix chain 'G' and resid 488 through 499 removed outlier: 3.765A pdb=" N ASP G 494 " --> pdb=" O VAL G 490 " (cutoff:3.500A) Processing helix chain 'G' and resid 504 through 508 Processing helix chain 'G' and resid 510 through 530 removed outlier: 3.738A pdb=" N ASP G 526 " --> pdb=" O ARG G 522 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS G 530 " --> pdb=" O ASP G 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 534 through 540 removed outlier: 3.531A pdb=" N HIS G 538 " --> pdb=" O ALA G 534 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 18 removed outlier: 3.788A pdb=" N LEU H 12 " --> pdb=" O ASN H 8 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR H 13 " --> pdb=" O ASN H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 47 No H-bonds generated for 'chain 'H' and resid 45 through 47' Processing helix chain 'H' and resid 49 through 54 removed outlier: 4.004A pdb=" N GLU H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 124 removed outlier: 3.522A pdb=" N GLU H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 127 No H-bonds generated for 'chain 'H' and resid 125 through 127' Processing helix chain 'H' and resid 201 through 205 removed outlier: 3.839A pdb=" N LYS H 204 " --> pdb=" O ASP H 201 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS H 205 " --> pdb=" O ASP H 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 201 through 205' Processing helix chain 'H' and resid 222 through 234 removed outlier: 3.554A pdb=" N LEU H 226 " --> pdb=" O ASN H 222 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA H 231 " --> pdb=" O ARG H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 260 through 280 removed outlier: 3.694A pdb=" N ALA H 264 " --> pdb=" O ALA H 260 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU H 268 " --> pdb=" O ALA H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 325 through 338 removed outlier: 3.711A pdb=" N PHE H 329 " --> pdb=" O SER H 325 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE H 331 " --> pdb=" O GLU H 327 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE H 335 " --> pdb=" O PHE H 331 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS H 338 " --> pdb=" O GLY H 334 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 347 removed outlier: 4.218A pdb=" N ALA H 344 " --> pdb=" O LYS H 340 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE H 345 " --> pdb=" O ALA H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 351 through 355 Processing helix chain 'H' and resid 402 through 420 removed outlier: 3.556A pdb=" N ILE H 411 " --> pdb=" O MET H 407 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP H 416 " --> pdb=" O LEU H 412 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE H 418 " --> pdb=" O GLY H 414 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER H 420 " --> pdb=" O ASP H 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 438 through 443 removed outlier: 3.772A pdb=" N LYS H 443 " --> pdb=" O SER H 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 488 through 499 removed outlier: 3.765A pdb=" N ASP H 494 " --> pdb=" O VAL H 490 " (cutoff:3.500A) Processing helix chain 'H' and resid 504 through 508 Processing helix chain 'H' and resid 510 through 530 removed outlier: 3.737A pdb=" N ASP H 526 " --> pdb=" O ARG H 522 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS H 530 " --> pdb=" O ASP H 526 " (cutoff:3.500A) Processing helix chain 'H' and resid 534 through 540 removed outlier: 3.531A pdb=" N HIS H 538 " --> pdb=" O ALA H 534 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 18 removed outlier: 3.787A pdb=" N LEU I 12 " --> pdb=" O ASN I 8 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR I 13 " --> pdb=" O ASN I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 47 No H-bonds generated for 'chain 'I' and resid 45 through 47' Processing helix chain 'I' and resid 49 through 54 removed outlier: 4.005A pdb=" N GLU I 53 " --> pdb=" O LEU I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 124 removed outlier: 3.522A pdb=" N GLU I 121 " --> pdb=" O LYS I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 127 No H-bonds generated for 'chain 'I' and resid 125 through 127' Processing helix chain 'I' and resid 201 through 205 removed outlier: 3.839A pdb=" N LYS I 204 " --> pdb=" O ASP I 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS I 205 " --> pdb=" O ASP I 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 201 through 205' Processing helix chain 'I' and resid 222 through 234 removed outlier: 3.554A pdb=" N LEU I 226 " --> pdb=" O ASN I 222 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA I 231 " --> pdb=" O ARG I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 260 through 280 removed outlier: 3.695A pdb=" N ALA I 264 " --> pdb=" O ALA I 260 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU I 268 " --> pdb=" O ALA I 264 " (cutoff:3.500A) Processing helix chain 'I' and resid 325 through 338 removed outlier: 3.711A pdb=" N PHE I 329 " --> pdb=" O SER I 325 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE I 331 " --> pdb=" O GLU I 327 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE I 335 " --> pdb=" O PHE I 331 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS I 338 " --> pdb=" O GLY I 334 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 347 removed outlier: 4.218A pdb=" N ALA I 344 " --> pdb=" O LYS I 340 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE I 345 " --> pdb=" O ALA I 341 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 355 Processing helix chain 'I' and resid 402 through 420 removed outlier: 3.556A pdb=" N ILE I 411 " --> pdb=" O MET I 407 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP I 416 " --> pdb=" O LEU I 412 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE I 418 " --> pdb=" O GLY I 414 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER I 420 " --> pdb=" O ASP I 416 " (cutoff:3.500A) Processing helix chain 'I' and resid 438 through 443 removed outlier: 3.772A pdb=" N LYS I 443 " --> pdb=" O SER I 439 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 499 removed outlier: 3.765A pdb=" N ASP I 494 " --> pdb=" O VAL I 490 " (cutoff:3.500A) Processing helix chain 'I' and resid 504 through 508 Processing helix chain 'I' and resid 510 through 530 removed outlier: 3.737A pdb=" N ASP I 526 " --> pdb=" O ARG I 522 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS I 530 " --> pdb=" O ASP I 526 " (cutoff:3.500A) Processing helix chain 'I' and resid 534 through 540 removed outlier: 3.532A pdb=" N HIS I 538 " --> pdb=" O ALA I 534 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 18 removed outlier: 3.787A pdb=" N LEU J 12 " --> pdb=" O ASN J 8 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR J 13 " --> pdb=" O ASN J 9 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 47 No H-bonds generated for 'chain 'J' and resid 45 through 47' Processing helix chain 'J' and resid 49 through 54 removed outlier: 4.005A pdb=" N GLU J 53 " --> pdb=" O LEU J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 124 removed outlier: 3.522A pdb=" N GLU J 121 " --> pdb=" O LYS J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 127 No H-bonds generated for 'chain 'J' and resid 125 through 127' Processing helix chain 'J' and resid 201 through 205 removed outlier: 3.838A pdb=" N LYS J 204 " --> pdb=" O ASP J 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS J 205 " --> pdb=" O ASP J 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 201 through 205' Processing helix chain 'J' and resid 222 through 234 removed outlier: 3.554A pdb=" N LEU J 226 " --> pdb=" O ASN J 222 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA J 231 " --> pdb=" O ARG J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 260 through 280 removed outlier: 3.694A pdb=" N ALA J 264 " --> pdb=" O ALA J 260 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU J 268 " --> pdb=" O ALA J 264 " (cutoff:3.500A) Processing helix chain 'J' and resid 325 through 338 removed outlier: 3.711A pdb=" N PHE J 329 " --> pdb=" O SER J 325 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE J 331 " --> pdb=" O GLU J 327 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE J 335 " --> pdb=" O PHE J 331 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS J 338 " --> pdb=" O GLY J 334 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 347 removed outlier: 4.218A pdb=" N ALA J 344 " --> pdb=" O LYS J 340 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N PHE J 345 " --> pdb=" O ALA J 341 " (cutoff:3.500A) Processing helix chain 'J' and resid 351 through 355 Processing helix chain 'J' and resid 402 through 420 removed outlier: 3.556A pdb=" N ILE J 411 " --> pdb=" O MET J 407 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP J 416 " --> pdb=" O LEU J 412 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE J 418 " --> pdb=" O GLY J 414 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER J 420 " --> pdb=" O ASP J 416 " (cutoff:3.500A) Processing helix chain 'J' and resid 438 through 443 removed outlier: 3.773A pdb=" N LYS J 443 " --> pdb=" O SER J 439 " (cutoff:3.500A) Processing helix chain 'J' and resid 488 through 499 removed outlier: 3.766A pdb=" N ASP J 494 " --> pdb=" O VAL J 490 " (cutoff:3.500A) Processing helix chain 'J' and resid 504 through 508 Processing helix chain 'J' and resid 510 through 530 removed outlier: 3.738A pdb=" N ASP J 526 " --> pdb=" O ARG J 522 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS J 530 " --> pdb=" O ASP J 526 " (cutoff:3.500A) Processing helix chain 'J' and resid 534 through 540 removed outlier: 3.532A pdb=" N HIS J 538 " --> pdb=" O ALA J 534 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 18 removed outlier: 3.788A pdb=" N LEU K 12 " --> pdb=" O ASN K 8 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR K 13 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 47 No H-bonds generated for 'chain 'K' and resid 45 through 47' Processing helix chain 'K' and resid 49 through 54 removed outlier: 4.004A pdb=" N GLU K 53 " --> pdb=" O LEU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 124 removed outlier: 3.521A pdb=" N GLU K 121 " --> pdb=" O LYS K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 127 No H-bonds generated for 'chain 'K' and resid 125 through 127' Processing helix chain 'K' and resid 201 through 205 removed outlier: 3.839A pdb=" N LYS K 204 " --> pdb=" O ASP K 201 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS K 205 " --> pdb=" O ASP K 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 201 through 205' Processing helix chain 'K' and resid 222 through 234 removed outlier: 3.553A pdb=" N LEU K 226 " --> pdb=" O ASN K 222 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA K 231 " --> pdb=" O ARG K 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 260 through 280 removed outlier: 3.694A pdb=" N ALA K 264 " --> pdb=" O ALA K 260 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU K 268 " --> pdb=" O ALA K 264 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 338 removed outlier: 3.711A pdb=" N PHE K 329 " --> pdb=" O SER K 325 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE K 331 " --> pdb=" O GLU K 327 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE K 335 " --> pdb=" O PHE K 331 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS K 338 " --> pdb=" O GLY K 334 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 347 removed outlier: 4.218A pdb=" N ALA K 344 " --> pdb=" O LYS K 340 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE K 345 " --> pdb=" O ALA K 341 " (cutoff:3.500A) Processing helix chain 'K' and resid 351 through 355 Processing helix chain 'K' and resid 402 through 420 removed outlier: 3.555A pdb=" N ILE K 411 " --> pdb=" O MET K 407 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP K 416 " --> pdb=" O LEU K 412 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE K 418 " --> pdb=" O GLY K 414 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER K 420 " --> pdb=" O ASP K 416 " (cutoff:3.500A) Processing helix chain 'K' and resid 438 through 443 removed outlier: 3.773A pdb=" N LYS K 443 " --> pdb=" O SER K 439 " (cutoff:3.500A) Processing helix chain 'K' and resid 488 through 499 removed outlier: 3.765A pdb=" N ASP K 494 " --> pdb=" O VAL K 490 " (cutoff:3.500A) Processing helix chain 'K' and resid 504 through 508 Processing helix chain 'K' and resid 510 through 530 removed outlier: 3.737A pdb=" N ASP K 526 " --> pdb=" O ARG K 522 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS K 530 " --> pdb=" O ASP K 526 " (cutoff:3.500A) Processing helix chain 'K' and resid 534 through 540 removed outlier: 3.531A pdb=" N HIS K 538 " --> pdb=" O ALA K 534 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 18 removed outlier: 3.788A pdb=" N LEU L 12 " --> pdb=" O ASN L 8 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR L 13 " --> pdb=" O ASN L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 47 No H-bonds generated for 'chain 'L' and resid 45 through 47' Processing helix chain 'L' and resid 49 through 54 removed outlier: 4.004A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 124 removed outlier: 3.521A pdb=" N GLU L 121 " --> pdb=" O LYS L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 127 No H-bonds generated for 'chain 'L' and resid 125 through 127' Processing helix chain 'L' and resid 201 through 205 removed outlier: 3.839A pdb=" N LYS L 204 " --> pdb=" O ASP L 201 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS L 205 " --> pdb=" O ASP L 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 201 through 205' Processing helix chain 'L' and resid 222 through 234 removed outlier: 3.554A pdb=" N LEU L 226 " --> pdb=" O ASN L 222 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA L 231 " --> pdb=" O ARG L 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 260 through 280 removed outlier: 3.695A pdb=" N ALA L 264 " --> pdb=" O ALA L 260 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU L 268 " --> pdb=" O ALA L 264 " (cutoff:3.500A) Processing helix chain 'L' and resid 325 through 338 removed outlier: 3.711A pdb=" N PHE L 329 " --> pdb=" O SER L 325 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE L 331 " --> pdb=" O GLU L 327 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE L 335 " --> pdb=" O PHE L 331 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS L 338 " --> pdb=" O GLY L 334 " (cutoff:3.500A) Processing helix chain 'L' and resid 338 through 347 removed outlier: 4.218A pdb=" N ALA L 344 " --> pdb=" O LYS L 340 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE L 345 " --> pdb=" O ALA L 341 " (cutoff:3.500A) Processing helix chain 'L' and resid 351 through 355 Processing helix chain 'L' and resid 402 through 420 removed outlier: 3.557A pdb=" N ILE L 411 " --> pdb=" O MET L 407 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP L 416 " --> pdb=" O LEU L 412 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE L 418 " --> pdb=" O GLY L 414 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER L 420 " --> pdb=" O ASP L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 438 through 443 removed outlier: 3.772A pdb=" N LYS L 443 " --> pdb=" O SER L 439 " (cutoff:3.500A) Processing helix chain 'L' and resid 488 through 499 removed outlier: 3.765A pdb=" N ASP L 494 " --> pdb=" O VAL L 490 " (cutoff:3.500A) Processing helix chain 'L' and resid 504 through 508 Processing helix chain 'L' and resid 510 through 530 removed outlier: 3.737A pdb=" N ASP L 526 " --> pdb=" O ARG L 522 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS L 530 " --> pdb=" O ASP L 526 " (cutoff:3.500A) Processing helix chain 'L' and resid 534 through 540 removed outlier: 3.531A pdb=" N HIS L 538 " --> pdb=" O ALA L 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 18 removed outlier: 3.788A pdb=" N LEU A 12 " --> pdb=" O ASN A 8 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 49 through 54 removed outlier: 4.005A pdb=" N GLU A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 124 removed outlier: 3.522A pdb=" N GLU A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 127 No H-bonds generated for 'chain 'A' and resid 125 through 127' Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.838A pdb=" N LYS A 204 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS A 205 " --> pdb=" O ASP A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 201 through 205' Processing helix chain 'A' and resid 222 through 234 removed outlier: 3.553A pdb=" N LEU A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 280 removed outlier: 3.695A pdb=" N ALA A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 338 removed outlier: 3.711A pdb=" N PHE A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 removed outlier: 4.219A pdb=" N ALA A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 402 through 420 removed outlier: 3.556A pdb=" N ILE A 411 " --> pdb=" O MET A 407 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A 418 " --> pdb=" O GLY A 414 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.773A pdb=" N LYS A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 499 removed outlier: 3.765A pdb=" N ASP A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 508 Processing helix chain 'A' and resid 510 through 530 removed outlier: 3.737A pdb=" N ASP A 526 " --> pdb=" O ARG A 522 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A 530 " --> pdb=" O ASP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 540 removed outlier: 3.531A pdb=" N HIS A 538 " --> pdb=" O ALA A 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 18 removed outlier: 3.787A pdb=" N LEU B 12 " --> pdb=" O ASN B 8 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR B 13 " --> pdb=" O ASN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 49 through 54 removed outlier: 4.004A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 124 removed outlier: 3.522A pdb=" N GLU B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 127 No H-bonds generated for 'chain 'B' and resid 125 through 127' Processing helix chain 'B' and resid 201 through 205 removed outlier: 3.838A pdb=" N LYS B 204 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS B 205 " --> pdb=" O ASP B 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 201 through 205' Processing helix chain 'B' and resid 222 through 234 removed outlier: 3.554A pdb=" N LEU B 226 " --> pdb=" O ASN B 222 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B 231 " --> pdb=" O ARG B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 280 removed outlier: 3.695A pdb=" N ALA B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 338 removed outlier: 3.711A pdb=" N PHE B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 335 " --> pdb=" O PHE B 331 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS B 338 " --> pdb=" O GLY B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 347 removed outlier: 4.218A pdb=" N ALA B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE B 345 " --> pdb=" O ALA B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 402 through 420 removed outlier: 3.556A pdb=" N ILE B 411 " --> pdb=" O MET B 407 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 418 " --> pdb=" O GLY B 414 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER B 420 " --> pdb=" O ASP B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.772A pdb=" N LYS B 443 " --> pdb=" O SER B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 499 removed outlier: 3.765A pdb=" N ASP B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 508 Processing helix chain 'B' and resid 510 through 530 removed outlier: 3.738A pdb=" N ASP B 526 " --> pdb=" O ARG B 522 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS B 530 " --> pdb=" O ASP B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 540 removed outlier: 3.531A pdb=" N HIS B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 18 removed outlier: 3.788A pdb=" N LEU C 12 " --> pdb=" O ASN C 8 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR C 13 " --> pdb=" O ASN C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'C' and resid 49 through 54 removed outlier: 4.004A pdb=" N GLU C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 124 removed outlier: 3.521A pdb=" N GLU C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 127 No H-bonds generated for 'chain 'C' and resid 125 through 127' Processing helix chain 'C' and resid 201 through 205 removed outlier: 3.839A pdb=" N LYS C 204 " --> pdb=" O ASP C 201 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS C 205 " --> pdb=" O ASP C 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 201 through 205' Processing helix chain 'C' and resid 222 through 234 removed outlier: 3.554A pdb=" N LEU C 226 " --> pdb=" O ASN C 222 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA C 231 " --> pdb=" O ARG C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 280 removed outlier: 3.695A pdb=" N ALA C 264 " --> pdb=" O ALA C 260 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 268 " --> pdb=" O ALA C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 338 removed outlier: 3.710A pdb=" N PHE C 329 " --> pdb=" O SER C 325 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE C 331 " --> pdb=" O GLU C 327 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE C 335 " --> pdb=" O PHE C 331 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS C 338 " --> pdb=" O GLY C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 347 removed outlier: 4.218A pdb=" N ALA C 344 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE C 345 " --> pdb=" O ALA C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 355 Processing helix chain 'C' and resid 402 through 420 removed outlier: 3.557A pdb=" N ILE C 411 " --> pdb=" O MET C 407 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP C 416 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE C 418 " --> pdb=" O GLY C 414 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER C 420 " --> pdb=" O ASP C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.772A pdb=" N LYS C 443 " --> pdb=" O SER C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 499 removed outlier: 3.766A pdb=" N ASP C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 508 Processing helix chain 'C' and resid 510 through 530 removed outlier: 3.737A pdb=" N ASP C 526 " --> pdb=" O ARG C 522 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS C 530 " --> pdb=" O ASP C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 540 removed outlier: 3.531A pdb=" N HIS C 538 " --> pdb=" O ALA C 534 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 18 removed outlier: 3.787A pdb=" N LEU E 12 " --> pdb=" O ASN E 8 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR E 13 " --> pdb=" O ASN E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 47 No H-bonds generated for 'chain 'E' and resid 45 through 47' Processing helix chain 'E' and resid 49 through 54 removed outlier: 4.004A pdb=" N GLU E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 124 removed outlier: 3.522A pdb=" N GLU E 121 " --> pdb=" O LYS E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 127 No H-bonds generated for 'chain 'E' and resid 125 through 127' Processing helix chain 'E' and resid 201 through 205 removed outlier: 3.838A pdb=" N LYS E 204 " --> pdb=" O ASP E 201 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS E 205 " --> pdb=" O ASP E 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 201 through 205' Processing helix chain 'E' and resid 222 through 234 removed outlier: 3.554A pdb=" N LEU E 226 " --> pdb=" O ASN E 222 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 280 removed outlier: 3.694A pdb=" N ALA E 264 " --> pdb=" O ALA E 260 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU E 268 " --> pdb=" O ALA E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 338 removed outlier: 3.710A pdb=" N PHE E 329 " --> pdb=" O SER E 325 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE E 331 " --> pdb=" O GLU E 327 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE E 335 " --> pdb=" O PHE E 331 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS E 338 " --> pdb=" O GLY E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 347 removed outlier: 4.218A pdb=" N ALA E 344 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N PHE E 345 " --> pdb=" O ALA E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 355 Processing helix chain 'E' and resid 402 through 420 removed outlier: 3.556A pdb=" N ILE E 411 " --> pdb=" O MET E 407 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP E 416 " --> pdb=" O LEU E 412 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE E 418 " --> pdb=" O GLY E 414 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER E 420 " --> pdb=" O ASP E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.773A pdb=" N LYS E 443 " --> pdb=" O SER E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 499 removed outlier: 3.766A pdb=" N ASP E 494 " --> pdb=" O VAL E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 504 through 508 Processing helix chain 'E' and resid 510 through 530 removed outlier: 3.738A pdb=" N ASP E 526 " --> pdb=" O ARG E 522 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS E 530 " --> pdb=" O ASP E 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 534 through 540 removed outlier: 3.531A pdb=" N HIS E 538 " --> pdb=" O ALA E 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 18 removed outlier: 3.787A pdb=" N LEU F 12 " --> pdb=" O ASN F 8 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 47 No H-bonds generated for 'chain 'F' and resid 45 through 47' Processing helix chain 'F' and resid 49 through 54 removed outlier: 4.004A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 124 removed outlier: 3.521A pdb=" N GLU F 121 " --> pdb=" O LYS F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 127 No H-bonds generated for 'chain 'F' and resid 125 through 127' Processing helix chain 'F' and resid 201 through 205 removed outlier: 3.839A pdb=" N LYS F 204 " --> pdb=" O ASP F 201 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS F 205 " --> pdb=" O ASP F 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 201 through 205' Processing helix chain 'F' and resid 222 through 234 removed outlier: 3.554A pdb=" N LEU F 226 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 280 removed outlier: 3.694A pdb=" N ALA F 264 " --> pdb=" O ALA F 260 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU F 268 " --> pdb=" O ALA F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 338 removed outlier: 3.711A pdb=" N PHE F 329 " --> pdb=" O SER F 325 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE F 331 " --> pdb=" O GLU F 327 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE F 335 " --> pdb=" O PHE F 331 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS F 338 " --> pdb=" O GLY F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 347 removed outlier: 4.218A pdb=" N ALA F 344 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE F 345 " --> pdb=" O ALA F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 355 Processing helix chain 'F' and resid 402 through 420 removed outlier: 3.556A pdb=" N ILE F 411 " --> pdb=" O MET F 407 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP F 416 " --> pdb=" O LEU F 412 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE F 418 " --> pdb=" O GLY F 414 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER F 420 " --> pdb=" O ASP F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 443 removed outlier: 3.772A pdb=" N LYS F 443 " --> pdb=" O SER F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 499 removed outlier: 3.766A pdb=" N ASP F 494 " --> pdb=" O VAL F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 504 through 508 Processing helix chain 'F' and resid 510 through 530 removed outlier: 3.738A pdb=" N ASP F 526 " --> pdb=" O ARG F 522 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS F 530 " --> pdb=" O ASP F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 540 removed outlier: 3.531A pdb=" N HIS F 538 " --> pdb=" O ALA F 534 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 4 removed outlier: 3.629A pdb=" N VAL D 4 " --> pdb=" O CYS D 83 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N CYS D 83 " --> pdb=" O VAL D 4 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET D 97 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N SER D 81 " --> pdb=" O ASN D 95 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N ASN D 95 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 9.299A pdb=" N CYS D 83 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 10.886A pdb=" N ILE D 93 " --> pdb=" O CYS D 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 4 removed outlier: 3.629A pdb=" N VAL D 4 " --> pdb=" O CYS D 83 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N CYS D 83 " --> pdb=" O VAL D 4 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET D 97 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N SER D 81 " --> pdb=" O ASN D 95 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N ASN D 95 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 9.299A pdb=" N CYS D 83 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 10.886A pdb=" N ILE D 93 " --> pdb=" O CYS D 83 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL D 23 " --> pdb=" O ASN D 92 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU D 94 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE D 25 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE D 96 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA D 27 " --> pdb=" O ILE D 96 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N CYS D 98 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ILE D 29 " --> pdb=" O CYS D 98 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N LYS D 39 " --> pdb=" O HIS K 244 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N HIS K 244 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR D 43 " --> pdb=" O GLN K 240 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN K 240 " --> pdb=" O TYR D 43 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N SER K 254 " --> pdb=" O GLN K 240 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N TYR K 242 " --> pdb=" O GLU K 252 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLU K 252 " --> pdb=" O TYR K 242 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N HIS K 244 " --> pdb=" O GLN K 250 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLN K 250 " --> pdb=" O HIS K 244 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE K 140 " --> pdb=" O HIS K 251 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 258 through 259 Processing sheet with id=AA4, first strand: chain 'D' and resid 258 through 259 Processing sheet with id=AA5, first strand: chain 'D' and resid 284 through 286 removed outlier: 3.509A pdb=" N PHE D 140 " --> pdb=" O HIS D 251 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLN D 250 " --> pdb=" O HIS D 244 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N HIS D 244 " --> pdb=" O GLN D 250 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLU D 252 " --> pdb=" O TYR D 242 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N TYR D 242 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER D 254 " --> pdb=" O GLN D 240 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN D 240 " --> pdb=" O TYR G 43 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR G 43 " --> pdb=" O GLN D 240 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N HIS D 244 " --> pdb=" O LYS G 39 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N LYS G 39 " --> pdb=" O HIS D 244 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N VAL G 23 " --> pdb=" O ASN G 92 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU G 94 " --> pdb=" O VAL G 23 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE G 25 " --> pdb=" O LEU G 94 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE G 96 " --> pdb=" O ILE G 25 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA G 27 " --> pdb=" O ILE G 96 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N CYS G 98 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ILE G 29 " --> pdb=" O CYS G 98 " (cutoff:3.500A) removed outlier: 10.885A pdb=" N ILE G 93 " --> pdb=" O CYS G 83 " (cutoff:3.500A) removed outlier: 9.299A pdb=" N CYS G 83 " --> pdb=" O ILE G 93 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N ASN G 95 " --> pdb=" O SER G 81 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N SER G 81 " --> pdb=" O ASN G 95 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET G 97 " --> pdb=" O ASP G 79 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N CYS G 83 " --> pdb=" O VAL G 4 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL G 4 " --> pdb=" O CYS G 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 284 through 286 removed outlier: 3.509A pdb=" N PHE D 140 " --> pdb=" O HIS D 251 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLN D 250 " --> pdb=" O HIS D 244 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N HIS D 244 " --> pdb=" O GLN D 250 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLU D 252 " --> pdb=" O TYR D 242 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N TYR D 242 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER D 254 " --> pdb=" O GLN D 240 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN D 240 " --> pdb=" O TYR G 43 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR G 43 " --> pdb=" O GLN D 240 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N HIS D 244 " --> pdb=" O LYS G 39 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N LYS G 39 " --> pdb=" O HIS D 244 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N VAL G 23 " --> pdb=" O ASN G 92 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU G 94 " --> pdb=" O VAL G 23 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE G 25 " --> pdb=" O LEU G 94 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE G 96 " --> pdb=" O ILE G 25 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA G 27 " --> pdb=" O ILE G 96 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N CYS G 98 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ILE G 29 " --> pdb=" O CYS G 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 145 through 149 removed outlier: 3.530A pdb=" N LYS D 145 " --> pdb=" O TYR D 160 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR D 156 " --> pdb=" O SER D 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 258 through 259 Processing sheet with id=AA9, first strand: chain 'G' and resid 258 through 259 Processing sheet with id=AB1, first strand: chain 'G' and resid 284 through 286 removed outlier: 3.509A pdb=" N PHE G 140 " --> pdb=" O HIS G 251 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLN G 250 " --> pdb=" O HIS G 244 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N HIS G 244 " --> pdb=" O GLN G 250 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLU G 252 " --> pdb=" O TYR G 242 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N TYR G 242 " --> pdb=" O GLU G 252 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER G 254 " --> pdb=" O GLN G 240 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN G 240 " --> pdb=" O TYR H 43 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR H 43 " --> pdb=" O GLN G 240 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N HIS G 244 " --> pdb=" O LYS H 39 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N LYS H 39 " --> pdb=" O HIS G 244 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL H 23 " --> pdb=" O ASN H 92 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU H 94 " --> pdb=" O VAL H 23 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE H 25 " --> pdb=" O LEU H 94 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE H 96 " --> pdb=" O ILE H 25 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA H 27 " --> pdb=" O ILE H 96 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N CYS H 98 " --> pdb=" O ALA H 27 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ILE H 29 " --> pdb=" O CYS H 98 " (cutoff:3.500A) removed outlier: 10.886A pdb=" N ILE H 93 " --> pdb=" O CYS H 83 " (cutoff:3.500A) removed outlier: 9.299A pdb=" N CYS H 83 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N ASN H 95 " --> pdb=" O SER H 81 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N SER H 81 " --> pdb=" O ASN H 95 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N MET H 97 " --> pdb=" O ASP H 79 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N CYS H 83 " --> pdb=" O VAL H 4 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL H 4 " --> pdb=" O CYS H 83 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 284 through 286 removed outlier: 3.509A pdb=" N PHE G 140 " --> pdb=" O HIS G 251 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLN G 250 " --> pdb=" O HIS G 244 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N HIS G 244 " --> pdb=" O GLN G 250 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLU G 252 " --> pdb=" O TYR G 242 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N TYR G 242 " --> pdb=" O GLU G 252 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER G 254 " --> pdb=" O GLN G 240 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN G 240 " --> pdb=" O TYR H 43 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR H 43 " --> pdb=" O GLN G 240 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N HIS G 244 " --> pdb=" O LYS H 39 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N LYS H 39 " --> pdb=" O HIS G 244 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL H 23 " --> pdb=" O ASN H 92 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU H 94 " --> pdb=" O VAL H 23 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE H 25 " --> pdb=" O LEU H 94 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE H 96 " --> pdb=" O ILE H 25 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA H 27 " --> pdb=" O ILE H 96 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N CYS H 98 " --> pdb=" O ALA H 27 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ILE H 29 " --> pdb=" O CYS H 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 145 through 149 removed outlier: 3.530A pdb=" N LYS G 145 " --> pdb=" O TYR G 160 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR G 156 " --> pdb=" O SER G 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 258 through 259 Processing sheet with id=AB5, first strand: chain 'H' and resid 258 through 259 Processing sheet with id=AB6, first strand: chain 'H' and resid 284 through 286 removed outlier: 3.509A pdb=" N PHE H 140 " --> pdb=" O HIS H 251 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLN H 250 " --> pdb=" O HIS H 244 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N HIS H 244 " --> pdb=" O GLN H 250 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLU H 252 " --> pdb=" O TYR H 242 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N TYR H 242 " --> pdb=" O GLU H 252 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER H 254 " --> pdb=" O GLN H 240 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN H 240 " --> pdb=" O TYR I 43 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR I 43 " --> pdb=" O GLN H 240 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N HIS H 244 " --> pdb=" O LYS I 39 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N LYS I 39 " --> pdb=" O HIS H 244 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N VAL I 23 " --> pdb=" O ASN I 92 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU I 94 " --> pdb=" O VAL I 23 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE I 25 " --> pdb=" O LEU I 94 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE I 96 " --> pdb=" O ILE I 25 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA I 27 " --> pdb=" O ILE I 96 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N CYS I 98 " --> pdb=" O ALA I 27 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ILE I 29 " --> pdb=" O CYS I 98 " (cutoff:3.500A) removed outlier: 10.885A pdb=" N ILE I 93 " --> pdb=" O CYS I 83 " (cutoff:3.500A) removed outlier: 9.299A pdb=" N CYS I 83 " --> pdb=" O ILE I 93 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N ASN I 95 " --> pdb=" O SER I 81 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N SER I 81 " --> pdb=" O ASN I 95 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET I 97 " --> pdb=" O ASP I 79 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N CYS I 83 " --> pdb=" O VAL I 4 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL I 4 " --> pdb=" O CYS I 83 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 284 through 286 removed outlier: 3.509A pdb=" N PHE H 140 " --> pdb=" O HIS H 251 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLN H 250 " --> pdb=" O HIS H 244 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N HIS H 244 " --> pdb=" O GLN H 250 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLU H 252 " --> pdb=" O TYR H 242 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N TYR H 242 " --> pdb=" O GLU H 252 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER H 254 " --> pdb=" O GLN H 240 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN H 240 " --> pdb=" O TYR I 43 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR I 43 " --> pdb=" O GLN H 240 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N HIS H 244 " --> pdb=" O LYS I 39 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N LYS I 39 " --> pdb=" O HIS H 244 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N VAL I 23 " --> pdb=" O ASN I 92 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU I 94 " --> pdb=" O VAL I 23 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE I 25 " --> pdb=" O LEU I 94 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE I 96 " --> pdb=" O ILE I 25 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA I 27 " --> pdb=" O ILE I 96 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N CYS I 98 " --> pdb=" O ALA I 27 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ILE I 29 " --> pdb=" O CYS I 98 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 145 through 149 removed outlier: 3.530A pdb=" N LYS H 145 " --> pdb=" O TYR H 160 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR H 156 " --> pdb=" O SER H 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 258 through 259 Processing sheet with id=AC1, first strand: chain 'I' and resid 258 through 259 Processing sheet with id=AC2, first strand: chain 'I' and resid 284 through 286 removed outlier: 3.509A pdb=" N PHE I 140 " --> pdb=" O HIS I 251 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLN I 250 " --> pdb=" O HIS I 244 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N HIS I 244 " --> pdb=" O GLN I 250 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLU I 252 " --> pdb=" O TYR I 242 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TYR I 242 " --> pdb=" O GLU I 252 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER I 254 " --> pdb=" O GLN I 240 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN I 240 " --> pdb=" O TYR J 43 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR J 43 " --> pdb=" O GLN I 240 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N HIS I 244 " --> pdb=" O LYS J 39 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N LYS J 39 " --> pdb=" O HIS I 244 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL J 23 " --> pdb=" O ASN J 92 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU J 94 " --> pdb=" O VAL J 23 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE J 25 " --> pdb=" O LEU J 94 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE J 96 " --> pdb=" O ILE J 25 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA J 27 " --> pdb=" O ILE J 96 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N CYS J 98 " --> pdb=" O ALA J 27 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ILE J 29 " --> pdb=" O CYS J 98 " (cutoff:3.500A) removed outlier: 10.885A pdb=" N ILE J 93 " --> pdb=" O CYS J 83 " (cutoff:3.500A) removed outlier: 9.299A pdb=" N CYS J 83 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N ASN J 95 " --> pdb=" O SER J 81 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N SER J 81 " --> pdb=" O ASN J 95 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET J 97 " --> pdb=" O ASP J 79 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N CYS J 83 " --> pdb=" O VAL J 4 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL J 4 " --> pdb=" O CYS J 83 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 284 through 286 removed outlier: 3.509A pdb=" N PHE I 140 " --> pdb=" O HIS I 251 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLN I 250 " --> pdb=" O HIS I 244 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N HIS I 244 " --> pdb=" O GLN I 250 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLU I 252 " --> pdb=" O TYR I 242 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TYR I 242 " --> pdb=" O GLU I 252 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER I 254 " --> pdb=" O GLN I 240 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN I 240 " --> pdb=" O TYR J 43 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR J 43 " --> pdb=" O GLN I 240 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N HIS I 244 " --> pdb=" O LYS J 39 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N LYS J 39 " --> pdb=" O HIS I 244 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL J 23 " --> pdb=" O ASN J 92 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU J 94 " --> pdb=" O VAL J 23 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE J 25 " --> pdb=" O LEU J 94 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE J 96 " --> pdb=" O ILE J 25 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA J 27 " --> pdb=" O ILE J 96 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N CYS J 98 " --> pdb=" O ALA J 27 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ILE J 29 " --> pdb=" O CYS J 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 145 through 149 removed outlier: 3.530A pdb=" N LYS I 145 " --> pdb=" O TYR I 160 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR I 156 " --> pdb=" O SER I 149 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 258 through 259 Processing sheet with id=AC6, first strand: chain 'J' and resid 258 through 259 Processing sheet with id=AC7, first strand: chain 'J' and resid 284 through 286 removed outlier: 3.509A pdb=" N PHE J 140 " --> pdb=" O HIS J 251 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLN J 250 " --> pdb=" O HIS J 244 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N HIS J 244 " --> pdb=" O GLN J 250 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLU J 252 " --> pdb=" O TYR J 242 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N TYR J 242 " --> pdb=" O GLU J 252 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER J 254 " --> pdb=" O GLN J 240 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN J 240 " --> pdb=" O TYR K 43 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR K 43 " --> pdb=" O GLN J 240 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N HIS J 244 " --> pdb=" O LYS K 39 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N LYS K 39 " --> pdb=" O HIS J 244 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL K 23 " --> pdb=" O ASN K 92 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU K 94 " --> pdb=" O VAL K 23 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE K 25 " --> pdb=" O LEU K 94 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE K 96 " --> pdb=" O ILE K 25 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA K 27 " --> pdb=" O ILE K 96 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N CYS K 98 " --> pdb=" O ALA K 27 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ILE K 29 " --> pdb=" O CYS K 98 " (cutoff:3.500A) removed outlier: 10.886A pdb=" N ILE K 93 " --> pdb=" O CYS K 83 " (cutoff:3.500A) removed outlier: 9.299A pdb=" N CYS K 83 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N ASN K 95 " --> pdb=" O SER K 81 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N SER K 81 " --> pdb=" O ASN K 95 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N MET K 97 " --> pdb=" O ASP K 79 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N CYS K 83 " --> pdb=" O VAL K 4 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL K 4 " --> pdb=" O CYS K 83 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 284 through 286 removed outlier: 3.509A pdb=" N PHE J 140 " --> pdb=" O HIS J 251 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLN J 250 " --> pdb=" O HIS J 244 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N HIS J 244 " --> pdb=" O GLN J 250 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLU J 252 " --> pdb=" O TYR J 242 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N TYR J 242 " --> pdb=" O GLU J 252 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER J 254 " --> pdb=" O GLN J 240 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN J 240 " --> pdb=" O TYR K 43 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR K 43 " --> pdb=" O GLN J 240 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N HIS J 244 " --> pdb=" O LYS K 39 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N LYS K 39 " --> pdb=" O HIS J 244 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL K 23 " --> pdb=" O ASN K 92 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU K 94 " --> pdb=" O VAL K 23 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE K 25 " --> pdb=" O LEU K 94 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE K 96 " --> pdb=" O ILE K 25 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA K 27 " --> pdb=" O ILE K 96 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N CYS K 98 " --> pdb=" O ALA K 27 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ILE K 29 " --> pdb=" O CYS K 98 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 145 through 149 removed outlier: 3.530A pdb=" N LYS J 145 " --> pdb=" O TYR J 160 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR J 156 " --> pdb=" O SER J 149 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 258 through 259 Processing sheet with id=AD2, first strand: chain 'K' and resid 258 through 259 Processing sheet with id=AD3, first strand: chain 'K' and resid 145 through 149 removed outlier: 3.530A pdb=" N LYS K 145 " --> pdb=" O TYR K 160 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR K 156 " --> pdb=" O SER K 149 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 3 through 4 removed outlier: 3.629A pdb=" N VAL L 4 " --> pdb=" O CYS L 83 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N CYS L 83 " --> pdb=" O VAL L 4 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET L 97 " --> pdb=" O ASP L 79 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N SER L 81 " --> pdb=" O ASN L 95 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N ASN L 95 " --> pdb=" O SER L 81 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N CYS L 83 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 10.886A pdb=" N ILE L 93 " --> pdb=" O CYS L 83 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 3 through 4 removed outlier: 3.629A pdb=" N VAL L 4 " --> pdb=" O CYS L 83 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N CYS L 83 " --> pdb=" O VAL L 4 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET L 97 " --> pdb=" O ASP L 79 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N SER L 81 " --> pdb=" O ASN L 95 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N ASN L 95 " --> pdb=" O SER L 81 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N CYS L 83 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 10.886A pdb=" N ILE L 93 " --> pdb=" O CYS L 83 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL L 23 " --> pdb=" O ASN L 92 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU L 94 " --> pdb=" O VAL L 23 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE L 25 " --> pdb=" O LEU L 94 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE L 96 " --> pdb=" O ILE L 25 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA L 27 " --> pdb=" O ILE L 96 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N CYS L 98 " --> pdb=" O ALA L 27 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ILE L 29 " --> pdb=" O CYS L 98 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N LYS L 39 " --> pdb=" O HIS F 244 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N HIS F 244 " --> pdb=" O LYS L 39 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR L 43 " --> pdb=" O GLN F 240 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN F 240 " --> pdb=" O TYR L 43 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N SER F 254 " --> pdb=" O GLN F 240 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N TYR F 242 " --> pdb=" O GLU F 252 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLU F 252 " --> pdb=" O TYR F 242 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N HIS F 244 " --> pdb=" O GLN F 250 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLN F 250 " --> pdb=" O HIS F 244 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE F 140 " --> pdb=" O HIS F 251 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 258 through 259 Processing sheet with id=AD7, first strand: chain 'L' and resid 258 through 259 Processing sheet with id=AD8, first strand: chain 'L' and resid 284 through 286 removed outlier: 3.509A pdb=" N PHE L 140 " --> pdb=" O HIS L 251 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLN L 250 " --> pdb=" O HIS L 244 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N HIS L 244 " --> pdb=" O GLN L 250 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLU L 252 " --> pdb=" O TYR L 242 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N TYR L 242 " --> pdb=" O GLU L 252 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER L 254 " --> pdb=" O GLN L 240 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN L 240 " --> pdb=" O TYR A 43 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR A 43 " --> pdb=" O GLN L 240 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N HIS L 244 " --> pdb=" O LYS A 39 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N LYS A 39 " --> pdb=" O HIS L 244 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL A 23 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU A 94 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE A 25 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE A 96 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA A 27 " --> pdb=" O ILE A 96 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N CYS A 98 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ILE A 29 " --> pdb=" O CYS A 98 " (cutoff:3.500A) removed outlier: 10.885A pdb=" N ILE A 93 " --> pdb=" O CYS A 83 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N CYS A 83 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N ASN A 95 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N SER A 81 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET A 97 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N CYS A 83 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A 4 " --> pdb=" O CYS A 83 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 284 through 286 removed outlier: 3.509A pdb=" N PHE L 140 " --> pdb=" O HIS L 251 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLN L 250 " --> pdb=" O HIS L 244 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N HIS L 244 " --> pdb=" O GLN L 250 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLU L 252 " --> pdb=" O TYR L 242 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N TYR L 242 " --> pdb=" O GLU L 252 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER L 254 " --> pdb=" O GLN L 240 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN L 240 " --> pdb=" O TYR A 43 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR A 43 " --> pdb=" O GLN L 240 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N HIS L 244 " --> pdb=" O LYS A 39 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N LYS A 39 " --> pdb=" O HIS L 244 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL A 23 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU A 94 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE A 25 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE A 96 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA A 27 " --> pdb=" O ILE A 96 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N CYS A 98 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ILE A 29 " --> pdb=" O CYS A 98 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 145 through 149 removed outlier: 3.530A pdb=" N LYS L 145 " --> pdb=" O TYR L 160 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR L 156 " --> pdb=" O SER L 149 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AE3, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AE4, first strand: chain 'A' and resid 284 through 286 removed outlier: 3.509A pdb=" N PHE A 140 " --> pdb=" O HIS A 251 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLN A 250 " --> pdb=" O HIS A 244 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N HIS A 244 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLU A 252 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TYR A 242 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER A 254 " --> pdb=" O GLN A 240 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN A 240 " --> pdb=" O TYR B 43 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR B 43 " --> pdb=" O GLN A 240 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N HIS A 244 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N LYS B 39 " --> pdb=" O HIS A 244 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N VAL B 23 " --> pdb=" O ASN B 92 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU B 94 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE B 25 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE B 96 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA B 27 " --> pdb=" O ILE B 96 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N CYS B 98 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ILE B 29 " --> pdb=" O CYS B 98 " (cutoff:3.500A) removed outlier: 10.885A pdb=" N ILE B 93 " --> pdb=" O CYS B 83 " (cutoff:3.500A) removed outlier: 9.299A pdb=" N CYS B 83 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 10.814A pdb=" N ASN B 95 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N SER B 81 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET B 97 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N CYS B 83 " --> pdb=" O VAL B 4 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B 4 " --> pdb=" O CYS B 83 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 284 through 286 removed outlier: 3.509A pdb=" N PHE A 140 " --> pdb=" O HIS A 251 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLN A 250 " --> pdb=" O HIS A 244 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N HIS A 244 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLU A 252 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TYR A 242 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER A 254 " --> pdb=" O GLN A 240 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN A 240 " --> pdb=" O TYR B 43 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR B 43 " --> pdb=" O GLN A 240 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N HIS A 244 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N LYS B 39 " --> pdb=" O HIS A 244 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N VAL B 23 " --> pdb=" O ASN B 92 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU B 94 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE B 25 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE B 96 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA B 27 " --> pdb=" O ILE B 96 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N CYS B 98 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ILE B 29 " --> pdb=" O CYS B 98 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 145 through 149 removed outlier: 3.530A pdb=" N LYS A 145 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A 156 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 258 through 259 Processing sheet with id=AE8, first strand: chain 'B' and resid 258 through 259 Processing sheet with id=AE9, first strand: chain 'B' and resid 284 through 286 removed outlier: 3.508A pdb=" N PHE B 140 " --> pdb=" O HIS B 251 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLN B 250 " --> pdb=" O HIS B 244 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N HIS B 244 " --> pdb=" O GLN B 250 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLU B 252 " --> pdb=" O TYR B 242 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N TYR B 242 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER B 254 " --> pdb=" O GLN B 240 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN B 240 " --> pdb=" O TYR C 43 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR C 43 " --> pdb=" O GLN B 240 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N HIS B 244 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N LYS C 39 " --> pdb=" O HIS B 244 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL C 23 " --> pdb=" O ASN C 92 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU C 94 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE C 25 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE C 96 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA C 27 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N CYS C 98 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ILE C 29 " --> pdb=" O CYS C 98 " (cutoff:3.500A) removed outlier: 10.886A pdb=" N ILE C 93 " --> pdb=" O CYS C 83 " (cutoff:3.500A) removed outlier: 9.299A pdb=" N CYS C 83 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N ASN C 95 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N SER C 81 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET C 97 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N CYS C 83 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL C 4 " --> pdb=" O CYS C 83 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 284 through 286 removed outlier: 3.508A pdb=" N PHE B 140 " --> pdb=" O HIS B 251 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLN B 250 " --> pdb=" O HIS B 244 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N HIS B 244 " --> pdb=" O GLN B 250 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLU B 252 " --> pdb=" O TYR B 242 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N TYR B 242 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER B 254 " --> pdb=" O GLN B 240 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN B 240 " --> pdb=" O TYR C 43 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR C 43 " --> pdb=" O GLN B 240 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N HIS B 244 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N LYS C 39 " --> pdb=" O HIS B 244 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL C 23 " --> pdb=" O ASN C 92 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU C 94 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE C 25 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE C 96 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA C 27 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N CYS C 98 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ILE C 29 " --> pdb=" O CYS C 98 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 145 through 149 removed outlier: 3.530A pdb=" N LYS B 145 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR B 156 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 258 through 259 Processing sheet with id=AF4, first strand: chain 'C' and resid 258 through 259 Processing sheet with id=AF5, first strand: chain 'C' and resid 284 through 286 removed outlier: 3.508A pdb=" N PHE C 140 " --> pdb=" O HIS C 251 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLN C 250 " --> pdb=" O HIS C 244 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N HIS C 244 " --> pdb=" O GLN C 250 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLU C 252 " --> pdb=" O TYR C 242 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N TYR C 242 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER C 254 " --> pdb=" O GLN C 240 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLN C 240 " --> pdb=" O TYR E 43 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR E 43 " --> pdb=" O GLN C 240 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N HIS C 244 " --> pdb=" O LYS E 39 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N LYS E 39 " --> pdb=" O HIS C 244 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N VAL E 23 " --> pdb=" O ASN E 92 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU E 94 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE E 25 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE E 96 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA E 27 " --> pdb=" O ILE E 96 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N CYS E 98 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ILE E 29 " --> pdb=" O CYS E 98 " (cutoff:3.500A) removed outlier: 10.886A pdb=" N ILE E 93 " --> pdb=" O CYS E 83 " (cutoff:3.500A) removed outlier: 9.299A pdb=" N CYS E 83 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N ASN E 95 " --> pdb=" O SER E 81 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N SER E 81 " --> pdb=" O ASN E 95 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET E 97 " --> pdb=" O ASP E 79 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N CYS E 83 " --> pdb=" O VAL E 4 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL E 4 " --> pdb=" O CYS E 83 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 284 through 286 removed outlier: 3.508A pdb=" N PHE C 140 " --> pdb=" O HIS C 251 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLN C 250 " --> pdb=" O HIS C 244 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N HIS C 244 " --> pdb=" O GLN C 250 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLU C 252 " --> pdb=" O TYR C 242 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N TYR C 242 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER C 254 " --> pdb=" O GLN C 240 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLN C 240 " --> pdb=" O TYR E 43 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR E 43 " --> pdb=" O GLN C 240 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N HIS C 244 " --> pdb=" O LYS E 39 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N LYS E 39 " --> pdb=" O HIS C 244 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N VAL E 23 " --> pdb=" O ASN E 92 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU E 94 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE E 25 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE E 96 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA E 27 " --> pdb=" O ILE E 96 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N CYS E 98 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ILE E 29 " --> pdb=" O CYS E 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 145 through 149 removed outlier: 3.531A pdb=" N LYS C 145 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR C 156 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 258 through 259 Processing sheet with id=AF9, first strand: chain 'E' and resid 258 through 259 Processing sheet with id=AG1, first strand: chain 'E' and resid 284 through 286 removed outlier: 3.509A pdb=" N PHE E 140 " --> pdb=" O HIS E 251 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLN E 250 " --> pdb=" O HIS E 244 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N HIS E 244 " --> pdb=" O GLN E 250 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLU E 252 " --> pdb=" O TYR E 242 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N TYR E 242 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER E 254 " --> pdb=" O GLN E 240 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLN E 240 " --> pdb=" O TYR F 43 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR F 43 " --> pdb=" O GLN E 240 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N HIS E 244 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N LYS F 39 " --> pdb=" O HIS E 244 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N VAL F 23 " --> pdb=" O ASN F 92 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU F 94 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE F 25 " --> pdb=" O LEU F 94 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE F 96 " --> pdb=" O ILE F 25 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA F 27 " --> pdb=" O ILE F 96 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N CYS F 98 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ILE F 29 " --> pdb=" O CYS F 98 " (cutoff:3.500A) removed outlier: 10.886A pdb=" N ILE F 93 " --> pdb=" O CYS F 83 " (cutoff:3.500A) removed outlier: 9.299A pdb=" N CYS F 83 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N ASN F 95 " --> pdb=" O SER F 81 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N SER F 81 " --> pdb=" O ASN F 95 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N MET F 97 " --> pdb=" O ASP F 79 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N CYS F 83 " --> pdb=" O VAL F 4 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL F 4 " --> pdb=" O CYS F 83 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 284 through 286 removed outlier: 3.509A pdb=" N PHE E 140 " --> pdb=" O HIS E 251 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLN E 250 " --> pdb=" O HIS E 244 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N HIS E 244 " --> pdb=" O GLN E 250 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLU E 252 " --> pdb=" O TYR E 242 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N TYR E 242 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER E 254 " --> pdb=" O GLN E 240 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLN E 240 " --> pdb=" O TYR F 43 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR F 43 " --> pdb=" O GLN E 240 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N HIS E 244 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N LYS F 39 " --> pdb=" O HIS E 244 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N VAL F 23 " --> pdb=" O ASN F 92 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU F 94 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE F 25 " --> pdb=" O LEU F 94 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE F 96 " --> pdb=" O ILE F 25 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA F 27 " --> pdb=" O ILE F 96 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N CYS F 98 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ILE F 29 " --> pdb=" O CYS F 98 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 145 through 149 removed outlier: 3.530A pdb=" N LYS E 145 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR E 156 " --> pdb=" O SER E 149 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 258 through 259 Processing sheet with id=AG5, first strand: chain 'F' and resid 258 through 259 Processing sheet with id=AG6, first strand: chain 'F' and resid 145 through 149 removed outlier: 3.530A pdb=" N LYS F 145 " --> pdb=" O TYR F 160 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR F 156 " --> pdb=" O SER F 149 " (cutoff:3.500A) 1798 hydrogen bonds defined for protein. 4788 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: 22.17 Time building geometry restraints manager: 20.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12479 1.33 - 1.45: 11410 1.45 - 1.57: 28299 1.57 - 1.69: 12 1.69 - 1.81: 384 Bond restraints: 52584 Sorted by residual: bond pdb=" CA ASP F 318 " pdb=" C ASP F 318 " ideal model delta sigma weight residual 1.521 1.585 -0.064 1.30e-02 5.92e+03 2.44e+01 bond pdb=" CA ASP K 318 " pdb=" C ASP K 318 " ideal model delta sigma weight residual 1.521 1.585 -0.064 1.30e-02 5.92e+03 2.42e+01 bond pdb=" CA ASP C 318 " pdb=" C ASP C 318 " ideal model delta sigma weight residual 1.521 1.585 -0.064 1.30e-02 5.92e+03 2.42e+01 bond pdb=" CA ASP H 318 " pdb=" C ASP H 318 " ideal model delta sigma weight residual 1.521 1.585 -0.064 1.30e-02 5.92e+03 2.42e+01 bond pdb=" CA ASP A 318 " pdb=" C ASP A 318 " ideal model delta sigma weight residual 1.521 1.585 -0.064 1.30e-02 5.92e+03 2.41e+01 ... (remaining 52579 not shown) Histogram of bond angle deviations from ideal: 97.67 - 105.46: 768 105.46 - 113.25: 27503 113.25 - 121.04: 28310 121.04 - 128.83: 14086 128.83 - 136.62: 289 Bond angle restraints: 70956 Sorted by residual: angle pdb=" C ASP J 318 " pdb=" N PRO J 319 " pdb=" CA PRO J 319 " ideal model delta sigma weight residual 119.84 135.30 -15.46 1.25e+00 6.40e-01 1.53e+02 angle pdb=" C ASP E 318 " pdb=" N PRO E 319 " pdb=" CA PRO E 319 " ideal model delta sigma weight residual 119.84 135.29 -15.45 1.25e+00 6.40e-01 1.53e+02 angle pdb=" C ASP H 318 " pdb=" N PRO H 319 " pdb=" CA PRO H 319 " ideal model delta sigma weight residual 119.84 135.28 -15.44 1.25e+00 6.40e-01 1.53e+02 angle pdb=" C ASP I 318 " pdb=" N PRO I 319 " pdb=" CA PRO I 319 " ideal model delta sigma weight residual 119.84 135.26 -15.42 1.25e+00 6.40e-01 1.52e+02 angle pdb=" C ASP K 318 " pdb=" N PRO K 319 " pdb=" CA PRO K 319 " ideal model delta sigma weight residual 119.84 135.26 -15.42 1.25e+00 6.40e-01 1.52e+02 ... (remaining 70951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.35: 28034 18.35 - 36.70: 2602 36.70 - 55.05: 684 55.05 - 73.40: 84 73.40 - 91.75: 48 Dihedral angle restraints: 31452 sinusoidal: 12684 harmonic: 18768 Sorted by residual: dihedral pdb=" CA LYS K 290 " pdb=" C LYS K 290 " pdb=" N PRO K 291 " pdb=" CA PRO K 291 " ideal model delta harmonic sigma weight residual 180.00 141.75 38.25 0 5.00e+00 4.00e-02 5.85e+01 dihedral pdb=" CA LYS G 290 " pdb=" C LYS G 290 " pdb=" N PRO G 291 " pdb=" CA PRO G 291 " ideal model delta harmonic sigma weight residual 180.00 141.77 38.23 0 5.00e+00 4.00e-02 5.85e+01 dihedral pdb=" CA LYS B 290 " pdb=" C LYS B 290 " pdb=" N PRO B 291 " pdb=" CA PRO B 291 " ideal model delta harmonic sigma weight residual 180.00 141.77 38.23 0 5.00e+00 4.00e-02 5.85e+01 ... (remaining 31449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 6387 0.092 - 0.184: 1037 0.184 - 0.276: 142 0.276 - 0.368: 66 0.368 - 0.460: 12 Chirality restraints: 7644 Sorted by residual: chirality pdb=" CA PHE A 473 " pdb=" N PHE A 473 " pdb=" C PHE A 473 " pdb=" CB PHE A 473 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.29e+00 chirality pdb=" CA PHE H 473 " pdb=" N PHE H 473 " pdb=" C PHE H 473 " pdb=" CB PHE H 473 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.28e+00 chirality pdb=" CA PHE C 473 " pdb=" N PHE C 473 " pdb=" C PHE C 473 " pdb=" CB PHE C 473 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.28e+00 ... (remaining 7641 not shown) Planarity restraints: 9048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS K 538 " 0.018 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C HIS K 538 " -0.066 2.00e-02 2.50e+03 pdb=" O HIS K 538 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU K 539 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS J 538 " 0.018 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C HIS J 538 " -0.065 2.00e-02 2.50e+03 pdb=" O HIS J 538 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU J 539 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 538 " -0.018 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C HIS D 538 " 0.065 2.00e-02 2.50e+03 pdb=" O HIS D 538 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU D 539 " -0.022 2.00e-02 2.50e+03 ... (remaining 9045 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 228 2.40 - 3.02: 27009 3.02 - 3.65: 72546 3.65 - 4.27: 116244 4.27 - 4.90: 197650 Nonbonded interactions: 413677 Sorted by model distance: nonbonded pdb=" O VAL H 445 " pdb=" O ASN H 475 " model vdw 1.770 3.040 nonbonded pdb=" O VAL B 445 " pdb=" O ASN B 475 " model vdw 1.770 3.040 nonbonded pdb=" O VAL I 445 " pdb=" O ASN I 475 " model vdw 1.770 3.040 nonbonded pdb=" O VAL K 445 " pdb=" O ASN K 475 " model vdw 1.770 3.040 nonbonded pdb=" O VAL C 445 " pdb=" O ASN C 475 " model vdw 1.770 3.040 ... (remaining 413672 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 9.640 Check model and map are aligned: 0.730 Set scattering table: 0.430 Process input model: 129.790 Find NCS groups from input model: 3.210 Set up NCS constraints: 0.310 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 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 : 0.009 0.064 52584 Z= 0.600 Angle : 1.233 15.460 70956 Z= 0.755 Chirality : 0.076 0.460 7644 Planarity : 0.007 0.083 9048 Dihedral : 15.686 91.751 19332 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.22 % Favored : 94.39 % Rotamer: Outliers : 3.11 % Allowed : 10.56 % Favored : 86.34 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % 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: -4.44 (0.09), residues: 6204 helix: -4.38 (0.05), residues: 1824 sheet: -2.18 (0.15), residues: 1020 loop : -2.32 (0.09), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 307 HIS 0.010 0.003 HIS C 434 PHE 0.020 0.002 PHE H 140 TYR 0.032 0.003 TYR F 242 ARG 0.003 0.000 ARG A 522 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1101 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 921 time to evaluate : 6.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.8931 (mmt) cc_final: 0.8630 (mmt) REVERT: D 97 MET cc_start: 0.8392 (mmt) cc_final: 0.8143 (mmt) REVERT: D 494 ASP cc_start: 0.7606 (m-30) cc_final: 0.7398 (m-30) REVERT: D 535 TYR cc_start: 0.9057 (t80) cc_final: 0.8810 (t80) REVERT: G 283 ARG cc_start: 0.8458 (mtt180) cc_final: 0.8233 (mtt180) REVERT: G 322 PHE cc_start: 0.8325 (m-80) cc_final: 0.8003 (m-80) REVERT: H 1 MET cc_start: 0.8966 (mmt) cc_final: 0.8513 (mmt) REVERT: H 79 ASP cc_start: 0.7513 (t70) cc_final: 0.7121 (t0) REVERT: H 494 ASP cc_start: 0.7650 (m-30) cc_final: 0.7170 (m-30) REVERT: I 1 MET cc_start: 0.8919 (mmt) cc_final: 0.8662 (mmt) REVERT: I 389 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6663 (mt-10) REVERT: I 535 TYR cc_start: 0.9056 (t80) cc_final: 0.8695 (t80) REVERT: J 1 MET cc_start: 0.8904 (mmt) cc_final: 0.8554 (mmt) REVERT: J 283 ARG cc_start: 0.8492 (mtt180) cc_final: 0.8248 (mtt180) REVERT: J 322 PHE cc_start: 0.8333 (m-80) cc_final: 0.7995 (m-80) REVERT: K 1 MET cc_start: 0.8971 (mmt) cc_final: 0.8447 (mmt) REVERT: K 30 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8811 (mm) REVERT: K 79 ASP cc_start: 0.7470 (t70) cc_final: 0.7061 (t0) REVERT: K 494 ASP cc_start: 0.7654 (m-30) cc_final: 0.7189 (m-30) REVERT: L 1 MET cc_start: 0.8973 (mmt) cc_final: 0.8448 (mmt) REVERT: L 79 ASP cc_start: 0.7691 (t70) cc_final: 0.7307 (t0) REVERT: L 494 ASP cc_start: 0.7644 (m-30) cc_final: 0.7179 (m-30) REVERT: A 1 MET cc_start: 0.8924 (mmt) cc_final: 0.8705 (mmt) REVERT: A 97 MET cc_start: 0.8420 (mmt) cc_final: 0.8200 (mmt) REVERT: A 494 ASP cc_start: 0.7622 (m-30) cc_final: 0.7395 (m-30) REVERT: A 535 TYR cc_start: 0.9059 (t80) cc_final: 0.8651 (t80) REVERT: B 1 MET cc_start: 0.8905 (mmt) cc_final: 0.8623 (mmt) REVERT: B 283 ARG cc_start: 0.8434 (mtt180) cc_final: 0.8176 (mtt180) REVERT: B 322 PHE cc_start: 0.8292 (m-80) cc_final: 0.7955 (m-80) REVERT: B 535 TYR cc_start: 0.9036 (t80) cc_final: 0.8759 (t80) REVERT: C 1 MET cc_start: 0.8971 (mmt) cc_final: 0.8472 (mmt) REVERT: C 30 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8792 (mm) REVERT: C 79 ASP cc_start: 0.7482 (t70) cc_final: 0.7061 (t0) REVERT: C 494 ASP cc_start: 0.7708 (m-30) cc_final: 0.7197 (m-30) REVERT: C 535 TYR cc_start: 0.8981 (t80) cc_final: 0.8357 (t80) REVERT: E 1 MET cc_start: 0.8959 (mmt) cc_final: 0.8630 (mmt) REVERT: E 97 MET cc_start: 0.8444 (mmt) cc_final: 0.8202 (mmt) REVERT: E 535 TYR cc_start: 0.9059 (t80) cc_final: 0.8710 (t80) REVERT: F 283 ARG cc_start: 0.8486 (mtt180) cc_final: 0.8247 (mtt180) REVERT: F 322 PHE cc_start: 0.8299 (m-80) cc_final: 0.7943 (m-80) REVERT: F 499 ASP cc_start: 0.7623 (t0) cc_final: 0.7098 (t0) outliers start: 180 outliers final: 73 residues processed: 1063 average time/residue: 0.7073 time to fit residues: 1182.1443 Evaluate side-chains 642 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 566 time to evaluate : 6.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 369 SER Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain G residue 8 ASN Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 369 SER Chi-restraints excluded: chain G residue 389 GLU Chi-restraints excluded: chain G residue 454 LEU Chi-restraints excluded: chain G residue 539 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 313 ILE Chi-restraints excluded: chain H residue 369 SER Chi-restraints excluded: chain H residue 450 ASN Chi-restraints excluded: chain H residue 539 LEU Chi-restraints excluded: chain I residue 8 ASN Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 313 ILE Chi-restraints excluded: chain I residue 369 SER Chi-restraints excluded: chain I residue 389 GLU Chi-restraints excluded: chain I residue 450 ASN Chi-restraints excluded: chain I residue 539 LEU Chi-restraints excluded: chain J residue 8 ASN Chi-restraints excluded: chain J residue 67 SER Chi-restraints excluded: chain J residue 313 ILE Chi-restraints excluded: chain J residue 369 SER Chi-restraints excluded: chain J residue 389 GLU Chi-restraints excluded: chain J residue 454 LEU Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 313 ILE Chi-restraints excluded: chain K residue 369 SER Chi-restraints excluded: chain K residue 450 ASN Chi-restraints excluded: chain K residue 539 LEU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 313 ILE Chi-restraints excluded: chain L residue 369 SER Chi-restraints excluded: chain L residue 450 ASN Chi-restraints excluded: chain L residue 539 LEU Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 369 SER Chi-restraints excluded: chain E residue 539 LEU Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 369 SER Chi-restraints excluded: chain F residue 454 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 526 optimal weight: 0.9990 chunk 472 optimal weight: 0.8980 chunk 262 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 319 optimal weight: 4.9990 chunk 252 optimal weight: 6.9990 chunk 489 optimal weight: 2.9990 chunk 189 optimal weight: 0.7980 chunk 297 optimal weight: 1.9990 chunk 364 optimal weight: 5.9990 chunk 566 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 ASN D 236 ASN ** D 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 HIS D 263 ASN D 303 ASN D 312 ASN D 351 ASN D 456 HIS G 136 ASN G 236 ASN G 243 HIS G 244 HIS G 263 ASN G 303 ASN G 312 ASN G 456 HIS H 136 ASN H 236 ASN ** H 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 244 HIS H 263 ASN H 303 ASN H 312 ASN ** H 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 456 HIS I 136 ASN I 236 ASN I 243 HIS I 244 HIS I 263 ASN I 312 ASN I 316 HIS I 351 ASN I 456 HIS I 515 GLN ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 236 ASN ** J 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 244 HIS ** J 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 303 ASN J 312 ASN ** J 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 456 HIS K 136 ASN K 236 ASN ** K 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 244 HIS K 263 ASN K 303 ASN K 312 ASN K 316 HIS K 456 HIS L 136 ASN L 236 ASN ** L 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 244 HIS L 251 HIS L 263 ASN L 303 ASN L 312 ASN L 316 HIS L 456 HIS A 136 ASN A 236 ASN ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS A 263 ASN A 303 ASN A 312 ASN A 316 HIS A 383 ASN A 456 HIS B 136 ASN B 236 ASN B 243 HIS B 244 HIS B 263 ASN B 303 ASN B 312 ASN B 456 HIS C 136 ASN C 236 ASN ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 HIS C 263 ASN C 303 ASN C 312 ASN C 351 ASN C 456 HIS E 136 ASN E 236 ASN E 243 HIS E 244 HIS E 263 ASN E 312 ASN E 316 HIS E 351 ASN E 383 ASN E 456 HIS F 136 ASN F 236 ASN ** F 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 244 HIS F 263 ASN F 303 ASN F 312 ASN F 456 HIS Total number of N/Q/H flips: 97 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 52584 Z= 0.186 Angle : 0.584 6.376 70956 Z= 0.318 Chirality : 0.045 0.169 7644 Planarity : 0.004 0.054 9048 Dihedral : 6.169 72.632 6928 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.77 % Favored : 96.03 % Rotamer: Outliers : 2.42 % Allowed : 13.89 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % 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: -3.14 (0.09), residues: 6204 helix: -2.42 (0.09), residues: 1836 sheet: -1.79 (0.14), residues: 1116 loop : -1.93 (0.10), residues: 3252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 307 HIS 0.008 0.001 HIS I 316 PHE 0.012 0.001 PHE G 75 TYR 0.025 0.002 TYR G 242 ARG 0.004 0.001 ARG E 391 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 685 time to evaluate : 5.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.8925 (mmt) cc_final: 0.8553 (mmt) REVERT: D 97 MET cc_start: 0.7941 (mmt) cc_final: 0.7549 (mmt) REVERT: D 324 LEU cc_start: 0.7678 (mt) cc_final: 0.7448 (mt) REVERT: G 1 MET cc_start: 0.8980 (mmt) cc_final: 0.8755 (tpp) REVERT: G 252 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7698 (tp30) REVERT: G 391 ARG cc_start: 0.7823 (mtm110) cc_final: 0.7432 (mtm110) REVERT: H 1 MET cc_start: 0.8851 (mmt) cc_final: 0.8362 (mmt) REVERT: H 240 GLN cc_start: 0.8763 (mt0) cc_final: 0.8516 (mt0) REVERT: H 252 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7375 (tp30) REVERT: H 494 ASP cc_start: 0.7597 (m-30) cc_final: 0.7202 (m-30) REVERT: I 1 MET cc_start: 0.8918 (mmt) cc_final: 0.8607 (mmt) REVERT: I 324 LEU cc_start: 0.7767 (mt) cc_final: 0.7476 (mt) REVERT: J 1 MET cc_start: 0.8869 (mmt) cc_final: 0.8531 (mmt) REVERT: J 22 ASP cc_start: 0.7648 (m-30) cc_final: 0.7362 (t0) REVERT: J 252 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7611 (tp30) REVERT: K 1 MET cc_start: 0.8865 (mmt) cc_final: 0.8329 (mmt) REVERT: K 240 GLN cc_start: 0.8738 (mt0) cc_final: 0.8474 (mt0) REVERT: K 252 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7382 (tp30) REVERT: K 494 ASP cc_start: 0.7626 (m-30) cc_final: 0.7215 (m-30) REVERT: L 1 MET cc_start: 0.8885 (mmt) cc_final: 0.8349 (mmt) REVERT: L 138 LEU cc_start: 0.8898 (mt) cc_final: 0.8691 (mp) REVERT: L 240 GLN cc_start: 0.8706 (mt0) cc_final: 0.8412 (mt0) REVERT: L 252 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7449 (tp30) REVERT: L 494 ASP cc_start: 0.7616 (m-30) cc_final: 0.7198 (m-30) REVERT: A 1 MET cc_start: 0.8894 (mmt) cc_final: 0.8586 (mmt) REVERT: A 97 MET cc_start: 0.8042 (mmt) cc_final: 0.7537 (mmt) REVERT: A 252 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7707 (tt0) REVERT: B 1 MET cc_start: 0.8856 (mmt) cc_final: 0.8554 (mmt) REVERT: B 106 PHE cc_start: 0.8056 (m-10) cc_final: 0.7835 (m-10) REVERT: B 252 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7527 (tp30) REVERT: C 1 MET cc_start: 0.8860 (mmt) cc_final: 0.8343 (mmt) REVERT: C 240 GLN cc_start: 0.8710 (mt0) cc_final: 0.8481 (mt0) REVERT: C 252 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7263 (tp30) REVERT: C 494 ASP cc_start: 0.7680 (m-30) cc_final: 0.7219 (m-30) REVERT: E 1 MET cc_start: 0.8978 (mmt) cc_final: 0.8610 (mmt) REVERT: E 97 MET cc_start: 0.8086 (mmt) cc_final: 0.7635 (mmt) REVERT: E 324 LEU cc_start: 0.7968 (mt) cc_final: 0.7647 (mt) REVERT: F 1 MET cc_start: 0.8998 (mmt) cc_final: 0.8752 (tpp) REVERT: F 22 ASP cc_start: 0.7536 (m-30) cc_final: 0.7281 (t0) REVERT: F 252 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7584 (tt0) outliers start: 140 outliers final: 43 residues processed: 786 average time/residue: 0.6326 time to fit residues: 823.3342 Evaluate side-chains 636 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 584 time to evaluate : 6.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 128 ILE Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 252 GLU Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 351 ASN Chi-restraints excluded: chain I residue 505 VAL Chi-restraints excluded: chain J residue 128 ILE Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain J residue 252 GLU Chi-restraints excluded: chain J residue 426 VAL Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 252 GLU Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 128 ILE Chi-restraints excluded: chain L residue 155 THR Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 252 GLU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 426 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 314 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 471 optimal weight: 3.9990 chunk 385 optimal weight: 0.0770 chunk 156 optimal weight: 8.9990 chunk 567 optimal weight: 5.9990 chunk 613 optimal weight: 10.0000 chunk 505 optimal weight: 0.7980 chunk 562 optimal weight: 0.1980 chunk 193 optimal weight: 3.9990 chunk 455 optimal weight: 5.9990 overall best weight: 1.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 243 HIS D 316 HIS D 500 HIS G 316 HIS G 347 ASN G 500 HIS ** H 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 316 HIS ** H 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 500 HIS I 316 HIS I 500 HIS J 136 ASN J 243 HIS J 263 ASN J 347 ASN ** J 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 500 HIS ** K 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 316 HIS K 500 HIS L 243 HIS L 251 HIS L 316 HIS ** L 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 500 HIS ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 HIS A 500 HIS B 347 ASN B 500 HIS ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 HIS C 500 HIS E 316 HIS ** E 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 500 HIS F 243 HIS F 316 HIS F 347 ASN F 500 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 52584 Z= 0.268 Angle : 0.577 7.439 70956 Z= 0.316 Chirality : 0.046 0.176 7644 Planarity : 0.004 0.065 9048 Dihedral : 5.182 34.836 6804 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.17 % Allowed : 16.15 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % 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: -2.22 (0.10), residues: 6204 helix: -1.05 (0.11), residues: 1848 sheet: -0.82 (0.17), residues: 864 loop : -1.92 (0.10), residues: 3492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 307 HIS 0.007 0.001 HIS D 316 PHE 0.014 0.001 PHE F 75 TYR 0.025 0.002 TYR D 242 ARG 0.005 0.000 ARG D 391 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 628 time to evaluate : 6.277 Fit side-chains revert: symmetry clash REVERT: D 1 MET cc_start: 0.9044 (mmt) cc_final: 0.8512 (mmt) REVERT: G 2 LYS cc_start: 0.8423 (ptpt) cc_final: 0.8219 (ptmt) REVERT: G 79 ASP cc_start: 0.7559 (t0) cc_final: 0.7117 (t0) REVERT: G 245 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7452 (mm-30) REVERT: G 252 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7371 (tt0) REVERT: G 253 ILE cc_start: 0.8041 (mm) cc_final: 0.7772 (mm) REVERT: G 347 ASN cc_start: 0.8684 (OUTLIER) cc_final: 0.8471 (p0) REVERT: H 252 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7719 (tp30) REVERT: H 494 ASP cc_start: 0.7587 (m-30) cc_final: 0.7156 (m-30) REVERT: I 1 MET cc_start: 0.9032 (mmt) cc_final: 0.8519 (mmt) REVERT: J 1 MET cc_start: 0.8954 (mmt) cc_final: 0.8465 (mmt) REVERT: J 22 ASP cc_start: 0.7570 (m-30) cc_final: 0.7333 (t0) REVERT: J 79 ASP cc_start: 0.7547 (t0) cc_final: 0.7081 (t0) REVERT: J 252 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7448 (tt0) REVERT: K 252 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7721 (tp30) REVERT: K 494 ASP cc_start: 0.7526 (m-30) cc_final: 0.7124 (m-30) REVERT: L 106 PHE cc_start: 0.8208 (m-10) cc_final: 0.7991 (m-10) REVERT: L 144 ASP cc_start: 0.7274 (m-30) cc_final: 0.6900 (m-30) REVERT: L 197 TYR cc_start: 0.4510 (OUTLIER) cc_final: 0.4259 (m-10) REVERT: L 240 GLN cc_start: 0.8826 (mt0) cc_final: 0.8617 (mt0) REVERT: L 252 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7751 (tp30) REVERT: L 494 ASP cc_start: 0.7544 (m-30) cc_final: 0.7134 (m-30) REVERT: A 1 MET cc_start: 0.9040 (mmt) cc_final: 0.8539 (mmt) REVERT: A 252 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7716 (tt0) REVERT: B 1 MET cc_start: 0.8974 (mmt) cc_final: 0.8526 (mmt) REVERT: B 22 ASP cc_start: 0.7539 (m-30) cc_final: 0.7296 (t0) REVERT: B 104 ASN cc_start: 0.7498 (OUTLIER) cc_final: 0.7061 (p0) REVERT: B 252 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7460 (tt0) REVERT: B 347 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8490 (p0) REVERT: C 252 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7746 (tp30) REVERT: C 494 ASP cc_start: 0.7542 (m-30) cc_final: 0.7123 (m-30) REVERT: E 1 MET cc_start: 0.9032 (mmt) cc_final: 0.8515 (mmt) REVERT: F 2 LYS cc_start: 0.8403 (ptpt) cc_final: 0.8187 (ptmt) REVERT: F 22 ASP cc_start: 0.7611 (m-30) cc_final: 0.7373 (t0) REVERT: F 245 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7288 (mm-30) REVERT: F 252 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: F 347 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8531 (p0) outliers start: 126 outliers final: 72 residues processed: 724 average time/residue: 0.6284 time to fit residues: 750.4299 Evaluate side-chains 671 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 585 time to evaluate : 5.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 419 LYS Chi-restraints excluded: chain G residue 8 ASN Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 214 THR Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 128 ILE Chi-restraints excluded: chain H residue 152 GLU Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 252 GLU Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain I residue 8 ASN Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain I residue 295 ASP Chi-restraints excluded: chain I residue 505 VAL Chi-restraints excluded: chain J residue 8 ASN Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 128 ILE Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain J residue 252 GLU Chi-restraints excluded: chain J residue 295 ASP Chi-restraints excluded: chain J residue 347 ASN Chi-restraints excluded: chain J residue 426 VAL Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 252 GLU Chi-restraints excluded: chain K residue 295 ASP Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 128 ILE Chi-restraints excluded: chain L residue 155 THR Chi-restraints excluded: chain L residue 197 TYR Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 252 GLU Chi-restraints excluded: chain L residue 295 ASP Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 347 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 560 optimal weight: 0.7980 chunk 426 optimal weight: 0.7980 chunk 294 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 270 optimal weight: 4.9990 chunk 381 optimal weight: 1.9990 chunk 569 optimal weight: 2.9990 chunk 603 optimal weight: 3.9990 chunk 297 optimal weight: 0.8980 chunk 539 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 316 HIS G 316 HIS G 347 ASN H 240 GLN ** H 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 316 HIS ** H 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 434 HIS I 316 HIS ** I 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 316 HIS J 347 ASN ** J 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 240 GLN ** K 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 316 HIS L 316 HIS ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 HIS B 347 ASN B 434 HIS C 240 GLN ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 HIS C 434 HIS E 316 HIS F 316 HIS F 347 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 52584 Z= 0.183 Angle : 0.510 6.944 70956 Z= 0.281 Chirality : 0.044 0.157 7644 Planarity : 0.004 0.053 9048 Dihedral : 4.857 32.140 6804 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.62 % Allowed : 17.37 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.10), residues: 6204 helix: -0.41 (0.11), residues: 1848 sheet: -0.69 (0.17), residues: 864 loop : -1.82 (0.10), residues: 3492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 307 HIS 0.008 0.001 HIS L 316 PHE 0.010 0.001 PHE E 75 TYR 0.014 0.001 TYR F 242 ARG 0.006 0.000 ARG A 391 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 605 time to evaluate : 6.243 Fit side-chains revert: symmetry clash REVERT: D 1 MET cc_start: 0.9024 (mmt) cc_final: 0.8590 (mmt) REVERT: D 104 ASN cc_start: 0.7493 (OUTLIER) cc_final: 0.6906 (p0) REVERT: D 106 PHE cc_start: 0.8291 (m-10) cc_final: 0.8070 (m-10) REVERT: D 235 MET cc_start: 0.8649 (mtp) cc_final: 0.8392 (mtm) REVERT: D 382 ILE cc_start: 0.7568 (mm) cc_final: 0.7330 (mt) REVERT: G 79 ASP cc_start: 0.7471 (t0) cc_final: 0.7031 (t0) REVERT: G 245 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7457 (mm-30) REVERT: G 252 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7428 (tt0) REVERT: H 1 MET cc_start: 0.8990 (mmt) cc_final: 0.8261 (mmt) REVERT: H 252 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7632 (tp30) REVERT: H 494 ASP cc_start: 0.7599 (m-30) cc_final: 0.7174 (m-30) REVERT: I 1 MET cc_start: 0.9009 (mmt) cc_final: 0.8516 (mmt) REVERT: I 429 GLU cc_start: 0.6995 (pp20) cc_final: 0.6672 (pp20) REVERT: J 1 MET cc_start: 0.8921 (mmt) cc_final: 0.8479 (mmt) REVERT: J 2 LYS cc_start: 0.8426 (ptpt) cc_final: 0.8224 (ptmt) REVERT: J 79 ASP cc_start: 0.7463 (t0) cc_final: 0.7005 (t0) REVERT: J 245 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7452 (mm-30) REVERT: J 252 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7355 (tt0) REVERT: K 1 MET cc_start: 0.8986 (mmt) cc_final: 0.8191 (mmt) REVERT: K 252 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7635 (tp30) REVERT: K 494 ASP cc_start: 0.7595 (m-30) cc_final: 0.7174 (m-30) REVERT: L 1 MET cc_start: 0.8994 (mmt) cc_final: 0.8192 (mmt) REVERT: L 144 ASP cc_start: 0.7346 (m-30) cc_final: 0.6912 (m-30) REVERT: L 197 TYR cc_start: 0.4666 (OUTLIER) cc_final: 0.4415 (m-10) REVERT: L 240 GLN cc_start: 0.8769 (mt0) cc_final: 0.8543 (mt0) REVERT: L 252 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7432 (tp30) REVERT: L 494 ASP cc_start: 0.7622 (m-30) cc_final: 0.7198 (m-30) REVERT: A 1 MET cc_start: 0.9004 (mmt) cc_final: 0.8490 (mmt) REVERT: A 104 ASN cc_start: 0.7488 (OUTLIER) cc_final: 0.6901 (p0) REVERT: A 106 PHE cc_start: 0.8294 (m-10) cc_final: 0.8081 (m-10) REVERT: A 252 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7634 (tt0) REVERT: A 253 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8329 (mm) REVERT: A 429 GLU cc_start: 0.6954 (pp20) cc_final: 0.6585 (pp20) REVERT: B 1 MET cc_start: 0.8888 (mmt) cc_final: 0.8473 (mmt) REVERT: B 22 ASP cc_start: 0.7593 (m-30) cc_final: 0.7361 (t0) REVERT: B 79 ASP cc_start: 0.7468 (t0) cc_final: 0.7252 (t0) REVERT: B 245 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7421 (mm-30) REVERT: B 252 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7366 (tt0) REVERT: B 347 ASN cc_start: 0.8618 (OUTLIER) cc_final: 0.8311 (p0) REVERT: C 1 MET cc_start: 0.8990 (mmt) cc_final: 0.8266 (mmt) REVERT: C 252 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7545 (tp30) REVERT: C 494 ASP cc_start: 0.7604 (m-30) cc_final: 0.7166 (m-30) REVERT: E 1 MET cc_start: 0.9012 (mmt) cc_final: 0.8496 (mmt) REVERT: E 429 GLU cc_start: 0.6947 (pp20) cc_final: 0.6732 (pp20) REVERT: E 535 TYR cc_start: 0.8829 (t80) cc_final: 0.8581 (t80) REVERT: F 104 ASN cc_start: 0.7607 (OUTLIER) cc_final: 0.7179 (p0) REVERT: F 245 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7438 (mm-30) REVERT: F 252 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7461 (tt0) REVERT: F 347 ASN cc_start: 0.8623 (OUTLIER) cc_final: 0.8321 (p0) outliers start: 152 outliers final: 96 residues processed: 705 average time/residue: 0.6455 time to fit residues: 745.5024 Evaluate side-chains 687 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 575 time to evaluate : 6.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 419 LYS Chi-restraints excluded: chain G residue 8 ASN Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 214 THR Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 295 ASP Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain H residue 75 PHE Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 128 ILE Chi-restraints excluded: chain H residue 152 GLU Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 252 GLU Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain H residue 398 ASP Chi-restraints excluded: chain H residue 434 HIS Chi-restraints excluded: chain I residue 8 ASN Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain I residue 295 ASP Chi-restraints excluded: chain I residue 362 THR Chi-restraints excluded: chain I residue 505 VAL Chi-restraints excluded: chain J residue 8 ASN Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 128 ILE Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain J residue 252 GLU Chi-restraints excluded: chain J residue 295 ASP Chi-restraints excluded: chain J residue 398 ASP Chi-restraints excluded: chain J residue 426 VAL Chi-restraints excluded: chain K residue 75 PHE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 104 ASN Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 252 GLU Chi-restraints excluded: chain K residue 295 ASP Chi-restraints excluded: chain K residue 398 ASP Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 104 ASN Chi-restraints excluded: chain L residue 128 ILE Chi-restraints excluded: chain L residue 197 TYR Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 252 GLU Chi-restraints excluded: chain L residue 295 ASP Chi-restraints excluded: chain L residue 398 ASP Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 104 ASN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 434 HIS Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 104 ASN Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 295 ASP Chi-restraints excluded: chain F residue 347 ASN Chi-restraints excluded: chain F residue 426 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 502 optimal weight: 6.9990 chunk 342 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 449 optimal weight: 4.9990 chunk 248 optimal weight: 0.5980 chunk 514 optimal weight: 6.9990 chunk 416 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 307 optimal weight: 2.9990 chunk 541 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 316 HIS G 347 ASN H 240 GLN ** H 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 294 ASN H 316 HIS ** H 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 316 HIS ** I 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 294 ASN K 316 HIS K 434 HIS L 294 ASN L 316 HIS A 243 HIS A 316 HIS B 316 HIS B 347 ASN C 240 GLN ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN C 316 HIS C 347 ASN E 316 HIS E 351 ASN F 294 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 52584 Z= 0.290 Angle : 0.555 6.928 70956 Z= 0.305 Chirality : 0.046 0.162 7644 Planarity : 0.004 0.058 9048 Dihedral : 5.010 34.512 6804 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.64 % Allowed : 18.18 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.10), residues: 6204 helix: -0.23 (0.11), residues: 1872 sheet: -0.54 (0.17), residues: 864 loop : -1.76 (0.10), residues: 3468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 307 HIS 0.018 0.001 HIS C 434 PHE 0.011 0.001 PHE E 75 TYR 0.014 0.002 TYR K 242 ARG 0.006 0.000 ARG G 391 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 578 time to evaluate : 6.026 Fit side-chains REVERT: D 1 MET cc_start: 0.9080 (mmt) cc_final: 0.8577 (mmt) REVERT: D 104 ASN cc_start: 0.7615 (OUTLIER) cc_final: 0.7048 (p0) REVERT: D 144 ASP cc_start: 0.7207 (m-30) cc_final: 0.6534 (m-30) REVERT: D 197 TYR cc_start: 0.5097 (OUTLIER) cc_final: 0.4585 (m-10) REVERT: D 382 ILE cc_start: 0.7833 (mm) cc_final: 0.7579 (mt) REVERT: G 79 ASP cc_start: 0.7587 (t0) cc_final: 0.7137 (t0) REVERT: G 116 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8619 (tt) REVERT: G 245 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7429 (tp30) REVERT: G 252 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7218 (tt0) REVERT: H 1 MET cc_start: 0.9111 (mmt) cc_final: 0.8895 (mmt) REVERT: H 252 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7288 (tp30) REVERT: H 494 ASP cc_start: 0.7547 (m-30) cc_final: 0.7090 (m-30) REVERT: I 1 MET cc_start: 0.9069 (mmt) cc_final: 0.8559 (mmt) REVERT: J 79 ASP cc_start: 0.7548 (t0) cc_final: 0.7082 (t0) REVERT: J 116 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8615 (tt) REVERT: J 252 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7329 (tt0) REVERT: K 1 MET cc_start: 0.9102 (mmt) cc_final: 0.8877 (mmt) REVERT: K 252 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7300 (tp30) REVERT: K 494 ASP cc_start: 0.7551 (m-30) cc_final: 0.7099 (m-30) REVERT: L 1 MET cc_start: 0.9107 (mmt) cc_final: 0.8883 (mmt) REVERT: L 104 ASN cc_start: 0.7668 (OUTLIER) cc_final: 0.7287 (p0) REVERT: L 144 ASP cc_start: 0.7494 (m-30) cc_final: 0.7012 (m-30) REVERT: L 197 TYR cc_start: 0.4969 (OUTLIER) cc_final: 0.4695 (m-10) REVERT: L 252 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7488 (tp30) REVERT: L 494 ASP cc_start: 0.7544 (m-30) cc_final: 0.7091 (m-30) REVERT: A 1 MET cc_start: 0.9056 (mmt) cc_final: 0.8490 (mmt) REVERT: A 104 ASN cc_start: 0.7525 (OUTLIER) cc_final: 0.6928 (p0) REVERT: A 252 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: A 253 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8444 (mm) REVERT: B 252 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7321 (tt0) REVERT: B 294 ASN cc_start: 0.8118 (m-40) cc_final: 0.7888 (m110) REVERT: C 1 MET cc_start: 0.9110 (mmt) cc_final: 0.8896 (mmt) REVERT: C 252 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7406 (tp30) REVERT: C 494 ASP cc_start: 0.7552 (m-30) cc_final: 0.7096 (m-30) REVERT: E 1 MET cc_start: 0.9052 (mmt) cc_final: 0.8484 (mmt) REVERT: E 429 GLU cc_start: 0.7095 (pp20) cc_final: 0.6870 (pp20) REVERT: F 104 ASN cc_start: 0.7490 (OUTLIER) cc_final: 0.7005 (p0) REVERT: F 116 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8651 (tt) REVERT: F 245 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7309 (mm-30) REVERT: F 252 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7477 (tt0) outliers start: 153 outliers final: 96 residues processed: 700 average time/residue: 0.6555 time to fit residues: 750.7083 Evaluate side-chains 670 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 555 time to evaluate : 6.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 419 LYS Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain G residue 8 ASN Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 214 THR Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 295 ASP Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 128 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 252 GLU Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain H residue 398 ASP Chi-restraints excluded: chain I residue 8 ASN Chi-restraints excluded: chain I residue 75 PHE Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain I residue 295 ASP Chi-restraints excluded: chain I residue 362 THR Chi-restraints excluded: chain I residue 505 VAL Chi-restraints excluded: chain J residue 8 ASN Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 128 ILE Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain J residue 252 GLU Chi-restraints excluded: chain J residue 295 ASP Chi-restraints excluded: chain J residue 398 ASP Chi-restraints excluded: chain J residue 426 VAL Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 104 ASN Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 252 GLU Chi-restraints excluded: chain K residue 295 ASP Chi-restraints excluded: chain K residue 398 ASP Chi-restraints excluded: chain K residue 434 HIS Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 104 ASN Chi-restraints excluded: chain L residue 128 ILE Chi-restraints excluded: chain L residue 197 TYR Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 252 GLU Chi-restraints excluded: chain L residue 295 ASP Chi-restraints excluded: chain L residue 398 ASP Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 104 ASN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 347 ASN Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 104 ASN Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 295 ASP Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain F residue 453 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 202 optimal weight: 0.0870 chunk 543 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 354 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 603 optimal weight: 0.9990 chunk 501 optimal weight: 3.9990 chunk 279 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 199 optimal weight: 7.9990 chunk 316 optimal weight: 4.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 316 HIS H 240 GLN ** H 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 316 HIS ** H 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 316 HIS I 434 HIS ** K 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 240 GLN L 316 HIS L 434 HIS A 316 HIS A 434 HIS ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 HIS C 347 ASN E 316 HIS E 434 HIS F 347 ASN ** F 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 52584 Z= 0.306 Angle : 0.561 6.926 70956 Z= 0.310 Chirality : 0.046 0.172 7644 Planarity : 0.004 0.061 9048 Dihedral : 5.059 34.417 6804 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.69 % Allowed : 19.25 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.10), residues: 6204 helix: -0.01 (0.12), residues: 1872 sheet: -0.84 (0.16), residues: 984 loop : -1.65 (0.10), residues: 3348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 307 HIS 0.016 0.001 HIS K 434 PHE 0.018 0.001 PHE L 322 TYR 0.020 0.002 TYR I 242 ARG 0.003 0.000 ARG D 162 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 563 time to evaluate : 6.215 Fit side-chains REVERT: D 1 MET cc_start: 0.9021 (mmt) cc_final: 0.8504 (mmt) REVERT: D 104 ASN cc_start: 0.7768 (OUTLIER) cc_final: 0.7444 (p0) REVERT: D 144 ASP cc_start: 0.7250 (m-30) cc_final: 0.6437 (m-30) REVERT: D 197 TYR cc_start: 0.5182 (OUTLIER) cc_final: 0.4656 (m-10) REVERT: D 382 ILE cc_start: 0.7876 (mm) cc_final: 0.7627 (mt) REVERT: G 116 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8653 (tt) REVERT: G 245 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7360 (mm-30) REVERT: G 252 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7415 (tt0) REVERT: H 1 MET cc_start: 0.9110 (mmt) cc_final: 0.8872 (mmt) REVERT: H 252 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7474 (tp30) REVERT: H 494 ASP cc_start: 0.7541 (m-30) cc_final: 0.7094 (m-30) REVERT: I 1 MET cc_start: 0.9012 (mmt) cc_final: 0.8490 (mmt) REVERT: I 389 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7769 (tm-30) REVERT: J 116 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8643 (tt) REVERT: J 245 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7399 (mm-30) REVERT: J 252 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7283 (tt0) REVERT: K 1 MET cc_start: 0.9089 (mmt) cc_final: 0.8844 (mmt) REVERT: K 252 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7394 (tp30) REVERT: K 494 ASP cc_start: 0.7543 (m-30) cc_final: 0.7092 (m-30) REVERT: L 1 MET cc_start: 0.9103 (mmt) cc_final: 0.8855 (mmt) REVERT: L 104 ASN cc_start: 0.7757 (OUTLIER) cc_final: 0.7370 (p0) REVERT: L 144 ASP cc_start: 0.7549 (m-30) cc_final: 0.6998 (m-30) REVERT: L 197 TYR cc_start: 0.5101 (OUTLIER) cc_final: 0.4814 (m-10) REVERT: L 252 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7435 (tp30) REVERT: L 494 ASP cc_start: 0.7540 (m-30) cc_final: 0.7094 (m-30) REVERT: A 1 MET cc_start: 0.9013 (mmt) cc_final: 0.8502 (mmt) REVERT: A 252 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7674 (tt0) REVERT: B 79 ASP cc_start: 0.7625 (t0) cc_final: 0.7364 (t0) REVERT: B 245 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7370 (mm-30) REVERT: B 252 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7299 (tt0) REVERT: B 257 TYR cc_start: 0.7808 (m-80) cc_final: 0.6683 (m-80) REVERT: B 389 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7213 (tm-30) REVERT: B 391 ARG cc_start: 0.7502 (mtt-85) cc_final: 0.6801 (mtt-85) REVERT: C 1 MET cc_start: 0.9115 (mmt) cc_final: 0.8873 (mmt) REVERT: C 252 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7446 (tp30) REVERT: C 494 ASP cc_start: 0.7541 (m-30) cc_final: 0.7079 (m-30) REVERT: E 1 MET cc_start: 0.8983 (mmt) cc_final: 0.8492 (mmt) REVERT: E 429 GLU cc_start: 0.6813 (pp20) cc_final: 0.6598 (pp20) REVERT: F 116 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8595 (tt) REVERT: F 245 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7252 (mm-30) REVERT: F 252 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7430 (tt0) REVERT: F 347 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.8319 (p0) REVERT: F 436 TYR cc_start: 0.5923 (m-10) cc_final: 0.5702 (m-10) outliers start: 156 outliers final: 109 residues processed: 691 average time/residue: 0.6515 time to fit residues: 735.8411 Evaluate side-chains 676 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 550 time to evaluate : 6.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 419 LYS Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain G residue 8 ASN Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 214 THR Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 295 ASP Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 485 ILE Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 128 ILE Chi-restraints excluded: chain H residue 152 GLU Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 242 TYR Chi-restraints excluded: chain H residue 252 GLU Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain H residue 321 THR Chi-restraints excluded: chain H residue 398 ASP Chi-restraints excluded: chain I residue 8 ASN Chi-restraints excluded: chain I residue 75 PHE Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain I residue 295 ASP Chi-restraints excluded: chain I residue 321 THR Chi-restraints excluded: chain I residue 434 HIS Chi-restraints excluded: chain I residue 505 VAL Chi-restraints excluded: chain J residue 8 ASN Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 128 ILE Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain J residue 252 GLU Chi-restraints excluded: chain J residue 295 ASP Chi-restraints excluded: chain J residue 398 ASP Chi-restraints excluded: chain J residue 453 ILE Chi-restraints excluded: chain J residue 485 ILE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 252 GLU Chi-restraints excluded: chain K residue 295 ASP Chi-restraints excluded: chain K residue 321 THR Chi-restraints excluded: chain K residue 398 ASP Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 104 ASN Chi-restraints excluded: chain L residue 128 ILE Chi-restraints excluded: chain L residue 152 GLU Chi-restraints excluded: chain L residue 197 TYR Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 252 GLU Chi-restraints excluded: chain L residue 295 ASP Chi-restraints excluded: chain L residue 321 THR Chi-restraints excluded: chain L residue 398 ASP Chi-restraints excluded: chain L residue 434 HIS Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 347 ASN Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 434 HIS Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 104 ASN Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 295 ASP Chi-restraints excluded: chain F residue 347 ASN Chi-restraints excluded: chain F residue 453 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 582 optimal weight: 5.9990 chunk 68 optimal weight: 0.3980 chunk 343 optimal weight: 1.9990 chunk 440 optimal weight: 0.6980 chunk 341 optimal weight: 5.9990 chunk 508 optimal weight: 0.2980 chunk 337 optimal weight: 0.8980 chunk 601 optimal weight: 6.9990 chunk 376 optimal weight: 0.0870 chunk 366 optimal weight: 4.9990 chunk 277 optimal weight: 3.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 347 ASN ** H 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 316 HIS ** J 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 240 GLN B 347 ASN E 21 ASN F 347 ASN ** F 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 52584 Z= 0.129 Angle : 0.475 6.958 70956 Z= 0.264 Chirality : 0.043 0.207 7644 Planarity : 0.004 0.054 9048 Dihedral : 4.568 30.223 6804 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.98 % Allowed : 19.96 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.11), residues: 6204 helix: 0.54 (0.12), residues: 1860 sheet: -0.71 (0.16), residues: 984 loop : -1.52 (0.11), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 307 HIS 0.019 0.001 HIS E 434 PHE 0.013 0.001 PHE L 322 TYR 0.023 0.001 TYR A 242 ARG 0.008 0.000 ARG F 391 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 614 time to evaluate : 6.583 Fit side-chains revert: symmetry clash REVERT: D 104 ASN cc_start: 0.7737 (OUTLIER) cc_final: 0.7452 (p0) REVERT: D 382 ILE cc_start: 0.7854 (mm) cc_final: 0.7597 (mt) REVERT: G 245 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7470 (mm-30) REVERT: G 252 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7459 (tt0) REVERT: H 1 MET cc_start: 0.8988 (mmt) cc_final: 0.8592 (tpp) REVERT: H 252 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7440 (tp30) REVERT: H 494 ASP cc_start: 0.7612 (m-30) cc_final: 0.7201 (m-30) REVERT: I 535 TYR cc_start: 0.8828 (t80) cc_final: 0.8549 (t80) REVERT: J 245 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7395 (mm-30) REVERT: J 252 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7317 (tt0) REVERT: K 1 MET cc_start: 0.8971 (mmt) cc_final: 0.8573 (tpp) REVERT: K 252 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7349 (tp30) REVERT: K 494 ASP cc_start: 0.7617 (m-30) cc_final: 0.7212 (m-30) REVERT: L 1 MET cc_start: 0.8975 (mmt) cc_final: 0.8580 (tpp) REVERT: L 104 ASN cc_start: 0.7774 (OUTLIER) cc_final: 0.7441 (p0) REVERT: L 144 ASP cc_start: 0.7439 (m-30) cc_final: 0.6827 (m-30) REVERT: L 197 TYR cc_start: 0.5156 (OUTLIER) cc_final: 0.4872 (m-10) REVERT: L 252 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7444 (tp30) REVERT: L 494 ASP cc_start: 0.7605 (m-30) cc_final: 0.7181 (m-30) REVERT: A 75 PHE cc_start: 0.7133 (OUTLIER) cc_final: 0.6807 (m-80) REVERT: A 104 ASN cc_start: 0.7674 (OUTLIER) cc_final: 0.7372 (p0) REVERT: B 245 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7253 (mm-30) REVERT: B 252 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7312 (tt0) REVERT: C 1 MET cc_start: 0.8992 (mmt) cc_final: 0.8586 (tpp) REVERT: C 494 ASP cc_start: 0.7614 (m-30) cc_final: 0.7199 (m-30) REVERT: E 535 TYR cc_start: 0.8830 (t80) cc_final: 0.8563 (t80) REVERT: F 245 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7313 (mm-30) REVERT: F 252 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7334 (tt0) outliers start: 115 outliers final: 70 residues processed: 691 average time/residue: 0.6673 time to fit residues: 756.0026 Evaluate side-chains 657 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 575 time to evaluate : 6.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 419 LYS Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 214 THR Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 295 ASP Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain H residue 75 PHE Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 128 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 252 GLU Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain H residue 321 THR Chi-restraints excluded: chain H residue 398 ASP Chi-restraints excluded: chain I residue 75 PHE Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 295 ASP Chi-restraints excluded: chain I residue 321 THR Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 128 ILE Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain J residue 252 GLU Chi-restraints excluded: chain J residue 295 ASP Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 75 PHE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 104 ASN Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 252 GLU Chi-restraints excluded: chain K residue 295 ASP Chi-restraints excluded: chain K residue 321 THR Chi-restraints excluded: chain K residue 381 LEU Chi-restraints excluded: chain L residue 104 ASN Chi-restraints excluded: chain L residue 128 ILE Chi-restraints excluded: chain L residue 197 TYR Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 252 GLU Chi-restraints excluded: chain L residue 295 ASP Chi-restraints excluded: chain L residue 321 THR Chi-restraints excluded: chain L residue 398 ASP Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 104 ASN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 104 ASN Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 295 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 372 optimal weight: 7.9990 chunk 240 optimal weight: 3.9990 chunk 359 optimal weight: 6.9990 chunk 181 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 382 optimal weight: 0.8980 chunk 409 optimal weight: 0.0020 chunk 297 optimal weight: 0.3980 chunk 56 optimal weight: 0.4980 chunk 472 optimal weight: 0.6980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 347 ASN H 240 GLN ** H 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 ASN ** H 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 316 HIS J 347 ASN ** J 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 240 GLN ** K 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 240 GLN C 240 GLN C 347 ASN ** F 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 52584 Z= 0.129 Angle : 0.473 6.972 70956 Z= 0.262 Chirality : 0.043 0.160 7644 Planarity : 0.003 0.051 9048 Dihedral : 4.367 29.809 6804 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.88 % Allowed : 20.03 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.11), residues: 6204 helix: 0.88 (0.12), residues: 1848 sheet: -0.59 (0.16), residues: 984 loop : -1.42 (0.11), residues: 3372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 307 HIS 0.004 0.000 HIS E 316 PHE 0.012 0.001 PHE E 428 TYR 0.021 0.001 TYR A 242 ARG 0.007 0.000 ARG F 391 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 604 time to evaluate : 6.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 104 ASN cc_start: 0.7753 (OUTLIER) cc_final: 0.7479 (p0) REVERT: D 535 TYR cc_start: 0.8803 (t80) cc_final: 0.8534 (t80) REVERT: G 245 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7464 (mm-30) REVERT: G 252 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7407 (tt0) REVERT: H 1 MET cc_start: 0.8965 (mmt) cc_final: 0.8592 (tpp) REVERT: H 494 ASP cc_start: 0.7605 (m-30) cc_final: 0.7291 (m-30) REVERT: J 245 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7290 (mm-30) REVERT: J 252 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7328 (tt0) REVERT: K 1 MET cc_start: 0.8954 (mmt) cc_final: 0.8577 (tpp) REVERT: K 252 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7598 (tp30) REVERT: K 494 ASP cc_start: 0.7614 (m-30) cc_final: 0.7295 (m-30) REVERT: L 1 MET cc_start: 0.8898 (mmt) cc_final: 0.8540 (tpp) REVERT: L 104 ASN cc_start: 0.7863 (OUTLIER) cc_final: 0.7547 (p0) REVERT: L 235 MET cc_start: 0.8617 (mtm) cc_final: 0.8367 (mtp) REVERT: L 245 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8070 (mm-30) REVERT: L 494 ASP cc_start: 0.7605 (m-30) cc_final: 0.7259 (m-30) REVERT: A 75 PHE cc_start: 0.7082 (OUTLIER) cc_final: 0.6786 (m-80) REVERT: A 104 ASN cc_start: 0.7726 (OUTLIER) cc_final: 0.7433 (p0) REVERT: A 429 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6662 (pp20) REVERT: A 535 TYR cc_start: 0.8818 (t80) cc_final: 0.8533 (t80) REVERT: B 79 ASP cc_start: 0.7330 (t0) cc_final: 0.7058 (t0) REVERT: B 245 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7495 (mm-30) REVERT: B 252 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7412 (tt0) REVERT: B 347 ASN cc_start: 0.8675 (p0) cc_final: 0.8423 (p0) REVERT: C 1 MET cc_start: 0.9003 (mmt) cc_final: 0.8625 (tpp) REVERT: C 252 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7542 (tp30) REVERT: C 494 ASP cc_start: 0.7600 (m-30) cc_final: 0.7251 (m-30) REVERT: E 535 TYR cc_start: 0.8823 (t80) cc_final: 0.8528 (t80) REVERT: F 245 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7377 (mm-30) REVERT: F 252 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7304 (tt0) outliers start: 109 outliers final: 76 residues processed: 671 average time/residue: 0.6424 time to fit residues: 705.7662 Evaluate side-chains 656 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 569 time to evaluate : 6.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 419 LYS Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 295 ASP Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain H residue 128 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 252 GLU Chi-restraints excluded: chain H residue 321 THR Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain I residue 8 ASN Chi-restraints excluded: chain I residue 75 PHE Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 295 ASP Chi-restraints excluded: chain I residue 321 THR Chi-restraints excluded: chain I residue 429 GLU Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 128 ILE Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain J residue 252 GLU Chi-restraints excluded: chain J residue 347 ASN Chi-restraints excluded: chain J residue 453 ILE Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 104 ASN Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 252 GLU Chi-restraints excluded: chain K residue 295 ASP Chi-restraints excluded: chain K residue 321 THR Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 104 ASN Chi-restraints excluded: chain L residue 128 ILE Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 252 GLU Chi-restraints excluded: chain L residue 321 THR Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 104 ASN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 347 ASN Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 104 ASN Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 295 ASP Chi-restraints excluded: chain F residue 453 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 547 optimal weight: 1.9990 chunk 576 optimal weight: 0.4980 chunk 525 optimal weight: 0.5980 chunk 560 optimal weight: 6.9990 chunk 337 optimal weight: 0.5980 chunk 244 optimal weight: 10.0000 chunk 440 optimal weight: 0.9980 chunk 171 optimal weight: 4.9990 chunk 506 optimal weight: 3.9990 chunk 530 optimal weight: 5.9990 chunk 558 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 347 ASN ** H 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 ASN ** H 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 347 ASN ** J 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 351 ASN A 316 HIS B 347 ASN C 240 GLN C 347 ASN E 316 HIS E 351 ASN ** F 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 52584 Z= 0.149 Angle : 0.479 6.999 70956 Z= 0.265 Chirality : 0.043 0.244 7644 Planarity : 0.004 0.051 9048 Dihedral : 4.345 29.998 6804 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.00 % Allowed : 19.96 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.11), residues: 6204 helix: 1.04 (0.12), residues: 1848 sheet: -0.50 (0.17), residues: 984 loop : -1.37 (0.11), residues: 3372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 307 HIS 0.005 0.001 HIS E 316 PHE 0.015 0.001 PHE K 322 TYR 0.021 0.001 TYR A 242 ARG 0.007 0.000 ARG G 391 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 583 time to evaluate : 6.656 Fit side-chains revert: symmetry clash REVERT: D 104 ASN cc_start: 0.7761 (OUTLIER) cc_final: 0.7486 (p0) REVERT: G 245 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7465 (mm-30) REVERT: G 252 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7482 (tp30) REVERT: H 1 MET cc_start: 0.9021 (mmt) cc_final: 0.8671 (tpp) REVERT: H 494 ASP cc_start: 0.7604 (m-30) cc_final: 0.7286 (m-30) REVERT: J 245 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7353 (mm-30) REVERT: J 252 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7441 (tt0) REVERT: J 436 TYR cc_start: 0.5875 (m-80) cc_final: 0.5596 (m-10) REVERT: K 1 MET cc_start: 0.8890 (mmt) cc_final: 0.8541 (tpp) REVERT: K 235 MET cc_start: 0.8664 (mtm) cc_final: 0.8401 (mtp) REVERT: K 494 ASP cc_start: 0.7617 (m-30) cc_final: 0.7348 (m-30) REVERT: L 1 MET cc_start: 0.8935 (mmt) cc_final: 0.8579 (tpp) REVERT: L 104 ASN cc_start: 0.7836 (OUTLIER) cc_final: 0.7530 (p0) REVERT: L 245 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8061 (mm-30) REVERT: L 346 CYS cc_start: 0.7868 (p) cc_final: 0.7345 (p) REVERT: L 494 ASP cc_start: 0.7610 (m-30) cc_final: 0.7306 (m-30) REVERT: A 75 PHE cc_start: 0.7105 (OUTLIER) cc_final: 0.6798 (m-80) REVERT: A 104 ASN cc_start: 0.7744 (OUTLIER) cc_final: 0.7455 (p0) REVERT: B 79 ASP cc_start: 0.7432 (t0) cc_final: 0.7198 (t0) REVERT: B 245 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7503 (mm-30) REVERT: B 252 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7412 (tt0) REVERT: C 1 MET cc_start: 0.9014 (mmt) cc_final: 0.8636 (tpp) REVERT: C 252 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7617 (tp30) REVERT: C 494 ASP cc_start: 0.7596 (m-30) cc_final: 0.7287 (m-30) REVERT: E 535 TYR cc_start: 0.8823 (t80) cc_final: 0.8524 (t80) REVERT: F 245 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7393 (mm-30) REVERT: F 252 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7291 (tt0) outliers start: 116 outliers final: 86 residues processed: 652 average time/residue: 0.6788 time to fit residues: 720.3202 Evaluate side-chains 665 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 570 time to evaluate : 5.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 419 LYS Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 295 ASP Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 485 ILE Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 75 PHE Chi-restraints excluded: chain H residue 128 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain H residue 321 THR Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain I residue 8 ASN Chi-restraints excluded: chain I residue 75 PHE Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 295 ASP Chi-restraints excluded: chain I residue 321 THR Chi-restraints excluded: chain I residue 419 LYS Chi-restraints excluded: chain I residue 429 GLU Chi-restraints excluded: chain J residue 128 ILE Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain J residue 252 GLU Chi-restraints excluded: chain J residue 347 ASN Chi-restraints excluded: chain J residue 407 MET Chi-restraints excluded: chain J residue 453 ILE Chi-restraints excluded: chain J residue 485 ILE Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 104 ASN Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 295 ASP Chi-restraints excluded: chain K residue 321 THR Chi-restraints excluded: chain K residue 434 HIS Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 104 ASN Chi-restraints excluded: chain L residue 128 ILE Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 252 GLU Chi-restraints excluded: chain L residue 321 THR Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 104 ASN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 347 ASN Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 104 ASN Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 295 ASP Chi-restraints excluded: chain F residue 453 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 368 optimal weight: 4.9990 chunk 592 optimal weight: 1.9990 chunk 361 optimal weight: 3.9990 chunk 281 optimal weight: 0.1980 chunk 411 optimal weight: 0.0470 chunk 621 optimal weight: 2.9990 chunk 572 optimal weight: 10.0000 chunk 495 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 382 optimal weight: 0.7980 chunk 303 optimal weight: 30.0000 overall best weight: 1.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 347 ASN H 347 ASN ** H 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 347 ASN ** J 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 ASN ** F 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 52584 Z= 0.197 Angle : 0.506 7.526 70956 Z= 0.281 Chirality : 0.045 0.199 7644 Planarity : 0.004 0.052 9048 Dihedral : 4.468 31.077 6804 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.92 % Allowed : 20.12 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -0.68 (0.11), residues: 6204 helix: 1.03 (0.12), residues: 1860 sheet: -0.48 (0.17), residues: 984 loop : -1.33 (0.11), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 307 HIS 0.003 0.001 HIS A 244 PHE 0.014 0.001 PHE K 322 TYR 0.027 0.001 TYR L 242 ARG 0.008 0.000 ARG C 241 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 577 time to evaluate : 5.359 Fit side-chains revert: symmetry clash REVERT: G 245 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7527 (mm-30) REVERT: G 252 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7505 (tt0) REVERT: G 436 TYR cc_start: 0.5919 (m-80) cc_final: 0.5534 (m-10) REVERT: H 1 MET cc_start: 0.9045 (mmt) cc_final: 0.8673 (tpp) REVERT: H 494 ASP cc_start: 0.7613 (m-30) cc_final: 0.7285 (m-30) REVERT: I 535 TYR cc_start: 0.8839 (t80) cc_final: 0.8562 (t80) REVERT: J 245 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7450 (mm-30) REVERT: J 252 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: J 436 TYR cc_start: 0.5983 (m-10) cc_final: 0.5616 (m-10) REVERT: K 1 MET cc_start: 0.8935 (mmt) cc_final: 0.8535 (tpp) REVERT: K 235 MET cc_start: 0.8655 (mtm) cc_final: 0.8373 (mtp) REVERT: K 494 ASP cc_start: 0.7622 (m-30) cc_final: 0.7290 (m-30) REVERT: L 1 MET cc_start: 0.9028 (mmt) cc_final: 0.8663 (tpp) REVERT: L 104 ASN cc_start: 0.7790 (OUTLIER) cc_final: 0.7464 (p0) REVERT: L 252 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7678 (tp30) REVERT: L 494 ASP cc_start: 0.7605 (m-30) cc_final: 0.7293 (m-30) REVERT: A 75 PHE cc_start: 0.7192 (OUTLIER) cc_final: 0.6986 (m-80) REVERT: A 535 TYR cc_start: 0.8829 (t80) cc_final: 0.8557 (t80) REVERT: B 79 ASP cc_start: 0.7468 (t0) cc_final: 0.7225 (t0) REVERT: B 245 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7407 (mm-30) REVERT: B 252 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7421 (tt0) REVERT: B 389 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7244 (tt0) REVERT: C 1 MET cc_start: 0.9055 (mmt) cc_final: 0.8619 (tpp) REVERT: C 252 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7511 (tp30) REVERT: C 494 ASP cc_start: 0.7612 (m-30) cc_final: 0.7281 (m-30) REVERT: F 245 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7474 (mm-30) REVERT: F 252 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7323 (tt0) outliers start: 111 outliers final: 90 residues processed: 654 average time/residue: 0.6668 time to fit residues: 706.6459 Evaluate side-chains 662 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 564 time to evaluate : 6.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 419 LYS Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 295 ASP Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 485 ILE Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 128 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain H residue 321 THR Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain I residue 8 ASN Chi-restraints excluded: chain I residue 75 PHE Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 295 ASP Chi-restraints excluded: chain I residue 321 THR Chi-restraints excluded: chain I residue 419 LYS Chi-restraints excluded: chain I residue 429 GLU Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 128 ILE Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain J residue 252 GLU Chi-restraints excluded: chain J residue 347 ASN Chi-restraints excluded: chain J residue 407 MET Chi-restraints excluded: chain J residue 453 ILE Chi-restraints excluded: chain J residue 485 ILE Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 104 ASN Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 252 GLU Chi-restraints excluded: chain K residue 295 ASP Chi-restraints excluded: chain K residue 321 THR Chi-restraints excluded: chain K residue 434 HIS Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 104 ASN Chi-restraints excluded: chain L residue 128 ILE Chi-restraints excluded: chain L residue 214 THR Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 252 GLU Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 295 ASP Chi-restraints excluded: chain L residue 321 THR Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 104 ASN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 347 ASN Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 104 ASN Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 295 ASP Chi-restraints excluded: chain F residue 407 MET Chi-restraints excluded: chain F residue 453 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 393 optimal weight: 6.9990 chunk 527 optimal weight: 8.9990 chunk 151 optimal weight: 1.9990 chunk 456 optimal weight: 0.3980 chunk 73 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 495 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 509 optimal weight: 9.9990 chunk 62 optimal weight: 0.0870 chunk 91 optimal weight: 7.9990 overall best weight: 1.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 347 ASN H 347 ASN ** H 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 347 ASN ** J 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 ASN ** F 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.151711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.116543 restraints weight = 65855.668| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.13 r_work: 0.3193 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 52584 Z= 0.184 Angle : 0.502 6.622 70956 Z= 0.279 Chirality : 0.045 0.221 7644 Planarity : 0.004 0.051 9048 Dihedral : 4.470 30.759 6804 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.92 % Allowed : 20.34 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % 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: -0.62 (0.11), residues: 6204 helix: 1.20 (0.12), residues: 1788 sheet: -0.46 (0.17), residues: 984 loop : -1.30 (0.11), residues: 3432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 307 HIS 0.003 0.001 HIS G 316 PHE 0.014 0.001 PHE G 322 TYR 0.023 0.001 TYR A 242 ARG 0.007 0.000 ARG G 391 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14264.47 seconds wall clock time: 257 minutes 5.31 seconds (15425.31 seconds total)