Starting phenix.real_space_refine on Wed Feb 21 08:26:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ae0_11735/02_2024/7ae0_11735.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ae0_11735/02_2024/7ae0_11735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ae0_11735/02_2024/7ae0_11735.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ae0_11735/02_2024/7ae0_11735.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ae0_11735/02_2024/7ae0_11735.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ae0_11735/02_2024/7ae0_11735.pdb" } resolution = 2.4 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= 0.012 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 270 5.16 5 C 59040 2.51 5 N 15300 2.21 5 O 18108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "3A TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3B TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3B PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3B TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3B TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3B TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3B PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3B TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3B TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3B TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3B TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3B TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3B TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3B TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3B PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3B PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3B PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3C TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3C PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3C TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3C TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3C TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3C PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3C PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3C TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3C TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3C TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3C TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3C TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3C TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3C TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3C PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3C PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3C PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3D TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3D TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3D TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3D TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3D PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3D PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3D TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3D TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3D TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3D TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3D TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3D TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3D TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3D PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3D PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3D PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3E TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3E PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3E TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3E TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3E TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3E PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3E PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3E TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3E TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3E TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3E TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3E TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3E TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3E TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3E PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3E PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3E PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3F TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3F PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3F PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3F TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3F TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3F TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3F TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3F PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3F PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3F TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3F TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3F TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3F TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3F TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3F TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3F TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3F TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3F PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3F PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3F PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4D TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4D TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4D TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4D TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4D PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4D PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4D TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4D TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4D TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4D TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4D TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4D TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4D TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4D PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4D PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4D PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4E TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4E PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4E TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4E TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4E TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4E PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4E PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4E TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4E TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4E TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4E TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4E TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4E TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4E TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4E PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4E PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4E PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4F TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4F PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4F PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4F TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4F TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4F TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4F TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4F PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4F PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4F TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4F TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4F TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4F TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4F TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4F TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4F TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4F TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4F PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4F PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4F PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5E TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5E PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5E TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5E TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5E TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5E PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5E PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5E TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5E TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5E TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5E TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5E TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5E TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5E TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5E PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5E PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5E PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5F TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5F PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5F PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5F TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5F TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5F TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5F TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5F PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5F PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5F TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5F TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5F TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5F TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5F TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5F TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5F TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5F TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5F PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5F PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5F PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3a PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3a TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3a PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3a TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3a GLU 96": "OE1" <-> "OE2" Residue "3b PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3b TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3b PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3b TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3b GLU 96": "OE1" <-> "OE2" Residue "3c PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3c TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3c PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3c TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3c GLU 96": "OE1" <-> "OE2" Residue "3d PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3d TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3d PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3d TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3d GLU 96": "OE1" <-> "OE2" Residue "3e PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3e TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3e PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3e TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3e GLU 96": "OE1" <-> "OE2" Residue "3f PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3f TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3f PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3f TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3f GLU 96": "OE1" <-> "OE2" Residue "4a PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4a TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4a PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4a TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4a GLU 96": "OE1" <-> "OE2" Residue "4b PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4b TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4b PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4b TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4b GLU 96": "OE1" <-> "OE2" Residue "4c PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4c TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4c PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4c TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4c GLU 96": "OE1" <-> "OE2" Residue "4d PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4d TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4d PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4d TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4d GLU 96": "OE1" <-> "OE2" Residue "4e PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4e TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4e PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4e TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4e GLU 96": "OE1" <-> "OE2" Residue "4f PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4f TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4f PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4f TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4f GLU 96": "OE1" <-> "OE2" Residue "5a PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5a TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5a PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5a TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5a GLU 96": "OE1" <-> "OE2" Residue "5b PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5b TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5b PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5b TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5b GLU 96": "OE1" <-> "OE2" Residue "5c PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5c TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5c PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5c TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5c GLU 96": "OE1" <-> "OE2" Residue "5d PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5d TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5d PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5d TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5d GLU 96": "OE1" <-> "OE2" Residue "5e PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5e TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5e PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5e TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5e GLU 96": "OE1" <-> "OE2" Residue "5f PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5f TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5f PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5f TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5f GLU 96": "OE1" <-> "OE2" Time to flip residues: 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 92718 Number of models: 1 Model: "" Number of chains: 36 Chain: "3A" Number of atoms: 4006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4006 Classifications: {'peptide': 511} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 482} Chain breaks: 1 Chain: "3B" Number of atoms: 4006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4006 Classifications: {'peptide': 511} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 482} Chain breaks: 1 Chain: "3C" Number of atoms: 4006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4006 Classifications: {'peptide': 511} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 482} Chain breaks: 1 Chain: "3D" Number of atoms: 4006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4006 Classifications: {'peptide': 511} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 482} Chain breaks: 1 Chain: "3E" Number of atoms: 4006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4006 Classifications: {'peptide': 511} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 482} Chain breaks: 1 Chain: "3F" Number of atoms: 4006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4006 Classifications: {'peptide': 511} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 482} Chain breaks: 1 Chain: "4A" Number of atoms: 4006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4006 Classifications: {'peptide': 511} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 482} Chain breaks: 1 Chain: "4B" Number of atoms: 4006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4006 Classifications: {'peptide': 511} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 482} Chain breaks: 1 Chain: "4C" Number of atoms: 4006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4006 Classifications: {'peptide': 511} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 482} Chain breaks: 1 Chain: "4D" Number of atoms: 4006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4006 Classifications: {'peptide': 511} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 482} Chain breaks: 1 Chain: "4E" Number of atoms: 4006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4006 Classifications: {'peptide': 511} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 482} Chain breaks: 1 Chain: "4F" Number of atoms: 4006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4006 Classifications: {'peptide': 511} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 482} Chain breaks: 1 Chain: "5A" Number of atoms: 4006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4006 Classifications: {'peptide': 511} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 482} Chain breaks: 1 Chain: "5B" Number of atoms: 4006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4006 Classifications: {'peptide': 511} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 482} Chain breaks: 1 Chain: "5C" Number of atoms: 4006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4006 Classifications: {'peptide': 511} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 482} Chain breaks: 1 Chain: "5D" Number of atoms: 4006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4006 Classifications: {'peptide': 511} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 482} Chain breaks: 1 Chain: "5E" Number of atoms: 4006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4006 Classifications: {'peptide': 511} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 482} Chain breaks: 1 Chain: "5F" Number of atoms: 4006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4006 Classifications: {'peptide': 511} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 482} Chain breaks: 1 Chain: "3a" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "3b" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "3c" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "3d" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "3e" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "3f" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "4a" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "4b" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "4c" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "4d" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "4e" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "4f" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "5a" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "5b" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "5c" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "5d" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "5e" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "5f" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Time building chain proxies: 34.41, per 1000 atoms: 0.37 Number of scatterers: 92718 At special positions: 0 Unit cell: (234.3, 236.5, 196.9, 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 270 16.00 O 18108 8.00 N 15300 7.00 C 59040 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: 25.19 Conformation dependent library (CDL) restraints added in 12.0 seconds 23256 Ramachandran restraints generated. 11628 Oldfield, 0 Emsley, 11628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 21924 Finding SS restraints... Secondary structure from input PDB file: 360 helices and 132 sheets defined 31.7% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.77 Creating SS restraints... Processing helix chain '3A' and resid 58 through 67 Processing helix chain '3A' and resid 104 through 115 Processing helix chain '3A' and resid 141 through 153 removed outlier: 3.719A pdb=" N LEU3A 145 " --> pdb=" O ASN3A 141 " (cutoff:3.500A) Processing helix chain '3A' and resid 171 through 190 Processing helix chain '3A' and resid 212 through 221 Processing helix chain '3A' and resid 224 through 229 Processing helix chain '3A' and resid 247 through 251 Processing helix chain '3A' and resid 261 through 271 Processing helix chain '3A' and resid 451 through 462 Processing helix chain '3A' and resid 477 through 481 Processing helix chain '3A' and resid 485 through 497 Processing helix chain '3A' and resid 505 through 520 Processing helix chain '3A' and resid 543 through 545 No H-bonds generated for 'chain '3A' and resid 543 through 545' Processing helix chain '3A' and resid 546 through 551 Processing helix chain '3A' and resid 586 through 605 Processing helix chain '3A' and resid 606 through 608 No H-bonds generated for 'chain '3A' and resid 606 through 608' Processing helix chain '3A' and resid 613 through 634 Processing helix chain '3A' and resid 641 through 644 Processing helix chain '3A' and resid 657 through 664 Processing helix chain '3B' and resid 58 through 67 Processing helix chain '3B' and resid 104 through 115 Processing helix chain '3B' and resid 141 through 153 removed outlier: 3.719A pdb=" N LEU3B 145 " --> pdb=" O ASN3B 141 " (cutoff:3.500A) Processing helix chain '3B' and resid 171 through 190 Processing helix chain '3B' and resid 212 through 221 Processing helix chain '3B' and resid 224 through 229 Processing helix chain '3B' and resid 247 through 251 Processing helix chain '3B' and resid 261 through 271 Processing helix chain '3B' and resid 451 through 462 Processing helix chain '3B' and resid 477 through 481 Processing helix chain '3B' and resid 485 through 497 Processing helix chain '3B' and resid 505 through 520 Processing helix chain '3B' and resid 543 through 545 No H-bonds generated for 'chain '3B' and resid 543 through 545' Processing helix chain '3B' and resid 546 through 551 Processing helix chain '3B' and resid 586 through 605 Processing helix chain '3B' and resid 606 through 608 No H-bonds generated for 'chain '3B' and resid 606 through 608' Processing helix chain '3B' and resid 613 through 634 Processing helix chain '3B' and resid 641 through 644 Processing helix chain '3B' and resid 657 through 664 Processing helix chain '3C' and resid 58 through 67 Processing helix chain '3C' and resid 104 through 115 Processing helix chain '3C' and resid 141 through 153 removed outlier: 3.719A pdb=" N LEU3C 145 " --> pdb=" O ASN3C 141 " (cutoff:3.500A) Processing helix chain '3C' and resid 171 through 190 Processing helix chain '3C' and resid 212 through 221 Processing helix chain '3C' and resid 224 through 229 Processing helix chain '3C' and resid 247 through 251 Processing helix chain '3C' and resid 261 through 271 Processing helix chain '3C' and resid 451 through 462 Processing helix chain '3C' and resid 477 through 481 Processing helix chain '3C' and resid 485 through 497 Processing helix chain '3C' and resid 505 through 520 Processing helix chain '3C' and resid 543 through 545 No H-bonds generated for 'chain '3C' and resid 543 through 545' Processing helix chain '3C' and resid 546 through 551 Processing helix chain '3C' and resid 586 through 605 Processing helix chain '3C' and resid 606 through 608 No H-bonds generated for 'chain '3C' and resid 606 through 608' Processing helix chain '3C' and resid 613 through 634 Processing helix chain '3C' and resid 641 through 644 Processing helix chain '3C' and resid 657 through 664 Processing helix chain '3D' and resid 58 through 67 Processing helix chain '3D' and resid 104 through 115 Processing helix chain '3D' and resid 141 through 153 removed outlier: 3.719A pdb=" N LEU3D 145 " --> pdb=" O ASN3D 141 " (cutoff:3.500A) Processing helix chain '3D' and resid 171 through 190 Processing helix chain '3D' and resid 212 through 221 Processing helix chain '3D' and resid 224 through 229 Processing helix chain '3D' and resid 247 through 251 Processing helix chain '3D' and resid 261 through 271 Processing helix chain '3D' and resid 451 through 462 Processing helix chain '3D' and resid 477 through 481 Processing helix chain '3D' and resid 485 through 497 Processing helix chain '3D' and resid 505 through 520 Processing helix chain '3D' and resid 543 through 545 No H-bonds generated for 'chain '3D' and resid 543 through 545' Processing helix chain '3D' and resid 546 through 551 Processing helix chain '3D' and resid 586 through 605 Processing helix chain '3D' and resid 606 through 608 No H-bonds generated for 'chain '3D' and resid 606 through 608' Processing helix chain '3D' and resid 613 through 634 Processing helix chain '3D' and resid 641 through 644 Processing helix chain '3D' and resid 657 through 664 Processing helix chain '3E' and resid 58 through 67 Processing helix chain '3E' and resid 104 through 115 Processing helix chain '3E' and resid 141 through 153 removed outlier: 3.720A pdb=" N LEU3E 145 " --> pdb=" O ASN3E 141 " (cutoff:3.500A) Processing helix chain '3E' and resid 171 through 190 Processing helix chain '3E' and resid 212 through 221 Processing helix chain '3E' and resid 224 through 229 Processing helix chain '3E' and resid 247 through 251 Processing helix chain '3E' and resid 261 through 271 Processing helix chain '3E' and resid 451 through 462 Processing helix chain '3E' and resid 477 through 481 Processing helix chain '3E' and resid 485 through 497 Processing helix chain '3E' and resid 505 through 520 Processing helix chain '3E' and resid 543 through 545 No H-bonds generated for 'chain '3E' and resid 543 through 545' Processing helix chain '3E' and resid 546 through 551 Processing helix chain '3E' and resid 586 through 605 Processing helix chain '3E' and resid 606 through 608 No H-bonds generated for 'chain '3E' and resid 606 through 608' Processing helix chain '3E' and resid 613 through 634 Processing helix chain '3E' and resid 641 through 644 Processing helix chain '3E' and resid 657 through 664 Processing helix chain '3F' and resid 58 through 67 Processing helix chain '3F' and resid 104 through 115 Processing helix chain '3F' and resid 141 through 153 removed outlier: 3.719A pdb=" N LEU3F 145 " --> pdb=" O ASN3F 141 " (cutoff:3.500A) Processing helix chain '3F' and resid 171 through 190 Processing helix chain '3F' and resid 212 through 221 Processing helix chain '3F' and resid 224 through 229 Processing helix chain '3F' and resid 247 through 251 Processing helix chain '3F' and resid 261 through 271 Processing helix chain '3F' and resid 451 through 462 Processing helix chain '3F' and resid 477 through 481 Processing helix chain '3F' and resid 485 through 497 Processing helix chain '3F' and resid 505 through 520 Processing helix chain '3F' and resid 543 through 545 No H-bonds generated for 'chain '3F' and resid 543 through 545' Processing helix chain '3F' and resid 546 through 551 Processing helix chain '3F' and resid 586 through 605 Processing helix chain '3F' and resid 606 through 608 No H-bonds generated for 'chain '3F' and resid 606 through 608' Processing helix chain '3F' and resid 613 through 634 Processing helix chain '3F' and resid 641 through 644 Processing helix chain '3F' and resid 657 through 664 Processing helix chain '4A' and resid 58 through 67 Processing helix chain '4A' and resid 104 through 115 Processing helix chain '4A' and resid 141 through 153 removed outlier: 3.719A pdb=" N LEU4A 145 " --> pdb=" O ASN4A 141 " (cutoff:3.500A) Processing helix chain '4A' and resid 171 through 190 Processing helix chain '4A' and resid 212 through 221 Processing helix chain '4A' and resid 224 through 229 Processing helix chain '4A' and resid 247 through 251 Processing helix chain '4A' and resid 261 through 271 Processing helix chain '4A' and resid 451 through 462 Processing helix chain '4A' and resid 477 through 481 Processing helix chain '4A' and resid 485 through 497 Processing helix chain '4A' and resid 505 through 520 Processing helix chain '4A' and resid 543 through 545 No H-bonds generated for 'chain '4A' and resid 543 through 545' Processing helix chain '4A' and resid 546 through 551 Processing helix chain '4A' and resid 586 through 605 Processing helix chain '4A' and resid 606 through 608 No H-bonds generated for 'chain '4A' and resid 606 through 608' Processing helix chain '4A' and resid 613 through 634 Processing helix chain '4A' and resid 641 through 644 Processing helix chain '4A' and resid 657 through 664 Processing helix chain '4B' and resid 58 through 67 Processing helix chain '4B' and resid 104 through 115 Processing helix chain '4B' and resid 141 through 153 removed outlier: 3.719A pdb=" N LEU4B 145 " --> pdb=" O ASN4B 141 " (cutoff:3.500A) Processing helix chain '4B' and resid 171 through 190 Processing helix chain '4B' and resid 212 through 221 Processing helix chain '4B' and resid 224 through 229 Processing helix chain '4B' and resid 247 through 251 Processing helix chain '4B' and resid 261 through 271 Processing helix chain '4B' and resid 451 through 462 Processing helix chain '4B' and resid 477 through 481 Processing helix chain '4B' and resid 485 through 497 Processing helix chain '4B' and resid 505 through 520 Processing helix chain '4B' and resid 543 through 545 No H-bonds generated for 'chain '4B' and resid 543 through 545' Processing helix chain '4B' and resid 546 through 551 Processing helix chain '4B' and resid 586 through 605 Processing helix chain '4B' and resid 606 through 608 No H-bonds generated for 'chain '4B' and resid 606 through 608' Processing helix chain '4B' and resid 613 through 634 Processing helix chain '4B' and resid 641 through 644 Processing helix chain '4B' and resid 657 through 664 Processing helix chain '4C' and resid 58 through 67 Processing helix chain '4C' and resid 104 through 115 Processing helix chain '4C' and resid 141 through 153 removed outlier: 3.719A pdb=" N LEU4C 145 " --> pdb=" O ASN4C 141 " (cutoff:3.500A) Processing helix chain '4C' and resid 171 through 190 Processing helix chain '4C' and resid 212 through 221 Processing helix chain '4C' and resid 224 through 229 Processing helix chain '4C' and resid 247 through 251 Processing helix chain '4C' and resid 261 through 271 Processing helix chain '4C' and resid 451 through 462 Processing helix chain '4C' and resid 477 through 481 Processing helix chain '4C' and resid 485 through 497 Processing helix chain '4C' and resid 505 through 520 Processing helix chain '4C' and resid 543 through 545 No H-bonds generated for 'chain '4C' and resid 543 through 545' Processing helix chain '4C' and resid 546 through 551 Processing helix chain '4C' and resid 586 through 605 Processing helix chain '4C' and resid 606 through 608 No H-bonds generated for 'chain '4C' and resid 606 through 608' Processing helix chain '4C' and resid 613 through 634 Processing helix chain '4C' and resid 641 through 644 Processing helix chain '4C' and resid 657 through 664 Processing helix chain '4D' and resid 58 through 67 Processing helix chain '4D' and resid 104 through 115 Processing helix chain '4D' and resid 141 through 153 removed outlier: 3.720A pdb=" N LEU4D 145 " --> pdb=" O ASN4D 141 " (cutoff:3.500A) Processing helix chain '4D' and resid 171 through 190 Processing helix chain '4D' and resid 212 through 221 Processing helix chain '4D' and resid 224 through 229 Processing helix chain '4D' and resid 247 through 251 Processing helix chain '4D' and resid 261 through 271 Processing helix chain '4D' and resid 451 through 462 Processing helix chain '4D' and resid 477 through 481 Processing helix chain '4D' and resid 485 through 497 Processing helix chain '4D' and resid 505 through 520 Processing helix chain '4D' and resid 543 through 545 No H-bonds generated for 'chain '4D' and resid 543 through 545' Processing helix chain '4D' and resid 546 through 551 Processing helix chain '4D' and resid 586 through 605 Processing helix chain '4D' and resid 606 through 608 No H-bonds generated for 'chain '4D' and resid 606 through 608' Processing helix chain '4D' and resid 613 through 634 Processing helix chain '4D' and resid 641 through 644 Processing helix chain '4D' and resid 657 through 664 Processing helix chain '4E' and resid 58 through 67 Processing helix chain '4E' and resid 104 through 115 Processing helix chain '4E' and resid 141 through 153 removed outlier: 3.719A pdb=" N LEU4E 145 " --> pdb=" O ASN4E 141 " (cutoff:3.500A) Processing helix chain '4E' and resid 171 through 190 Processing helix chain '4E' and resid 212 through 221 Processing helix chain '4E' and resid 224 through 229 Processing helix chain '4E' and resid 247 through 251 Processing helix chain '4E' and resid 261 through 271 Processing helix chain '4E' and resid 451 through 462 Processing helix chain '4E' and resid 477 through 481 Processing helix chain '4E' and resid 485 through 497 Processing helix chain '4E' and resid 505 through 520 Processing helix chain '4E' and resid 543 through 545 No H-bonds generated for 'chain '4E' and resid 543 through 545' Processing helix chain '4E' and resid 546 through 551 Processing helix chain '4E' and resid 586 through 605 Processing helix chain '4E' and resid 606 through 608 No H-bonds generated for 'chain '4E' and resid 606 through 608' Processing helix chain '4E' and resid 613 through 634 Processing helix chain '4E' and resid 641 through 644 Processing helix chain '4E' and resid 657 through 664 Processing helix chain '4F' and resid 58 through 67 Processing helix chain '4F' and resid 104 through 115 Processing helix chain '4F' and resid 141 through 153 removed outlier: 3.720A pdb=" N LEU4F 145 " --> pdb=" O ASN4F 141 " (cutoff:3.500A) Processing helix chain '4F' and resid 171 through 190 Processing helix chain '4F' and resid 212 through 221 Processing helix chain '4F' and resid 224 through 229 Processing helix chain '4F' and resid 247 through 251 Processing helix chain '4F' and resid 261 through 271 Processing helix chain '4F' and resid 451 through 462 Processing helix chain '4F' and resid 477 through 481 Processing helix chain '4F' and resid 485 through 497 Processing helix chain '4F' and resid 505 through 520 Processing helix chain '4F' and resid 543 through 545 No H-bonds generated for 'chain '4F' and resid 543 through 545' Processing helix chain '4F' and resid 546 through 551 Processing helix chain '4F' and resid 586 through 605 Processing helix chain '4F' and resid 606 through 608 No H-bonds generated for 'chain '4F' and resid 606 through 608' Processing helix chain '4F' and resid 613 through 634 Processing helix chain '4F' and resid 641 through 644 Processing helix chain '4F' and resid 657 through 664 Processing helix chain '5A' and resid 58 through 67 Processing helix chain '5A' and resid 104 through 115 Processing helix chain '5A' and resid 141 through 153 removed outlier: 3.718A pdb=" N LEU5A 145 " --> pdb=" O ASN5A 141 " (cutoff:3.500A) Processing helix chain '5A' and resid 171 through 190 Processing helix chain '5A' and resid 212 through 221 Processing helix chain '5A' and resid 224 through 229 Processing helix chain '5A' and resid 247 through 251 Processing helix chain '5A' and resid 261 through 271 Processing helix chain '5A' and resid 451 through 462 Processing helix chain '5A' and resid 477 through 481 Processing helix chain '5A' and resid 485 through 497 Processing helix chain '5A' and resid 505 through 520 Processing helix chain '5A' and resid 543 through 545 No H-bonds generated for 'chain '5A' and resid 543 through 545' Processing helix chain '5A' and resid 546 through 551 Processing helix chain '5A' and resid 586 through 605 Processing helix chain '5A' and resid 606 through 608 No H-bonds generated for 'chain '5A' and resid 606 through 608' Processing helix chain '5A' and resid 613 through 634 Processing helix chain '5A' and resid 641 through 644 Processing helix chain '5A' and resid 657 through 664 Processing helix chain '5B' and resid 58 through 67 Processing helix chain '5B' and resid 104 through 115 Processing helix chain '5B' and resid 141 through 153 removed outlier: 3.719A pdb=" N LEU5B 145 " --> pdb=" O ASN5B 141 " (cutoff:3.500A) Processing helix chain '5B' and resid 171 through 190 Processing helix chain '5B' and resid 212 through 221 Processing helix chain '5B' and resid 224 through 229 Processing helix chain '5B' and resid 247 through 251 Processing helix chain '5B' and resid 261 through 271 Processing helix chain '5B' and resid 451 through 462 Processing helix chain '5B' and resid 477 through 481 Processing helix chain '5B' and resid 485 through 497 Processing helix chain '5B' and resid 505 through 520 Processing helix chain '5B' and resid 543 through 545 No H-bonds generated for 'chain '5B' and resid 543 through 545' Processing helix chain '5B' and resid 546 through 551 Processing helix chain '5B' and resid 586 through 605 Processing helix chain '5B' and resid 606 through 608 No H-bonds generated for 'chain '5B' and resid 606 through 608' Processing helix chain '5B' and resid 613 through 634 Processing helix chain '5B' and resid 641 through 644 Processing helix chain '5B' and resid 657 through 664 Processing helix chain '5C' and resid 58 through 67 Processing helix chain '5C' and resid 104 through 115 Processing helix chain '5C' and resid 141 through 153 removed outlier: 3.719A pdb=" N LEU5C 145 " --> pdb=" O ASN5C 141 " (cutoff:3.500A) Processing helix chain '5C' and resid 171 through 190 Processing helix chain '5C' and resid 212 through 221 Processing helix chain '5C' and resid 224 through 229 Processing helix chain '5C' and resid 247 through 251 Processing helix chain '5C' and resid 261 through 271 Processing helix chain '5C' and resid 451 through 462 Processing helix chain '5C' and resid 477 through 481 Processing helix chain '5C' and resid 485 through 497 Processing helix chain '5C' and resid 505 through 520 Processing helix chain '5C' and resid 543 through 545 No H-bonds generated for 'chain '5C' and resid 543 through 545' Processing helix chain '5C' and resid 546 through 551 Processing helix chain '5C' and resid 586 through 605 Processing helix chain '5C' and resid 606 through 608 No H-bonds generated for 'chain '5C' and resid 606 through 608' Processing helix chain '5C' and resid 613 through 634 Processing helix chain '5C' and resid 641 through 644 Processing helix chain '5C' and resid 657 through 664 Processing helix chain '5D' and resid 58 through 67 Processing helix chain '5D' and resid 104 through 115 Processing helix chain '5D' and resid 141 through 153 removed outlier: 3.719A pdb=" N LEU5D 145 " --> pdb=" O ASN5D 141 " (cutoff:3.500A) Processing helix chain '5D' and resid 171 through 190 Processing helix chain '5D' and resid 212 through 221 Processing helix chain '5D' and resid 224 through 229 Processing helix chain '5D' and resid 247 through 251 Processing helix chain '5D' and resid 261 through 271 Processing helix chain '5D' and resid 451 through 462 Processing helix chain '5D' and resid 477 through 481 Processing helix chain '5D' and resid 485 through 497 Processing helix chain '5D' and resid 505 through 520 Processing helix chain '5D' and resid 543 through 545 No H-bonds generated for 'chain '5D' and resid 543 through 545' Processing helix chain '5D' and resid 546 through 551 Processing helix chain '5D' and resid 586 through 605 Processing helix chain '5D' and resid 606 through 608 No H-bonds generated for 'chain '5D' and resid 606 through 608' Processing helix chain '5D' and resid 613 through 634 Processing helix chain '5D' and resid 641 through 644 Processing helix chain '5D' and resid 657 through 664 Processing helix chain '5E' and resid 58 through 67 Processing helix chain '5E' and resid 104 through 115 Processing helix chain '5E' and resid 141 through 153 removed outlier: 3.720A pdb=" N LEU5E 145 " --> pdb=" O ASN5E 141 " (cutoff:3.500A) Processing helix chain '5E' and resid 171 through 190 Processing helix chain '5E' and resid 212 through 221 Processing helix chain '5E' and resid 224 through 229 Processing helix chain '5E' and resid 247 through 251 Processing helix chain '5E' and resid 261 through 271 Processing helix chain '5E' and resid 451 through 462 Processing helix chain '5E' and resid 477 through 481 Processing helix chain '5E' and resid 485 through 497 Processing helix chain '5E' and resid 505 through 520 Processing helix chain '5E' and resid 543 through 545 No H-bonds generated for 'chain '5E' and resid 543 through 545' Processing helix chain '5E' and resid 546 through 551 Processing helix chain '5E' and resid 586 through 605 Processing helix chain '5E' and resid 606 through 608 No H-bonds generated for 'chain '5E' and resid 606 through 608' Processing helix chain '5E' and resid 613 through 634 Processing helix chain '5E' and resid 641 through 644 Processing helix chain '5E' and resid 657 through 664 Processing helix chain '5F' and resid 58 through 67 Processing helix chain '5F' and resid 104 through 115 Processing helix chain '5F' and resid 141 through 153 removed outlier: 3.719A pdb=" N LEU5F 145 " --> pdb=" O ASN5F 141 " (cutoff:3.500A) Processing helix chain '5F' and resid 171 through 190 Processing helix chain '5F' and resid 212 through 221 Processing helix chain '5F' and resid 224 through 229 Processing helix chain '5F' and resid 247 through 251 Processing helix chain '5F' and resid 261 through 271 Processing helix chain '5F' and resid 451 through 462 Processing helix chain '5F' and resid 477 through 481 Processing helix chain '5F' and resid 485 through 497 Processing helix chain '5F' and resid 505 through 520 Processing helix chain '5F' and resid 543 through 545 No H-bonds generated for 'chain '5F' and resid 543 through 545' Processing helix chain '5F' and resid 546 through 551 Processing helix chain '5F' and resid 586 through 605 Processing helix chain '5F' and resid 606 through 608 No H-bonds generated for 'chain '5F' and resid 606 through 608' Processing helix chain '5F' and resid 613 through 634 Processing helix chain '5F' and resid 641 through 644 Processing helix chain '5F' and resid 657 through 664 Processing helix chain '3a' and resid 69 through 76 Processing helix chain '3b' and resid 69 through 76 Processing helix chain '3c' and resid 69 through 76 Processing helix chain '3d' and resid 69 through 76 Processing helix chain '3e' and resid 69 through 76 Processing helix chain '3f' and resid 69 through 76 Processing helix chain '4a' and resid 69 through 76 Processing helix chain '4b' and resid 69 through 76 Processing helix chain '4c' and resid 69 through 76 Processing helix chain '4d' and resid 69 through 76 Processing helix chain '4e' and resid 69 through 76 Processing helix chain '4f' and resid 69 through 76 Processing helix chain '5a' and resid 69 through 76 Processing helix chain '5b' and resid 69 through 76 Processing helix chain '5c' and resid 69 through 76 Processing helix chain '5d' and resid 69 through 76 Processing helix chain '5e' and resid 69 through 76 Processing helix chain '5f' and resid 69 through 76 Processing sheet with id=AA1, first strand: chain '3A' and resid 8 through 13 removed outlier: 6.290A pdb=" N GLY3A 8 " --> pdb=" O ILE3B 681 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU3B 683 " --> pdb=" O GLY3A 8 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR3A 10 " --> pdb=" O LEU3B 683 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N PHE3B 685 " --> pdb=" O TYR3A 10 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU3A 12 " --> pdb=" O PHE3B 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '3A' and resid 54 through 56 removed outlier: 7.457A pdb=" N THR3A 35 " --> pdb=" O THR3A 125 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL3A 127 " --> pdb=" O THR3A 35 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE3A 195 " --> pdb=" O LEU3A 161 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N ASN3A 559 " --> pdb=" O GLY3A 231 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA3A 233 " --> pdb=" O ASN3A 559 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE3A 561 " --> pdb=" O ALA3A 233 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR3A 235 " --> pdb=" O ILE3A 561 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N SER3A 563 " --> pdb=" O TYR3A 235 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3A' and resid 87 through 93 Processing sheet with id=AA4, first strand: chain '3A' and resid 204 through 205 Processing sheet with id=AA5, first strand: chain '3A' and resid 502 through 503 removed outlier: 3.543A pdb=" N LYS3A 536 " --> pdb=" O GLN3A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '3A' and resid 646 through 649 removed outlier: 6.297A pdb=" N MET3A 666 " --> pdb=" O ILE4A 682 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LYS4A 684 " --> pdb=" O MET3A 666 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL3A 668 " --> pdb=" O LYS4A 684 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N SER4A 686 " --> pdb=" O VAL3A 668 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE3A 670 " --> pdb=" O SER4A 686 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '3A' and resid 680 through 685 Processing sheet with id=AA8, first strand: chain '3B' and resid 8 through 13 removed outlier: 6.290A pdb=" N GLY3B 8 " --> pdb=" O ILE3C 681 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU3C 683 " --> pdb=" O GLY3B 8 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TYR3B 10 " --> pdb=" O LEU3C 683 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N PHE3C 685 " --> pdb=" O TYR3B 10 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU3B 12 " --> pdb=" O PHE3C 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain '3B' and resid 54 through 56 removed outlier: 7.456A pdb=" N THR3B 35 " --> pdb=" O THR3B 125 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL3B 127 " --> pdb=" O THR3B 35 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE3B 195 " --> pdb=" O LEU3B 161 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N ASN3B 559 " --> pdb=" O GLY3B 231 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA3B 233 " --> pdb=" O ASN3B 559 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE3B 561 " --> pdb=" O ALA3B 233 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR3B 235 " --> pdb=" O ILE3B 561 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N SER3B 563 " --> pdb=" O TYR3B 235 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3B' and resid 87 through 93 Processing sheet with id=AB2, first strand: chain '3B' and resid 204 through 205 Processing sheet with id=AB3, first strand: chain '3B' and resid 502 through 503 removed outlier: 3.542A pdb=" N LYS3B 536 " --> pdb=" O GLN3B 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '3B' and resid 646 through 649 removed outlier: 6.296A pdb=" N MET3B 666 " --> pdb=" O ILE4B 682 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LYS4B 684 " --> pdb=" O MET3B 666 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL3B 668 " --> pdb=" O LYS4B 684 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N SER4B 686 " --> pdb=" O VAL3B 668 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE3B 670 " --> pdb=" O SER4B 686 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLY4A 8 " --> pdb=" O ILE4B 681 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU4B 683 " --> pdb=" O GLY4A 8 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR4A 10 " --> pdb=" O LEU4B 683 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N PHE4B 685 " --> pdb=" O TYR4A 10 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU4A 12 " --> pdb=" O PHE4B 685 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N HIS4B 687 " --> pdb=" O GLU4A 12 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '3C' and resid 8 through 13 removed outlier: 6.289A pdb=" N GLY3C 8 " --> pdb=" O ILE3D 681 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU3D 683 " --> pdb=" O GLY3C 8 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR3C 10 " --> pdb=" O LEU3D 683 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N PHE3D 685 " --> pdb=" O TYR3C 10 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLU3C 12 " --> pdb=" O PHE3D 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain '3C' and resid 54 through 56 removed outlier: 7.457A pdb=" N THR3C 35 " --> pdb=" O THR3C 125 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL3C 127 " --> pdb=" O THR3C 35 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE3C 195 " --> pdb=" O LEU3C 161 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N ASN3C 559 " --> pdb=" O GLY3C 231 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA3C 233 " --> pdb=" O ASN3C 559 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE3C 561 " --> pdb=" O ALA3C 233 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR3C 235 " --> pdb=" O ILE3C 561 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N SER3C 563 " --> pdb=" O TYR3C 235 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '3C' and resid 87 through 93 Processing sheet with id=AB8, first strand: chain '3C' and resid 204 through 205 Processing sheet with id=AB9, first strand: chain '3C' and resid 502 through 503 removed outlier: 3.543A pdb=" N LYS3C 536 " --> pdb=" O GLN3C 239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '3C' and resid 646 through 649 removed outlier: 6.297A pdb=" N MET3C 666 " --> pdb=" O ILE4C 682 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LYS4C 684 " --> pdb=" O MET3C 666 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL3C 668 " --> pdb=" O LYS4C 684 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N SER4C 686 " --> pdb=" O VAL3C 668 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE3C 670 " --> pdb=" O SER4C 686 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLY4B 8 " --> pdb=" O ILE4C 681 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU4C 683 " --> pdb=" O GLY4B 8 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TYR4B 10 " --> pdb=" O LEU4C 683 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N PHE4C 685 " --> pdb=" O TYR4B 10 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU4B 12 " --> pdb=" O PHE4C 685 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N HIS4C 687 " --> pdb=" O GLU4B 12 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '3D' and resid 8 through 13 removed outlier: 6.290A pdb=" N GLY3D 8 " --> pdb=" O ILE3E 681 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU3E 683 " --> pdb=" O GLY3D 8 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR3D 10 " --> pdb=" O LEU3E 683 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N PHE3E 685 " --> pdb=" O TYR3D 10 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLU3D 12 " --> pdb=" O PHE3E 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain '3D' and resid 54 through 56 removed outlier: 7.457A pdb=" N THR3D 35 " --> pdb=" O THR3D 125 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL3D 127 " --> pdb=" O THR3D 35 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE3D 195 " --> pdb=" O LEU3D 161 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N ASN3D 559 " --> pdb=" O GLY3D 231 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA3D 233 " --> pdb=" O ASN3D 559 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ILE3D 561 " --> pdb=" O ALA3D 233 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR3D 235 " --> pdb=" O ILE3D 561 " (cutoff:3.500A) removed outlier: 9.120A pdb=" N SER3D 563 " --> pdb=" O TYR3D 235 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '3D' and resid 87 through 93 Processing sheet with id=AC5, first strand: chain '3D' and resid 204 through 205 Processing sheet with id=AC6, first strand: chain '3D' and resid 502 through 503 removed outlier: 3.543A pdb=" N LYS3D 536 " --> pdb=" O GLN3D 239 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '3D' and resid 646 through 649 removed outlier: 6.299A pdb=" N MET3D 666 " --> pdb=" O ILE4D 682 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LYS4D 684 " --> pdb=" O MET3D 666 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL3D 668 " --> pdb=" O LYS4D 684 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N SER4D 686 " --> pdb=" O VAL3D 668 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE3D 670 " --> pdb=" O SER4D 686 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY4C 8 " --> pdb=" O ILE4D 681 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU4D 683 " --> pdb=" O GLY4C 8 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TYR4C 10 " --> pdb=" O LEU4D 683 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N PHE4D 685 " --> pdb=" O TYR4C 10 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLU4C 12 " --> pdb=" O PHE4D 685 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N HIS4D 687 " --> pdb=" O GLU4C 12 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '3E' and resid 8 through 13 removed outlier: 6.289A pdb=" N GLY3E 8 " --> pdb=" O ILE3F 681 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU3F 683 " --> pdb=" O GLY3E 8 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR3E 10 " --> pdb=" O LEU3F 683 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N PHE3F 685 " --> pdb=" O TYR3E 10 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU3E 12 " --> pdb=" O PHE3F 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain '3E' and resid 54 through 56 removed outlier: 7.457A pdb=" N THR3E 35 " --> pdb=" O THR3E 125 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL3E 127 " --> pdb=" O THR3E 35 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE3E 195 " --> pdb=" O LEU3E 161 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N ASN3E 559 " --> pdb=" O GLY3E 231 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA3E 233 " --> pdb=" O ASN3E 559 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE3E 561 " --> pdb=" O ALA3E 233 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR3E 235 " --> pdb=" O ILE3E 561 " (cutoff:3.500A) removed outlier: 9.120A pdb=" N SER3E 563 " --> pdb=" O TYR3E 235 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '3E' and resid 87 through 93 Processing sheet with id=AD2, first strand: chain '3E' and resid 204 through 205 Processing sheet with id=AD3, first strand: chain '3E' and resid 502 through 503 removed outlier: 3.542A pdb=" N LYS3E 536 " --> pdb=" O GLN3E 239 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '3E' and resid 646 through 649 removed outlier: 6.299A pdb=" N MET3E 666 " --> pdb=" O ILE4E 682 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LYS4E 684 " --> pdb=" O MET3E 666 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL3E 668 " --> pdb=" O LYS4E 684 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N SER4E 686 " --> pdb=" O VAL3E 668 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE3E 670 " --> pdb=" O SER4E 686 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY4D 8 " --> pdb=" O ILE4E 681 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU4E 683 " --> pdb=" O GLY4D 8 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR4D 10 " --> pdb=" O LEU4E 683 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N PHE4E 685 " --> pdb=" O TYR4D 10 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLU4D 12 " --> pdb=" O PHE4E 685 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N HIS4E 687 " --> pdb=" O GLU4D 12 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '3F' and resid 54 through 56 removed outlier: 7.457A pdb=" N THR3F 35 " --> pdb=" O THR3F 125 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL3F 127 " --> pdb=" O THR3F 35 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE3F 195 " --> pdb=" O LEU3F 161 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N ASN3F 559 " --> pdb=" O GLY3F 231 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA3F 233 " --> pdb=" O ASN3F 559 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE3F 561 " --> pdb=" O ALA3F 233 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR3F 235 " --> pdb=" O ILE3F 561 " (cutoff:3.500A) removed outlier: 9.120A pdb=" N SER3F 563 " --> pdb=" O TYR3F 235 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '3F' and resid 87 through 93 Processing sheet with id=AD7, first strand: chain '3F' and resid 204 through 205 Processing sheet with id=AD8, first strand: chain '3F' and resid 502 through 503 removed outlier: 3.542A pdb=" N LYS3F 536 " --> pdb=" O GLN3F 239 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '3F' and resid 646 through 649 removed outlier: 6.298A pdb=" N MET3F 666 " --> pdb=" O ILE4F 682 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LYS4F 684 " --> pdb=" O MET3F 666 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL3F 668 " --> pdb=" O LYS4F 684 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N SER4F 686 " --> pdb=" O VAL3F 668 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE3F 670 " --> pdb=" O SER4F 686 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY4E 8 " --> pdb=" O ILE4F 681 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LEU4F 683 " --> pdb=" O GLY4E 8 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR4E 10 " --> pdb=" O LEU4F 683 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N PHE4F 685 " --> pdb=" O TYR4E 10 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU4E 12 " --> pdb=" O PHE4F 685 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N HIS4F 687 " --> pdb=" O GLU4E 12 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '4A' and resid 54 through 56 removed outlier: 7.458A pdb=" N THR4A 35 " --> pdb=" O THR4A 125 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL4A 127 " --> pdb=" O THR4A 35 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE4A 195 " --> pdb=" O LEU4A 161 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N ASN4A 559 " --> pdb=" O GLY4A 231 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA4A 233 " --> pdb=" O ASN4A 559 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE4A 561 " --> pdb=" O ALA4A 233 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR4A 235 " --> pdb=" O ILE4A 561 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N SER4A 563 " --> pdb=" O TYR4A 235 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '4A' and resid 87 through 93 Processing sheet with id=AE3, first strand: chain '4A' and resid 204 through 205 Processing sheet with id=AE4, first strand: chain '4A' and resid 502 through 503 removed outlier: 3.544A pdb=" N LYS4A 536 " --> pdb=" O GLN4A 239 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain '4A' and resid 646 through 649 removed outlier: 6.301A pdb=" N MET4A 666 " --> pdb=" O ILE5A 682 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LYS5A 684 " --> pdb=" O MET4A 666 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL4A 668 " --> pdb=" O LYS5A 684 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N SER5A 686 " --> pdb=" O VAL4A 668 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE4A 670 " --> pdb=" O SER5A 686 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '4B' and resid 54 through 56 removed outlier: 7.456A pdb=" N THR4B 35 " --> pdb=" O THR4B 125 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL4B 127 " --> pdb=" O THR4B 35 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE4B 195 " --> pdb=" O LEU4B 161 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N ASN4B 559 " --> pdb=" O GLY4B 231 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA4B 233 " --> pdb=" O ASN4B 559 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE4B 561 " --> pdb=" O ALA4B 233 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR4B 235 " --> pdb=" O ILE4B 561 " (cutoff:3.500A) removed outlier: 9.120A pdb=" N SER4B 563 " --> pdb=" O TYR4B 235 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain '4B' and resid 87 through 93 Processing sheet with id=AE8, first strand: chain '4B' and resid 204 through 205 Processing sheet with id=AE9, first strand: chain '4B' and resid 502 through 503 removed outlier: 3.543A pdb=" N LYS4B 536 " --> pdb=" O GLN4B 239 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain '4B' and resid 646 through 649 removed outlier: 6.300A pdb=" N MET4B 666 " --> pdb=" O ILE5B 682 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LYS5B 684 " --> pdb=" O MET4B 666 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL4B 668 " --> pdb=" O LYS5B 684 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N SER5B 686 " --> pdb=" O VAL4B 668 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE4B 670 " --> pdb=" O SER5B 686 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLY5A 8 " --> pdb=" O ILE5B 681 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU5B 683 " --> pdb=" O GLY5A 8 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR5A 10 " --> pdb=" O LEU5B 683 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N PHE5B 685 " --> pdb=" O TYR5A 10 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU5A 12 " --> pdb=" O PHE5B 685 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N HIS5B 687 " --> pdb=" O GLU5A 12 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain '4C' and resid 54 through 56 removed outlier: 7.457A pdb=" N THR4C 35 " --> pdb=" O THR4C 125 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL4C 127 " --> pdb=" O THR4C 35 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE4C 195 " --> pdb=" O LEU4C 161 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N ASN4C 559 " --> pdb=" O GLY4C 231 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA4C 233 " --> pdb=" O ASN4C 559 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE4C 561 " --> pdb=" O ALA4C 233 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR4C 235 " --> pdb=" O ILE4C 561 " (cutoff:3.500A) removed outlier: 9.120A pdb=" N SER4C 563 " --> pdb=" O TYR4C 235 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain '4C' and resid 87 through 93 Processing sheet with id=AF4, first strand: chain '4C' and resid 204 through 205 Processing sheet with id=AF5, first strand: chain '4C' and resid 502 through 503 removed outlier: 3.544A pdb=" N LYS4C 536 " --> pdb=" O GLN4C 239 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain '4C' and resid 646 through 649 removed outlier: 6.300A pdb=" N MET4C 666 " --> pdb=" O ILE5C 682 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LYS5C 684 " --> pdb=" O MET4C 666 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL4C 668 " --> pdb=" O LYS5C 684 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N SER5C 686 " --> pdb=" O VAL4C 668 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE4C 670 " --> pdb=" O SER5C 686 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY5B 8 " --> pdb=" O ILE5C 681 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU5C 683 " --> pdb=" O GLY5B 8 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TYR5B 10 " --> pdb=" O LEU5C 683 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N PHE5C 685 " --> pdb=" O TYR5B 10 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU5B 12 " --> pdb=" O PHE5C 685 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N HIS5C 687 " --> pdb=" O GLU5B 12 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain '4D' and resid 54 through 56 removed outlier: 7.456A pdb=" N THR4D 35 " --> pdb=" O THR4D 125 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL4D 127 " --> pdb=" O THR4D 35 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE4D 195 " --> pdb=" O LEU4D 161 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N ASN4D 559 " --> pdb=" O GLY4D 231 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA4D 233 " --> pdb=" O ASN4D 559 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ILE4D 561 " --> pdb=" O ALA4D 233 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR4D 235 " --> pdb=" O ILE4D 561 " (cutoff:3.500A) removed outlier: 9.120A pdb=" N SER4D 563 " --> pdb=" O TYR4D 235 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain '4D' and resid 87 through 93 Processing sheet with id=AF9, first strand: chain '4D' and resid 204 through 205 Processing sheet with id=AG1, first strand: chain '4D' and resid 502 through 503 removed outlier: 3.543A pdb=" N LYS4D 536 " --> pdb=" O GLN4D 239 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain '4D' and resid 646 through 649 removed outlier: 6.299A pdb=" N MET4D 666 " --> pdb=" O ILE5D 682 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LYS5D 684 " --> pdb=" O MET4D 666 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL4D 668 " --> pdb=" O LYS5D 684 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N SER5D 686 " --> pdb=" O VAL4D 668 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE4D 670 " --> pdb=" O SER5D 686 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY5C 8 " --> pdb=" O ILE5D 681 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU5D 683 " --> pdb=" O GLY5C 8 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR5C 10 " --> pdb=" O LEU5D 683 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N PHE5D 685 " --> pdb=" O TYR5C 10 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLU5C 12 " --> pdb=" O PHE5D 685 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N HIS5D 687 " --> pdb=" O GLU5C 12 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain '4E' and resid 54 through 56 removed outlier: 7.457A pdb=" N THR4E 35 " --> pdb=" O THR4E 125 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL4E 127 " --> pdb=" O THR4E 35 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE4E 195 " --> pdb=" O LEU4E 161 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N ASN4E 559 " --> pdb=" O GLY4E 231 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA4E 233 " --> pdb=" O ASN4E 559 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE4E 561 " --> pdb=" O ALA4E 233 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR4E 235 " --> pdb=" O ILE4E 561 " (cutoff:3.500A) removed outlier: 9.120A pdb=" N SER4E 563 " --> pdb=" O TYR4E 235 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain '4E' and resid 87 through 93 Processing sheet with id=AG5, first strand: chain '4E' and resid 204 through 205 Processing sheet with id=AG6, first strand: chain '4E' and resid 502 through 503 removed outlier: 3.542A pdb=" N LYS4E 536 " --> pdb=" O GLN4E 239 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain '4E' and resid 646 through 649 removed outlier: 6.300A pdb=" N MET4E 666 " --> pdb=" O ILE5E 682 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LYS5E 684 " --> pdb=" O MET4E 666 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL4E 668 " --> pdb=" O LYS5E 684 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N SER5E 686 " --> pdb=" O VAL4E 668 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE4E 670 " --> pdb=" O SER5E 686 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLY5D 8 " --> pdb=" O ILE5E 681 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LEU5E 683 " --> pdb=" O GLY5D 8 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR5D 10 " --> pdb=" O LEU5E 683 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N PHE5E 685 " --> pdb=" O TYR5D 10 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU5D 12 " --> pdb=" O PHE5E 685 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N HIS5E 687 " --> pdb=" O GLU5D 12 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain '4F' and resid 54 through 56 removed outlier: 7.457A pdb=" N THR4F 35 " --> pdb=" O THR4F 125 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL4F 127 " --> pdb=" O THR4F 35 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE4F 195 " --> pdb=" O LEU4F 161 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N ASN4F 559 " --> pdb=" O GLY4F 231 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA4F 233 " --> pdb=" O ASN4F 559 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE4F 561 " --> pdb=" O ALA4F 233 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR4F 235 " --> pdb=" O ILE4F 561 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N SER4F 563 " --> pdb=" O TYR4F 235 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain '4F' and resid 87 through 93 Processing sheet with id=AH1, first strand: chain '4F' and resid 204 through 205 Processing sheet with id=AH2, first strand: chain '4F' and resid 502 through 503 removed outlier: 3.542A pdb=" N LYS4F 536 " --> pdb=" O GLN4F 239 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '4F' and resid 646 through 649 removed outlier: 6.301A pdb=" N MET4F 666 " --> pdb=" O ILE5F 682 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LYS5F 684 " --> pdb=" O MET4F 666 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL4F 668 " --> pdb=" O LYS5F 684 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N SER5F 686 " --> pdb=" O VAL4F 668 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE4F 670 " --> pdb=" O SER5F 686 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLY5E 8 " --> pdb=" O ILE5F 681 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LEU5F 683 " --> pdb=" O GLY5E 8 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR5E 10 " --> pdb=" O LEU5F 683 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N PHE5F 685 " --> pdb=" O TYR5E 10 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU5E 12 " --> pdb=" O PHE5F 685 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N HIS5F 687 " --> pdb=" O GLU5E 12 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain '5A' and resid 54 through 56 removed outlier: 7.457A pdb=" N THR5A 35 " --> pdb=" O THR5A 125 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL5A 127 " --> pdb=" O THR5A 35 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE5A 195 " --> pdb=" O LEU5A 161 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N ASN5A 559 " --> pdb=" O GLY5A 231 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA5A 233 " --> pdb=" O ASN5A 559 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE5A 561 " --> pdb=" O ALA5A 233 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR5A 235 " --> pdb=" O ILE5A 561 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N SER5A 563 " --> pdb=" O TYR5A 235 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain '5A' and resid 87 through 93 Processing sheet with id=AH6, first strand: chain '5A' and resid 204 through 205 Processing sheet with id=AH7, first strand: chain '5A' and resid 502 through 503 removed outlier: 3.544A pdb=" N LYS5A 536 " --> pdb=" O GLN5A 239 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain '5A' and resid 646 through 649 Processing sheet with id=AH9, first strand: chain '5B' and resid 54 through 56 removed outlier: 7.457A pdb=" N THR5B 35 " --> pdb=" O THR5B 125 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL5B 127 " --> pdb=" O THR5B 35 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE5B 195 " --> pdb=" O LEU5B 161 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N ASN5B 559 " --> pdb=" O GLY5B 231 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA5B 233 " --> pdb=" O ASN5B 559 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE5B 561 " --> pdb=" O ALA5B 233 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N TYR5B 235 " --> pdb=" O ILE5B 561 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N SER5B 563 " --> pdb=" O TYR5B 235 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain '5B' and resid 87 through 93 Processing sheet with id=AI2, first strand: chain '5B' and resid 204 through 205 Processing sheet with id=AI3, first strand: chain '5B' and resid 502 through 503 removed outlier: 3.543A pdb=" N LYS5B 536 " --> pdb=" O GLN5B 239 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain '5B' and resid 646 through 649 Processing sheet with id=AI5, first strand: chain '5C' and resid 54 through 56 removed outlier: 7.457A pdb=" N THR5C 35 " --> pdb=" O THR5C 125 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL5C 127 " --> pdb=" O THR5C 35 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE5C 195 " --> pdb=" O LEU5C 161 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N ASN5C 559 " --> pdb=" O GLY5C 231 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA5C 233 " --> pdb=" O ASN5C 559 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE5C 561 " --> pdb=" O ALA5C 233 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR5C 235 " --> pdb=" O ILE5C 561 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N SER5C 563 " --> pdb=" O TYR5C 235 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain '5C' and resid 87 through 93 Processing sheet with id=AI7, first strand: chain '5C' and resid 204 through 205 Processing sheet with id=AI8, first strand: chain '5C' and resid 502 through 503 removed outlier: 3.543A pdb=" N LYS5C 536 " --> pdb=" O GLN5C 239 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain '5C' and resid 646 through 649 Processing sheet with id=AJ1, first strand: chain '5D' and resid 54 through 56 removed outlier: 7.456A pdb=" N THR5D 35 " --> pdb=" O THR5D 125 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL5D 127 " --> pdb=" O THR5D 35 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE5D 195 " --> pdb=" O LEU5D 161 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N ASN5D 559 " --> pdb=" O GLY5D 231 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA5D 233 " --> pdb=" O ASN5D 559 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ILE5D 561 " --> pdb=" O ALA5D 233 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR5D 235 " --> pdb=" O ILE5D 561 " (cutoff:3.500A) removed outlier: 9.120A pdb=" N SER5D 563 " --> pdb=" O TYR5D 235 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain '5D' and resid 87 through 93 Processing sheet with id=AJ3, first strand: chain '5D' and resid 204 through 205 Processing sheet with id=AJ4, first strand: chain '5D' and resid 502 through 503 removed outlier: 3.543A pdb=" N LYS5D 536 " --> pdb=" O GLN5D 239 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain '5D' and resid 646 through 649 Processing sheet with id=AJ6, first strand: chain '5E' and resid 54 through 56 removed outlier: 7.457A pdb=" N THR5E 35 " --> pdb=" O THR5E 125 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL5E 127 " --> pdb=" O THR5E 35 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE5E 195 " --> pdb=" O LEU5E 161 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N ASN5E 559 " --> pdb=" O GLY5E 231 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA5E 233 " --> pdb=" O ASN5E 559 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE5E 561 " --> pdb=" O ALA5E 233 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR5E 235 " --> pdb=" O ILE5E 561 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N SER5E 563 " --> pdb=" O TYR5E 235 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain '5E' and resid 87 through 93 Processing sheet with id=AJ8, first strand: chain '5E' and resid 204 through 205 Processing sheet with id=AJ9, first strand: chain '5E' and resid 502 through 503 removed outlier: 3.543A pdb=" N LYS5E 536 " --> pdb=" O GLN5E 239 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain '5E' and resid 646 through 649 Processing sheet with id=AK2, first strand: chain '5F' and resid 54 through 56 removed outlier: 7.456A pdb=" N THR5F 35 " --> pdb=" O THR5F 125 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL5F 127 " --> pdb=" O THR5F 35 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE5F 195 " --> pdb=" O LEU5F 161 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N ASN5F 559 " --> pdb=" O GLY5F 231 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA5F 233 " --> pdb=" O ASN5F 559 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE5F 561 " --> pdb=" O ALA5F 233 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N TYR5F 235 " --> pdb=" O ILE5F 561 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N SER5F 563 " --> pdb=" O TYR5F 235 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain '5F' and resid 87 through 93 Processing sheet with id=AK4, first strand: chain '5F' and resid 204 through 205 Processing sheet with id=AK5, first strand: chain '5F' and resid 502 through 503 removed outlier: 3.542A pdb=" N LYS5F 536 " --> pdb=" O GLN5F 239 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain '5F' and resid 646 through 649 Processing sheet with id=AK7, first strand: chain '3a' and resid 10 through 13 removed outlier: 5.285A pdb=" N ARG3a 86 " --> pdb=" O ASN3a 107 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN3a 107 " --> pdb=" O ARG3a 86 " (cutoff:3.500A) removed outlier: 16.660A pdb=" N ASN3a 107 " --> pdb=" O GLU3b 35 " (cutoff:3.500A) removed outlier: 12.598A pdb=" N GLU3b 35 " --> pdb=" O ASN3a 107 " (cutoff:3.500A) removed outlier: 13.300A pdb=" N TRP3a 109 " --> pdb=" O ILE3b 33 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N ILE3b 33 " --> pdb=" O TRP3a 109 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU3a 111 " --> pdb=" O THR3b 31 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ASP3b 28 " --> pdb=" O PHE3b 55 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N PHE3b 55 " --> pdb=" O ASP3b 28 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLU3b 30 " --> pdb=" O GLN3b 53 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLN3b 53 " --> pdb=" O GLU3b 30 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU3b 32 " --> pdb=" O GLY3b 51 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain '3a' and resid 137 through 140 removed outlier: 6.362A pdb=" N ALA3a 133 " --> pdb=" O PRO3a 110 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain '3a' and resid 47 through 55 removed outlier: 4.990A pdb=" N GLU3a 32 " --> pdb=" O GLY3a 51 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLN3a 53 " --> pdb=" O GLU3a 30 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLU3a 30 " --> pdb=" O GLN3a 53 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N PHE3a 55 " --> pdb=" O ASP3a 28 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ASP3a 28 " --> pdb=" O PHE3a 55 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU3f 111 " --> pdb=" O THR3a 31 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N ILE3a 33 " --> pdb=" O TRP3f 109 " (cutoff:3.500A) removed outlier: 13.300A pdb=" N TRP3f 109 " --> pdb=" O ILE3a 33 " (cutoff:3.500A) removed outlier: 12.598A pdb=" N GLU3a 35 " --> pdb=" O ASN3f 107 " (cutoff:3.500A) removed outlier: 16.660A pdb=" N ASN3f 107 " --> pdb=" O GLU3a 35 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN3f 107 " --> pdb=" O ARG3f 86 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ARG3f 86 " --> pdb=" O ASN3f 107 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain '3e' and resid 118 through 119 removed outlier: 6.362A pdb=" N ALA3f 133 " --> pdb=" O PRO3f 110 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain '3a' and resid 118 through 119 removed outlier: 6.361A pdb=" N ALA3b 133 " --> pdb=" O PRO3b 110 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain '3b' and resid 10 through 13 removed outlier: 5.285A pdb=" N ARG3b 86 " --> pdb=" O ASN3b 107 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN3b 107 " --> pdb=" O ARG3b 86 " (cutoff:3.500A) removed outlier: 16.659A pdb=" N ASN3b 107 " --> pdb=" O GLU3c 35 " (cutoff:3.500A) removed outlier: 12.599A pdb=" N GLU3c 35 " --> pdb=" O ASN3b 107 " (cutoff:3.500A) removed outlier: 13.301A pdb=" N TRP3b 109 " --> pdb=" O ILE3c 33 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N ILE3c 33 " --> pdb=" O TRP3b 109 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU3b 111 " --> pdb=" O THR3c 31 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ASP3c 28 " --> pdb=" O PHE3c 55 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N PHE3c 55 " --> pdb=" O ASP3c 28 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLU3c 30 " --> pdb=" O GLN3c 53 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLN3c 53 " --> pdb=" O GLU3c 30 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU3c 32 " --> pdb=" O GLY3c 51 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain '3b' and resid 118 through 119 removed outlier: 6.362A pdb=" N ALA3c 133 " --> pdb=" O PRO3c 110 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain '3c' and resid 10 through 13 removed outlier: 5.285A pdb=" N ARG3c 86 " --> pdb=" O ASN3c 107 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN3c 107 " --> pdb=" O ARG3c 86 " (cutoff:3.500A) removed outlier: 16.660A pdb=" N ASN3c 107 " --> pdb=" O GLU3d 35 " (cutoff:3.500A) removed outlier: 12.599A pdb=" N GLU3d 35 " --> pdb=" O ASN3c 107 " (cutoff:3.500A) removed outlier: 13.301A pdb=" N TRP3c 109 " --> pdb=" O ILE3d 33 " (cutoff:3.500A) removed outlier: 10.068A pdb=" N ILE3d 33 " --> pdb=" O TRP3c 109 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU3c 111 " --> pdb=" O THR3d 31 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ASP3d 28 " --> pdb=" O PHE3d 55 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N PHE3d 55 " --> pdb=" O ASP3d 28 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLU3d 30 " --> pdb=" O GLN3d 53 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLN3d 53 " --> pdb=" O GLU3d 30 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU3d 32 " --> pdb=" O GLY3d 51 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain '3c' and resid 118 through 119 removed outlier: 6.361A pdb=" N ALA3d 133 " --> pdb=" O PRO3d 110 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain '3d' and resid 10 through 13 removed outlier: 5.285A pdb=" N ARG3d 86 " --> pdb=" O ASN3d 107 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN3d 107 " --> pdb=" O ARG3d 86 " (cutoff:3.500A) removed outlier: 16.660A pdb=" N ASN3d 107 " --> pdb=" O GLU3e 35 " (cutoff:3.500A) removed outlier: 12.598A pdb=" N GLU3e 35 " --> pdb=" O ASN3d 107 " (cutoff:3.500A) removed outlier: 13.301A pdb=" N TRP3d 109 " --> pdb=" O ILE3e 33 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N ILE3e 33 " --> pdb=" O TRP3d 109 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU3d 111 " --> pdb=" O THR3e 31 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ASP3e 28 " --> pdb=" O PHE3e 55 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N PHE3e 55 " --> pdb=" O ASP3e 28 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLU3e 30 " --> pdb=" O GLN3e 53 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLN3e 53 " --> pdb=" O GLU3e 30 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N GLU3e 32 " --> pdb=" O GLY3e 51 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain '3d' and resid 118 through 119 removed outlier: 6.361A pdb=" N ALA3e 133 " --> pdb=" O PRO3e 110 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain '3e' and resid 10 through 13 removed outlier: 5.285A pdb=" N ARG3e 86 " --> pdb=" O ASN3e 107 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN3e 107 " --> pdb=" O ARG3e 86 " (cutoff:3.500A) removed outlier: 16.660A pdb=" N ASN3e 107 " --> pdb=" O GLU3f 35 " (cutoff:3.500A) removed outlier: 12.598A pdb=" N GLU3f 35 " --> pdb=" O ASN3e 107 " (cutoff:3.500A) removed outlier: 13.300A pdb=" N TRP3e 109 " --> pdb=" O ILE3f 33 " (cutoff:3.500A) removed outlier: 10.068A pdb=" N ILE3f 33 " --> pdb=" O TRP3e 109 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU3e 111 " --> pdb=" O THR3f 31 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ASP3f 28 " --> pdb=" O PHE3f 55 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N PHE3f 55 " --> pdb=" O ASP3f 28 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU3f 30 " --> pdb=" O GLN3f 53 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLN3f 53 " --> pdb=" O GLU3f 30 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU3f 32 " --> pdb=" O GLY3f 51 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain '4a' and resid 10 through 13 removed outlier: 5.284A pdb=" N ARG4a 86 " --> pdb=" O ASN4a 107 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN4a 107 " --> pdb=" O ARG4a 86 " (cutoff:3.500A) removed outlier: 16.659A pdb=" N ASN4a 107 " --> pdb=" O GLU4b 35 " (cutoff:3.500A) removed outlier: 12.598A pdb=" N GLU4b 35 " --> pdb=" O ASN4a 107 " (cutoff:3.500A) removed outlier: 13.300A pdb=" N TRP4a 109 " --> pdb=" O ILE4b 33 " (cutoff:3.500A) removed outlier: 10.068A pdb=" N ILE4b 33 " --> pdb=" O TRP4a 109 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU4a 111 " --> pdb=" O THR4b 31 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ASP4b 28 " --> pdb=" O PHE4b 55 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N PHE4b 55 " --> pdb=" O ASP4b 28 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLU4b 30 " --> pdb=" O GLN4b 53 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLN4b 53 " --> pdb=" O GLU4b 30 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU4b 32 " --> pdb=" O GLY4b 51 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain '4a' and resid 137 through 140 removed outlier: 6.362A pdb=" N ALA4a 133 " --> pdb=" O PRO4a 110 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain '4a' and resid 47 through 55 removed outlier: 4.989A pdb=" N GLU4a 32 " --> pdb=" O GLY4a 51 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLN4a 53 " --> pdb=" O GLU4a 30 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLU4a 30 " --> pdb=" O GLN4a 53 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N PHE4a 55 " --> pdb=" O ASP4a 28 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ASP4a 28 " --> pdb=" O PHE4a 55 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU4f 111 " --> pdb=" O THR4a 31 " (cutoff:3.500A) removed outlier: 10.068A pdb=" N ILE4a 33 " --> pdb=" O TRP4f 109 " (cutoff:3.500A) removed outlier: 13.301A pdb=" N TRP4f 109 " --> pdb=" O ILE4a 33 " (cutoff:3.500A) removed outlier: 12.597A pdb=" N GLU4a 35 " --> pdb=" O ASN4f 107 " (cutoff:3.500A) removed outlier: 16.660A pdb=" N ASN4f 107 " --> pdb=" O GLU4a 35 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN4f 107 " --> pdb=" O ARG4f 86 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ARG4f 86 " --> pdb=" O ASN4f 107 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain '4e' and resid 118 through 119 removed outlier: 6.362A pdb=" N ALA4f 133 " --> pdb=" O PRO4f 110 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain '4a' and resid 118 through 119 removed outlier: 6.362A pdb=" N ALA4b 133 " --> pdb=" O PRO4b 110 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain '4b' and resid 10 through 13 removed outlier: 5.285A pdb=" N ARG4b 86 " --> pdb=" O ASN4b 107 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN4b 107 " --> pdb=" O ARG4b 86 " (cutoff:3.500A) removed outlier: 16.659A pdb=" N ASN4b 107 " --> pdb=" O GLU4c 35 " (cutoff:3.500A) removed outlier: 12.598A pdb=" N GLU4c 35 " --> pdb=" O ASN4b 107 " (cutoff:3.500A) removed outlier: 13.300A pdb=" N TRP4b 109 " --> pdb=" O ILE4c 33 " (cutoff:3.500A) removed outlier: 10.068A pdb=" N ILE4c 33 " --> pdb=" O TRP4b 109 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU4b 111 " --> pdb=" O THR4c 31 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ASP4c 28 " --> pdb=" O PHE4c 55 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N PHE4c 55 " --> pdb=" O ASP4c 28 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLU4c 30 " --> pdb=" O GLN4c 53 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLN4c 53 " --> pdb=" O GLU4c 30 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU4c 32 " --> pdb=" O GLY4c 51 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain '4b' and resid 118 through 119 removed outlier: 6.361A pdb=" N ALA4c 133 " --> pdb=" O PRO4c 110 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain '4c' and resid 10 through 13 removed outlier: 5.285A pdb=" N ARG4c 86 " --> pdb=" O ASN4c 107 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN4c 107 " --> pdb=" O ARG4c 86 " (cutoff:3.500A) removed outlier: 16.660A pdb=" N ASN4c 107 " --> pdb=" O GLU4d 35 " (cutoff:3.500A) removed outlier: 12.599A pdb=" N GLU4d 35 " --> pdb=" O ASN4c 107 " (cutoff:3.500A) removed outlier: 13.301A pdb=" N TRP4c 109 " --> pdb=" O ILE4d 33 " (cutoff:3.500A) removed outlier: 10.068A pdb=" N ILE4d 33 " --> pdb=" O TRP4c 109 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU4c 111 " --> pdb=" O THR4d 31 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ASP4d 28 " --> pdb=" O PHE4d 55 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N PHE4d 55 " --> pdb=" O ASP4d 28 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLU4d 30 " --> pdb=" O GLN4d 53 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLN4d 53 " --> pdb=" O GLU4d 30 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU4d 32 " --> pdb=" O GLY4d 51 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain '4c' and resid 118 through 119 removed outlier: 6.362A pdb=" N ALA4d 133 " --> pdb=" O PRO4d 110 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain '4d' and resid 10 through 13 removed outlier: 5.285A pdb=" N ARG4d 86 " --> pdb=" O ASN4d 107 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN4d 107 " --> pdb=" O ARG4d 86 " (cutoff:3.500A) removed outlier: 16.659A pdb=" N ASN4d 107 " --> pdb=" O GLU4e 35 " (cutoff:3.500A) removed outlier: 12.598A pdb=" N GLU4e 35 " --> pdb=" O ASN4d 107 " (cutoff:3.500A) removed outlier: 13.300A pdb=" N TRP4d 109 " --> pdb=" O ILE4e 33 " (cutoff:3.500A) removed outlier: 10.068A pdb=" N ILE4e 33 " --> pdb=" O TRP4d 109 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU4d 111 " --> pdb=" O THR4e 31 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ASP4e 28 " --> pdb=" O PHE4e 55 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N PHE4e 55 " --> pdb=" O ASP4e 28 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLU4e 30 " --> pdb=" O GLN4e 53 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLN4e 53 " --> pdb=" O GLU4e 30 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU4e 32 " --> pdb=" O GLY4e 51 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain '4d' and resid 118 through 119 removed outlier: 6.362A pdb=" N ALA4e 133 " --> pdb=" O PRO4e 110 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain '4e' and resid 10 through 13 removed outlier: 5.285A pdb=" N ARG4e 86 " --> pdb=" O ASN4e 107 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN4e 107 " --> pdb=" O ARG4e 86 " (cutoff:3.500A) removed outlier: 16.660A pdb=" N ASN4e 107 " --> pdb=" O GLU4f 35 " (cutoff:3.500A) removed outlier: 12.598A pdb=" N GLU4f 35 " --> pdb=" O ASN4e 107 " (cutoff:3.500A) removed outlier: 13.301A pdb=" N TRP4e 109 " --> pdb=" O ILE4f 33 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N ILE4f 33 " --> pdb=" O TRP4e 109 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU4e 111 " --> pdb=" O THR4f 31 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ASP4f 28 " --> pdb=" O PHE4f 55 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N PHE4f 55 " --> pdb=" O ASP4f 28 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU4f 30 " --> pdb=" O GLN4f 53 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLN4f 53 " --> pdb=" O GLU4f 30 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU4f 32 " --> pdb=" O GLY4f 51 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain '5a' and resid 10 through 13 removed outlier: 5.284A pdb=" N ARG5a 86 " --> pdb=" O ASN5a 107 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN5a 107 " --> pdb=" O ARG5a 86 " (cutoff:3.500A) removed outlier: 16.660A pdb=" N ASN5a 107 " --> pdb=" O GLU5b 35 " (cutoff:3.500A) removed outlier: 12.599A pdb=" N GLU5b 35 " --> pdb=" O ASN5a 107 " (cutoff:3.500A) removed outlier: 13.300A pdb=" N TRP5a 109 " --> pdb=" O ILE5b 33 " (cutoff:3.500A) removed outlier: 10.068A pdb=" N ILE5b 33 " --> pdb=" O TRP5a 109 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU5a 111 " --> pdb=" O THR5b 31 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ASP5b 28 " --> pdb=" O PHE5b 55 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N PHE5b 55 " --> pdb=" O ASP5b 28 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLU5b 30 " --> pdb=" O GLN5b 53 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLN5b 53 " --> pdb=" O GLU5b 30 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU5b 32 " --> pdb=" O GLY5b 51 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain '5a' and resid 137 through 140 removed outlier: 6.362A pdb=" N ALA5a 133 " --> pdb=" O PRO5a 110 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain '5a' and resid 47 through 55 removed outlier: 4.989A pdb=" N GLU5a 32 " --> pdb=" O GLY5a 51 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLN5a 53 " --> pdb=" O GLU5a 30 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLU5a 30 " --> pdb=" O GLN5a 53 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N PHE5a 55 " --> pdb=" O ASP5a 28 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ASP5a 28 " --> pdb=" O PHE5a 55 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU5f 111 " --> pdb=" O THR5a 31 " (cutoff:3.500A) removed outlier: 10.068A pdb=" N ILE5a 33 " --> pdb=" O TRP5f 109 " (cutoff:3.500A) removed outlier: 13.300A pdb=" N TRP5f 109 " --> pdb=" O ILE5a 33 " (cutoff:3.500A) removed outlier: 12.598A pdb=" N GLU5a 35 " --> pdb=" O ASN5f 107 " (cutoff:3.500A) removed outlier: 16.659A pdb=" N ASN5f 107 " --> pdb=" O GLU5a 35 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN5f 107 " --> pdb=" O ARG5f 86 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ARG5f 86 " --> pdb=" O ASN5f 107 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain '5e' and resid 118 through 119 removed outlier: 6.362A pdb=" N ALA5f 133 " --> pdb=" O PRO5f 110 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain '5a' and resid 118 through 119 removed outlier: 6.362A pdb=" N ALA5b 133 " --> pdb=" O PRO5b 110 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain '5b' and resid 10 through 13 removed outlier: 5.284A pdb=" N ARG5b 86 " --> pdb=" O ASN5b 107 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN5b 107 " --> pdb=" O ARG5b 86 " (cutoff:3.500A) removed outlier: 16.660A pdb=" N ASN5b 107 " --> pdb=" O GLU5c 35 " (cutoff:3.500A) removed outlier: 12.598A pdb=" N GLU5c 35 " --> pdb=" O ASN5b 107 " (cutoff:3.500A) removed outlier: 13.300A pdb=" N TRP5b 109 " --> pdb=" O ILE5c 33 " (cutoff:3.500A) removed outlier: 10.068A pdb=" N ILE5c 33 " --> pdb=" O TRP5b 109 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU5b 111 " --> pdb=" O THR5c 31 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ASP5c 28 " --> pdb=" O PHE5c 55 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N PHE5c 55 " --> pdb=" O ASP5c 28 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLU5c 30 " --> pdb=" O GLN5c 53 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLN5c 53 " --> pdb=" O GLU5c 30 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU5c 32 " --> pdb=" O GLY5c 51 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain '5b' and resid 118 through 119 removed outlier: 6.362A pdb=" N ALA5c 133 " --> pdb=" O PRO5c 110 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain '5c' and resid 10 through 13 removed outlier: 5.285A pdb=" N ARG5c 86 " --> pdb=" O ASN5c 107 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN5c 107 " --> pdb=" O ARG5c 86 " (cutoff:3.500A) removed outlier: 16.660A pdb=" N ASN5c 107 " --> pdb=" O GLU5d 35 " (cutoff:3.500A) removed outlier: 12.598A pdb=" N GLU5d 35 " --> pdb=" O ASN5c 107 " (cutoff:3.500A) removed outlier: 13.301A pdb=" N TRP5c 109 " --> pdb=" O ILE5d 33 " (cutoff:3.500A) removed outlier: 10.068A pdb=" N ILE5d 33 " --> pdb=" O TRP5c 109 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU5c 111 " --> pdb=" O THR5d 31 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ASP5d 28 " --> pdb=" O PHE5d 55 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N PHE5d 55 " --> pdb=" O ASP5d 28 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLU5d 30 " --> pdb=" O GLN5d 53 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLN5d 53 " --> pdb=" O GLU5d 30 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N GLU5d 32 " --> pdb=" O GLY5d 51 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain '5c' and resid 118 through 119 removed outlier: 6.362A pdb=" N ALA5d 133 " --> pdb=" O PRO5d 110 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain '5d' and resid 10 through 13 removed outlier: 5.285A pdb=" N ARG5d 86 " --> pdb=" O ASN5d 107 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN5d 107 " --> pdb=" O ARG5d 86 " (cutoff:3.500A) removed outlier: 16.660A pdb=" N ASN5d 107 " --> pdb=" O GLU5e 35 " (cutoff:3.500A) removed outlier: 12.598A pdb=" N GLU5e 35 " --> pdb=" O ASN5d 107 " (cutoff:3.500A) removed outlier: 13.300A pdb=" N TRP5d 109 " --> pdb=" O ILE5e 33 " (cutoff:3.500A) removed outlier: 10.068A pdb=" N ILE5e 33 " --> pdb=" O TRP5d 109 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU5d 111 " --> pdb=" O THR5e 31 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ASP5e 28 " --> pdb=" O PHE5e 55 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N PHE5e 55 " --> pdb=" O ASP5e 28 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLU5e 30 " --> pdb=" O GLN5e 53 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLN5e 53 " --> pdb=" O GLU5e 30 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU5e 32 " --> pdb=" O GLY5e 51 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain '5d' and resid 118 through 119 removed outlier: 6.363A pdb=" N ALA5e 133 " --> pdb=" O PRO5e 110 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain '5e' and resid 10 through 13 removed outlier: 5.284A pdb=" N ARG5e 86 " --> pdb=" O ASN5e 107 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN5e 107 " --> pdb=" O ARG5e 86 " (cutoff:3.500A) removed outlier: 16.660A pdb=" N ASN5e 107 " --> pdb=" O GLU5f 35 " (cutoff:3.500A) removed outlier: 12.598A pdb=" N GLU5f 35 " --> pdb=" O ASN5e 107 " (cutoff:3.500A) removed outlier: 13.300A pdb=" N TRP5e 109 " --> pdb=" O ILE5f 33 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N ILE5f 33 " --> pdb=" O TRP5e 109 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU5e 111 " --> pdb=" O THR5f 31 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ASP5f 28 " --> pdb=" O PHE5f 55 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N PHE5f 55 " --> pdb=" O ASP5f 28 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLU5f 30 " --> pdb=" O GLN5f 53 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLN5f 53 " --> pdb=" O GLU5f 30 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU5f 32 " --> pdb=" O GLY5f 51 " (cutoff:3.500A) 3831 hydrogen bonds defined for protein. 10665 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: 52.41 Time building geometry restraints manager: 28.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 17645 1.32 - 1.45: 25359 1.45 - 1.58: 51171 1.58 - 1.72: 163 1.72 - 1.85: 504 Bond restraints: 94842 Sorted by residual: bond pdb=" CB LEU4B 478 " pdb=" CG LEU4B 478 " ideal model delta sigma weight residual 1.530 1.437 0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" CB LEU3B 478 " pdb=" CG LEU3B 478 " ideal model delta sigma weight residual 1.530 1.437 0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" CB LEU5E 478 " pdb=" CG LEU5E 478 " ideal model delta sigma weight residual 1.530 1.438 0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" CB LEU5B 478 " pdb=" CG LEU5B 478 " ideal model delta sigma weight residual 1.530 1.438 0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" CB LEU4A 478 " pdb=" CG LEU4A 478 " ideal model delta sigma weight residual 1.530 1.438 0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 94837 not shown) Histogram of bond angle deviations from ideal: 97.26 - 105.01: 2024 105.01 - 112.75: 44582 112.75 - 120.50: 47224 120.50 - 128.25: 34528 128.25 - 136.00: 648 Bond angle restraints: 129006 Sorted by residual: angle pdb=" C PRO5E 18 " pdb=" N PRO5E 19 " pdb=" CA PRO5E 19 " ideal model delta sigma weight residual 120.03 128.04 -8.01 9.90e-01 1.02e+00 6.54e+01 angle pdb=" C PRO5F 18 " pdb=" N PRO5F 19 " pdb=" CA PRO5F 19 " ideal model delta sigma weight residual 120.03 128.02 -7.99 9.90e-01 1.02e+00 6.52e+01 angle pdb=" C PRO3F 18 " pdb=" N PRO3F 19 " pdb=" CA PRO3F 19 " ideal model delta sigma weight residual 120.03 128.02 -7.99 9.90e-01 1.02e+00 6.52e+01 angle pdb=" C PRO5A 18 " pdb=" N PRO5A 19 " pdb=" CA PRO5A 19 " ideal model delta sigma weight residual 120.03 128.02 -7.99 9.90e-01 1.02e+00 6.51e+01 angle pdb=" C PRO4C 18 " pdb=" N PRO4C 19 " pdb=" CA PRO4C 19 " ideal model delta sigma weight residual 120.03 128.01 -7.98 9.90e-01 1.02e+00 6.51e+01 ... (remaining 129001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.74: 53674 14.74 - 29.49: 2126 29.49 - 44.23: 504 44.23 - 58.97: 90 58.97 - 73.71: 162 Dihedral angle restraints: 56556 sinusoidal: 22392 harmonic: 34164 Sorted by residual: dihedral pdb=" C ILE5F 214 " pdb=" N ILE5F 214 " pdb=" CA ILE5F 214 " pdb=" CB ILE5F 214 " ideal model delta harmonic sigma weight residual -122.00 -131.51 9.51 0 2.50e+00 1.60e-01 1.45e+01 dihedral pdb=" C TYR4B 204 " pdb=" N TYR4B 204 " pdb=" CA TYR4B 204 " pdb=" CB TYR4B 204 " ideal model delta harmonic sigma weight residual -122.60 -132.11 9.51 0 2.50e+00 1.60e-01 1.45e+01 dihedral pdb=" C TYR5C 204 " pdb=" N TYR5C 204 " pdb=" CA TYR5C 204 " pdb=" CB TYR5C 204 " ideal model delta harmonic sigma weight residual -122.60 -132.10 9.50 0 2.50e+00 1.60e-01 1.44e+01 ... (remaining 56553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 12473 0.143 - 0.286: 1782 0.286 - 0.429: 73 0.429 - 0.572: 0 0.572 - 0.715: 18 Chirality restraints: 14346 Sorted by residual: chirality pdb=" CG LEU4e 80 " pdb=" CB LEU4e 80 " pdb=" CD1 LEU4e 80 " pdb=" CD2 LEU4e 80 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" CG LEU4c 80 " pdb=" CB LEU4c 80 " pdb=" CD1 LEU4c 80 " pdb=" CD2 LEU4c 80 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" CG LEU5a 80 " pdb=" CB LEU5a 80 " pdb=" CD1 LEU5a 80 " pdb=" CD2 LEU5a 80 " both_signs ideal model delta sigma weight residual False -2.59 -1.88 -0.71 2.00e-01 2.50e+01 1.28e+01 ... (remaining 14343 not shown) Planarity restraints: 16776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU4f 30 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" CD GLU4f 30 " 0.062 2.00e-02 2.50e+03 pdb=" OE1 GLU4f 30 " -0.022 2.00e-02 2.50e+03 pdb=" OE2 GLU4f 30 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU5d 30 " -0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" CD GLU5d 30 " 0.062 2.00e-02 2.50e+03 pdb=" OE1 GLU5d 30 " -0.022 2.00e-02 2.50e+03 pdb=" OE2 GLU5d 30 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU3c 30 " -0.017 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" CD GLU3c 30 " 0.062 2.00e-02 2.50e+03 pdb=" OE1 GLU3c 30 " -0.022 2.00e-02 2.50e+03 pdb=" OE2 GLU3c 30 " -0.022 2.00e-02 2.50e+03 ... (remaining 16773 not shown) Histogram of nonbonded interaction distances: 1.12 - 1.87: 36 1.87 - 2.63: 812 2.63 - 3.39: 109883 3.39 - 4.14: 224125 4.14 - 4.90: 391533 Nonbonded interactions: 726389 Sorted by model distance: nonbonded pdb=" OG SER3B 43 " pdb=" CG2 THR4B 91 " model vdw 1.115 3.460 nonbonded pdb=" OG SER3C 43 " pdb=" CG2 THR4C 91 " model vdw 1.115 3.460 nonbonded pdb=" OG SER4D 43 " pdb=" CG2 THR5D 91 " model vdw 1.118 3.460 nonbonded pdb=" OG SER4E 43 " pdb=" CG2 THR5E 91 " model vdw 1.121 3.460 nonbonded pdb=" OG SER3A 43 " pdb=" CG2 THR4A 91 " model vdw 1.122 3.460 ... (remaining 726384 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 '3A' selection = chain '3B' selection = chain '3C' selection = chain '3D' selection = chain '3E' selection = chain '3F' selection = chain '4A' selection = chain '4B' selection = chain '4C' selection = chain '4D' selection = chain '4E' selection = chain '4F' selection = chain '5A' selection = chain '5B' selection = chain '5C' selection = chain '5D' selection = chain '5E' selection = chain '5F' } ncs_group { reference = chain '3a' selection = chain '3b' selection = chain '3c' selection = chain '3d' selection = chain '3e' selection = chain '3f' selection = chain '4a' selection = chain '4b' selection = chain '4c' selection = chain '4d' selection = chain '4e' selection = chain '4f' selection = chain '5a' selection = chain '5b' selection = chain '5c' selection = chain '5d' selection = chain '5e' selection = chain '5f' } 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: 3.680 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: 0.060 Extract box with map and model: 15.940 Check model and map are aligned: 0.990 Set scattering table: 0.630 Process input model: 196.900 Find NCS groups from input model: 5.480 Set up NCS constraints: 1.120 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: 0.030 Load rotamer database and sin/cos tables:14.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 238.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 : 0.015 0.093 94842 Z= 1.005 Angle : 1.665 10.716 129006 Z= 1.143 Chirality : 0.097 0.715 14346 Planarity : 0.008 0.044 16776 Dihedral : 9.993 73.714 34632 Min Nonbonded Distance : 1.115 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.03 % 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: 0.61 (0.08), residues: 11628 helix: 0.53 (0.09), residues: 3240 sheet: 1.63 (0.11), residues: 1980 loop : 0.02 (0.08), residues: 6408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.007 TRP4D 617 HIS 0.007 0.002 HIS3f 9 PHE 0.024 0.006 PHE4B 680 TYR 0.043 0.007 TYR4B 176 ARG 0.013 0.001 ARG5A 591 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23256 Ramachandran restraints generated. 11628 Oldfield, 0 Emsley, 11628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23256 Ramachandran restraints generated. 11628 Oldfield, 0 Emsley, 11628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2303 residues out of total 10152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2303 time to evaluate : 7.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3B 623 MET cc_start: 0.8345 (tmm) cc_final: 0.8101 (tmm) REVERT: 3C 111 MET cc_start: 0.9193 (mmm) cc_final: 0.8904 (mmp) REVERT: 3C 549 MET cc_start: 0.8771 (mtp) cc_final: 0.8471 (mtp) REVERT: 3D 60 LEU cc_start: 0.7779 (mt) cc_final: 0.7568 (mt) REVERT: 3E 623 MET cc_start: 0.8370 (tmm) cc_final: 0.8168 (tmm) REVERT: 3F 226 ASP cc_start: 0.6690 (m-30) cc_final: 0.6490 (m-30) REVERT: 3F 549 MET cc_start: 0.8762 (mtp) cc_final: 0.8510 (mtp) REVERT: 4A 111 MET cc_start: 0.9305 (mmm) cc_final: 0.8931 (mmm) REVERT: 4A 549 MET cc_start: 0.8693 (mtp) cc_final: 0.8073 (mtp) REVERT: 4A 623 MET cc_start: 0.8408 (tmm) cc_final: 0.8195 (tmm) REVERT: 4B 249 ASP cc_start: 0.7488 (m-30) cc_final: 0.7246 (m-30) REVERT: 4B 623 MET cc_start: 0.8266 (tmm) cc_final: 0.7942 (tmm) REVERT: 4C 111 MET cc_start: 0.9268 (mmm) cc_final: 0.8911 (mmp) REVERT: 4C 184 MET cc_start: 0.8047 (mtm) cc_final: 0.7844 (mtp) REVERT: 4D 111 MET cc_start: 0.9302 (mmm) cc_final: 0.8905 (mmm) REVERT: 4D 549 MET cc_start: 0.8702 (mtp) cc_final: 0.8152 (mtp) REVERT: 4D 623 MET cc_start: 0.8392 (tmm) cc_final: 0.8189 (tmm) REVERT: 4E 249 ASP cc_start: 0.7451 (m-30) cc_final: 0.7222 (m-30) REVERT: 4E 623 MET cc_start: 0.8251 (tmm) cc_final: 0.7913 (tmm) REVERT: 4F 111 MET cc_start: 0.9251 (mmm) cc_final: 0.8889 (mmp) REVERT: 4F 184 MET cc_start: 0.8040 (mtm) cc_final: 0.7827 (mtp) REVERT: 5A 509 MET cc_start: 0.9009 (mmm) cc_final: 0.8686 (mmm) REVERT: 5B 111 MET cc_start: 0.9276 (mmm) cc_final: 0.9072 (mmm) REVERT: 5B 656 MET cc_start: 0.9153 (mtm) cc_final: 0.8897 (mtm) REVERT: 5C 111 MET cc_start: 0.9260 (mmm) cc_final: 0.8942 (mmt) REVERT: 5C 519 ASP cc_start: 0.6944 (m-30) cc_final: 0.6723 (m-30) REVERT: 5C 656 MET cc_start: 0.9143 (mtm) cc_final: 0.8739 (mtm) REVERT: 5D 509 MET cc_start: 0.9013 (mmm) cc_final: 0.8711 (mmm) REVERT: 5E 656 MET cc_start: 0.9162 (mtm) cc_final: 0.8923 (mtm) REVERT: 5F 111 MET cc_start: 0.9242 (mmm) cc_final: 0.8734 (mmm) REVERT: 5F 519 ASP cc_start: 0.6935 (m-30) cc_final: 0.6715 (m-30) REVERT: 5F 656 MET cc_start: 0.9120 (mtm) cc_final: 0.8622 (mtm) REVERT: 3a 52 MET cc_start: 0.8489 (mtp) cc_final: 0.8255 (mtm) REVERT: 3b 52 MET cc_start: 0.8461 (mtp) cc_final: 0.8225 (mtp) REVERT: 3d 49 MET cc_start: 0.9063 (ptt) cc_final: 0.8823 (ptt) REVERT: 3d 52 MET cc_start: 0.8519 (mtp) cc_final: 0.8301 (mtm) REVERT: 3e 52 MET cc_start: 0.8457 (mtp) cc_final: 0.8155 (mtp) REVERT: 4a 73 GLN cc_start: 0.8657 (mt0) cc_final: 0.8353 (mt0) REVERT: 4b 52 MET cc_start: 0.8691 (mtp) cc_final: 0.8146 (mtm) REVERT: 4c 111 LEU cc_start: 0.8692 (mt) cc_final: 0.8177 (mp) REVERT: 4d 73 GLN cc_start: 0.8662 (mt0) cc_final: 0.8363 (mt0) REVERT: 4e 52 MET cc_start: 0.8672 (mtp) cc_final: 0.8101 (mtm) REVERT: 4f 52 MET cc_start: 0.8516 (mtp) cc_final: 0.8028 (mtm) REVERT: 4f 111 LEU cc_start: 0.8683 (mt) cc_final: 0.8170 (mp) REVERT: 5a 73 GLN cc_start: 0.8679 (mt0) cc_final: 0.8464 (mt0) REVERT: 5b 73 GLN cc_start: 0.8700 (mt0) cc_final: 0.8474 (mt0) REVERT: 5c 49 MET cc_start: 0.8961 (ptt) cc_final: 0.8271 (ptp) REVERT: 5c 73 GLN cc_start: 0.8716 (mt0) cc_final: 0.8395 (mt0) REVERT: 5e 73 GLN cc_start: 0.8682 (mt0) cc_final: 0.8446 (mt0) REVERT: 5f 49 MET cc_start: 0.8936 (ptt) cc_final: 0.8263 (ptp) REVERT: 5f 73 GLN cc_start: 0.8670 (mt0) cc_final: 0.8338 (mt0) outliers start: 0 outliers final: 3 residues processed: 2303 average time/residue: 1.8248 time to fit residues: 5551.0948 Evaluate side-chains 1255 residues out of total 10152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1252 time to evaluate : 7.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3C residue 156 ASP Chi-restraints excluded: chain 3F residue 156 ASP Chi-restraints excluded: chain 3a residue 35 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1170 random chunks: chunk 987 optimal weight: 2.9990 chunk 886 optimal weight: 6.9990 chunk 492 optimal weight: 5.9990 chunk 302 optimal weight: 8.9990 chunk 598 optimal weight: 2.9990 chunk 473 optimal weight: 5.9990 chunk 917 optimal weight: 1.9990 chunk 354 optimal weight: 0.9990 chunk 557 optimal weight: 0.0030 chunk 682 optimal weight: 6.9990 chunk 1062 optimal weight: 0.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3A 219 ASN 3A 626 ASN 3B 73 GLN 3B 626 ASN 3B 654 GLN 3C 23 GLN 3C 239 GLN 3C 626 ASN 3D 626 ASN 3E 73 GLN 3E 626 ASN 3E 654 GLN 3F 23 GLN 3F 239 GLN 3F 626 ASN ** 4A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4B 470 ASN 4B 474 ASN ** 4B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4B 626 ASN 4C 190 GLN 4C 219 ASN 4C 470 ASN 4C 474 ASN ** 4C 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4C 626 ASN 4D 490 ASN 4E 470 ASN 4E 474 ASN ** 4E 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4E 626 ASN 4F 190 GLN 4F 470 ASN 4F 474 ASN ** 4F 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4F 626 ASN 5A 36 GLN 5A 490 ASN 5B 93 ASN 5B 190 GLN ** 5B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5B 518 ASN 5C 23 GLN 5C 36 GLN ** 5C 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5D 36 GLN 5D 490 ASN 5E 93 ASN 5E 190 GLN 5E 518 ASN 5F 23 GLN 5F 36 GLN 3c 9 HIS 3c 73 GLN 3f 9 HIS 4a 9 HIS 4a 140 GLN 4b 9 HIS 4c 9 HIS 4c 140 GLN 4d 9 HIS 4d 140 GLN 4e 9 HIS 4f 9 HIS 4f 140 GLN 5a 9 HIS 5b 9 HIS 5c 9 HIS 5c 140 GLN 5d 9 HIS 5e 9 HIS 5f 9 HIS 5f 140 GLN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 94842 Z= 0.202 Angle : 0.649 7.288 129006 Z= 0.372 Chirality : 0.047 0.193 14346 Planarity : 0.005 0.037 16776 Dihedral : 4.904 37.602 12661 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.60 % Allowed : 8.85 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.83 (0.08), residues: 11628 helix: 1.93 (0.09), residues: 3240 sheet: 1.10 (0.11), residues: 2178 loop : -0.39 (0.08), residues: 6210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP5d 109 HIS 0.006 0.001 HIS4C 552 PHE 0.021 0.002 PHE3A 175 TYR 0.019 0.002 TYR5C 489 ARG 0.007 0.001 ARG3E 520 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23256 Ramachandran restraints generated. 11628 Oldfield, 0 Emsley, 11628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23256 Ramachandran restraints generated. 11628 Oldfield, 0 Emsley, 11628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1615 residues out of total 10152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 1351 time to evaluate : 8.797 Fit side-chains REVERT: 3A 610 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: 3B 52 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7467 (mptp) REVERT: 3B 239 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8057 (tp40) REVERT: 3B 610 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6739 (mp0) REVERT: 3B 675 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8264 (p) REVERT: 3C 606 GLN cc_start: 0.7864 (pt0) cc_final: 0.7582 (pt0) REVERT: 3C 610 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: 3C 675 VAL cc_start: 0.8500 (OUTLIER) cc_final: 0.8255 (p) REVERT: 3D 239 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8195 (tp40) REVERT: 3D 610 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7141 (mp0) REVERT: 3E 52 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7481 (mptp) REVERT: 3E 239 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7969 (tp40) REVERT: 3E 610 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.6728 (mp0) REVERT: 3E 675 VAL cc_start: 0.8501 (OUTLIER) cc_final: 0.8214 (p) REVERT: 3F 606 GLN cc_start: 0.7865 (pt0) cc_final: 0.7563 (pt0) REVERT: 3F 610 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: 4A 111 MET cc_start: 0.9236 (mmm) cc_final: 0.8941 (mmm) REVERT: 4A 605 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7853 (mt-10) REVERT: 4A 676 ARG cc_start: 0.7695 (mtt90) cc_final: 0.6854 (mpt180) REVERT: 4A 689 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.6563 (ppp) REVERT: 4B 253 ILE cc_start: 0.6491 (mt) cc_final: 0.6246 (mt) REVERT: 4B 595 MET cc_start: 0.8180 (tmm) cc_final: 0.7957 (tmt) REVERT: 4C 111 MET cc_start: 0.9141 (mmm) cc_final: 0.8810 (mmp) REVERT: 4D 111 MET cc_start: 0.9225 (mmm) cc_final: 0.8941 (mmm) REVERT: 4D 605 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7841 (mt-10) REVERT: 4D 676 ARG cc_start: 0.7674 (mtt90) cc_final: 0.6848 (mpt180) REVERT: 4D 689 MET cc_start: 0.6698 (OUTLIER) cc_final: 0.6366 (ppp) REVERT: 4E 253 ILE cc_start: 0.6411 (mt) cc_final: 0.6170 (mt) REVERT: 4E 595 MET cc_start: 0.8188 (tmm) cc_final: 0.7959 (tmt) REVERT: 4F 100 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8439 (mtpp) REVERT: 4F 111 MET cc_start: 0.9154 (mmm) cc_final: 0.8830 (mmp) REVERT: 5A 73 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7422 (mt0) REVERT: 5A 509 MET cc_start: 0.8920 (mmm) cc_final: 0.8326 (mmm) REVERT: 5B 605 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7697 (mt-10) REVERT: 5C 105 MET cc_start: 0.7907 (ttp) cc_final: 0.7680 (tpp) REVERT: 5C 111 MET cc_start: 0.9178 (mmm) cc_final: 0.8611 (mmm) REVERT: 5C 656 MET cc_start: 0.8945 (mtm) cc_final: 0.8413 (mtm) REVERT: 5D 73 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7379 (mt0) REVERT: 5D 509 MET cc_start: 0.8968 (mmm) cc_final: 0.8370 (mmm) REVERT: 5E 605 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7716 (mt-10) REVERT: 5F 61 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7107 (m-30) REVERT: 5F 105 MET cc_start: 0.8161 (mmm) cc_final: 0.7931 (mmm) REVERT: 5F 111 MET cc_start: 0.9161 (mmm) cc_final: 0.8733 (mmm) REVERT: 5F 656 MET cc_start: 0.8930 (mtm) cc_final: 0.8351 (mtm) REVERT: 3a 114 GLN cc_start: 0.8339 (mt0) cc_final: 0.8097 (mt0) REVERT: 3a 124 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7560 (pm20) REVERT: 3b 35 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7566 (mt-10) REVERT: 3b 52 MET cc_start: 0.8423 (mtp) cc_final: 0.7946 (mmm) REVERT: 3c 124 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7605 (pm20) REVERT: 3d 52 MET cc_start: 0.8509 (mtp) cc_final: 0.8282 (mtm) REVERT: 3d 124 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7551 (pm20) REVERT: 3e 35 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7534 (mt-10) REVERT: 3e 52 MET cc_start: 0.8443 (mtp) cc_final: 0.7978 (mmm) REVERT: 3f 73 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8394 (mt0) REVERT: 3f 124 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7628 (pm20) REVERT: 4a 114 GLN cc_start: 0.8290 (mt0) cc_final: 0.8047 (mt0) REVERT: 4b 52 MET cc_start: 0.8707 (mtp) cc_final: 0.8356 (mtm) REVERT: 4c 124 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7636 (pm20) REVERT: 4d 114 GLN cc_start: 0.8313 (mt0) cc_final: 0.8079 (mt0) REVERT: 4e 52 MET cc_start: 0.8720 (mtp) cc_final: 0.8367 (mtm) REVERT: 4f 124 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7653 (pm20) REVERT: 5b 52 MET cc_start: 0.8338 (mtp) cc_final: 0.8138 (mtm) REVERT: 5c 33 ILE cc_start: 0.8794 (mt) cc_final: 0.8515 (mt) REVERT: 5c 49 MET cc_start: 0.9043 (ptt) cc_final: 0.8322 (ptp) REVERT: 5c 82 LYS cc_start: 0.8572 (mmtm) cc_final: 0.8356 (mmtm) REVERT: 5f 33 ILE cc_start: 0.8803 (mt) cc_final: 0.8550 (mt) REVERT: 5f 49 MET cc_start: 0.9054 (ptt) cc_final: 0.8357 (ptp) REVERT: 5f 82 LYS cc_start: 0.8572 (mmtm) cc_final: 0.8358 (mmtm) outliers start: 264 outliers final: 74 residues processed: 1514 average time/residue: 1.6684 time to fit residues: 3417.9911 Evaluate side-chains 1249 residues out of total 10152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1142 time to evaluate : 8.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 61 ASP Chi-restraints excluded: chain 3A residue 98 THR Chi-restraints excluded: chain 3A residue 610 GLU Chi-restraints excluded: chain 3B residue 52 LYS Chi-restraints excluded: chain 3B residue 61 ASP Chi-restraints excluded: chain 3B residue 98 THR Chi-restraints excluded: chain 3B residue 159 THR Chi-restraints excluded: chain 3B residue 209 GLU Chi-restraints excluded: chain 3B residue 239 GLN Chi-restraints excluded: chain 3B residue 545 GLU Chi-restraints excluded: chain 3B residue 601 LYS Chi-restraints excluded: chain 3B residue 610 GLU Chi-restraints excluded: chain 3B residue 675 VAL Chi-restraints excluded: chain 3C residue 20 SER Chi-restraints excluded: chain 3C residue 77 VAL Chi-restraints excluded: chain 3C residue 98 THR Chi-restraints excluded: chain 3C residue 100 LYS Chi-restraints excluded: chain 3C residue 610 GLU Chi-restraints excluded: chain 3C residue 675 VAL Chi-restraints excluded: chain 3D residue 61 ASP Chi-restraints excluded: chain 3D residue 98 THR Chi-restraints excluded: chain 3D residue 239 GLN Chi-restraints excluded: chain 3D residue 610 GLU Chi-restraints excluded: chain 3E residue 52 LYS Chi-restraints excluded: chain 3E residue 61 ASP Chi-restraints excluded: chain 3E residue 98 THR Chi-restraints excluded: chain 3E residue 159 THR Chi-restraints excluded: chain 3E residue 209 GLU Chi-restraints excluded: chain 3E residue 239 GLN Chi-restraints excluded: chain 3E residue 545 GLU Chi-restraints excluded: chain 3E residue 601 LYS Chi-restraints excluded: chain 3E residue 610 GLU Chi-restraints excluded: chain 3E residue 675 VAL Chi-restraints excluded: chain 3F residue 98 THR Chi-restraints excluded: chain 3F residue 100 LYS Chi-restraints excluded: chain 3F residue 605 GLU Chi-restraints excluded: chain 3F residue 610 GLU Chi-restraints excluded: chain 4A residue 605 GLU Chi-restraints excluded: chain 4A residue 675 VAL Chi-restraints excluded: chain 4A residue 689 MET Chi-restraints excluded: chain 4B residue 21 VAL Chi-restraints excluded: chain 4B residue 61 ASP Chi-restraints excluded: chain 4B residue 506 SER Chi-restraints excluded: chain 4B residue 517 ASP Chi-restraints excluded: chain 4B residue 675 VAL Chi-restraints excluded: chain 4C residue 506 SER Chi-restraints excluded: chain 4C residue 601 LYS Chi-restraints excluded: chain 4C residue 675 VAL Chi-restraints excluded: chain 4D residue 605 GLU Chi-restraints excluded: chain 4D residue 675 VAL Chi-restraints excluded: chain 4D residue 689 MET Chi-restraints excluded: chain 4E residue 21 VAL Chi-restraints excluded: chain 4E residue 61 ASP Chi-restraints excluded: chain 4E residue 517 ASP Chi-restraints excluded: chain 4E residue 675 VAL Chi-restraints excluded: chain 4F residue 100 LYS Chi-restraints excluded: chain 4F residue 506 SER Chi-restraints excluded: chain 4F residue 601 LYS Chi-restraints excluded: chain 4F residue 675 VAL Chi-restraints excluded: chain 5A residue 21 VAL Chi-restraints excluded: chain 5A residue 40 THR Chi-restraints excluded: chain 5A residue 73 GLN Chi-restraints excluded: chain 5A residue 151 VAL Chi-restraints excluded: chain 5A residue 605 GLU Chi-restraints excluded: chain 5A residue 675 VAL Chi-restraints excluded: chain 5B residue 40 THR Chi-restraints excluded: chain 5B residue 61 ASP Chi-restraints excluded: chain 5B residue 136 THR Chi-restraints excluded: chain 5B residue 151 VAL Chi-restraints excluded: chain 5B residue 605 GLU Chi-restraints excluded: chain 5B residue 675 VAL Chi-restraints excluded: chain 5C residue 21 VAL Chi-restraints excluded: chain 5C residue 61 ASP Chi-restraints excluded: chain 5C residue 157 GLU Chi-restraints excluded: chain 5C residue 206 ASP Chi-restraints excluded: chain 5C residue 601 LYS Chi-restraints excluded: chain 5C residue 605 GLU Chi-restraints excluded: chain 5C residue 675 VAL Chi-restraints excluded: chain 5D residue 21 VAL Chi-restraints excluded: chain 5D residue 40 THR Chi-restraints excluded: chain 5D residue 73 GLN Chi-restraints excluded: chain 5D residue 151 VAL Chi-restraints excluded: chain 5D residue 605 GLU Chi-restraints excluded: chain 5D residue 675 VAL Chi-restraints excluded: chain 5E residue 40 THR Chi-restraints excluded: chain 5E residue 61 ASP Chi-restraints excluded: chain 5E residue 136 THR Chi-restraints excluded: chain 5E residue 151 VAL Chi-restraints excluded: chain 5E residue 605 GLU Chi-restraints excluded: chain 5E residue 675 VAL Chi-restraints excluded: chain 5F residue 61 ASP Chi-restraints excluded: chain 5F residue 206 ASP Chi-restraints excluded: chain 5F residue 601 LYS Chi-restraints excluded: chain 5F residue 605 GLU Chi-restraints excluded: chain 5F residue 675 VAL Chi-restraints excluded: chain 3a residue 124 GLU Chi-restraints excluded: chain 3b residue 35 GLU Chi-restraints excluded: chain 3c residue 124 GLU Chi-restraints excluded: chain 3d residue 124 GLU Chi-restraints excluded: chain 3e residue 35 GLU Chi-restraints excluded: chain 3f residue 73 GLN Chi-restraints excluded: chain 3f residue 124 GLU Chi-restraints excluded: chain 4a residue 22 THR Chi-restraints excluded: chain 4c residue 56 SER Chi-restraints excluded: chain 4c residue 124 GLU Chi-restraints excluded: chain 4f residue 56 SER Chi-restraints excluded: chain 4f residue 124 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1170 random chunks: chunk 590 optimal weight: 30.0000 chunk 329 optimal weight: 8.9990 chunk 884 optimal weight: 9.9990 chunk 723 optimal weight: 2.9990 chunk 293 optimal weight: 8.9990 chunk 1064 optimal weight: 5.9990 chunk 1149 optimal weight: 10.0000 chunk 947 optimal weight: 0.0010 chunk 1055 optimal weight: 9.9990 chunk 362 optimal weight: 0.6980 chunk 853 optimal weight: 6.9990 overall best weight: 3.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3A 205 ASN 3B 205 ASN 3C 73 GLN 3C 239 GLN 3D 205 ASN 3E 205 ASN 3F 23 GLN 3F 73 GLN 3F 239 GLN 4A 205 ASN 4A 490 ASN 4A 654 GLN 4B 470 ASN 4B 490 ASN 4B 528 ASN 4B 626 ASN 4C 474 ASN 4C 490 ASN 4C 528 ASN ** 4C 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4C 626 ASN 4D 205 ASN 4D 490 ASN 4D 654 GLN 4E 470 ASN 4E 490 ASN 4E 528 ASN 4E 626 ASN 4F 470 ASN 4F 490 ASN 4F 528 ASN ** 4F 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4F 626 ASN 5B 71 ASN ** 5B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5B 490 ASN 5C 490 ASN 5E 71 ASN ** 5E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5E 490 ASN 5F 490 ASN 3a 9 HIS 3a 140 GLN 3b 9 HIS 3d 9 HIS 3d 140 GLN 3e 9 HIS 4d 140 GLN 5a 140 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 94842 Z= 0.247 Angle : 0.703 11.074 129006 Z= 0.394 Chirality : 0.048 0.240 14346 Planarity : 0.005 0.049 16776 Dihedral : 4.960 20.067 12654 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.31 % Allowed : 10.40 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.33 (0.08), residues: 11628 helix: 1.58 (0.09), residues: 3366 sheet: 0.77 (0.11), residues: 2304 loop : -0.81 (0.08), residues: 5958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP5A 131 HIS 0.006 0.002 HIS3c 38 PHE 0.024 0.003 PHE3A 175 TYR 0.024 0.002 TYR5C 489 ARG 0.009 0.001 ARG4A 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23256 Ramachandran restraints generated. 11628 Oldfield, 0 Emsley, 11628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23256 Ramachandran restraints generated. 11628 Oldfield, 0 Emsley, 11628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1499 residues out of total 10152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 1163 time to evaluate : 8.118 Fit side-chains REVERT: 3A 154 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7539 (mtpp) REVERT: 3A 610 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: 3B 52 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7596 (mptp) REVERT: 3B 675 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8395 (p) REVERT: 3B 689 MET cc_start: 0.6330 (OUTLIER) cc_final: 0.4678 (pmm) REVERT: 3C 606 GLN cc_start: 0.7938 (pt0) cc_final: 0.7642 (pt0) REVERT: 3C 610 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: 3D 154 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7548 (mtpp) REVERT: 3D 610 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: 3E 52 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7581 (mptp) REVERT: 3E 239 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8104 (tp-100) REVERT: 3E 517 ASP cc_start: 0.7088 (m-30) cc_final: 0.6875 (m-30) REVERT: 3E 610 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: 3E 675 VAL cc_start: 0.8672 (OUTLIER) cc_final: 0.8382 (p) REVERT: 3E 689 MET cc_start: 0.6295 (OUTLIER) cc_final: 0.4643 (pmm) REVERT: 3F 606 GLN cc_start: 0.7938 (pt0) cc_final: 0.7625 (pt0) REVERT: 3F 610 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: 4A 605 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7957 (mt-10) REVERT: 4A 659 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7781 (tp40) REVERT: 4A 689 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6711 (ppp) REVERT: 4B 48 ASP cc_start: 0.7072 (OUTLIER) cc_final: 0.6823 (m-30) REVERT: 4C 100 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8421 (mtpp) REVERT: 4C 111 MET cc_start: 0.9174 (mmm) cc_final: 0.8905 (mmm) REVERT: 4C 202 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7100 (mp10) REVERT: 4C 602 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8067 (ttpt) REVERT: 4D 100 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8693 (mttp) REVERT: 4D 605 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7931 (mt-10) REVERT: 4D 659 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7801 (tp40) REVERT: 4D 689 MET cc_start: 0.6665 (OUTLIER) cc_final: 0.6015 (pp-130) REVERT: 4E 48 ASP cc_start: 0.7067 (OUTLIER) cc_final: 0.6825 (m-30) REVERT: 4F 100 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8405 (mtpp) REVERT: 4F 111 MET cc_start: 0.9173 (mmm) cc_final: 0.8913 (mmm) REVERT: 4F 202 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7100 (mp10) REVERT: 4F 602 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8074 (ttpt) REVERT: 5A 73 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7536 (mt0) REVERT: 5A 157 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7322 (tt0) REVERT: 5A 509 MET cc_start: 0.9042 (mmm) cc_final: 0.8619 (mmm) REVERT: 5B 146 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7119 (mt-10) REVERT: 5B 197 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7238 (m-30) REVERT: 5B 605 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7584 (mt-10) REVERT: 5C 73 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7564 (mt0) REVERT: 5C 96 GLU cc_start: 0.6762 (tt0) cc_final: 0.6504 (mt-10) REVERT: 5C 250 GLU cc_start: 0.7656 (mm-30) cc_final: 0.6973 (tp30) REVERT: 5D 73 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7500 (mt0) REVERT: 5D 509 MET cc_start: 0.9043 (mmm) cc_final: 0.8537 (mmm) REVERT: 5E 197 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7342 (m-30) REVERT: 5F 73 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7532 (mt0) REVERT: 5F 105 MET cc_start: 0.8208 (mmm) cc_final: 0.7796 (mmm) REVERT: 3a 124 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7573 (pm20) REVERT: 3b 35 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7489 (mt-10) REVERT: 3b 52 MET cc_start: 0.8550 (mtp) cc_final: 0.7881 (mmm) REVERT: 3b 114 GLN cc_start: 0.7920 (mt0) cc_final: 0.7640 (mt0) REVERT: 3c 114 GLN cc_start: 0.8425 (mt0) cc_final: 0.8218 (mt0) REVERT: 3d 52 MET cc_start: 0.8650 (mtp) cc_final: 0.8444 (mtm) REVERT: 3d 124 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7554 (pm20) REVERT: 3e 28 ASP cc_start: 0.7877 (m-30) cc_final: 0.7647 (m-30) REVERT: 3e 35 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7517 (mt-10) REVERT: 3e 52 MET cc_start: 0.8561 (mtp) cc_final: 0.7872 (mmm) REVERT: 3e 114 GLN cc_start: 0.7930 (mt0) cc_final: 0.7670 (mt0) REVERT: 3f 73 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8597 (mt0) REVERT: 3f 114 GLN cc_start: 0.8378 (mt0) cc_final: 0.8134 (mt0) REVERT: 4a 130 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8626 (ttp) REVERT: 4b 52 MET cc_start: 0.8815 (mtp) cc_final: 0.8454 (mtm) REVERT: 4c 124 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7617 (pm20) REVERT: 4d 130 MET cc_start: 0.8874 (ttp) cc_final: 0.8617 (ttp) REVERT: 4e 52 MET cc_start: 0.8835 (mtp) cc_final: 0.8447 (mtm) REVERT: 4f 73 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8546 (mt0) REVERT: 4f 124 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7588 (pm20) REVERT: 5b 30 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6795 (pm20) REVERT: 5b 52 MET cc_start: 0.8441 (mtp) cc_final: 0.8235 (mtm) REVERT: 5c 49 MET cc_start: 0.9071 (ptt) cc_final: 0.8535 (ptp) REVERT: 5e 30 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6861 (pm20) REVERT: 5f 49 MET cc_start: 0.9063 (ptt) cc_final: 0.8533 (ptp) outliers start: 336 outliers final: 150 residues processed: 1366 average time/residue: 1.7420 time to fit residues: 3204.3261 Evaluate side-chains 1278 residues out of total 10152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1079 time to evaluate : 7.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 61 ASP Chi-restraints excluded: chain 3A residue 98 THR Chi-restraints excluded: chain 3A residue 105 MET Chi-restraints excluded: chain 3A residue 154 LYS Chi-restraints excluded: chain 3A residue 529 ILE Chi-restraints excluded: chain 3A residue 610 GLU Chi-restraints excluded: chain 3A residue 662 LEU Chi-restraints excluded: chain 3B residue 52 LYS Chi-restraints excluded: chain 3B residue 61 ASP Chi-restraints excluded: chain 3B residue 98 THR Chi-restraints excluded: chain 3B residue 130 ASP Chi-restraints excluded: chain 3B residue 135 GLU Chi-restraints excluded: chain 3B residue 159 THR Chi-restraints excluded: chain 3B residue 209 GLU Chi-restraints excluded: chain 3B residue 545 GLU Chi-restraints excluded: chain 3B residue 601 LYS Chi-restraints excluded: chain 3B residue 662 LEU Chi-restraints excluded: chain 3B residue 675 VAL Chi-restraints excluded: chain 3B residue 689 MET Chi-restraints excluded: chain 3C residue 20 SER Chi-restraints excluded: chain 3C residue 98 THR Chi-restraints excluded: chain 3C residue 100 LYS Chi-restraints excluded: chain 3C residue 130 ASP Chi-restraints excluded: chain 3C residue 491 THR Chi-restraints excluded: chain 3C residue 529 ILE Chi-restraints excluded: chain 3C residue 605 GLU Chi-restraints excluded: chain 3C residue 610 GLU Chi-restraints excluded: chain 3C residue 675 VAL Chi-restraints excluded: chain 3D residue 61 ASP Chi-restraints excluded: chain 3D residue 98 THR Chi-restraints excluded: chain 3D residue 105 MET Chi-restraints excluded: chain 3D residue 134 SER Chi-restraints excluded: chain 3D residue 154 LYS Chi-restraints excluded: chain 3D residue 529 ILE Chi-restraints excluded: chain 3D residue 565 VAL Chi-restraints excluded: chain 3D residue 601 LYS Chi-restraints excluded: chain 3D residue 610 GLU Chi-restraints excluded: chain 3D residue 662 LEU Chi-restraints excluded: chain 3E residue 52 LYS Chi-restraints excluded: chain 3E residue 61 ASP Chi-restraints excluded: chain 3E residue 98 THR Chi-restraints excluded: chain 3E residue 130 ASP Chi-restraints excluded: chain 3E residue 135 GLU Chi-restraints excluded: chain 3E residue 209 GLU Chi-restraints excluded: chain 3E residue 239 GLN Chi-restraints excluded: chain 3E residue 472 LYS Chi-restraints excluded: chain 3E residue 545 GLU Chi-restraints excluded: chain 3E residue 601 LYS Chi-restraints excluded: chain 3E residue 610 GLU Chi-restraints excluded: chain 3E residue 662 LEU Chi-restraints excluded: chain 3E residue 675 VAL Chi-restraints excluded: chain 3E residue 689 MET Chi-restraints excluded: chain 3F residue 98 THR Chi-restraints excluded: chain 3F residue 100 LYS Chi-restraints excluded: chain 3F residue 130 ASP Chi-restraints excluded: chain 3F residue 605 GLU Chi-restraints excluded: chain 3F residue 610 GLU Chi-restraints excluded: chain 4A residue 61 ASP Chi-restraints excluded: chain 4A residue 91 THR Chi-restraints excluded: chain 4A residue 105 MET Chi-restraints excluded: chain 4A residue 132 SER Chi-restraints excluded: chain 4A residue 485 ASP Chi-restraints excluded: chain 4A residue 601 LYS Chi-restraints excluded: chain 4A residue 605 GLU Chi-restraints excluded: chain 4A residue 659 GLN Chi-restraints excluded: chain 4A residue 662 LEU Chi-restraints excluded: chain 4A residue 675 VAL Chi-restraints excluded: chain 4A residue 689 MET Chi-restraints excluded: chain 4B residue 21 VAL Chi-restraints excluded: chain 4B residue 48 ASP Chi-restraints excluded: chain 4B residue 61 ASP Chi-restraints excluded: chain 4B residue 91 THR Chi-restraints excluded: chain 4B residue 132 SER Chi-restraints excluded: chain 4B residue 481 ILE Chi-restraints excluded: chain 4B residue 601 LYS Chi-restraints excluded: chain 4B residue 675 VAL Chi-restraints excluded: chain 4C residue 21 VAL Chi-restraints excluded: chain 4C residue 91 THR Chi-restraints excluded: chain 4C residue 100 LYS Chi-restraints excluded: chain 4C residue 132 SER Chi-restraints excluded: chain 4C residue 202 GLN Chi-restraints excluded: chain 4C residue 506 SER Chi-restraints excluded: chain 4C residue 602 LYS Chi-restraints excluded: chain 4D residue 61 ASP Chi-restraints excluded: chain 4D residue 91 THR Chi-restraints excluded: chain 4D residue 100 LYS Chi-restraints excluded: chain 4D residue 105 MET Chi-restraints excluded: chain 4D residue 132 SER Chi-restraints excluded: chain 4D residue 212 ASP Chi-restraints excluded: chain 4D residue 485 ASP Chi-restraints excluded: chain 4D residue 601 LYS Chi-restraints excluded: chain 4D residue 605 GLU Chi-restraints excluded: chain 4D residue 659 GLN Chi-restraints excluded: chain 4D residue 662 LEU Chi-restraints excluded: chain 4D residue 675 VAL Chi-restraints excluded: chain 4D residue 689 MET Chi-restraints excluded: chain 4E residue 21 VAL Chi-restraints excluded: chain 4E residue 48 ASP Chi-restraints excluded: chain 4E residue 61 ASP Chi-restraints excluded: chain 4E residue 91 THR Chi-restraints excluded: chain 4E residue 130 ASP Chi-restraints excluded: chain 4E residue 132 SER Chi-restraints excluded: chain 4E residue 481 ILE Chi-restraints excluded: chain 4E residue 601 LYS Chi-restraints excluded: chain 4E residue 675 VAL Chi-restraints excluded: chain 4F residue 21 VAL Chi-restraints excluded: chain 4F residue 91 THR Chi-restraints excluded: chain 4F residue 100 LYS Chi-restraints excluded: chain 4F residue 132 SER Chi-restraints excluded: chain 4F residue 202 GLN Chi-restraints excluded: chain 4F residue 506 SER Chi-restraints excluded: chain 4F residue 602 LYS Chi-restraints excluded: chain 5A residue 40 THR Chi-restraints excluded: chain 5A residue 61 ASP Chi-restraints excluded: chain 5A residue 73 GLN Chi-restraints excluded: chain 5A residue 130 ASP Chi-restraints excluded: chain 5A residue 136 THR Chi-restraints excluded: chain 5A residue 151 VAL Chi-restraints excluded: chain 5A residue 156 ASP Chi-restraints excluded: chain 5A residue 157 GLU Chi-restraints excluded: chain 5A residue 605 GLU Chi-restraints excluded: chain 5A residue 675 VAL Chi-restraints excluded: chain 5B residue 40 THR Chi-restraints excluded: chain 5B residue 61 ASP Chi-restraints excluded: chain 5B residue 130 ASP Chi-restraints excluded: chain 5B residue 136 THR Chi-restraints excluded: chain 5B residue 146 GLU Chi-restraints excluded: chain 5B residue 151 VAL Chi-restraints excluded: chain 5B residue 197 ASP Chi-restraints excluded: chain 5B residue 605 GLU Chi-restraints excluded: chain 5B residue 625 GLU Chi-restraints excluded: chain 5B residue 662 LEU Chi-restraints excluded: chain 5C residue 21 VAL Chi-restraints excluded: chain 5C residue 61 ASP Chi-restraints excluded: chain 5C residue 73 GLN Chi-restraints excluded: chain 5C residue 98 THR Chi-restraints excluded: chain 5C residue 132 SER Chi-restraints excluded: chain 5C residue 157 GLU Chi-restraints excluded: chain 5C residue 206 ASP Chi-restraints excluded: chain 5C residue 506 SER Chi-restraints excluded: chain 5C residue 605 GLU Chi-restraints excluded: chain 5C residue 675 VAL Chi-restraints excluded: chain 5D residue 40 THR Chi-restraints excluded: chain 5D residue 61 ASP Chi-restraints excluded: chain 5D residue 73 GLN Chi-restraints excluded: chain 5D residue 130 ASP Chi-restraints excluded: chain 5D residue 136 THR Chi-restraints excluded: chain 5D residue 151 VAL Chi-restraints excluded: chain 5D residue 156 ASP Chi-restraints excluded: chain 5D residue 675 VAL Chi-restraints excluded: chain 5E residue 40 THR Chi-restraints excluded: chain 5E residue 61 ASP Chi-restraints excluded: chain 5E residue 130 ASP Chi-restraints excluded: chain 5E residue 136 THR Chi-restraints excluded: chain 5E residue 151 VAL Chi-restraints excluded: chain 5E residue 197 ASP Chi-restraints excluded: chain 5E residue 625 GLU Chi-restraints excluded: chain 5E residue 662 LEU Chi-restraints excluded: chain 5F residue 21 VAL Chi-restraints excluded: chain 5F residue 61 ASP Chi-restraints excluded: chain 5F residue 73 GLN Chi-restraints excluded: chain 5F residue 98 THR Chi-restraints excluded: chain 5F residue 132 SER Chi-restraints excluded: chain 5F residue 157 GLU Chi-restraints excluded: chain 5F residue 206 ASP Chi-restraints excluded: chain 5F residue 506 SER Chi-restraints excluded: chain 5F residue 605 GLU Chi-restraints excluded: chain 5F residue 675 VAL Chi-restraints excluded: chain 3a residue 124 GLU Chi-restraints excluded: chain 3b residue 35 GLU Chi-restraints excluded: chain 3b residue 82 LYS Chi-restraints excluded: chain 3b residue 124 GLU Chi-restraints excluded: chain 3c residue 124 GLU Chi-restraints excluded: chain 3d residue 124 GLU Chi-restraints excluded: chain 3e residue 35 GLU Chi-restraints excluded: chain 3e residue 82 LYS Chi-restraints excluded: chain 3e residue 124 GLU Chi-restraints excluded: chain 3f residue 73 GLN Chi-restraints excluded: chain 3f residue 124 GLU Chi-restraints excluded: chain 4a residue 2 SER Chi-restraints excluded: chain 4a residue 22 THR Chi-restraints excluded: chain 4a residue 130 MET Chi-restraints excluded: chain 4b residue 66 LYS Chi-restraints excluded: chain 4c residue 56 SER Chi-restraints excluded: chain 4c residue 124 GLU Chi-restraints excluded: chain 4d residue 2 SER Chi-restraints excluded: chain 4e residue 66 LYS Chi-restraints excluded: chain 4f residue 56 SER Chi-restraints excluded: chain 4f residue 73 GLN Chi-restraints excluded: chain 4f residue 124 GLU Chi-restraints excluded: chain 5a residue 17 THR Chi-restraints excluded: chain 5b residue 17 THR Chi-restraints excluded: chain 5b residue 30 GLU Chi-restraints excluded: chain 5b residue 112 LYS Chi-restraints excluded: chain 5c residue 17 THR Chi-restraints excluded: chain 5d residue 17 THR Chi-restraints excluded: chain 5e residue 17 THR Chi-restraints excluded: chain 5e residue 30 GLU Chi-restraints excluded: chain 5f residue 17 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1170 random chunks: chunk 1051 optimal weight: 10.0000 chunk 800 optimal weight: 9.9990 chunk 552 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 507 optimal weight: 9.9990 chunk 714 optimal weight: 5.9990 chunk 1068 optimal weight: 3.9990 chunk 1130 optimal weight: 5.9990 chunk 558 optimal weight: 5.9990 chunk 1012 optimal weight: 5.9990 chunk 304 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3A 205 ASN 3B 606 GLN 3C 205 ASN 3C 239 GLN 3D 205 ASN 3E 606 GLN 3F 23 GLN 3F 205 ASN 3F 239 GLN 4A 205 ASN 4C 93 ASN 4C 474 ASN ** 4C 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4D 205 ASN 4D 490 ASN 4E 490 ASN 4F 93 ASN ** 4F 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5A 205 ASN 5A 606 GLN 5B 190 GLN ** 5B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5D 205 ASN 5D 606 GLN 5E 190 GLN ** 5E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3a 140 GLN 3d 140 GLN 4a 114 GLN 4d 114 GLN 4d 140 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 94842 Z= 0.342 Angle : 0.803 8.977 129006 Z= 0.449 Chirality : 0.051 0.226 14346 Planarity : 0.006 0.067 16776 Dihedral : 5.296 19.912 12654 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.74 % Allowed : 10.41 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.06 (0.08), residues: 11628 helix: 1.38 (0.09), residues: 3222 sheet: 0.67 (0.11), residues: 2250 loop : -1.13 (0.07), residues: 6156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP3E 131 HIS 0.007 0.002 HIS4c 97 PHE 0.025 0.003 PHE3D 175 TYR 0.026 0.003 TYR5C 489 ARG 0.008 0.001 ARG3E 520 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23256 Ramachandran restraints generated. 11628 Oldfield, 0 Emsley, 11628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23256 Ramachandran restraints generated. 11628 Oldfield, 0 Emsley, 11628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1478 residues out of total 10152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 380 poor density : 1098 time to evaluate : 7.908 Fit side-chains REVERT: 3A 154 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7631 (mtpp) REVERT: 3A 610 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7047 (mp0) REVERT: 3B 52 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7678 (mptp) REVERT: 3B 79 LEU cc_start: 0.6359 (mt) cc_final: 0.6061 (mt) REVERT: 3B 91 THR cc_start: 0.6472 (m) cc_final: 0.6263 (t) REVERT: 3B 669 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8135 (mt-10) REVERT: 3B 689 MET cc_start: 0.6440 (OUTLIER) cc_final: 0.4573 (pmm) REVERT: 3C 606 GLN cc_start: 0.8102 (pt0) cc_final: 0.7901 (pt0) REVERT: 3D 154 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7626 (mtpp) REVERT: 3D 610 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7049 (mp0) REVERT: 3D 659 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7428 (tm-30) REVERT: 3E 41 LYS cc_start: 0.7035 (OUTLIER) cc_final: 0.6741 (mptt) REVERT: 3E 79 LEU cc_start: 0.6366 (mt) cc_final: 0.6056 (mt) REVERT: 3E 689 MET cc_start: 0.6463 (OUTLIER) cc_final: 0.4957 (pmm) REVERT: 3F 606 GLN cc_start: 0.8046 (pt0) cc_final: 0.7836 (pt0) REVERT: 4A 48 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.7081 (m-30) REVERT: 4A 605 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7972 (mt-10) REVERT: 4A 643 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7251 (pm20) REVERT: 4A 689 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.6699 (ppp) REVERT: 4B 41 LYS cc_start: 0.7441 (OUTLIER) cc_final: 0.6907 (mmtm) REVERT: 4B 130 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7327 (OUTLIER) REVERT: 4B 154 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7560 (mtpm) REVERT: 4C 73 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7287 (mt0) REVERT: 4C 111 MET cc_start: 0.9191 (mmm) cc_final: 0.8954 (mmm) REVERT: 4C 202 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7180 (mp10) REVERT: 4C 669 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8071 (mt-10) REVERT: 4D 48 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.7080 (m-30) REVERT: 4D 100 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8691 (mttp) REVERT: 4D 605 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7985 (mt-10) REVERT: 4D 643 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7244 (pm20) REVERT: 4D 689 MET cc_start: 0.6668 (OUTLIER) cc_final: 0.6070 (pp-130) REVERT: 4E 41 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.6922 (mmtm) REVERT: 4E 130 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7320 (OUTLIER) REVERT: 4E 154 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7538 (mtpm) REVERT: 4F 73 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7377 (mt0) REVERT: 4F 100 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8477 (mtpp) REVERT: 4F 111 MET cc_start: 0.9187 (mmm) cc_final: 0.8952 (mmm) REVERT: 4F 202 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7182 (mp10) REVERT: 4F 669 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8072 (mt-10) REVERT: 5A 73 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7520 (mt0) REVERT: 5A 549 MET cc_start: 0.8941 (mtp) cc_final: 0.8539 (mtp) REVERT: 5B 23 GLN cc_start: 0.7464 (mp10) cc_final: 0.7232 (mp10) REVERT: 5B 73 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.6967 (mm110) REVERT: 5B 197 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7478 (m-30) REVERT: 5B 605 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7664 (mt-10) REVERT: 5C 73 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.7558 (mt0) REVERT: 5C 96 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6876 (mt-10) REVERT: 5C 250 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7074 (tp30) REVERT: 5D 73 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7515 (mt0) REVERT: 5D 549 MET cc_start: 0.8922 (mtp) cc_final: 0.8548 (mtp) REVERT: 5E 23 GLN cc_start: 0.7456 (mp10) cc_final: 0.7139 (mp10) REVERT: 5E 73 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7051 (mm110) REVERT: 5E 197 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7474 (m-30) REVERT: 5F 73 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7567 (mt0) REVERT: 5F 96 GLU cc_start: 0.7129 (tt0) cc_final: 0.6886 (mt-10) REVERT: 5F 105 MET cc_start: 0.8178 (mmm) cc_final: 0.7758 (mmm) REVERT: 5F 250 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7068 (tp30) REVERT: 3a 87 ASP cc_start: 0.7556 (m-30) cc_final: 0.7110 (m-30) REVERT: 3b 28 ASP cc_start: 0.7864 (m-30) cc_final: 0.7615 (m-30) REVERT: 3b 35 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7506 (mt-10) REVERT: 3b 52 MET cc_start: 0.8630 (mtp) cc_final: 0.7938 (mmm) REVERT: 3d 87 ASP cc_start: 0.7590 (m-30) cc_final: 0.7106 (m-30) REVERT: 3e 28 ASP cc_start: 0.7874 (m-30) cc_final: 0.7610 (m-30) REVERT: 3e 35 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7501 (mt-10) REVERT: 3e 52 MET cc_start: 0.8650 (mtp) cc_final: 0.8003 (mmm) REVERT: 3e 114 GLN cc_start: 0.7968 (mt0) cc_final: 0.7750 (mt0) REVERT: 3f 73 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8586 (mt0) REVERT: 3f 114 GLN cc_start: 0.8357 (mt0) cc_final: 0.8143 (mt0) REVERT: 4a 130 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8586 (ttp) REVERT: 4b 52 MET cc_start: 0.8810 (mtp) cc_final: 0.8449 (mtm) REVERT: 4c 73 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8553 (mt0) REVERT: 4c 124 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7602 (pm20) REVERT: 4d 130 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8617 (ttp) REVERT: 4e 52 MET cc_start: 0.8837 (mtp) cc_final: 0.8446 (mtm) REVERT: 4f 52 MET cc_start: 0.8577 (mtm) cc_final: 0.8345 (mtm) REVERT: 4f 73 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8558 (mt0) REVERT: 4f 124 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7545 (pm20) REVERT: 5b 124 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7625 (pt0) REVERT: 5c 49 MET cc_start: 0.9107 (ptt) cc_final: 0.8630 (ptp) REVERT: 5e 30 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7046 (pm20) REVERT: 5f 49 MET cc_start: 0.9115 (ptt) cc_final: 0.8633 (ptp) outliers start: 380 outliers final: 195 residues processed: 1343 average time/residue: 1.7166 time to fit residues: 3104.1032 Evaluate side-chains 1308 residues out of total 10152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 1062 time to evaluate : 7.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 61 ASP Chi-restraints excluded: chain 3A residue 79 LEU Chi-restraints excluded: chain 3A residue 98 THR Chi-restraints excluded: chain 3A residue 134 SER Chi-restraints excluded: chain 3A residue 154 LYS Chi-restraints excluded: chain 3A residue 184 MET Chi-restraints excluded: chain 3A residue 529 ILE Chi-restraints excluded: chain 3A residue 545 GLU Chi-restraints excluded: chain 3A residue 610 GLU Chi-restraints excluded: chain 3A residue 662 LEU Chi-restraints excluded: chain 3B residue 52 LYS Chi-restraints excluded: chain 3B residue 61 ASP Chi-restraints excluded: chain 3B residue 98 THR Chi-restraints excluded: chain 3B residue 130 ASP Chi-restraints excluded: chain 3B residue 135 GLU Chi-restraints excluded: chain 3B residue 209 GLU Chi-restraints excluded: chain 3B residue 506 SER Chi-restraints excluded: chain 3B residue 529 ILE Chi-restraints excluded: chain 3B residue 545 GLU Chi-restraints excluded: chain 3B residue 565 VAL Chi-restraints excluded: chain 3B residue 601 LYS Chi-restraints excluded: chain 3B residue 662 LEU Chi-restraints excluded: chain 3B residue 669 GLU Chi-restraints excluded: chain 3B residue 675 VAL Chi-restraints excluded: chain 3B residue 689 MET Chi-restraints excluded: chain 3C residue 20 SER Chi-restraints excluded: chain 3C residue 79 LEU Chi-restraints excluded: chain 3C residue 100 LYS Chi-restraints excluded: chain 3C residue 130 ASP Chi-restraints excluded: chain 3C residue 202 GLN Chi-restraints excluded: chain 3C residue 481 ILE Chi-restraints excluded: chain 3C residue 491 THR Chi-restraints excluded: chain 3C residue 529 ILE Chi-restraints excluded: chain 3C residue 675 VAL Chi-restraints excluded: chain 3D residue 61 ASP Chi-restraints excluded: chain 3D residue 79 LEU Chi-restraints excluded: chain 3D residue 98 THR Chi-restraints excluded: chain 3D residue 134 SER Chi-restraints excluded: chain 3D residue 154 LYS Chi-restraints excluded: chain 3D residue 529 ILE Chi-restraints excluded: chain 3D residue 545 GLU Chi-restraints excluded: chain 3D residue 565 VAL Chi-restraints excluded: chain 3D residue 601 LYS Chi-restraints excluded: chain 3D residue 610 GLU Chi-restraints excluded: chain 3D residue 659 GLN Chi-restraints excluded: chain 3D residue 662 LEU Chi-restraints excluded: chain 3E residue 41 LYS Chi-restraints excluded: chain 3E residue 52 LYS Chi-restraints excluded: chain 3E residue 61 ASP Chi-restraints excluded: chain 3E residue 98 THR Chi-restraints excluded: chain 3E residue 130 ASP Chi-restraints excluded: chain 3E residue 209 GLU Chi-restraints excluded: chain 3E residue 472 LYS Chi-restraints excluded: chain 3E residue 506 SER Chi-restraints excluded: chain 3E residue 529 ILE Chi-restraints excluded: chain 3E residue 565 VAL Chi-restraints excluded: chain 3E residue 601 LYS Chi-restraints excluded: chain 3E residue 662 LEU Chi-restraints excluded: chain 3E residue 675 VAL Chi-restraints excluded: chain 3E residue 689 MET Chi-restraints excluded: chain 3F residue 79 LEU Chi-restraints excluded: chain 3F residue 98 THR Chi-restraints excluded: chain 3F residue 100 LYS Chi-restraints excluded: chain 3F residue 130 ASP Chi-restraints excluded: chain 3F residue 202 GLN Chi-restraints excluded: chain 3F residue 491 THR Chi-restraints excluded: chain 3F residue 605 GLU Chi-restraints excluded: chain 4A residue 48 ASP Chi-restraints excluded: chain 4A residue 61 ASP Chi-restraints excluded: chain 4A residue 91 THR Chi-restraints excluded: chain 4A residue 105 MET Chi-restraints excluded: chain 4A residue 130 ASP Chi-restraints excluded: chain 4A residue 132 SER Chi-restraints excluded: chain 4A residue 212 ASP Chi-restraints excluded: chain 4A residue 485 ASP Chi-restraints excluded: chain 4A residue 601 LYS Chi-restraints excluded: chain 4A residue 605 GLU Chi-restraints excluded: chain 4A residue 643 GLU Chi-restraints excluded: chain 4A residue 662 LEU Chi-restraints excluded: chain 4A residue 675 VAL Chi-restraints excluded: chain 4A residue 689 MET Chi-restraints excluded: chain 4B residue 21 VAL Chi-restraints excluded: chain 4B residue 41 LYS Chi-restraints excluded: chain 4B residue 61 ASP Chi-restraints excluded: chain 4B residue 91 THR Chi-restraints excluded: chain 4B residue 130 ASP Chi-restraints excluded: chain 4B residue 154 LYS Chi-restraints excluded: chain 4B residue 481 ILE Chi-restraints excluded: chain 4B residue 506 SER Chi-restraints excluded: chain 4B residue 517 ASP Chi-restraints excluded: chain 4B residue 529 ILE Chi-restraints excluded: chain 4B residue 601 LYS Chi-restraints excluded: chain 4B residue 675 VAL Chi-restraints excluded: chain 4C residue 48 ASP Chi-restraints excluded: chain 4C residue 73 GLN Chi-restraints excluded: chain 4C residue 91 THR Chi-restraints excluded: chain 4C residue 132 SER Chi-restraints excluded: chain 4C residue 157 GLU Chi-restraints excluded: chain 4C residue 202 GLN Chi-restraints excluded: chain 4C residue 474 ASN Chi-restraints excluded: chain 4C residue 506 SER Chi-restraints excluded: chain 4C residue 601 LYS Chi-restraints excluded: chain 4C residue 662 LEU Chi-restraints excluded: chain 4C residue 669 GLU Chi-restraints excluded: chain 4D residue 48 ASP Chi-restraints excluded: chain 4D residue 61 ASP Chi-restraints excluded: chain 4D residue 91 THR Chi-restraints excluded: chain 4D residue 100 LYS Chi-restraints excluded: chain 4D residue 105 MET Chi-restraints excluded: chain 4D residue 130 ASP Chi-restraints excluded: chain 4D residue 132 SER Chi-restraints excluded: chain 4D residue 485 ASP Chi-restraints excluded: chain 4D residue 601 LYS Chi-restraints excluded: chain 4D residue 605 GLU Chi-restraints excluded: chain 4D residue 643 GLU Chi-restraints excluded: chain 4D residue 662 LEU Chi-restraints excluded: chain 4D residue 675 VAL Chi-restraints excluded: chain 4D residue 689 MET Chi-restraints excluded: chain 4E residue 21 VAL Chi-restraints excluded: chain 4E residue 41 LYS Chi-restraints excluded: chain 4E residue 61 ASP Chi-restraints excluded: chain 4E residue 91 THR Chi-restraints excluded: chain 4E residue 130 ASP Chi-restraints excluded: chain 4E residue 136 THR Chi-restraints excluded: chain 4E residue 154 LYS Chi-restraints excluded: chain 4E residue 481 ILE Chi-restraints excluded: chain 4E residue 506 SER Chi-restraints excluded: chain 4E residue 517 ASP Chi-restraints excluded: chain 4E residue 529 ILE Chi-restraints excluded: chain 4E residue 601 LYS Chi-restraints excluded: chain 4E residue 675 VAL Chi-restraints excluded: chain 4F residue 48 ASP Chi-restraints excluded: chain 4F residue 73 GLN Chi-restraints excluded: chain 4F residue 91 THR Chi-restraints excluded: chain 4F residue 100 LYS Chi-restraints excluded: chain 4F residue 132 SER Chi-restraints excluded: chain 4F residue 157 GLU Chi-restraints excluded: chain 4F residue 202 GLN Chi-restraints excluded: chain 4F residue 506 SER Chi-restraints excluded: chain 4F residue 601 LYS Chi-restraints excluded: chain 4F residue 662 LEU Chi-restraints excluded: chain 4F residue 669 GLU Chi-restraints excluded: chain 5A residue 40 THR Chi-restraints excluded: chain 5A residue 73 GLN Chi-restraints excluded: chain 5A residue 136 THR Chi-restraints excluded: chain 5A residue 151 VAL Chi-restraints excluded: chain 5A residue 529 ILE Chi-restraints excluded: chain 5A residue 601 LYS Chi-restraints excluded: chain 5A residue 605 GLU Chi-restraints excluded: chain 5B residue 40 THR Chi-restraints excluded: chain 5B residue 61 ASP Chi-restraints excluded: chain 5B residue 73 GLN Chi-restraints excluded: chain 5B residue 136 THR Chi-restraints excluded: chain 5B residue 151 VAL Chi-restraints excluded: chain 5B residue 197 ASP Chi-restraints excluded: chain 5B residue 506 SER Chi-restraints excluded: chain 5B residue 529 ILE Chi-restraints excluded: chain 5B residue 605 GLU Chi-restraints excluded: chain 5B residue 625 GLU Chi-restraints excluded: chain 5B residue 662 LEU Chi-restraints excluded: chain 5C residue 21 VAL Chi-restraints excluded: chain 5C residue 48 ASP Chi-restraints excluded: chain 5C residue 61 ASP Chi-restraints excluded: chain 5C residue 73 GLN Chi-restraints excluded: chain 5C residue 96 GLU Chi-restraints excluded: chain 5C residue 98 THR Chi-restraints excluded: chain 5C residue 132 SER Chi-restraints excluded: chain 5C residue 157 GLU Chi-restraints excluded: chain 5C residue 206 ASP Chi-restraints excluded: chain 5C residue 506 SER Chi-restraints excluded: chain 5C residue 601 LYS Chi-restraints excluded: chain 5C residue 605 GLU Chi-restraints excluded: chain 5C residue 625 GLU Chi-restraints excluded: chain 5C residue 662 LEU Chi-restraints excluded: chain 5C residue 675 VAL Chi-restraints excluded: chain 5D residue 40 THR Chi-restraints excluded: chain 5D residue 73 GLN Chi-restraints excluded: chain 5D residue 136 THR Chi-restraints excluded: chain 5D residue 151 VAL Chi-restraints excluded: chain 5D residue 529 ILE Chi-restraints excluded: chain 5D residue 601 LYS Chi-restraints excluded: chain 5D residue 605 GLU Chi-restraints excluded: chain 5E residue 40 THR Chi-restraints excluded: chain 5E residue 61 ASP Chi-restraints excluded: chain 5E residue 73 GLN Chi-restraints excluded: chain 5E residue 77 VAL Chi-restraints excluded: chain 5E residue 136 THR Chi-restraints excluded: chain 5E residue 151 VAL Chi-restraints excluded: chain 5E residue 197 ASP Chi-restraints excluded: chain 5E residue 506 SER Chi-restraints excluded: chain 5E residue 529 ILE Chi-restraints excluded: chain 5E residue 625 GLU Chi-restraints excluded: chain 5E residue 662 LEU Chi-restraints excluded: chain 5F residue 21 VAL Chi-restraints excluded: chain 5F residue 61 ASP Chi-restraints excluded: chain 5F residue 73 GLN Chi-restraints excluded: chain 5F residue 132 SER Chi-restraints excluded: chain 5F residue 157 GLU Chi-restraints excluded: chain 5F residue 506 SER Chi-restraints excluded: chain 5F residue 601 LYS Chi-restraints excluded: chain 5F residue 605 GLU Chi-restraints excluded: chain 5F residue 662 LEU Chi-restraints excluded: chain 5F residue 675 VAL Chi-restraints excluded: chain 3a residue 124 GLU Chi-restraints excluded: chain 3b residue 22 THR Chi-restraints excluded: chain 3b residue 35 GLU Chi-restraints excluded: chain 3b residue 82 LYS Chi-restraints excluded: chain 3b residue 124 GLU Chi-restraints excluded: chain 3c residue 124 GLU Chi-restraints excluded: chain 3d residue 124 GLU Chi-restraints excluded: chain 3e residue 22 THR Chi-restraints excluded: chain 3e residue 35 GLU Chi-restraints excluded: chain 3e residue 82 LYS Chi-restraints excluded: chain 3e residue 124 GLU Chi-restraints excluded: chain 3e residue 130 MET Chi-restraints excluded: chain 3f residue 73 GLN Chi-restraints excluded: chain 3f residue 124 GLU Chi-restraints excluded: chain 4a residue 2 SER Chi-restraints excluded: chain 4a residue 22 THR Chi-restraints excluded: chain 4a residue 130 MET Chi-restraints excluded: chain 4c residue 56 SER Chi-restraints excluded: chain 4c residue 73 GLN Chi-restraints excluded: chain 4c residue 124 GLU Chi-restraints excluded: chain 4d residue 2 SER Chi-restraints excluded: chain 4d residue 22 THR Chi-restraints excluded: chain 4d residue 130 MET Chi-restraints excluded: chain 4f residue 56 SER Chi-restraints excluded: chain 4f residue 73 GLN Chi-restraints excluded: chain 4f residue 124 GLU Chi-restraints excluded: chain 5a residue 17 THR Chi-restraints excluded: chain 5a residue 119 LYS Chi-restraints excluded: chain 5b residue 17 THR Chi-restraints excluded: chain 5b residue 30 GLU Chi-restraints excluded: chain 5b residue 56 SER Chi-restraints excluded: chain 5b residue 112 LYS Chi-restraints excluded: chain 5b residue 124 GLU Chi-restraints excluded: chain 5c residue 17 THR Chi-restraints excluded: chain 5c residue 73 GLN Chi-restraints excluded: chain 5d residue 17 THR Chi-restraints excluded: chain 5d residue 119 LYS Chi-restraints excluded: chain 5e residue 17 THR Chi-restraints excluded: chain 5e residue 30 GLU Chi-restraints excluded: chain 5e residue 56 SER Chi-restraints excluded: chain 5e residue 124 GLU Chi-restraints excluded: chain 5f residue 17 THR Chi-restraints excluded: chain 5f residue 73 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1170 random chunks: chunk 941 optimal weight: 0.9980 chunk 641 optimal weight: 30.0000 chunk 16 optimal weight: 10.0000 chunk 842 optimal weight: 10.0000 chunk 466 optimal weight: 0.9980 chunk 965 optimal weight: 5.9990 chunk 781 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 577 optimal weight: 0.7980 chunk 1015 optimal weight: 5.9990 chunk 285 optimal weight: 0.7980 overall best weight: 1.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3B 626 ASN 3C 23 GLN 3C 239 GLN 3F 23 GLN 3F 239 GLN 4A 205 ASN 4B 490 ASN ** 4B 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4C 474 ASN ** 4C 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4D 205 ASN ** 4E 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4F 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5A 606 GLN 5B 93 ASN ** 5B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5C 606 GLN ** 5D 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5D 606 GLN 5E 93 ASN ** 5E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5F 606 GLN 3a 140 GLN 3d 114 GLN 3d 140 GLN 4a 140 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 94842 Z= 0.178 Angle : 0.600 7.140 129006 Z= 0.333 Chirality : 0.045 0.174 14346 Planarity : 0.005 0.056 16776 Dihedral : 4.893 19.482 12654 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.67 % Allowed : 11.91 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.16 (0.08), residues: 11628 helix: 1.63 (0.09), residues: 3330 sheet: 0.60 (0.11), residues: 2340 loop : -1.01 (0.08), residues: 5958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP5f 109 HIS 0.004 0.001 HIS4a 38 PHE 0.017 0.002 PHE5F 175 TYR 0.025 0.001 TYR5F 489 ARG 0.006 0.000 ARG3B 520 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23256 Ramachandran restraints generated. 11628 Oldfield, 0 Emsley, 11628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23256 Ramachandran restraints generated. 11628 Oldfield, 0 Emsley, 11628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1398 residues out of total 10152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 1127 time to evaluate : 8.008 Fit side-chains REVERT: 3A 154 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7542 (mtpp) REVERT: 3A 239 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8202 (tp40) REVERT: 3A 529 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8060 (mt) REVERT: 3A 610 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: 3B 41 LYS cc_start: 0.7013 (OUTLIER) cc_final: 0.6701 (mptt) REVERT: 3B 79 LEU cc_start: 0.6351 (mt) cc_final: 0.6069 (mt) REVERT: 3B 610 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: 3B 675 VAL cc_start: 0.8813 (OUTLIER) cc_final: 0.8517 (p) REVERT: 3D 154 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7541 (mtpp) REVERT: 3D 610 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: 3E 79 LEU cc_start: 0.6354 (mt) cc_final: 0.6065 (mt) REVERT: 3E 610 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: 3E 675 VAL cc_start: 0.8816 (OUTLIER) cc_final: 0.8521 (p) REVERT: 3E 689 MET cc_start: 0.6429 (OUTLIER) cc_final: 0.4707 (pmm) REVERT: 4A 48 ASP cc_start: 0.7342 (OUTLIER) cc_final: 0.7077 (m-30) REVERT: 4A 605 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7862 (mt-10) REVERT: 4B 41 LYS cc_start: 0.7357 (OUTLIER) cc_final: 0.6735 (mmtm) REVERT: 4B 154 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7441 (mtpm) REVERT: 4B 529 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8189 (mm) REVERT: 4C 111 MET cc_start: 0.9118 (mmm) cc_final: 0.8887 (mmm) REVERT: 4C 202 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7137 (mp10) REVERT: 4D 48 ASP cc_start: 0.7336 (OUTLIER) cc_final: 0.7078 (m-30) REVERT: 4D 100 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8703 (mttp) REVERT: 4D 605 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7850 (mt-10) REVERT: 4D 689 MET cc_start: 0.6630 (OUTLIER) cc_final: 0.5958 (pp-130) REVERT: 4E 41 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.6752 (mmtm) REVERT: 4E 154 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7450 (mtpm) REVERT: 4E 529 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8196 (mm) REVERT: 4F 73 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7369 (mt0) REVERT: 4F 111 MET cc_start: 0.9115 (mmm) cc_final: 0.8884 (mmm) REVERT: 4F 202 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7092 (mp10) REVERT: 5A 73 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7484 (mt0) REVERT: 5A 509 MET cc_start: 0.8960 (mmm) cc_final: 0.8392 (mmm) REVERT: 5A 549 MET cc_start: 0.8895 (mtp) cc_final: 0.8567 (mtp) REVERT: 5B 23 GLN cc_start: 0.7295 (mp10) cc_final: 0.7082 (mp10) REVERT: 5B 197 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7415 (m-30) REVERT: 5B 605 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7568 (mt-10) REVERT: 5C 73 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7544 (mt0) REVERT: 5C 96 GLU cc_start: 0.7091 (tt0) cc_final: 0.6883 (mt-10) REVERT: 5C 250 GLU cc_start: 0.7546 (mm-30) cc_final: 0.6974 (tp30) REVERT: 5D 73 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7478 (mt0) REVERT: 5D 549 MET cc_start: 0.8878 (mtp) cc_final: 0.8577 (mtp) REVERT: 5E 23 GLN cc_start: 0.7287 (mp10) cc_final: 0.6996 (mp10) REVERT: 5E 197 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7403 (m-30) REVERT: 5E 601 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8532 (ptmm) REVERT: 5F 73 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7549 (mt0) REVERT: 5F 96 GLU cc_start: 0.7152 (tt0) cc_final: 0.6899 (mt-10) REVERT: 5F 105 MET cc_start: 0.8137 (mmm) cc_final: 0.7792 (mmm) REVERT: 5F 250 GLU cc_start: 0.7576 (mm-30) cc_final: 0.6977 (tp30) REVERT: 3a 124 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7542 (pm20) REVERT: 3b 35 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7467 (mt-10) REVERT: 3b 52 MET cc_start: 0.8556 (mtp) cc_final: 0.7973 (mmm) REVERT: 3d 124 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7551 (pm20) REVERT: 3e 35 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7456 (mt-10) REVERT: 3e 52 MET cc_start: 0.8572 (mtp) cc_final: 0.7985 (mmm) REVERT: 3f 73 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8590 (mt0) REVERT: 3f 114 GLN cc_start: 0.8319 (mt0) cc_final: 0.8108 (mt0) REVERT: 4b 52 MET cc_start: 0.8764 (mtp) cc_final: 0.8428 (mtm) REVERT: 4c 73 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8518 (mt0) REVERT: 4c 124 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7570 (pm20) REVERT: 4d 130 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8601 (ttp) REVERT: 4e 52 MET cc_start: 0.8790 (mtp) cc_final: 0.8396 (mtm) REVERT: 4f 73 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8535 (mt0) REVERT: 4f 124 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7536 (pm20) REVERT: 5b 30 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6681 (pm20) REVERT: 5c 49 MET cc_start: 0.9046 (ptt) cc_final: 0.8440 (ptp) REVERT: 5e 30 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6750 (pm20) REVERT: 5f 49 MET cc_start: 0.9041 (ptt) cc_final: 0.8435 (ptp) outliers start: 271 outliers final: 131 residues processed: 1298 average time/residue: 1.7498 time to fit residues: 3051.1236 Evaluate side-chains 1252 residues out of total 10152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1074 time to evaluate : 9.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 61 ASP Chi-restraints excluded: chain 3A residue 105 MET Chi-restraints excluded: chain 3A residue 134 SER Chi-restraints excluded: chain 3A residue 154 LYS Chi-restraints excluded: chain 3A residue 239 GLN Chi-restraints excluded: chain 3A residue 529 ILE Chi-restraints excluded: chain 3A residue 610 GLU Chi-restraints excluded: chain 3B residue 41 LYS Chi-restraints excluded: chain 3B residue 61 ASP Chi-restraints excluded: chain 3B residue 98 THR Chi-restraints excluded: chain 3B residue 209 GLU Chi-restraints excluded: chain 3B residue 481 ILE Chi-restraints excluded: chain 3B residue 485 ASP Chi-restraints excluded: chain 3B residue 529 ILE Chi-restraints excluded: chain 3B residue 545 GLU Chi-restraints excluded: chain 3B residue 601 LYS Chi-restraints excluded: chain 3B residue 610 GLU Chi-restraints excluded: chain 3B residue 675 VAL Chi-restraints excluded: chain 3C residue 100 LYS Chi-restraints excluded: chain 3C residue 130 ASP Chi-restraints excluded: chain 3C residue 485 ASP Chi-restraints excluded: chain 3C residue 491 THR Chi-restraints excluded: chain 3C residue 529 ILE Chi-restraints excluded: chain 3C residue 605 GLU Chi-restraints excluded: chain 3C residue 675 VAL Chi-restraints excluded: chain 3D residue 61 ASP Chi-restraints excluded: chain 3D residue 105 MET Chi-restraints excluded: chain 3D residue 130 ASP Chi-restraints excluded: chain 3D residue 134 SER Chi-restraints excluded: chain 3D residue 154 LYS Chi-restraints excluded: chain 3D residue 529 ILE Chi-restraints excluded: chain 3D residue 601 LYS Chi-restraints excluded: chain 3D residue 610 GLU Chi-restraints excluded: chain 3E residue 61 ASP Chi-restraints excluded: chain 3E residue 98 THR Chi-restraints excluded: chain 3E residue 209 GLU Chi-restraints excluded: chain 3E residue 601 LYS Chi-restraints excluded: chain 3E residue 610 GLU Chi-restraints excluded: chain 3E residue 675 VAL Chi-restraints excluded: chain 3E residue 689 MET Chi-restraints excluded: chain 3F residue 100 LYS Chi-restraints excluded: chain 3F residue 130 ASP Chi-restraints excluded: chain 3F residue 485 ASP Chi-restraints excluded: chain 3F residue 605 GLU Chi-restraints excluded: chain 4A residue 48 ASP Chi-restraints excluded: chain 4A residue 61 ASP Chi-restraints excluded: chain 4A residue 91 THR Chi-restraints excluded: chain 4A residue 105 MET Chi-restraints excluded: chain 4A residue 130 ASP Chi-restraints excluded: chain 4A residue 485 ASP Chi-restraints excluded: chain 4A residue 601 LYS Chi-restraints excluded: chain 4A residue 605 GLU Chi-restraints excluded: chain 4A residue 675 VAL Chi-restraints excluded: chain 4B residue 20 SER Chi-restraints excluded: chain 4B residue 21 VAL Chi-restraints excluded: chain 4B residue 41 LYS Chi-restraints excluded: chain 4B residue 61 ASP Chi-restraints excluded: chain 4B residue 91 THR Chi-restraints excluded: chain 4B residue 136 THR Chi-restraints excluded: chain 4B residue 154 LYS Chi-restraints excluded: chain 4B residue 481 ILE Chi-restraints excluded: chain 4B residue 517 ASP Chi-restraints excluded: chain 4B residue 529 ILE Chi-restraints excluded: chain 4B residue 675 VAL Chi-restraints excluded: chain 4C residue 48 ASP Chi-restraints excluded: chain 4C residue 61 ASP Chi-restraints excluded: chain 4C residue 91 THR Chi-restraints excluded: chain 4C residue 132 SER Chi-restraints excluded: chain 4C residue 202 GLN Chi-restraints excluded: chain 4C residue 474 ASN Chi-restraints excluded: chain 4C residue 601 LYS Chi-restraints excluded: chain 4D residue 48 ASP Chi-restraints excluded: chain 4D residue 61 ASP Chi-restraints excluded: chain 4D residue 91 THR Chi-restraints excluded: chain 4D residue 100 LYS Chi-restraints excluded: chain 4D residue 105 MET Chi-restraints excluded: chain 4D residue 130 ASP Chi-restraints excluded: chain 4D residue 601 LYS Chi-restraints excluded: chain 4D residue 605 GLU Chi-restraints excluded: chain 4D residue 675 VAL Chi-restraints excluded: chain 4D residue 689 MET Chi-restraints excluded: chain 4E residue 20 SER Chi-restraints excluded: chain 4E residue 21 VAL Chi-restraints excluded: chain 4E residue 41 LYS Chi-restraints excluded: chain 4E residue 61 ASP Chi-restraints excluded: chain 4E residue 154 LYS Chi-restraints excluded: chain 4E residue 481 ILE Chi-restraints excluded: chain 4E residue 517 ASP Chi-restraints excluded: chain 4E residue 529 ILE Chi-restraints excluded: chain 4E residue 675 VAL Chi-restraints excluded: chain 4F residue 48 ASP Chi-restraints excluded: chain 4F residue 61 ASP Chi-restraints excluded: chain 4F residue 73 GLN Chi-restraints excluded: chain 4F residue 91 THR Chi-restraints excluded: chain 4F residue 132 SER Chi-restraints excluded: chain 4F residue 202 GLN Chi-restraints excluded: chain 4F residue 601 LYS Chi-restraints excluded: chain 5A residue 21 VAL Chi-restraints excluded: chain 5A residue 40 THR Chi-restraints excluded: chain 5A residue 73 GLN Chi-restraints excluded: chain 5A residue 130 ASP Chi-restraints excluded: chain 5A residue 151 VAL Chi-restraints excluded: chain 5A residue 156 ASP Chi-restraints excluded: chain 5A residue 601 LYS Chi-restraints excluded: chain 5B residue 40 THR Chi-restraints excluded: chain 5B residue 61 ASP Chi-restraints excluded: chain 5B residue 77 VAL Chi-restraints excluded: chain 5B residue 197 ASP Chi-restraints excluded: chain 5B residue 605 GLU Chi-restraints excluded: chain 5B residue 625 GLU Chi-restraints excluded: chain 5C residue 21 VAL Chi-restraints excluded: chain 5C residue 48 ASP Chi-restraints excluded: chain 5C residue 61 ASP Chi-restraints excluded: chain 5C residue 73 GLN Chi-restraints excluded: chain 5C residue 98 THR Chi-restraints excluded: chain 5C residue 132 SER Chi-restraints excluded: chain 5C residue 156 ASP Chi-restraints excluded: chain 5C residue 157 GLU Chi-restraints excluded: chain 5C residue 206 ASP Chi-restraints excluded: chain 5C residue 601 LYS Chi-restraints excluded: chain 5C residue 605 GLU Chi-restraints excluded: chain 5C residue 662 LEU Chi-restraints excluded: chain 5C residue 675 VAL Chi-restraints excluded: chain 5D residue 21 VAL Chi-restraints excluded: chain 5D residue 40 THR Chi-restraints excluded: chain 5D residue 48 ASP Chi-restraints excluded: chain 5D residue 73 GLN Chi-restraints excluded: chain 5D residue 130 ASP Chi-restraints excluded: chain 5D residue 151 VAL Chi-restraints excluded: chain 5D residue 529 ILE Chi-restraints excluded: chain 5D residue 601 LYS Chi-restraints excluded: chain 5D residue 605 GLU Chi-restraints excluded: chain 5E residue 40 THR Chi-restraints excluded: chain 5E residue 61 ASP Chi-restraints excluded: chain 5E residue 197 ASP Chi-restraints excluded: chain 5E residue 601 LYS Chi-restraints excluded: chain 5E residue 625 GLU Chi-restraints excluded: chain 5F residue 21 VAL Chi-restraints excluded: chain 5F residue 48 ASP Chi-restraints excluded: chain 5F residue 73 GLN Chi-restraints excluded: chain 5F residue 156 ASP Chi-restraints excluded: chain 5F residue 157 GLU Chi-restraints excluded: chain 5F residue 601 LYS Chi-restraints excluded: chain 5F residue 605 GLU Chi-restraints excluded: chain 5F residue 675 VAL Chi-restraints excluded: chain 3a residue 22 THR Chi-restraints excluded: chain 3a residue 124 GLU Chi-restraints excluded: chain 3b residue 22 THR Chi-restraints excluded: chain 3b residue 35 GLU Chi-restraints excluded: chain 3b residue 82 LYS Chi-restraints excluded: chain 3c residue 124 GLU Chi-restraints excluded: chain 3d residue 124 GLU Chi-restraints excluded: chain 3e residue 22 THR Chi-restraints excluded: chain 3e residue 35 GLU Chi-restraints excluded: chain 3e residue 82 LYS Chi-restraints excluded: chain 3e residue 130 MET Chi-restraints excluded: chain 3f residue 73 GLN Chi-restraints excluded: chain 3f residue 121 ASP Chi-restraints excluded: chain 3f residue 124 GLU Chi-restraints excluded: chain 4a residue 2 SER Chi-restraints excluded: chain 4a residue 22 THR Chi-restraints excluded: chain 4c residue 56 SER Chi-restraints excluded: chain 4c residue 73 GLN Chi-restraints excluded: chain 4c residue 124 GLU Chi-restraints excluded: chain 4d residue 2 SER Chi-restraints excluded: chain 4d residue 22 THR Chi-restraints excluded: chain 4d residue 130 MET Chi-restraints excluded: chain 4f residue 56 SER Chi-restraints excluded: chain 4f residue 73 GLN Chi-restraints excluded: chain 4f residue 124 GLU Chi-restraints excluded: chain 5a residue 17 THR Chi-restraints excluded: chain 5a residue 124 GLU Chi-restraints excluded: chain 5b residue 30 GLU Chi-restraints excluded: chain 5b residue 56 SER Chi-restraints excluded: chain 5b residue 112 LYS Chi-restraints excluded: chain 5c residue 73 GLN Chi-restraints excluded: chain 5e residue 30 GLU Chi-restraints excluded: chain 5f residue 73 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1170 random chunks: chunk 380 optimal weight: 5.9990 chunk 1018 optimal weight: 1.9990 chunk 223 optimal weight: 20.0000 chunk 663 optimal weight: 6.9990 chunk 279 optimal weight: 10.0000 chunk 1132 optimal weight: 0.0060 chunk 939 optimal weight: 9.9990 chunk 524 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 chunk 374 optimal weight: 10.0000 chunk 594 optimal weight: 6.9990 overall best weight: 3.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3C 23 GLN 3C 239 GLN 3E 626 ASN 3F 23 GLN 3F 239 GLN 4A 205 ASN 4C 474 ASN ** 4C 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4D 205 ASN ** 4F 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5A 606 GLN ** 5B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5C 490 ASN 5D 606 GLN ** 5E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3a 114 GLN 3a 140 GLN 3d 140 GLN 3e 114 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 94842 Z= 0.227 Angle : 0.655 8.115 129006 Z= 0.363 Chirality : 0.047 0.194 14346 Planarity : 0.005 0.057 16776 Dihedral : 4.936 19.902 12654 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.17 % Allowed : 11.80 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.11 (0.08), residues: 11628 helix: 1.57 (0.09), residues: 3330 sheet: 0.62 (0.11), residues: 2358 loop : -1.06 (0.08), residues: 5940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP3B 131 HIS 0.005 0.001 HIS4d 38 PHE 0.021 0.002 PHE5C 175 TYR 0.027 0.002 TYR5F 489 ARG 0.008 0.001 ARG3E 520 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23256 Ramachandran restraints generated. 11628 Oldfield, 0 Emsley, 11628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23256 Ramachandran restraints generated. 11628 Oldfield, 0 Emsley, 11628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1419 residues out of total 10152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 322 poor density : 1097 time to evaluate : 7.873 Fit side-chains REVERT: 3A 154 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7568 (mtpp) REVERT: 3A 610 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6977 (mp0) REVERT: 3B 41 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6672 (mptt) REVERT: 3B 52 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7579 (mptp) REVERT: 3B 79 LEU cc_start: 0.6394 (mt) cc_final: 0.6117 (mt) REVERT: 3B 610 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: 3B 659 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7816 (mm-40) REVERT: 3B 689 MET cc_start: 0.6549 (OUTLIER) cc_final: 0.4782 (pmm) REVERT: 3C 659 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7404 (tm-30) REVERT: 3C 663 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6885 (mt-10) REVERT: 3D 154 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7567 (mtpp) REVERT: 3D 610 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: 3D 659 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7329 (tm-30) REVERT: 3E 41 LYS cc_start: 0.7020 (OUTLIER) cc_final: 0.6650 (mptt) REVERT: 3E 52 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7569 (mptp) REVERT: 3E 79 LEU cc_start: 0.6368 (mt) cc_final: 0.6105 (mt) REVERT: 3E 610 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: 3E 659 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7816 (mm-40) REVERT: 3E 689 MET cc_start: 0.6505 (OUTLIER) cc_final: 0.4781 (pmm) REVERT: 4A 48 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.7191 (m-30) REVERT: 4A 605 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7899 (mt-10) REVERT: 4B 41 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.6762 (mmtm) REVERT: 4B 154 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7469 (mtpm) REVERT: 4C 73 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7319 (mt0) REVERT: 4C 111 MET cc_start: 0.9127 (mmm) cc_final: 0.8894 (mmm) REVERT: 4C 202 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7130 (mp10) REVERT: 4D 48 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7191 (m-30) REVERT: 4D 605 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7889 (mt-10) REVERT: 4D 689 MET cc_start: 0.6653 (OUTLIER) cc_final: 0.6052 (pp-130) REVERT: 4E 41 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.6782 (mmtm) REVERT: 4E 154 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7358 (mtpm) REVERT: 4F 73 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7386 (mt0) REVERT: 4F 111 MET cc_start: 0.9126 (mmm) cc_final: 0.8893 (mmm) REVERT: 4F 202 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7129 (mp10) REVERT: 5A 73 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7488 (mt0) REVERT: 5B 79 LEU cc_start: 0.6070 (OUTLIER) cc_final: 0.5833 (mp) REVERT: 5B 197 ASP cc_start: 0.7668 (OUTLIER) cc_final: 0.7440 (m-30) REVERT: 5B 605 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7593 (mt-10) REVERT: 5C 73 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7428 (mt0) REVERT: 5C 96 GLU cc_start: 0.7129 (tt0) cc_final: 0.6922 (mt-10) REVERT: 5C 250 GLU cc_start: 0.7557 (mm-30) cc_final: 0.6986 (tp30) REVERT: 5C 520 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.7160 (mtm180) REVERT: 5D 73 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7489 (mt0) REVERT: 5D 549 MET cc_start: 0.8902 (mtp) cc_final: 0.8629 (mtp) REVERT: 5E 23 GLN cc_start: 0.7391 (mp10) cc_final: 0.7106 (mp10) REVERT: 5E 73 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7073 (mm110) REVERT: 5E 79 LEU cc_start: 0.6073 (OUTLIER) cc_final: 0.5850 (mp) REVERT: 5E 146 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7286 (mt-10) REVERT: 5E 197 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7430 (m-30) REVERT: 5E 601 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8508 (ptmm) REVERT: 5F 61 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7611 (m-30) REVERT: 5F 73 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7426 (mt0) REVERT: 5F 96 GLU cc_start: 0.7146 (tt0) cc_final: 0.6894 (mt-10) REVERT: 5F 105 MET cc_start: 0.8169 (mmm) cc_final: 0.7876 (mmm) REVERT: 5F 135 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6881 (mp0) REVERT: 5F 250 GLU cc_start: 0.7566 (mm-30) cc_final: 0.6975 (tp30) REVERT: 5F 520 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.7164 (mtm180) REVERT: 3a 124 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7568 (pm20) REVERT: 3b 13 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7405 (mm-30) REVERT: 3b 35 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7482 (mt-10) REVERT: 3b 52 MET cc_start: 0.8627 (mtp) cc_final: 0.8000 (mmm) REVERT: 3d 124 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7571 (pm20) REVERT: 3e 35 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7475 (mt-10) REVERT: 3e 52 MET cc_start: 0.8643 (mtp) cc_final: 0.8003 (mmm) REVERT: 3f 73 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8601 (mt0) REVERT: 4a 130 MET cc_start: 0.8857 (ttp) cc_final: 0.8629 (ttp) REVERT: 4b 52 MET cc_start: 0.8762 (mtp) cc_final: 0.8443 (mtm) REVERT: 4c 73 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8532 (mt0) REVERT: 4c 124 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7604 (pm20) REVERT: 4d 130 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8661 (ttp) REVERT: 4e 52 MET cc_start: 0.8786 (mtp) cc_final: 0.8424 (mtm) REVERT: 4f 73 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8531 (mt0) REVERT: 4f 124 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7604 (pm20) REVERT: 5b 30 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6830 (pm20) REVERT: 5b 124 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7527 (pt0) REVERT: 5c 49 MET cc_start: 0.9054 (ptt) cc_final: 0.8531 (ptp) REVERT: 5e 30 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6883 (pm20) REVERT: 5f 49 MET cc_start: 0.9063 (ptt) cc_final: 0.8531 (ptp) outliers start: 322 outliers final: 169 residues processed: 1291 average time/residue: 1.7917 time to fit residues: 3149.7004 Evaluate side-chains 1306 residues out of total 10152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1078 time to evaluate : 7.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 61 ASP Chi-restraints excluded: chain 3A residue 79 LEU Chi-restraints excluded: chain 3A residue 98 THR Chi-restraints excluded: chain 3A residue 105 MET Chi-restraints excluded: chain 3A residue 134 SER Chi-restraints excluded: chain 3A residue 154 LYS Chi-restraints excluded: chain 3A residue 529 ILE Chi-restraints excluded: chain 3A residue 610 GLU Chi-restraints excluded: chain 3A residue 662 LEU Chi-restraints excluded: chain 3B residue 41 LYS Chi-restraints excluded: chain 3B residue 52 LYS Chi-restraints excluded: chain 3B residue 61 ASP Chi-restraints excluded: chain 3B residue 98 THR Chi-restraints excluded: chain 3B residue 209 GLU Chi-restraints excluded: chain 3B residue 481 ILE Chi-restraints excluded: chain 3B residue 485 ASP Chi-restraints excluded: chain 3B residue 529 ILE Chi-restraints excluded: chain 3B residue 545 GLU Chi-restraints excluded: chain 3B residue 610 GLU Chi-restraints excluded: chain 3B residue 659 GLN Chi-restraints excluded: chain 3B residue 675 VAL Chi-restraints excluded: chain 3B residue 689 MET Chi-restraints excluded: chain 3C residue 100 LYS Chi-restraints excluded: chain 3C residue 202 GLN Chi-restraints excluded: chain 3C residue 481 ILE Chi-restraints excluded: chain 3C residue 485 ASP Chi-restraints excluded: chain 3C residue 491 THR Chi-restraints excluded: chain 3C residue 529 ILE Chi-restraints excluded: chain 3C residue 605 GLU Chi-restraints excluded: chain 3C residue 659 GLN Chi-restraints excluded: chain 3C residue 675 VAL Chi-restraints excluded: chain 3D residue 61 ASP Chi-restraints excluded: chain 3D residue 79 LEU Chi-restraints excluded: chain 3D residue 98 THR Chi-restraints excluded: chain 3D residue 154 LYS Chi-restraints excluded: chain 3D residue 529 ILE Chi-restraints excluded: chain 3D residue 601 LYS Chi-restraints excluded: chain 3D residue 610 GLU Chi-restraints excluded: chain 3D residue 659 GLN Chi-restraints excluded: chain 3D residue 662 LEU Chi-restraints excluded: chain 3E residue 41 LYS Chi-restraints excluded: chain 3E residue 52 LYS Chi-restraints excluded: chain 3E residue 61 ASP Chi-restraints excluded: chain 3E residue 98 THR Chi-restraints excluded: chain 3E residue 209 GLU Chi-restraints excluded: chain 3E residue 472 LYS Chi-restraints excluded: chain 3E residue 481 ILE Chi-restraints excluded: chain 3E residue 529 ILE Chi-restraints excluded: chain 3E residue 610 GLU Chi-restraints excluded: chain 3E residue 659 GLN Chi-restraints excluded: chain 3E residue 675 VAL Chi-restraints excluded: chain 3E residue 689 MET Chi-restraints excluded: chain 3F residue 100 LYS Chi-restraints excluded: chain 3F residue 202 GLN Chi-restraints excluded: chain 3F residue 481 ILE Chi-restraints excluded: chain 3F residue 485 ASP Chi-restraints excluded: chain 3F residue 491 THR Chi-restraints excluded: chain 3F residue 605 GLU Chi-restraints excluded: chain 4A residue 48 ASP Chi-restraints excluded: chain 4A residue 61 ASP Chi-restraints excluded: chain 4A residue 91 THR Chi-restraints excluded: chain 4A residue 105 MET Chi-restraints excluded: chain 4A residue 130 ASP Chi-restraints excluded: chain 4A residue 485 ASP Chi-restraints excluded: chain 4A residue 601 LYS Chi-restraints excluded: chain 4A residue 605 GLU Chi-restraints excluded: chain 4A residue 662 LEU Chi-restraints excluded: chain 4A residue 675 VAL Chi-restraints excluded: chain 4B residue 20 SER Chi-restraints excluded: chain 4B residue 21 VAL Chi-restraints excluded: chain 4B residue 41 LYS Chi-restraints excluded: chain 4B residue 61 ASP Chi-restraints excluded: chain 4B residue 91 THR Chi-restraints excluded: chain 4B residue 136 THR Chi-restraints excluded: chain 4B residue 154 LYS Chi-restraints excluded: chain 4B residue 481 ILE Chi-restraints excluded: chain 4B residue 517 ASP Chi-restraints excluded: chain 4B residue 529 ILE Chi-restraints excluded: chain 4B residue 675 VAL Chi-restraints excluded: chain 4C residue 48 ASP Chi-restraints excluded: chain 4C residue 73 GLN Chi-restraints excluded: chain 4C residue 91 THR Chi-restraints excluded: chain 4C residue 132 SER Chi-restraints excluded: chain 4C residue 202 GLN Chi-restraints excluded: chain 4C residue 474 ASN Chi-restraints excluded: chain 4C residue 601 LYS Chi-restraints excluded: chain 4D residue 48 ASP Chi-restraints excluded: chain 4D residue 61 ASP Chi-restraints excluded: chain 4D residue 91 THR Chi-restraints excluded: chain 4D residue 105 MET Chi-restraints excluded: chain 4D residue 130 ASP Chi-restraints excluded: chain 4D residue 485 ASP Chi-restraints excluded: chain 4D residue 601 LYS Chi-restraints excluded: chain 4D residue 605 GLU Chi-restraints excluded: chain 4D residue 662 LEU Chi-restraints excluded: chain 4D residue 675 VAL Chi-restraints excluded: chain 4D residue 689 MET Chi-restraints excluded: chain 4E residue 20 SER Chi-restraints excluded: chain 4E residue 21 VAL Chi-restraints excluded: chain 4E residue 41 LYS Chi-restraints excluded: chain 4E residue 61 ASP Chi-restraints excluded: chain 4E residue 91 THR Chi-restraints excluded: chain 4E residue 154 LYS Chi-restraints excluded: chain 4E residue 481 ILE Chi-restraints excluded: chain 4E residue 506 SER Chi-restraints excluded: chain 4E residue 517 ASP Chi-restraints excluded: chain 4E residue 529 ILE Chi-restraints excluded: chain 4E residue 675 VAL Chi-restraints excluded: chain 4F residue 48 ASP Chi-restraints excluded: chain 4F residue 73 GLN Chi-restraints excluded: chain 4F residue 91 THR Chi-restraints excluded: chain 4F residue 132 SER Chi-restraints excluded: chain 4F residue 202 GLN Chi-restraints excluded: chain 4F residue 601 LYS Chi-restraints excluded: chain 5A residue 21 VAL Chi-restraints excluded: chain 5A residue 40 THR Chi-restraints excluded: chain 5A residue 73 GLN Chi-restraints excluded: chain 5A residue 136 THR Chi-restraints excluded: chain 5A residue 151 VAL Chi-restraints excluded: chain 5A residue 156 ASP Chi-restraints excluded: chain 5A residue 192 ARG Chi-restraints excluded: chain 5A residue 529 ILE Chi-restraints excluded: chain 5A residue 601 LYS Chi-restraints excluded: chain 5A residue 605 GLU Chi-restraints excluded: chain 5B residue 40 THR Chi-restraints excluded: chain 5B residue 61 ASP Chi-restraints excluded: chain 5B residue 77 VAL Chi-restraints excluded: chain 5B residue 79 LEU Chi-restraints excluded: chain 5B residue 136 THR Chi-restraints excluded: chain 5B residue 197 ASP Chi-restraints excluded: chain 5B residue 605 GLU Chi-restraints excluded: chain 5B residue 625 GLU Chi-restraints excluded: chain 5B residue 662 LEU Chi-restraints excluded: chain 5C residue 21 VAL Chi-restraints excluded: chain 5C residue 48 ASP Chi-restraints excluded: chain 5C residue 61 ASP Chi-restraints excluded: chain 5C residue 73 GLN Chi-restraints excluded: chain 5C residue 98 THR Chi-restraints excluded: chain 5C residue 132 SER Chi-restraints excluded: chain 5C residue 156 ASP Chi-restraints excluded: chain 5C residue 157 GLU Chi-restraints excluded: chain 5C residue 206 ASP Chi-restraints excluded: chain 5C residue 520 ARG Chi-restraints excluded: chain 5C residue 601 LYS Chi-restraints excluded: chain 5C residue 605 GLU Chi-restraints excluded: chain 5C residue 625 GLU Chi-restraints excluded: chain 5C residue 662 LEU Chi-restraints excluded: chain 5C residue 675 VAL Chi-restraints excluded: chain 5D residue 21 VAL Chi-restraints excluded: chain 5D residue 40 THR Chi-restraints excluded: chain 5D residue 48 ASP Chi-restraints excluded: chain 5D residue 73 GLN Chi-restraints excluded: chain 5D residue 130 ASP Chi-restraints excluded: chain 5D residue 136 THR Chi-restraints excluded: chain 5D residue 151 VAL Chi-restraints excluded: chain 5D residue 156 ASP Chi-restraints excluded: chain 5D residue 192 ARG Chi-restraints excluded: chain 5D residue 206 ASP Chi-restraints excluded: chain 5D residue 529 ILE Chi-restraints excluded: chain 5D residue 601 LYS Chi-restraints excluded: chain 5D residue 605 GLU Chi-restraints excluded: chain 5E residue 40 THR Chi-restraints excluded: chain 5E residue 61 ASP Chi-restraints excluded: chain 5E residue 73 GLN Chi-restraints excluded: chain 5E residue 79 LEU Chi-restraints excluded: chain 5E residue 136 THR Chi-restraints excluded: chain 5E residue 146 GLU Chi-restraints excluded: chain 5E residue 197 ASP Chi-restraints excluded: chain 5E residue 601 LYS Chi-restraints excluded: chain 5E residue 625 GLU Chi-restraints excluded: chain 5E residue 662 LEU Chi-restraints excluded: chain 5F residue 21 VAL Chi-restraints excluded: chain 5F residue 48 ASP Chi-restraints excluded: chain 5F residue 61 ASP Chi-restraints excluded: chain 5F residue 73 GLN Chi-restraints excluded: chain 5F residue 135 GLU Chi-restraints excluded: chain 5F residue 156 ASP Chi-restraints excluded: chain 5F residue 157 GLU Chi-restraints excluded: chain 5F residue 520 ARG Chi-restraints excluded: chain 5F residue 601 LYS Chi-restraints excluded: chain 5F residue 605 GLU Chi-restraints excluded: chain 5F residue 662 LEU Chi-restraints excluded: chain 5F residue 675 VAL Chi-restraints excluded: chain 3a residue 22 THR Chi-restraints excluded: chain 3a residue 124 GLU Chi-restraints excluded: chain 3b residue 13 GLU Chi-restraints excluded: chain 3b residue 22 THR Chi-restraints excluded: chain 3b residue 35 GLU Chi-restraints excluded: chain 3b residue 82 LYS Chi-restraints excluded: chain 3b residue 124 GLU Chi-restraints excluded: chain 3c residue 124 GLU Chi-restraints excluded: chain 3d residue 124 GLU Chi-restraints excluded: chain 3e residue 22 THR Chi-restraints excluded: chain 3e residue 35 GLU Chi-restraints excluded: chain 3e residue 82 LYS Chi-restraints excluded: chain 3e residue 124 GLU Chi-restraints excluded: chain 3e residue 130 MET Chi-restraints excluded: chain 3f residue 73 GLN Chi-restraints excluded: chain 3f residue 124 GLU Chi-restraints excluded: chain 4a residue 2 SER Chi-restraints excluded: chain 4a residue 22 THR Chi-restraints excluded: chain 4c residue 56 SER Chi-restraints excluded: chain 4c residue 73 GLN Chi-restraints excluded: chain 4c residue 124 GLU Chi-restraints excluded: chain 4d residue 2 SER Chi-restraints excluded: chain 4d residue 22 THR Chi-restraints excluded: chain 4d residue 130 MET Chi-restraints excluded: chain 4f residue 56 SER Chi-restraints excluded: chain 4f residue 73 GLN Chi-restraints excluded: chain 4f residue 124 GLU Chi-restraints excluded: chain 5a residue 17 THR Chi-restraints excluded: chain 5a residue 119 LYS Chi-restraints excluded: chain 5a residue 124 GLU Chi-restraints excluded: chain 5b residue 17 THR Chi-restraints excluded: chain 5b residue 30 GLU Chi-restraints excluded: chain 5b residue 56 SER Chi-restraints excluded: chain 5b residue 112 LYS Chi-restraints excluded: chain 5b residue 124 GLU Chi-restraints excluded: chain 5c residue 17 THR Chi-restraints excluded: chain 5c residue 73 GLN Chi-restraints excluded: chain 5c residue 119 LYS Chi-restraints excluded: chain 5d residue 17 THR Chi-restraints excluded: chain 5d residue 119 LYS Chi-restraints excluded: chain 5e residue 17 THR Chi-restraints excluded: chain 5e residue 30 GLU Chi-restraints excluded: chain 5e residue 56 SER Chi-restraints excluded: chain 5f residue 17 THR Chi-restraints excluded: chain 5f residue 73 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1170 random chunks: chunk 1091 optimal weight: 5.9990 chunk 127 optimal weight: 20.0000 chunk 644 optimal weight: 10.0000 chunk 826 optimal weight: 5.9990 chunk 640 optimal weight: 7.9990 chunk 952 optimal weight: 6.9990 chunk 632 optimal weight: 0.0870 chunk 1127 optimal weight: 2.9990 chunk 705 optimal weight: 9.9990 chunk 687 optimal weight: 0.9990 chunk 520 optimal weight: 10.0000 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3C 23 GLN 3C 239 GLN 3F 23 GLN 3F 239 GLN 4A 205 ASN 4C 474 ASN ** 4C 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4D 205 ASN ** 4F 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5A 606 GLN ** 5B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5C 490 ASN ** 5E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3a 140 GLN 3d 140 GLN 3e 114 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 94842 Z= 0.224 Angle : 0.650 7.949 129006 Z= 0.360 Chirality : 0.047 0.186 14346 Planarity : 0.005 0.058 16776 Dihedral : 4.934 19.812 12654 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.07 % Allowed : 12.10 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.09 (0.08), residues: 11628 helix: 1.58 (0.09), residues: 3330 sheet: 0.60 (0.11), residues: 2358 loop : -1.08 (0.08), residues: 5940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP4B 131 HIS 0.004 0.001 HIS4d 38 PHE 0.021 0.002 PHE5F 175 TYR 0.027 0.002 TYR5C 489 ARG 0.009 0.001 ARG3E 520 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23256 Ramachandran restraints generated. 11628 Oldfield, 0 Emsley, 11628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23256 Ramachandran restraints generated. 11628 Oldfield, 0 Emsley, 11628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1424 residues out of total 10152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 1112 time to evaluate : 8.101 Fit side-chains REVERT: 3A 154 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7549 (mtpp) REVERT: 3A 610 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6980 (mp0) REVERT: 3B 41 LYS cc_start: 0.6957 (OUTLIER) cc_final: 0.6597 (mptt) REVERT: 3B 52 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7559 (mptp) REVERT: 3B 79 LEU cc_start: 0.6401 (mt) cc_final: 0.6138 (mt) REVERT: 3B 610 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: 3B 659 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7831 (mm-40) REVERT: 3B 689 MET cc_start: 0.6461 (OUTLIER) cc_final: 0.4719 (pmm) REVERT: 3C 659 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: 3C 663 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6865 (mt-10) REVERT: 3D 154 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7542 (mtpp) REVERT: 3D 610 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: 3D 659 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7379 (tm-30) REVERT: 3E 41 LYS cc_start: 0.7024 (OUTLIER) cc_final: 0.6654 (mptt) REVERT: 3E 52 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7565 (mptp) REVERT: 3E 79 LEU cc_start: 0.6381 (mt) cc_final: 0.6107 (mt) REVERT: 3E 610 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: 3E 659 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7829 (mm-40) REVERT: 3E 689 MET cc_start: 0.6476 (OUTLIER) cc_final: 0.4853 (pmm) REVERT: 3F 659 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7415 (tm-30) REVERT: 3F 663 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6871 (mt-10) REVERT: 4A 48 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.7140 (m-30) REVERT: 4A 605 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7885 (mt-10) REVERT: 4B 41 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.6745 (mmtm) REVERT: 4B 154 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7459 (mtpm) REVERT: 4C 73 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7333 (mt0) REVERT: 4C 111 MET cc_start: 0.9121 (mmm) cc_final: 0.8896 (mmm) REVERT: 4C 202 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7150 (mp10) REVERT: 4D 48 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.7140 (m-30) REVERT: 4D 605 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7882 (mt-10) REVERT: 4D 689 MET cc_start: 0.6655 (OUTLIER) cc_final: 0.6060 (pp-130) REVERT: 4E 41 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.6766 (mmtm) REVERT: 4E 154 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7382 (mtpm) REVERT: 4F 73 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7368 (mt0) REVERT: 4F 100 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8415 (mtpp) REVERT: 4F 111 MET cc_start: 0.9119 (mmm) cc_final: 0.8897 (mmm) REVERT: 4F 202 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7121 (mp10) REVERT: 5A 73 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7501 (mt0) REVERT: 5A 99 PHE cc_start: 0.8699 (m-80) cc_final: 0.8487 (m-80) REVERT: 5A 549 MET cc_start: 0.8922 (mtp) cc_final: 0.8618 (mtp) REVERT: 5B 73 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7024 (mm110) REVERT: 5B 197 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7439 (m-30) REVERT: 5B 605 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7587 (mt-10) REVERT: 5C 73 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7390 (mt0) REVERT: 5C 96 GLU cc_start: 0.7136 (tt0) cc_final: 0.6928 (mt-10) REVERT: 5C 250 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7086 (tp30) REVERT: 5C 520 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7164 (mtm180) REVERT: 5D 73 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7472 (mt0) REVERT: 5D 549 MET cc_start: 0.8908 (mtp) cc_final: 0.8587 (mtp) REVERT: 5E 23 GLN cc_start: 0.7385 (mp10) cc_final: 0.7118 (mp10) REVERT: 5E 146 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7294 (mt-10) REVERT: 5E 197 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7387 (m-30) REVERT: 5E 601 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8478 (ptmm) REVERT: 5E 605 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7482 (mt-10) REVERT: 5F 73 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7431 (mt0) REVERT: 5F 96 GLU cc_start: 0.7153 (tt0) cc_final: 0.6907 (mt-10) REVERT: 5F 105 MET cc_start: 0.8238 (mmm) cc_final: 0.7964 (mmm) REVERT: 5F 135 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6841 (mp0) REVERT: 5F 250 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7071 (tp30) REVERT: 5F 520 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7182 (mtm180) REVERT: 3a 124 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7561 (pm20) REVERT: 3b 13 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7369 (mm-30) REVERT: 3b 35 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7477 (mt-10) REVERT: 3b 52 MET cc_start: 0.8619 (mtp) cc_final: 0.8002 (mmm) REVERT: 3d 124 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7565 (pm20) REVERT: 3e 35 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7474 (mt-10) REVERT: 3e 52 MET cc_start: 0.8635 (mtp) cc_final: 0.8009 (mmm) REVERT: 3f 73 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8601 (mt0) REVERT: 4a 130 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8639 (ttp) REVERT: 4b 52 MET cc_start: 0.8760 (mtp) cc_final: 0.8443 (mtm) REVERT: 4c 54 LYS cc_start: 0.8485 (mtmt) cc_final: 0.8146 (ptmt) REVERT: 4c 73 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8530 (mt0) REVERT: 4c 124 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7587 (pm20) REVERT: 4d 130 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8660 (ttp) REVERT: 4e 52 MET cc_start: 0.8791 (mtp) cc_final: 0.8433 (mtm) REVERT: 4f 73 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8537 (mt0) REVERT: 4f 124 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7582 (pm20) REVERT: 5b 30 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6826 (pm20) REVERT: 5b 124 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7543 (pt0) REVERT: 5c 49 MET cc_start: 0.9050 (ptt) cc_final: 0.8529 (ptp) REVERT: 5e 30 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6877 (pm20) REVERT: 5f 49 MET cc_start: 0.9055 (ptt) cc_final: 0.8477 (ptp) outliers start: 312 outliers final: 181 residues processed: 1298 average time/residue: 1.6992 time to fit residues: 2977.0892 Evaluate side-chains 1326 residues out of total 10152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1085 time to evaluate : 7.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 61 ASP Chi-restraints excluded: chain 3A residue 79 LEU Chi-restraints excluded: chain 3A residue 98 THR Chi-restraints excluded: chain 3A residue 105 MET Chi-restraints excluded: chain 3A residue 134 SER Chi-restraints excluded: chain 3A residue 154 LYS Chi-restraints excluded: chain 3A residue 485 ASP Chi-restraints excluded: chain 3A residue 529 ILE Chi-restraints excluded: chain 3A residue 610 GLU Chi-restraints excluded: chain 3A residue 662 LEU Chi-restraints excluded: chain 3B residue 41 LYS Chi-restraints excluded: chain 3B residue 52 LYS Chi-restraints excluded: chain 3B residue 61 ASP Chi-restraints excluded: chain 3B residue 98 THR Chi-restraints excluded: chain 3B residue 481 ILE Chi-restraints excluded: chain 3B residue 485 ASP Chi-restraints excluded: chain 3B residue 529 ILE Chi-restraints excluded: chain 3B residue 545 GLU Chi-restraints excluded: chain 3B residue 601 LYS Chi-restraints excluded: chain 3B residue 610 GLU Chi-restraints excluded: chain 3B residue 659 GLN Chi-restraints excluded: chain 3B residue 662 LEU Chi-restraints excluded: chain 3B residue 675 VAL Chi-restraints excluded: chain 3B residue 689 MET Chi-restraints excluded: chain 3C residue 100 LYS Chi-restraints excluded: chain 3C residue 130 ASP Chi-restraints excluded: chain 3C residue 202 GLN Chi-restraints excluded: chain 3C residue 481 ILE Chi-restraints excluded: chain 3C residue 485 ASP Chi-restraints excluded: chain 3C residue 491 THR Chi-restraints excluded: chain 3C residue 529 ILE Chi-restraints excluded: chain 3C residue 605 GLU Chi-restraints excluded: chain 3C residue 659 GLN Chi-restraints excluded: chain 3C residue 675 VAL Chi-restraints excluded: chain 3D residue 40 THR Chi-restraints excluded: chain 3D residue 61 ASP Chi-restraints excluded: chain 3D residue 79 LEU Chi-restraints excluded: chain 3D residue 98 THR Chi-restraints excluded: chain 3D residue 154 LYS Chi-restraints excluded: chain 3D residue 529 ILE Chi-restraints excluded: chain 3D residue 601 LYS Chi-restraints excluded: chain 3D residue 610 GLU Chi-restraints excluded: chain 3D residue 659 GLN Chi-restraints excluded: chain 3D residue 662 LEU Chi-restraints excluded: chain 3E residue 41 LYS Chi-restraints excluded: chain 3E residue 52 LYS Chi-restraints excluded: chain 3E residue 61 ASP Chi-restraints excluded: chain 3E residue 98 THR Chi-restraints excluded: chain 3E residue 209 GLU Chi-restraints excluded: chain 3E residue 472 LYS Chi-restraints excluded: chain 3E residue 481 ILE Chi-restraints excluded: chain 3E residue 529 ILE Chi-restraints excluded: chain 3E residue 601 LYS Chi-restraints excluded: chain 3E residue 610 GLU Chi-restraints excluded: chain 3E residue 659 GLN Chi-restraints excluded: chain 3E residue 662 LEU Chi-restraints excluded: chain 3E residue 675 VAL Chi-restraints excluded: chain 3E residue 689 MET Chi-restraints excluded: chain 3F residue 79 LEU Chi-restraints excluded: chain 3F residue 100 LYS Chi-restraints excluded: chain 3F residue 130 ASP Chi-restraints excluded: chain 3F residue 184 MET Chi-restraints excluded: chain 3F residue 202 GLN Chi-restraints excluded: chain 3F residue 481 ILE Chi-restraints excluded: chain 3F residue 485 ASP Chi-restraints excluded: chain 3F residue 491 THR Chi-restraints excluded: chain 3F residue 602 LYS Chi-restraints excluded: chain 3F residue 605 GLU Chi-restraints excluded: chain 3F residue 659 GLN Chi-restraints excluded: chain 4A residue 48 ASP Chi-restraints excluded: chain 4A residue 61 ASP Chi-restraints excluded: chain 4A residue 91 THR Chi-restraints excluded: chain 4A residue 105 MET Chi-restraints excluded: chain 4A residue 130 ASP Chi-restraints excluded: chain 4A residue 132 SER Chi-restraints excluded: chain 4A residue 485 ASP Chi-restraints excluded: chain 4A residue 601 LYS Chi-restraints excluded: chain 4A residue 605 GLU Chi-restraints excluded: chain 4A residue 662 LEU Chi-restraints excluded: chain 4A residue 675 VAL Chi-restraints excluded: chain 4B residue 20 SER Chi-restraints excluded: chain 4B residue 21 VAL Chi-restraints excluded: chain 4B residue 41 LYS Chi-restraints excluded: chain 4B residue 61 ASP Chi-restraints excluded: chain 4B residue 91 THR Chi-restraints excluded: chain 4B residue 136 THR Chi-restraints excluded: chain 4B residue 154 LYS Chi-restraints excluded: chain 4B residue 481 ILE Chi-restraints excluded: chain 4B residue 517 ASP Chi-restraints excluded: chain 4B residue 529 ILE Chi-restraints excluded: chain 4B residue 675 VAL Chi-restraints excluded: chain 4C residue 48 ASP Chi-restraints excluded: chain 4C residue 73 GLN Chi-restraints excluded: chain 4C residue 91 THR Chi-restraints excluded: chain 4C residue 132 SER Chi-restraints excluded: chain 4C residue 157 GLU Chi-restraints excluded: chain 4C residue 202 GLN Chi-restraints excluded: chain 4C residue 474 ASN Chi-restraints excluded: chain 4C residue 506 SER Chi-restraints excluded: chain 4C residue 601 LYS Chi-restraints excluded: chain 4D residue 48 ASP Chi-restraints excluded: chain 4D residue 61 ASP Chi-restraints excluded: chain 4D residue 91 THR Chi-restraints excluded: chain 4D residue 105 MET Chi-restraints excluded: chain 4D residue 130 ASP Chi-restraints excluded: chain 4D residue 132 SER Chi-restraints excluded: chain 4D residue 485 ASP Chi-restraints excluded: chain 4D residue 601 LYS Chi-restraints excluded: chain 4D residue 605 GLU Chi-restraints excluded: chain 4D residue 662 LEU Chi-restraints excluded: chain 4D residue 675 VAL Chi-restraints excluded: chain 4D residue 689 MET Chi-restraints excluded: chain 4E residue 20 SER Chi-restraints excluded: chain 4E residue 21 VAL Chi-restraints excluded: chain 4E residue 41 LYS Chi-restraints excluded: chain 4E residue 61 ASP Chi-restraints excluded: chain 4E residue 91 THR Chi-restraints excluded: chain 4E residue 136 THR Chi-restraints excluded: chain 4E residue 154 LYS Chi-restraints excluded: chain 4E residue 481 ILE Chi-restraints excluded: chain 4E residue 517 ASP Chi-restraints excluded: chain 4E residue 529 ILE Chi-restraints excluded: chain 4E residue 675 VAL Chi-restraints excluded: chain 4F residue 48 ASP Chi-restraints excluded: chain 4F residue 73 GLN Chi-restraints excluded: chain 4F residue 91 THR Chi-restraints excluded: chain 4F residue 100 LYS Chi-restraints excluded: chain 4F residue 132 SER Chi-restraints excluded: chain 4F residue 157 GLU Chi-restraints excluded: chain 4F residue 202 GLN Chi-restraints excluded: chain 4F residue 506 SER Chi-restraints excluded: chain 4F residue 601 LYS Chi-restraints excluded: chain 5A residue 21 VAL Chi-restraints excluded: chain 5A residue 40 THR Chi-restraints excluded: chain 5A residue 73 GLN Chi-restraints excluded: chain 5A residue 136 THR Chi-restraints excluded: chain 5A residue 151 VAL Chi-restraints excluded: chain 5A residue 192 ARG Chi-restraints excluded: chain 5A residue 529 ILE Chi-restraints excluded: chain 5A residue 601 LYS Chi-restraints excluded: chain 5A residue 605 GLU Chi-restraints excluded: chain 5B residue 40 THR Chi-restraints excluded: chain 5B residue 61 ASP Chi-restraints excluded: chain 5B residue 73 GLN Chi-restraints excluded: chain 5B residue 77 VAL Chi-restraints excluded: chain 5B residue 136 THR Chi-restraints excluded: chain 5B residue 197 ASP Chi-restraints excluded: chain 5B residue 605 GLU Chi-restraints excluded: chain 5B residue 625 GLU Chi-restraints excluded: chain 5B residue 662 LEU Chi-restraints excluded: chain 5C residue 21 VAL Chi-restraints excluded: chain 5C residue 61 ASP Chi-restraints excluded: chain 5C residue 73 GLN Chi-restraints excluded: chain 5C residue 98 THR Chi-restraints excluded: chain 5C residue 156 ASP Chi-restraints excluded: chain 5C residue 157 GLU Chi-restraints excluded: chain 5C residue 520 ARG Chi-restraints excluded: chain 5C residue 601 LYS Chi-restraints excluded: chain 5C residue 605 GLU Chi-restraints excluded: chain 5C residue 662 LEU Chi-restraints excluded: chain 5C residue 675 VAL Chi-restraints excluded: chain 5D residue 21 VAL Chi-restraints excluded: chain 5D residue 40 THR Chi-restraints excluded: chain 5D residue 48 ASP Chi-restraints excluded: chain 5D residue 73 GLN Chi-restraints excluded: chain 5D residue 151 VAL Chi-restraints excluded: chain 5D residue 156 ASP Chi-restraints excluded: chain 5D residue 192 ARG Chi-restraints excluded: chain 5D residue 529 ILE Chi-restraints excluded: chain 5D residue 601 LYS Chi-restraints excluded: chain 5D residue 605 GLU Chi-restraints excluded: chain 5E residue 40 THR Chi-restraints excluded: chain 5E residue 61 ASP Chi-restraints excluded: chain 5E residue 146 GLU Chi-restraints excluded: chain 5E residue 197 ASP Chi-restraints excluded: chain 5E residue 601 LYS Chi-restraints excluded: chain 5E residue 605 GLU Chi-restraints excluded: chain 5E residue 625 GLU Chi-restraints excluded: chain 5E residue 662 LEU Chi-restraints excluded: chain 5F residue 21 VAL Chi-restraints excluded: chain 5F residue 48 ASP Chi-restraints excluded: chain 5F residue 73 GLN Chi-restraints excluded: chain 5F residue 135 GLU Chi-restraints excluded: chain 5F residue 156 ASP Chi-restraints excluded: chain 5F residue 157 GLU Chi-restraints excluded: chain 5F residue 520 ARG Chi-restraints excluded: chain 5F residue 601 LYS Chi-restraints excluded: chain 5F residue 605 GLU Chi-restraints excluded: chain 5F residue 662 LEU Chi-restraints excluded: chain 5F residue 675 VAL Chi-restraints excluded: chain 3a residue 22 THR Chi-restraints excluded: chain 3a residue 124 GLU Chi-restraints excluded: chain 3b residue 13 GLU Chi-restraints excluded: chain 3b residue 22 THR Chi-restraints excluded: chain 3b residue 35 GLU Chi-restraints excluded: chain 3b residue 82 LYS Chi-restraints excluded: chain 3b residue 124 GLU Chi-restraints excluded: chain 3c residue 124 GLU Chi-restraints excluded: chain 3d residue 124 GLU Chi-restraints excluded: chain 3e residue 22 THR Chi-restraints excluded: chain 3e residue 35 GLU Chi-restraints excluded: chain 3e residue 82 LYS Chi-restraints excluded: chain 3e residue 124 GLU Chi-restraints excluded: chain 3e residue 130 MET Chi-restraints excluded: chain 3f residue 73 GLN Chi-restraints excluded: chain 3f residue 121 ASP Chi-restraints excluded: chain 3f residue 124 GLU Chi-restraints excluded: chain 4a residue 2 SER Chi-restraints excluded: chain 4a residue 22 THR Chi-restraints excluded: chain 4a residue 114 GLN Chi-restraints excluded: chain 4a residue 130 MET Chi-restraints excluded: chain 4b residue 22 THR Chi-restraints excluded: chain 4c residue 56 SER Chi-restraints excluded: chain 4c residue 73 GLN Chi-restraints excluded: chain 4c residue 124 GLU Chi-restraints excluded: chain 4d residue 2 SER Chi-restraints excluded: chain 4d residue 22 THR Chi-restraints excluded: chain 4d residue 114 GLN Chi-restraints excluded: chain 4d residue 130 MET Chi-restraints excluded: chain 4e residue 22 THR Chi-restraints excluded: chain 4f residue 56 SER Chi-restraints excluded: chain 4f residue 73 GLN Chi-restraints excluded: chain 4f residue 124 GLU Chi-restraints excluded: chain 5a residue 17 THR Chi-restraints excluded: chain 5a residue 119 LYS Chi-restraints excluded: chain 5a residue 124 GLU Chi-restraints excluded: chain 5b residue 17 THR Chi-restraints excluded: chain 5b residue 30 GLU Chi-restraints excluded: chain 5b residue 56 SER Chi-restraints excluded: chain 5b residue 112 LYS Chi-restraints excluded: chain 5b residue 124 GLU Chi-restraints excluded: chain 5c residue 17 THR Chi-restraints excluded: chain 5c residue 73 GLN Chi-restraints excluded: chain 5c residue 119 LYS Chi-restraints excluded: chain 5d residue 17 THR Chi-restraints excluded: chain 5d residue 119 LYS Chi-restraints excluded: chain 5e residue 17 THR Chi-restraints excluded: chain 5e residue 30 GLU Chi-restraints excluded: chain 5e residue 56 SER Chi-restraints excluded: chain 5f residue 17 THR Chi-restraints excluded: chain 5f residue 73 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1170 random chunks: chunk 697 optimal weight: 9.9990 chunk 450 optimal weight: 10.0000 chunk 673 optimal weight: 6.9990 chunk 339 optimal weight: 20.0000 chunk 221 optimal weight: 9.9990 chunk 218 optimal weight: 9.9990 chunk 716 optimal weight: 9.9990 chunk 768 optimal weight: 20.0000 chunk 557 optimal weight: 4.9990 chunk 105 optimal weight: 20.0000 chunk 886 optimal weight: 10.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3C 23 GLN 3C 239 GLN 3F 23 GLN 3F 239 GLN 4A 205 ASN 4B 205 ASN 4C 474 ASN 4D 205 ASN 4E 205 ASN 4F 205 ASN 4F 470 ASN 5A 36 GLN 5A 73 GLN 5A 606 GLN 5B 518 ASN 5D 36 GLN 5D 73 GLN 3a 140 GLN 3d 140 GLN 3f 114 GLN 5a 53 GLN 5d 53 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 94842 Z= 0.464 Angle : 0.914 9.671 129006 Z= 0.507 Chirality : 0.056 0.246 14346 Planarity : 0.007 0.082 16776 Dihedral : 5.475 20.282 12654 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.38 % Allowed : 12.23 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.38 (0.07), residues: 11628 helix: 1.11 (0.09), residues: 3222 sheet: 0.53 (0.11), residues: 2250 loop : -1.35 (0.07), residues: 6156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP3A 584 HIS 0.010 0.002 HIS3d 97 PHE 0.026 0.004 PHE3E 62 TYR 0.030 0.003 TYR5D 179 ARG 0.010 0.002 ARG3B 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23256 Ramachandran restraints generated. 11628 Oldfield, 0 Emsley, 11628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23256 Ramachandran restraints generated. 11628 Oldfield, 0 Emsley, 11628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1421 residues out of total 10152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 343 poor density : 1078 time to evaluate : 8.013 Fit side-chains REVERT: 3A 154 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7670 (mtpp) REVERT: 3A 610 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: 3B 79 LEU cc_start: 0.6609 (mt) cc_final: 0.6329 (mt) REVERT: 3B 689 MET cc_start: 0.6264 (OUTLIER) cc_final: 0.4828 (pmm) REVERT: 3C 659 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7355 (tm-30) REVERT: 3C 663 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6966 (mt-10) REVERT: 3D 154 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7639 (mtpp) REVERT: 3D 245 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8172 (tp-100) REVERT: 3D 610 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: 3D 659 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7421 (tm-30) REVERT: 3E 41 LYS cc_start: 0.6981 (OUTLIER) cc_final: 0.6589 (mptt) REVERT: 3E 79 LEU cc_start: 0.6545 (mt) cc_final: 0.6290 (mt) REVERT: 3E 659 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7929 (mm-40) REVERT: 3E 689 MET cc_start: 0.6221 (OUTLIER) cc_final: 0.5191 (pmm) REVERT: 3F 659 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7398 (tm-30) REVERT: 4A 605 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7971 (mt-10) REVERT: 4A 643 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7270 (pm20) REVERT: 4B 41 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.6904 (mmtm) REVERT: 4B 154 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7591 (mtpm) REVERT: 4B 492 ILE cc_start: 0.6565 (mt) cc_final: 0.6349 (mm) REVERT: 4C 73 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7406 (mt0) REVERT: 4C 111 MET cc_start: 0.9136 (mmm) cc_final: 0.8917 (mmm) REVERT: 4C 192 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7887 (mtt180) REVERT: 4C 202 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7169 (mp10) REVERT: 4C 669 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: 4D 605 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7967 (mt-10) REVERT: 4D 643 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7257 (pm20) REVERT: 4D 689 MET cc_start: 0.6699 (OUTLIER) cc_final: 0.6132 (pp-130) REVERT: 4E 41 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.6916 (mmtm) REVERT: 4E 689 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.7025 (pmm) REVERT: 4F 73 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7402 (mt0) REVERT: 4F 100 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8513 (mtpp) REVERT: 4F 111 MET cc_start: 0.9138 (mmm) cc_final: 0.8919 (mmm) REVERT: 4F 192 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7877 (mtt180) REVERT: 4F 202 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7218 (mp10) REVERT: 4F 669 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: 5A 135 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7234 (mm-30) REVERT: 5A 549 MET cc_start: 0.8994 (mtp) cc_final: 0.8690 (mtp) REVERT: 5B 73 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7050 (mm110) REVERT: 5B 130 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7343 (t0) REVERT: 5B 197 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7513 (m-30) REVERT: 5B 601 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8562 (ptmm) REVERT: 5B 605 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7733 (mt-10) REVERT: 5C 73 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7433 (mt0) REVERT: 5C 96 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6947 (mt-10) REVERT: 5C 192 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7985 (mtt180) REVERT: 5C 250 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7068 (tp30) REVERT: 5C 509 MET cc_start: 0.9087 (mmm) cc_final: 0.8760 (mmm) REVERT: 5C 520 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7234 (mtm180) REVERT: 5D 549 MET cc_start: 0.8979 (mtp) cc_final: 0.8690 (mtp) REVERT: 5E 73 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7138 (mm110) REVERT: 5E 146 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7435 (mt-10) REVERT: 5E 197 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7503 (m-30) REVERT: 5E 601 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8551 (ptmm) REVERT: 5E 605 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7667 (mt-10) REVERT: 5F 73 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7436 (mt0) REVERT: 5F 96 GLU cc_start: 0.7159 (tt0) cc_final: 0.6932 (mt-10) REVERT: 5F 105 MET cc_start: 0.8212 (mmm) cc_final: 0.7808 (mmm) REVERT: 5F 135 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6841 (mp0) REVERT: 5F 250 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7067 (tp30) REVERT: 5F 509 MET cc_start: 0.9158 (mmm) cc_final: 0.8774 (mmm) REVERT: 5F 520 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7249 (mtm180) REVERT: 3b 35 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7574 (mt-10) REVERT: 3b 52 MET cc_start: 0.8680 (mtp) cc_final: 0.8053 (mmm) REVERT: 3e 35 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7572 (mt-10) REVERT: 3e 52 MET cc_start: 0.8700 (mtp) cc_final: 0.8073 (mmm) REVERT: 3f 73 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8608 (mt0) REVERT: 4a 130 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8640 (ttp) REVERT: 4b 52 MET cc_start: 0.8812 (mtp) cc_final: 0.8455 (mtm) REVERT: 4c 124 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7638 (pm20) REVERT: 4d 130 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8526 (ttp) REVERT: 5b 35 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: 5c 49 MET cc_start: 0.9096 (ptt) cc_final: 0.8646 (ptp) REVERT: 5f 49 MET cc_start: 0.9088 (ptt) cc_final: 0.8625 (ptp) outliers start: 343 outliers final: 207 residues processed: 1301 average time/residue: 1.7796 time to fit residues: 3118.8722 Evaluate side-chains 1326 residues out of total 10152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1065 time to evaluate : 7.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 40 THR Chi-restraints excluded: chain 3A residue 61 ASP Chi-restraints excluded: chain 3A residue 79 LEU Chi-restraints excluded: chain 3A residue 105 MET Chi-restraints excluded: chain 3A residue 134 SER Chi-restraints excluded: chain 3A residue 154 LYS Chi-restraints excluded: chain 3A residue 494 LEU Chi-restraints excluded: chain 3A residue 529 ILE Chi-restraints excluded: chain 3A residue 545 GLU Chi-restraints excluded: chain 3A residue 610 GLU Chi-restraints excluded: chain 3A residue 662 LEU Chi-restraints excluded: chain 3B residue 52 LYS Chi-restraints excluded: chain 3B residue 61 ASP Chi-restraints excluded: chain 3B residue 98 THR Chi-restraints excluded: chain 3B residue 130 ASP Chi-restraints excluded: chain 3B residue 209 GLU Chi-restraints excluded: chain 3B residue 481 ILE Chi-restraints excluded: chain 3B residue 491 THR Chi-restraints excluded: chain 3B residue 506 SER Chi-restraints excluded: chain 3B residue 529 ILE Chi-restraints excluded: chain 3B residue 545 GLU Chi-restraints excluded: chain 3B residue 601 LYS Chi-restraints excluded: chain 3B residue 662 LEU Chi-restraints excluded: chain 3B residue 675 VAL Chi-restraints excluded: chain 3B residue 689 MET Chi-restraints excluded: chain 3C residue 79 LEU Chi-restraints excluded: chain 3C residue 100 LYS Chi-restraints excluded: chain 3C residue 130 ASP Chi-restraints excluded: chain 3C residue 202 GLN Chi-restraints excluded: chain 3C residue 481 ILE Chi-restraints excluded: chain 3C residue 491 THR Chi-restraints excluded: chain 3C residue 529 ILE Chi-restraints excluded: chain 3C residue 659 GLN Chi-restraints excluded: chain 3C residue 675 VAL Chi-restraints excluded: chain 3D residue 48 ASP Chi-restraints excluded: chain 3D residue 61 ASP Chi-restraints excluded: chain 3D residue 79 LEU Chi-restraints excluded: chain 3D residue 130 ASP Chi-restraints excluded: chain 3D residue 154 LYS Chi-restraints excluded: chain 3D residue 245 GLN Chi-restraints excluded: chain 3D residue 494 LEU Chi-restraints excluded: chain 3D residue 529 ILE Chi-restraints excluded: chain 3D residue 545 GLU Chi-restraints excluded: chain 3D residue 601 LYS Chi-restraints excluded: chain 3D residue 610 GLU Chi-restraints excluded: chain 3D residue 659 GLN Chi-restraints excluded: chain 3D residue 662 LEU Chi-restraints excluded: chain 3E residue 41 LYS Chi-restraints excluded: chain 3E residue 52 LYS Chi-restraints excluded: chain 3E residue 61 ASP Chi-restraints excluded: chain 3E residue 98 THR Chi-restraints excluded: chain 3E residue 209 GLU Chi-restraints excluded: chain 3E residue 472 LYS Chi-restraints excluded: chain 3E residue 481 ILE Chi-restraints excluded: chain 3E residue 506 SER Chi-restraints excluded: chain 3E residue 529 ILE Chi-restraints excluded: chain 3E residue 601 LYS Chi-restraints excluded: chain 3E residue 659 GLN Chi-restraints excluded: chain 3E residue 662 LEU Chi-restraints excluded: chain 3E residue 675 VAL Chi-restraints excluded: chain 3E residue 689 MET Chi-restraints excluded: chain 3F residue 79 LEU Chi-restraints excluded: chain 3F residue 100 LYS Chi-restraints excluded: chain 3F residue 130 ASP Chi-restraints excluded: chain 3F residue 202 GLN Chi-restraints excluded: chain 3F residue 481 ILE Chi-restraints excluded: chain 3F residue 491 THR Chi-restraints excluded: chain 3F residue 494 LEU Chi-restraints excluded: chain 3F residue 602 LYS Chi-restraints excluded: chain 3F residue 659 GLN Chi-restraints excluded: chain 4A residue 48 ASP Chi-restraints excluded: chain 4A residue 61 ASP Chi-restraints excluded: chain 4A residue 91 THR Chi-restraints excluded: chain 4A residue 105 MET Chi-restraints excluded: chain 4A residue 130 ASP Chi-restraints excluded: chain 4A residue 132 SER Chi-restraints excluded: chain 4A residue 157 GLU Chi-restraints excluded: chain 4A residue 212 ASP Chi-restraints excluded: chain 4A residue 485 ASP Chi-restraints excluded: chain 4A residue 601 LYS Chi-restraints excluded: chain 4A residue 605 GLU Chi-restraints excluded: chain 4A residue 643 GLU Chi-restraints excluded: chain 4A residue 662 LEU Chi-restraints excluded: chain 4A residue 675 VAL Chi-restraints excluded: chain 4B residue 20 SER Chi-restraints excluded: chain 4B residue 21 VAL Chi-restraints excluded: chain 4B residue 41 LYS Chi-restraints excluded: chain 4B residue 61 ASP Chi-restraints excluded: chain 4B residue 91 THR Chi-restraints excluded: chain 4B residue 130 ASP Chi-restraints excluded: chain 4B residue 136 THR Chi-restraints excluded: chain 4B residue 154 LYS Chi-restraints excluded: chain 4B residue 481 ILE Chi-restraints excluded: chain 4B residue 506 SER Chi-restraints excluded: chain 4B residue 517 ASP Chi-restraints excluded: chain 4B residue 529 ILE Chi-restraints excluded: chain 4B residue 675 VAL Chi-restraints excluded: chain 4C residue 48 ASP Chi-restraints excluded: chain 4C residue 73 GLN Chi-restraints excluded: chain 4C residue 132 SER Chi-restraints excluded: chain 4C residue 157 GLU Chi-restraints excluded: chain 4C residue 192 ARG Chi-restraints excluded: chain 4C residue 202 GLN Chi-restraints excluded: chain 4C residue 506 SER Chi-restraints excluded: chain 4C residue 601 LYS Chi-restraints excluded: chain 4C residue 669 GLU Chi-restraints excluded: chain 4D residue 48 ASP Chi-restraints excluded: chain 4D residue 61 ASP Chi-restraints excluded: chain 4D residue 91 THR Chi-restraints excluded: chain 4D residue 105 MET Chi-restraints excluded: chain 4D residue 130 ASP Chi-restraints excluded: chain 4D residue 132 SER Chi-restraints excluded: chain 4D residue 157 GLU Chi-restraints excluded: chain 4D residue 212 ASP Chi-restraints excluded: chain 4D residue 601 LYS Chi-restraints excluded: chain 4D residue 605 GLU Chi-restraints excluded: chain 4D residue 643 GLU Chi-restraints excluded: chain 4D residue 662 LEU Chi-restraints excluded: chain 4D residue 675 VAL Chi-restraints excluded: chain 4D residue 689 MET Chi-restraints excluded: chain 4E residue 20 SER Chi-restraints excluded: chain 4E residue 21 VAL Chi-restraints excluded: chain 4E residue 41 LYS Chi-restraints excluded: chain 4E residue 61 ASP Chi-restraints excluded: chain 4E residue 91 THR Chi-restraints excluded: chain 4E residue 130 ASP Chi-restraints excluded: chain 4E residue 136 THR Chi-restraints excluded: chain 4E residue 481 ILE Chi-restraints excluded: chain 4E residue 506 SER Chi-restraints excluded: chain 4E residue 517 ASP Chi-restraints excluded: chain 4E residue 529 ILE Chi-restraints excluded: chain 4E residue 675 VAL Chi-restraints excluded: chain 4E residue 689 MET Chi-restraints excluded: chain 4F residue 48 ASP Chi-restraints excluded: chain 4F residue 73 GLN Chi-restraints excluded: chain 4F residue 100 LYS Chi-restraints excluded: chain 4F residue 132 SER Chi-restraints excluded: chain 4F residue 157 GLU Chi-restraints excluded: chain 4F residue 192 ARG Chi-restraints excluded: chain 4F residue 202 GLN Chi-restraints excluded: chain 4F residue 506 SER Chi-restraints excluded: chain 4F residue 601 LYS Chi-restraints excluded: chain 4F residue 669 GLU Chi-restraints excluded: chain 5A residue 21 VAL Chi-restraints excluded: chain 5A residue 40 THR Chi-restraints excluded: chain 5A residue 48 ASP Chi-restraints excluded: chain 5A residue 73 GLN Chi-restraints excluded: chain 5A residue 151 VAL Chi-restraints excluded: chain 5A residue 192 ARG Chi-restraints excluded: chain 5A residue 529 ILE Chi-restraints excluded: chain 5A residue 601 LYS Chi-restraints excluded: chain 5A residue 605 GLU Chi-restraints excluded: chain 5B residue 48 ASP Chi-restraints excluded: chain 5B residue 61 ASP Chi-restraints excluded: chain 5B residue 73 GLN Chi-restraints excluded: chain 5B residue 77 VAL Chi-restraints excluded: chain 5B residue 130 ASP Chi-restraints excluded: chain 5B residue 151 VAL Chi-restraints excluded: chain 5B residue 197 ASP Chi-restraints excluded: chain 5B residue 506 SER Chi-restraints excluded: chain 5B residue 601 LYS Chi-restraints excluded: chain 5B residue 605 GLU Chi-restraints excluded: chain 5B residue 625 GLU Chi-restraints excluded: chain 5B residue 662 LEU Chi-restraints excluded: chain 5C residue 21 VAL Chi-restraints excluded: chain 5C residue 48 ASP Chi-restraints excluded: chain 5C residue 61 ASP Chi-restraints excluded: chain 5C residue 73 GLN Chi-restraints excluded: chain 5C residue 96 GLU Chi-restraints excluded: chain 5C residue 98 THR Chi-restraints excluded: chain 5C residue 135 GLU Chi-restraints excluded: chain 5C residue 156 ASP Chi-restraints excluded: chain 5C residue 157 GLU Chi-restraints excluded: chain 5C residue 192 ARG Chi-restraints excluded: chain 5C residue 206 ASP Chi-restraints excluded: chain 5C residue 506 SER Chi-restraints excluded: chain 5C residue 520 ARG Chi-restraints excluded: chain 5C residue 601 LYS Chi-restraints excluded: chain 5C residue 605 GLU Chi-restraints excluded: chain 5C residue 625 GLU Chi-restraints excluded: chain 5C residue 662 LEU Chi-restraints excluded: chain 5D residue 21 VAL Chi-restraints excluded: chain 5D residue 40 THR Chi-restraints excluded: chain 5D residue 48 ASP Chi-restraints excluded: chain 5D residue 73 GLN Chi-restraints excluded: chain 5D residue 151 VAL Chi-restraints excluded: chain 5D residue 192 ARG Chi-restraints excluded: chain 5D residue 529 ILE Chi-restraints excluded: chain 5D residue 601 LYS Chi-restraints excluded: chain 5D residue 605 GLU Chi-restraints excluded: chain 5E residue 48 ASP Chi-restraints excluded: chain 5E residue 61 ASP Chi-restraints excluded: chain 5E residue 73 GLN Chi-restraints excluded: chain 5E residue 77 VAL Chi-restraints excluded: chain 5E residue 136 THR Chi-restraints excluded: chain 5E residue 146 GLU Chi-restraints excluded: chain 5E residue 151 VAL Chi-restraints excluded: chain 5E residue 197 ASP Chi-restraints excluded: chain 5E residue 506 SER Chi-restraints excluded: chain 5E residue 601 LYS Chi-restraints excluded: chain 5E residue 605 GLU Chi-restraints excluded: chain 5E residue 625 GLU Chi-restraints excluded: chain 5E residue 662 LEU Chi-restraints excluded: chain 5F residue 21 VAL Chi-restraints excluded: chain 5F residue 48 ASP Chi-restraints excluded: chain 5F residue 73 GLN Chi-restraints excluded: chain 5F residue 98 THR Chi-restraints excluded: chain 5F residue 135 GLU Chi-restraints excluded: chain 5F residue 157 GLU Chi-restraints excluded: chain 5F residue 506 SER Chi-restraints excluded: chain 5F residue 520 ARG Chi-restraints excluded: chain 5F residue 601 LYS Chi-restraints excluded: chain 5F residue 605 GLU Chi-restraints excluded: chain 5F residue 662 LEU Chi-restraints excluded: chain 3a residue 22 THR Chi-restraints excluded: chain 3a residue 124 GLU Chi-restraints excluded: chain 3b residue 22 THR Chi-restraints excluded: chain 3b residue 35 GLU Chi-restraints excluded: chain 3b residue 82 LYS Chi-restraints excluded: chain 3b residue 124 GLU Chi-restraints excluded: chain 3c residue 124 GLU Chi-restraints excluded: chain 3d residue 124 GLU Chi-restraints excluded: chain 3e residue 22 THR Chi-restraints excluded: chain 3e residue 35 GLU Chi-restraints excluded: chain 3e residue 82 LYS Chi-restraints excluded: chain 3e residue 124 GLU Chi-restraints excluded: chain 3e residue 130 MET Chi-restraints excluded: chain 3f residue 73 GLN Chi-restraints excluded: chain 3f residue 124 GLU Chi-restraints excluded: chain 4a residue 2 SER Chi-restraints excluded: chain 4a residue 22 THR Chi-restraints excluded: chain 4a residue 130 MET Chi-restraints excluded: chain 4b residue 22 THR Chi-restraints excluded: chain 4c residue 56 SER Chi-restraints excluded: chain 4c residue 124 GLU Chi-restraints excluded: chain 4d residue 2 SER Chi-restraints excluded: chain 4d residue 22 THR Chi-restraints excluded: chain 4d residue 130 MET Chi-restraints excluded: chain 4e residue 22 THR Chi-restraints excluded: chain 4e residue 66 LYS Chi-restraints excluded: chain 4e residue 82 LYS Chi-restraints excluded: chain 4f residue 56 SER Chi-restraints excluded: chain 4f residue 124 GLU Chi-restraints excluded: chain 5a residue 17 THR Chi-restraints excluded: chain 5a residue 119 LYS Chi-restraints excluded: chain 5b residue 17 THR Chi-restraints excluded: chain 5b residue 22 THR Chi-restraints excluded: chain 5b residue 30 GLU Chi-restraints excluded: chain 5b residue 35 GLU Chi-restraints excluded: chain 5b residue 56 SER Chi-restraints excluded: chain 5b residue 112 LYS Chi-restraints excluded: chain 5c residue 17 THR Chi-restraints excluded: chain 5c residue 73 GLN Chi-restraints excluded: chain 5c residue 119 LYS Chi-restraints excluded: chain 5d residue 17 THR Chi-restraints excluded: chain 5d residue 119 LYS Chi-restraints excluded: chain 5e residue 17 THR Chi-restraints excluded: chain 5e residue 22 THR Chi-restraints excluded: chain 5e residue 56 SER Chi-restraints excluded: chain 5f residue 17 THR Chi-restraints excluded: chain 5f residue 73 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1170 random chunks: chunk 1025 optimal weight: 3.9990 chunk 1080 optimal weight: 1.9990 chunk 985 optimal weight: 1.9990 chunk 1050 optimal weight: 6.9990 chunk 632 optimal weight: 0.0020 chunk 457 optimal weight: 8.9990 chunk 825 optimal weight: 9.9990 chunk 322 optimal weight: 10.0000 chunk 949 optimal weight: 3.9990 chunk 993 optimal weight: 1.9990 chunk 1047 optimal weight: 3.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3C 23 GLN 3C 239 GLN 3F 23 GLN 3F 239 GLN 4A 205 ASN 4B 205 ASN 4C 93 ASN 4C 474 ASN ** 4C 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4D 205 ASN 4E 205 ASN ** 4E 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4F 93 ASN ** 4F 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5A 73 GLN 5A 606 GLN 5B 202 GLN ** 5B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5D 73 GLN ** 5D 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5E 202 GLN ** 5E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3a 114 GLN 3a 140 GLN 3d 140 GLN 3f 114 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 94842 Z= 0.182 Angle : 0.603 7.497 129006 Z= 0.335 Chirality : 0.046 0.170 14346 Planarity : 0.005 0.058 16776 Dihedral : 4.966 19.211 12654 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.14 % Allowed : 13.49 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.00 (0.08), residues: 11628 helix: 1.56 (0.09), residues: 3330 sheet: 0.48 (0.11), residues: 2340 loop : -1.15 (0.08), residues: 5958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP4f 103 HIS 0.004 0.001 HIS3d 97 PHE 0.017 0.002 PHE5A 175 TYR 0.027 0.001 TYR5F 489 ARG 0.009 0.001 ARG4F 520 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23256 Ramachandran restraints generated. 11628 Oldfield, 0 Emsley, 11628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23256 Ramachandran restraints generated. 11628 Oldfield, 0 Emsley, 11628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1301 residues out of total 10152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1084 time to evaluate : 8.071 Fit side-chains REVERT: 3A 154 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7481 (mtpp) REVERT: 3A 529 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8119 (mt) REVERT: 3A 610 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: 3B 79 LEU cc_start: 0.6500 (mt) cc_final: 0.6250 (mt) REVERT: 3D 154 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7476 (mtpp) REVERT: 3D 529 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8081 (mt) REVERT: 3D 610 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: 3E 79 LEU cc_start: 0.6477 (mt) cc_final: 0.6219 (mt) REVERT: 3F 659 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7302 (tm-30) REVERT: 4A 48 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.7096 (m-30) REVERT: 4A 605 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: 4B 154 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7413 (mtpm) REVERT: 4B 492 ILE cc_start: 0.6377 (mt) cc_final: 0.6067 (mt) REVERT: 4B 529 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8184 (mm) REVERT: 4C 73 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7330 (mt0) REVERT: 4C 111 MET cc_start: 0.9108 (mmm) cc_final: 0.8882 (mmm) REVERT: 4C 202 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7154 (mp10) REVERT: 4D 48 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.7094 (m-30) REVERT: 4D 605 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7862 (mt-10) REVERT: 4D 689 MET cc_start: 0.6644 (OUTLIER) cc_final: 0.5993 (pp-130) REVERT: 4E 529 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8191 (mm) REVERT: 4F 73 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7368 (mt0) REVERT: 4F 100 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8460 (mtpp) REVERT: 4F 111 MET cc_start: 0.9106 (mmm) cc_final: 0.8879 (mmm) REVERT: 4F 202 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7139 (mp10) REVERT: 4F 492 ILE cc_start: 0.6580 (OUTLIER) cc_final: 0.6224 (mp) REVERT: 5A 509 MET cc_start: 0.8962 (mmm) cc_final: 0.8424 (mmm) REVERT: 5B 73 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.6991 (mm110) REVERT: 5B 79 LEU cc_start: 0.5972 (OUTLIER) cc_final: 0.5648 (mp) REVERT: 5B 146 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7296 (mt-10) REVERT: 5B 197 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7427 (m-30) REVERT: 5B 605 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7568 (mt-10) REVERT: 5C 73 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7360 (mt0) REVERT: 5C 96 GLU cc_start: 0.7050 (tt0) cc_final: 0.6822 (mt-10) REVERT: 5C 250 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7146 (tp30) REVERT: 5D 509 MET cc_start: 0.8961 (mmm) cc_final: 0.8427 (mmm) REVERT: 5E 73 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7117 (mm110) REVERT: 5E 79 LEU cc_start: 0.5942 (OUTLIER) cc_final: 0.5632 (mp) REVERT: 5E 146 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7302 (mt-10) REVERT: 5E 197 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7414 (m-30) REVERT: 5E 601 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8529 (ptmm) REVERT: 5F 73 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7458 (mt0) REVERT: 5F 96 GLU cc_start: 0.7064 (tt0) cc_final: 0.6857 (mt-10) REVERT: 5F 105 MET cc_start: 0.8227 (mmm) cc_final: 0.7974 (mmm) REVERT: 5F 250 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7141 (tp30) REVERT: 5F 509 MET cc_start: 0.9090 (mmm) cc_final: 0.8744 (mmm) REVERT: 5F 529 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7837 (mt) REVERT: 3a 87 ASP cc_start: 0.7564 (m-30) cc_final: 0.7104 (m-30) REVERT: 3a 124 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7502 (pm20) REVERT: 3b 35 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7436 (mt-10) REVERT: 3b 52 MET cc_start: 0.8589 (mtp) cc_final: 0.7989 (mmm) REVERT: 3d 87 ASP cc_start: 0.7571 (m-30) cc_final: 0.7117 (m-30) REVERT: 3d 124 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7505 (pm20) REVERT: 3e 35 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7438 (mt-10) REVERT: 3e 52 MET cc_start: 0.8600 (mtp) cc_final: 0.7992 (mmm) REVERT: 3f 73 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8590 (mt0) REVERT: 3f 114 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: 4a 130 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8589 (ttp) REVERT: 4c 124 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7481 (pm20) REVERT: 4d 130 MET cc_start: 0.8885 (ttp) cc_final: 0.8595 (ttp) REVERT: 4e 52 MET cc_start: 0.8770 (mtp) cc_final: 0.8413 (mtm) REVERT: 4f 124 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7529 (pm20) REVERT: 5b 30 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6686 (pm20) REVERT: 5c 49 MET cc_start: 0.9045 (ptt) cc_final: 0.8480 (ptp) REVERT: 5f 49 MET cc_start: 0.9027 (ptt) cc_final: 0.8484 (ptp) outliers start: 217 outliers final: 132 residues processed: 1226 average time/residue: 1.7299 time to fit residues: 2855.7140 Evaluate side-chains 1236 residues out of total 10152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1060 time to evaluate : 7.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 61 ASP Chi-restraints excluded: chain 3A residue 105 MET Chi-restraints excluded: chain 3A residue 134 SER Chi-restraints excluded: chain 3A residue 154 LYS Chi-restraints excluded: chain 3A residue 485 ASP Chi-restraints excluded: chain 3A residue 529 ILE Chi-restraints excluded: chain 3A residue 545 GLU Chi-restraints excluded: chain 3A residue 610 GLU Chi-restraints excluded: chain 3B residue 61 ASP Chi-restraints excluded: chain 3B residue 98 THR Chi-restraints excluded: chain 3B residue 481 ILE Chi-restraints excluded: chain 3B residue 485 ASP Chi-restraints excluded: chain 3B residue 529 ILE Chi-restraints excluded: chain 3B residue 545 GLU Chi-restraints excluded: chain 3B residue 675 VAL Chi-restraints excluded: chain 3C residue 100 LYS Chi-restraints excluded: chain 3C residue 130 ASP Chi-restraints excluded: chain 3C residue 481 ILE Chi-restraints excluded: chain 3C residue 485 ASP Chi-restraints excluded: chain 3C residue 529 ILE Chi-restraints excluded: chain 3C residue 610 GLU Chi-restraints excluded: chain 3C residue 675 VAL Chi-restraints excluded: chain 3D residue 61 ASP Chi-restraints excluded: chain 3D residue 130 ASP Chi-restraints excluded: chain 3D residue 154 LYS Chi-restraints excluded: chain 3D residue 485 ASP Chi-restraints excluded: chain 3D residue 529 ILE Chi-restraints excluded: chain 3D residue 601 LYS Chi-restraints excluded: chain 3D residue 610 GLU Chi-restraints excluded: chain 3E residue 61 ASP Chi-restraints excluded: chain 3E residue 98 THR Chi-restraints excluded: chain 3E residue 130 ASP Chi-restraints excluded: chain 3E residue 209 GLU Chi-restraints excluded: chain 3E residue 472 LYS Chi-restraints excluded: chain 3E residue 675 VAL Chi-restraints excluded: chain 3F residue 100 LYS Chi-restraints excluded: chain 3F residue 130 ASP Chi-restraints excluded: chain 3F residue 481 ILE Chi-restraints excluded: chain 3F residue 485 ASP Chi-restraints excluded: chain 3F residue 610 GLU Chi-restraints excluded: chain 3F residue 659 GLN Chi-restraints excluded: chain 4A residue 48 ASP Chi-restraints excluded: chain 4A residue 61 ASP Chi-restraints excluded: chain 4A residue 91 THR Chi-restraints excluded: chain 4A residue 105 MET Chi-restraints excluded: chain 4A residue 130 ASP Chi-restraints excluded: chain 4A residue 157 GLU Chi-restraints excluded: chain 4A residue 485 ASP Chi-restraints excluded: chain 4A residue 601 LYS Chi-restraints excluded: chain 4A residue 605 GLU Chi-restraints excluded: chain 4A residue 675 VAL Chi-restraints excluded: chain 4B residue 20 SER Chi-restraints excluded: chain 4B residue 61 ASP Chi-restraints excluded: chain 4B residue 130 ASP Chi-restraints excluded: chain 4B residue 154 LYS Chi-restraints excluded: chain 4B residue 481 ILE Chi-restraints excluded: chain 4B residue 517 ASP Chi-restraints excluded: chain 4B residue 529 ILE Chi-restraints excluded: chain 4B residue 675 VAL Chi-restraints excluded: chain 4C residue 48 ASP Chi-restraints excluded: chain 4C residue 73 GLN Chi-restraints excluded: chain 4C residue 132 SER Chi-restraints excluded: chain 4C residue 157 GLU Chi-restraints excluded: chain 4C residue 202 GLN Chi-restraints excluded: chain 4C residue 506 SER Chi-restraints excluded: chain 4C residue 601 LYS Chi-restraints excluded: chain 4D residue 48 ASP Chi-restraints excluded: chain 4D residue 61 ASP Chi-restraints excluded: chain 4D residue 91 THR Chi-restraints excluded: chain 4D residue 105 MET Chi-restraints excluded: chain 4D residue 130 ASP Chi-restraints excluded: chain 4D residue 157 GLU Chi-restraints excluded: chain 4D residue 601 LYS Chi-restraints excluded: chain 4D residue 605 GLU Chi-restraints excluded: chain 4D residue 675 VAL Chi-restraints excluded: chain 4D residue 689 MET Chi-restraints excluded: chain 4E residue 20 SER Chi-restraints excluded: chain 4E residue 61 ASP Chi-restraints excluded: chain 4E residue 91 THR Chi-restraints excluded: chain 4E residue 130 ASP Chi-restraints excluded: chain 4E residue 481 ILE Chi-restraints excluded: chain 4E residue 517 ASP Chi-restraints excluded: chain 4E residue 529 ILE Chi-restraints excluded: chain 4E residue 675 VAL Chi-restraints excluded: chain 4F residue 48 ASP Chi-restraints excluded: chain 4F residue 73 GLN Chi-restraints excluded: chain 4F residue 100 LYS Chi-restraints excluded: chain 4F residue 132 SER Chi-restraints excluded: chain 4F residue 157 GLU Chi-restraints excluded: chain 4F residue 202 GLN Chi-restraints excluded: chain 4F residue 492 ILE Chi-restraints excluded: chain 4F residue 506 SER Chi-restraints excluded: chain 4F residue 601 LYS Chi-restraints excluded: chain 5A residue 21 VAL Chi-restraints excluded: chain 5A residue 40 THR Chi-restraints excluded: chain 5A residue 48 ASP Chi-restraints excluded: chain 5A residue 151 VAL Chi-restraints excluded: chain 5A residue 192 ARG Chi-restraints excluded: chain 5A residue 529 ILE Chi-restraints excluded: chain 5A residue 601 LYS Chi-restraints excluded: chain 5A residue 605 GLU Chi-restraints excluded: chain 5B residue 48 ASP Chi-restraints excluded: chain 5B residue 61 ASP Chi-restraints excluded: chain 5B residue 73 GLN Chi-restraints excluded: chain 5B residue 79 LEU Chi-restraints excluded: chain 5B residue 146 GLU Chi-restraints excluded: chain 5B residue 197 ASP Chi-restraints excluded: chain 5B residue 605 GLU Chi-restraints excluded: chain 5B residue 625 GLU Chi-restraints excluded: chain 5B residue 662 LEU Chi-restraints excluded: chain 5C residue 21 VAL Chi-restraints excluded: chain 5C residue 61 ASP Chi-restraints excluded: chain 5C residue 73 GLN Chi-restraints excluded: chain 5C residue 98 THR Chi-restraints excluded: chain 5C residue 157 GLU Chi-restraints excluded: chain 5C residue 492 ILE Chi-restraints excluded: chain 5C residue 601 LYS Chi-restraints excluded: chain 5C residue 605 GLU Chi-restraints excluded: chain 5C residue 625 GLU Chi-restraints excluded: chain 5D residue 21 VAL Chi-restraints excluded: chain 5D residue 40 THR Chi-restraints excluded: chain 5D residue 151 VAL Chi-restraints excluded: chain 5D residue 192 ARG Chi-restraints excluded: chain 5D residue 529 ILE Chi-restraints excluded: chain 5D residue 601 LYS Chi-restraints excluded: chain 5D residue 605 GLU Chi-restraints excluded: chain 5E residue 48 ASP Chi-restraints excluded: chain 5E residue 61 ASP Chi-restraints excluded: chain 5E residue 73 GLN Chi-restraints excluded: chain 5E residue 79 LEU Chi-restraints excluded: chain 5E residue 146 GLU Chi-restraints excluded: chain 5E residue 197 ASP Chi-restraints excluded: chain 5E residue 601 LYS Chi-restraints excluded: chain 5E residue 625 GLU Chi-restraints excluded: chain 5E residue 662 LEU Chi-restraints excluded: chain 5F residue 21 VAL Chi-restraints excluded: chain 5F residue 48 ASP Chi-restraints excluded: chain 5F residue 73 GLN Chi-restraints excluded: chain 5F residue 157 GLU Chi-restraints excluded: chain 5F residue 529 ILE Chi-restraints excluded: chain 5F residue 601 LYS Chi-restraints excluded: chain 5F residue 605 GLU Chi-restraints excluded: chain 3a residue 124 GLU Chi-restraints excluded: chain 3b residue 22 THR Chi-restraints excluded: chain 3b residue 35 GLU Chi-restraints excluded: chain 3b residue 82 LYS Chi-restraints excluded: chain 3b residue 124 GLU Chi-restraints excluded: chain 3c residue 124 GLU Chi-restraints excluded: chain 3d residue 124 GLU Chi-restraints excluded: chain 3e residue 22 THR Chi-restraints excluded: chain 3e residue 35 GLU Chi-restraints excluded: chain 3e residue 82 LYS Chi-restraints excluded: chain 3e residue 124 GLU Chi-restraints excluded: chain 3f residue 73 GLN Chi-restraints excluded: chain 3f residue 114 GLN Chi-restraints excluded: chain 3f residue 124 GLU Chi-restraints excluded: chain 4a residue 2 SER Chi-restraints excluded: chain 4a residue 22 THR Chi-restraints excluded: chain 4a residue 130 MET Chi-restraints excluded: chain 4c residue 22 THR Chi-restraints excluded: chain 4c residue 56 SER Chi-restraints excluded: chain 4c residue 124 GLU Chi-restraints excluded: chain 4d residue 2 SER Chi-restraints excluded: chain 4d residue 22 THR Chi-restraints excluded: chain 4f residue 22 THR Chi-restraints excluded: chain 4f residue 56 SER Chi-restraints excluded: chain 4f residue 124 GLU Chi-restraints excluded: chain 5b residue 30 GLU Chi-restraints excluded: chain 5b residue 56 SER Chi-restraints excluded: chain 5b residue 112 LYS Chi-restraints excluded: chain 5c residue 73 GLN Chi-restraints excluded: chain 5c residue 119 LYS Chi-restraints excluded: chain 5d residue 17 THR Chi-restraints excluded: chain 5e residue 56 SER Chi-restraints excluded: chain 5f residue 17 THR Chi-restraints excluded: chain 5f residue 73 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1170 random chunks: chunk 690 optimal weight: 20.0000 chunk 1111 optimal weight: 6.9990 chunk 678 optimal weight: 3.9990 chunk 527 optimal weight: 9.9990 chunk 772 optimal weight: 20.0000 chunk 1165 optimal weight: 1.9990 chunk 1072 optimal weight: 9.9990 chunk 928 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 716 optimal weight: 8.9990 chunk 569 optimal weight: 0.5980 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3C 23 GLN 3C 239 GLN 3F 23 GLN 3F 239 GLN 4A 205 ASN 4B 205 ASN ** 4C 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4D 205 ASN 5A 606 GLN ** 5B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5C 490 ASN 5D 36 GLN 3a 140 GLN 3d 140 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 94842 Z= 0.257 Angle : 0.696 8.414 129006 Z= 0.385 Chirality : 0.048 0.202 14346 Planarity : 0.006 0.061 16776 Dihedral : 5.055 19.713 12654 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.34 % Allowed : 13.58 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.09 (0.08), residues: 11628 helix: 1.57 (0.09), residues: 3222 sheet: 0.50 (0.11), residues: 2358 loop : -1.25 (0.07), residues: 6048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP3D 584 HIS 0.005 0.001 HIS4c 97 PHE 0.022 0.002 PHE5F 175 TYR 0.027 0.002 TYR5C 489 ARG 0.008 0.001 ARG4C 520 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23256 Ramachandran restraints generated. 11628 Oldfield, 0 Emsley, 11628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23256 Ramachandran restraints generated. 11628 Oldfield, 0 Emsley, 11628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1293 residues out of total 10152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 1055 time to evaluate : 8.018 Fit side-chains REVERT: 3A 154 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7535 (mtpp) REVERT: 3A 610 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7008 (mp0) REVERT: 3B 79 LEU cc_start: 0.6578 (mt) cc_final: 0.6320 (mt) REVERT: 3B 689 MET cc_start: 0.6341 (OUTLIER) cc_final: 0.4556 (pmm) REVERT: 3D 154 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7531 (mtpp) REVERT: 3D 610 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7005 (mp0) REVERT: 3E 41 LYS cc_start: 0.6912 (OUTLIER) cc_final: 0.6529 (mptt) REVERT: 3E 79 LEU cc_start: 0.6526 (mt) cc_final: 0.6268 (mt) REVERT: 3F 659 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7376 (tm-30) REVERT: 4A 48 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.7106 (m-30) REVERT: 4A 605 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: 4B 41 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.6798 (mmtm) REVERT: 4B 154 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7463 (mtpm) REVERT: 4B 492 ILE cc_start: 0.6515 (mt) cc_final: 0.6190 (mt) REVERT: 4C 73 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7333 (mt0) REVERT: 4C 111 MET cc_start: 0.9138 (mmm) cc_final: 0.8924 (mmm) REVERT: 4C 202 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7169 (mp10) REVERT: 4D 48 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.7102 (m-30) REVERT: 4D 605 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7886 (mt-10) REVERT: 4D 689 MET cc_start: 0.6661 (OUTLIER) cc_final: 0.6082 (pp-130) REVERT: 4E 41 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.6810 (mmtm) REVERT: 4F 73 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7369 (mt0) REVERT: 4F 100 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8434 (mtpp) REVERT: 4F 111 MET cc_start: 0.9137 (mmm) cc_final: 0.8925 (mmm) REVERT: 4F 202 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7173 (mp10) REVERT: 5A 73 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7636 (mt0) REVERT: 5A 549 MET cc_start: 0.8937 (mtp) cc_final: 0.8592 (mtp) REVERT: 5B 73 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7028 (mm110) REVERT: 5B 130 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7372 (t0) REVERT: 5B 146 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7345 (mt-10) REVERT: 5B 197 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7468 (m-30) REVERT: 5B 601 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8463 (ptmm) REVERT: 5B 605 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7508 (mt-10) REVERT: 5C 73 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7404 (mt0) REVERT: 5C 96 GLU cc_start: 0.7060 (tt0) cc_final: 0.6813 (mt-10) REVERT: 5C 192 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7742 (mtt180) REVERT: 5C 250 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7152 (tp30) REVERT: 5C 509 MET cc_start: 0.9059 (mmm) cc_final: 0.8796 (mmm) REVERT: 5D 73 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7633 (mt0) REVERT: 5D 549 MET cc_start: 0.8918 (mtp) cc_final: 0.8598 (mtp) REVERT: 5E 73 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7120 (mm110) REVERT: 5E 79 LEU cc_start: 0.6029 (OUTLIER) cc_final: 0.5738 (mp) REVERT: 5E 135 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: 5E 146 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7355 (mt-10) REVERT: 5E 197 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7459 (m-30) REVERT: 5E 601 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8487 (ptmm) REVERT: 5E 605 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7516 (mt-10) REVERT: 5F 73 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7408 (mt0) REVERT: 5F 96 GLU cc_start: 0.7080 (tt0) cc_final: 0.6834 (mt-10) REVERT: 5F 105 MET cc_start: 0.8255 (mmm) cc_final: 0.8017 (mmm) REVERT: 5F 209 GLU cc_start: 0.7202 (pt0) cc_final: 0.6890 (pt0) REVERT: 5F 509 MET cc_start: 0.9127 (mmm) cc_final: 0.8804 (mmm) REVERT: 5F 520 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7156 (mtm180) REVERT: 3a 87 ASP cc_start: 0.7597 (m-30) cc_final: 0.7174 (m-30) REVERT: 3b 35 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7495 (mt-10) REVERT: 3b 52 MET cc_start: 0.8652 (mtp) cc_final: 0.8030 (mmm) REVERT: 3d 87 ASP cc_start: 0.7624 (m-30) cc_final: 0.7167 (m-30) REVERT: 3e 35 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7507 (mt-10) REVERT: 3e 52 MET cc_start: 0.8666 (mtp) cc_final: 0.8043 (mmm) REVERT: 3f 73 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8609 (mt0) REVERT: 4a 130 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8671 (ttp) REVERT: 4c 124 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7636 (pm20) REVERT: 4d 130 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8660 (ttp) REVERT: 4e 52 MET cc_start: 0.8784 (mtp) cc_final: 0.8433 (mtm) REVERT: 4f 124 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7594 (pm20) REVERT: 5b 30 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6846 (pm20) REVERT: 5c 49 MET cc_start: 0.9050 (ptt) cc_final: 0.8559 (ptp) REVERT: 5e 30 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6932 (pm20) REVERT: 5f 49 MET cc_start: 0.9046 (ptt) cc_final: 0.8531 (ptp) outliers start: 238 outliers final: 160 residues processed: 1211 average time/residue: 1.7322 time to fit residues: 2817.0681 Evaluate side-chains 1267 residues out of total 10152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1059 time to evaluate : 7.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 61 ASP Chi-restraints excluded: chain 3A residue 105 MET Chi-restraints excluded: chain 3A residue 134 SER Chi-restraints excluded: chain 3A residue 154 LYS Chi-restraints excluded: chain 3A residue 485 ASP Chi-restraints excluded: chain 3A residue 529 ILE Chi-restraints excluded: chain 3A residue 545 GLU Chi-restraints excluded: chain 3A residue 610 GLU Chi-restraints excluded: chain 3B residue 61 ASP Chi-restraints excluded: chain 3B residue 98 THR Chi-restraints excluded: chain 3B residue 209 GLU Chi-restraints excluded: chain 3B residue 481 ILE Chi-restraints excluded: chain 3B residue 485 ASP Chi-restraints excluded: chain 3B residue 529 ILE Chi-restraints excluded: chain 3B residue 545 GLU Chi-restraints excluded: chain 3B residue 601 LYS Chi-restraints excluded: chain 3B residue 675 VAL Chi-restraints excluded: chain 3B residue 689 MET Chi-restraints excluded: chain 3C residue 100 LYS Chi-restraints excluded: chain 3C residue 130 ASP Chi-restraints excluded: chain 3C residue 481 ILE Chi-restraints excluded: chain 3C residue 485 ASP Chi-restraints excluded: chain 3C residue 529 ILE Chi-restraints excluded: chain 3C residue 610 GLU Chi-restraints excluded: chain 3C residue 675 VAL Chi-restraints excluded: chain 3D residue 48 ASP Chi-restraints excluded: chain 3D residue 61 ASP Chi-restraints excluded: chain 3D residue 154 LYS Chi-restraints excluded: chain 3D residue 485 ASP Chi-restraints excluded: chain 3D residue 529 ILE Chi-restraints excluded: chain 3D residue 601 LYS Chi-restraints excluded: chain 3D residue 610 GLU Chi-restraints excluded: chain 3E residue 41 LYS Chi-restraints excluded: chain 3E residue 61 ASP Chi-restraints excluded: chain 3E residue 98 THR Chi-restraints excluded: chain 3E residue 130 ASP Chi-restraints excluded: chain 3E residue 209 GLU Chi-restraints excluded: chain 3E residue 472 LYS Chi-restraints excluded: chain 3E residue 506 SER Chi-restraints excluded: chain 3E residue 601 LYS Chi-restraints excluded: chain 3E residue 675 VAL Chi-restraints excluded: chain 3F residue 100 LYS Chi-restraints excluded: chain 3F residue 130 ASP Chi-restraints excluded: chain 3F residue 481 ILE Chi-restraints excluded: chain 3F residue 485 ASP Chi-restraints excluded: chain 3F residue 602 LYS Chi-restraints excluded: chain 3F residue 610 GLU Chi-restraints excluded: chain 3F residue 659 GLN Chi-restraints excluded: chain 4A residue 48 ASP Chi-restraints excluded: chain 4A residue 61 ASP Chi-restraints excluded: chain 4A residue 91 THR Chi-restraints excluded: chain 4A residue 105 MET Chi-restraints excluded: chain 4A residue 130 ASP Chi-restraints excluded: chain 4A residue 157 GLU Chi-restraints excluded: chain 4A residue 485 ASP Chi-restraints excluded: chain 4A residue 601 LYS Chi-restraints excluded: chain 4A residue 605 GLU Chi-restraints excluded: chain 4A residue 675 VAL Chi-restraints excluded: chain 4B residue 20 SER Chi-restraints excluded: chain 4B residue 41 LYS Chi-restraints excluded: chain 4B residue 48 ASP Chi-restraints excluded: chain 4B residue 61 ASP Chi-restraints excluded: chain 4B residue 130 ASP Chi-restraints excluded: chain 4B residue 154 LYS Chi-restraints excluded: chain 4B residue 481 ILE Chi-restraints excluded: chain 4B residue 506 SER Chi-restraints excluded: chain 4B residue 517 ASP Chi-restraints excluded: chain 4B residue 529 ILE Chi-restraints excluded: chain 4B residue 675 VAL Chi-restraints excluded: chain 4C residue 41 LYS Chi-restraints excluded: chain 4C residue 48 ASP Chi-restraints excluded: chain 4C residue 73 GLN Chi-restraints excluded: chain 4C residue 132 SER Chi-restraints excluded: chain 4C residue 157 GLU Chi-restraints excluded: chain 4C residue 202 GLN Chi-restraints excluded: chain 4C residue 506 SER Chi-restraints excluded: chain 4C residue 601 LYS Chi-restraints excluded: chain 4D residue 48 ASP Chi-restraints excluded: chain 4D residue 61 ASP Chi-restraints excluded: chain 4D residue 91 THR Chi-restraints excluded: chain 4D residue 105 MET Chi-restraints excluded: chain 4D residue 130 ASP Chi-restraints excluded: chain 4D residue 157 GLU Chi-restraints excluded: chain 4D residue 601 LYS Chi-restraints excluded: chain 4D residue 605 GLU Chi-restraints excluded: chain 4D residue 675 VAL Chi-restraints excluded: chain 4D residue 689 MET Chi-restraints excluded: chain 4E residue 20 SER Chi-restraints excluded: chain 4E residue 41 LYS Chi-restraints excluded: chain 4E residue 48 ASP Chi-restraints excluded: chain 4E residue 61 ASP Chi-restraints excluded: chain 4E residue 91 THR Chi-restraints excluded: chain 4E residue 130 ASP Chi-restraints excluded: chain 4E residue 136 THR Chi-restraints excluded: chain 4E residue 481 ILE Chi-restraints excluded: chain 4E residue 517 ASP Chi-restraints excluded: chain 4E residue 529 ILE Chi-restraints excluded: chain 4E residue 675 VAL Chi-restraints excluded: chain 4F residue 48 ASP Chi-restraints excluded: chain 4F residue 73 GLN Chi-restraints excluded: chain 4F residue 100 LYS Chi-restraints excluded: chain 4F residue 132 SER Chi-restraints excluded: chain 4F residue 157 GLU Chi-restraints excluded: chain 4F residue 202 GLN Chi-restraints excluded: chain 4F residue 506 SER Chi-restraints excluded: chain 4F residue 601 LYS Chi-restraints excluded: chain 5A residue 21 VAL Chi-restraints excluded: chain 5A residue 40 THR Chi-restraints excluded: chain 5A residue 48 ASP Chi-restraints excluded: chain 5A residue 73 GLN Chi-restraints excluded: chain 5A residue 151 VAL Chi-restraints excluded: chain 5A residue 192 ARG Chi-restraints excluded: chain 5A residue 529 ILE Chi-restraints excluded: chain 5A residue 601 LYS Chi-restraints excluded: chain 5A residue 605 GLU Chi-restraints excluded: chain 5B residue 48 ASP Chi-restraints excluded: chain 5B residue 61 ASP Chi-restraints excluded: chain 5B residue 73 GLN Chi-restraints excluded: chain 5B residue 130 ASP Chi-restraints excluded: chain 5B residue 146 GLU Chi-restraints excluded: chain 5B residue 197 ASP Chi-restraints excluded: chain 5B residue 601 LYS Chi-restraints excluded: chain 5B residue 605 GLU Chi-restraints excluded: chain 5B residue 625 GLU Chi-restraints excluded: chain 5B residue 662 LEU Chi-restraints excluded: chain 5C residue 21 VAL Chi-restraints excluded: chain 5C residue 48 ASP Chi-restraints excluded: chain 5C residue 61 ASP Chi-restraints excluded: chain 5C residue 73 GLN Chi-restraints excluded: chain 5C residue 98 THR Chi-restraints excluded: chain 5C residue 156 ASP Chi-restraints excluded: chain 5C residue 157 GLU Chi-restraints excluded: chain 5C residue 192 ARG Chi-restraints excluded: chain 5C residue 601 LYS Chi-restraints excluded: chain 5C residue 605 GLU Chi-restraints excluded: chain 5C residue 625 GLU Chi-restraints excluded: chain 5D residue 21 VAL Chi-restraints excluded: chain 5D residue 40 THR Chi-restraints excluded: chain 5D residue 48 ASP Chi-restraints excluded: chain 5D residue 73 GLN Chi-restraints excluded: chain 5D residue 151 VAL Chi-restraints excluded: chain 5D residue 192 ARG Chi-restraints excluded: chain 5D residue 529 ILE Chi-restraints excluded: chain 5D residue 601 LYS Chi-restraints excluded: chain 5D residue 605 GLU Chi-restraints excluded: chain 5E residue 48 ASP Chi-restraints excluded: chain 5E residue 61 ASP Chi-restraints excluded: chain 5E residue 73 GLN Chi-restraints excluded: chain 5E residue 79 LEU Chi-restraints excluded: chain 5E residue 135 GLU Chi-restraints excluded: chain 5E residue 146 GLU Chi-restraints excluded: chain 5E residue 197 ASP Chi-restraints excluded: chain 5E residue 601 LYS Chi-restraints excluded: chain 5E residue 605 GLU Chi-restraints excluded: chain 5E residue 625 GLU Chi-restraints excluded: chain 5E residue 662 LEU Chi-restraints excluded: chain 5F residue 21 VAL Chi-restraints excluded: chain 5F residue 48 ASP Chi-restraints excluded: chain 5F residue 73 GLN Chi-restraints excluded: chain 5F residue 132 SER Chi-restraints excluded: chain 5F residue 157 GLU Chi-restraints excluded: chain 5F residue 520 ARG Chi-restraints excluded: chain 5F residue 601 LYS Chi-restraints excluded: chain 5F residue 605 GLU Chi-restraints excluded: chain 5F residue 625 GLU Chi-restraints excluded: chain 5F residue 662 LEU Chi-restraints excluded: chain 3a residue 124 GLU Chi-restraints excluded: chain 3b residue 22 THR Chi-restraints excluded: chain 3b residue 35 GLU Chi-restraints excluded: chain 3b residue 82 LYS Chi-restraints excluded: chain 3b residue 124 GLU Chi-restraints excluded: chain 3c residue 114 GLN Chi-restraints excluded: chain 3c residue 124 GLU Chi-restraints excluded: chain 3d residue 124 GLU Chi-restraints excluded: chain 3e residue 22 THR Chi-restraints excluded: chain 3e residue 35 GLU Chi-restraints excluded: chain 3e residue 82 LYS Chi-restraints excluded: chain 3e residue 124 GLU Chi-restraints excluded: chain 3f residue 73 GLN Chi-restraints excluded: chain 3f residue 124 GLU Chi-restraints excluded: chain 4a residue 2 SER Chi-restraints excluded: chain 4a residue 22 THR Chi-restraints excluded: chain 4a residue 54 LYS Chi-restraints excluded: chain 4a residue 114 GLN Chi-restraints excluded: chain 4a residue 130 MET Chi-restraints excluded: chain 4c residue 22 THR Chi-restraints excluded: chain 4c residue 56 SER Chi-restraints excluded: chain 4c residue 124 GLU Chi-restraints excluded: chain 4d residue 2 SER Chi-restraints excluded: chain 4d residue 22 THR Chi-restraints excluded: chain 4d residue 54 LYS Chi-restraints excluded: chain 4d residue 114 GLN Chi-restraints excluded: chain 4d residue 130 MET Chi-restraints excluded: chain 4f residue 22 THR Chi-restraints excluded: chain 4f residue 56 SER Chi-restraints excluded: chain 4f residue 124 GLU Chi-restraints excluded: chain 5a residue 119 LYS Chi-restraints excluded: chain 5b residue 30 GLU Chi-restraints excluded: chain 5b residue 56 SER Chi-restraints excluded: chain 5b residue 112 LYS Chi-restraints excluded: chain 5c residue 73 GLN Chi-restraints excluded: chain 5c residue 119 LYS Chi-restraints excluded: chain 5d residue 17 THR Chi-restraints excluded: chain 5d residue 119 LYS Chi-restraints excluded: chain 5e residue 30 GLU Chi-restraints excluded: chain 5e residue 56 SER Chi-restraints excluded: chain 5f residue 17 THR Chi-restraints excluded: chain 5f residue 73 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1170 random chunks: chunk 737 optimal weight: 9.9990 chunk 988 optimal weight: 3.9990 chunk 284 optimal weight: 20.0000 chunk 855 optimal weight: 20.0000 chunk 137 optimal weight: 0.0170 chunk 257 optimal weight: 8.9990 chunk 929 optimal weight: 5.9990 chunk 389 optimal weight: 6.9990 chunk 954 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 171 optimal weight: 20.0000 overall best weight: 5.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3C 23 GLN 3C 239 GLN 3F 23 GLN 3F 239 GLN 4A 205 ASN 4B 205 ASN ** 4C 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4D 205 ASN 5A 606 GLN ** 5B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5C 490 ASN 3a 140 GLN 3d 140 GLN 3f 114 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.167806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.147150 restraints weight = 81176.390| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.30 r_work: 0.3236 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 94842 Z= 0.316 Angle : 0.766 9.000 129006 Z= 0.425 Chirality : 0.050 0.215 14346 Planarity : 0.006 0.068 16776 Dihedral : 5.223 19.811 12654 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.54 % Allowed : 13.37 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.07), residues: 11628 helix: 1.40 (0.09), residues: 3222 sheet: 0.49 (0.11), residues: 2250 loop : -1.32 (0.07), residues: 6156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP3A 584 HIS 0.006 0.002 HIS4c 97 PHE 0.024 0.003 PHE4E 62 TYR 0.028 0.002 TYR5C 489 ARG 0.008 0.001 ARG4F 520 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 42003.13 seconds wall clock time: 725 minutes 7.95 seconds (43507.95 seconds total)