Starting phenix.real_space_refine on Mon Mar 25 04:39:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pev_20333/03_2024/6pev_20333.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pev_20333/03_2024/6pev_20333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pev_20333/03_2024/6pev_20333.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pev_20333/03_2024/6pev_20333.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pev_20333/03_2024/6pev_20333.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pev_20333/03_2024/6pev_20333.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 24 6.06 5 S 252 5.16 5 C 29628 2.51 5 N 7848 2.21 5 O 8616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 7": "OE1" <-> "OE2" Residue "A GLU 34": "OE1" <-> "OE2" Residue "A GLU 45": "OE1" <-> "OE2" Residue "A GLU 53": "OE1" <-> "OE2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A GLU 111": "OE1" <-> "OE2" Residue "A ASP 168": "OD1" <-> "OD2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A ASP 297": "OD1" <-> "OD2" Residue "A PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "A PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "A ASP 449": "OD1" <-> "OD2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 504": "OD1" <-> "OD2" Residue "A GLU 538": "OE1" <-> "OE2" Residue "A ASP 569": "OD1" <-> "OD2" Residue "B GLU 7": "OE1" <-> "OE2" Residue "B GLU 34": "OE1" <-> "OE2" Residue "B GLU 45": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B ASP 168": "OD1" <-> "OD2" Residue "B GLU 293": "OE1" <-> "OE2" Residue "B ASP 297": "OD1" <-> "OD2" Residue "B PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B GLU 386": "OE1" <-> "OE2" Residue "B PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B GLU 419": "OE1" <-> "OE2" Residue "B GLU 445": "OE1" <-> "OE2" Residue "B ASP 449": "OD1" <-> "OD2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 504": "OD1" <-> "OD2" Residue "B GLU 538": "OE1" <-> "OE2" Residue "B ASP 569": "OD1" <-> "OD2" Residue "C GLU 7": "OE1" <-> "OE2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C GLU 45": "OE1" <-> "OE2" Residue "C GLU 53": "OE1" <-> "OE2" Residue "C GLU 60": "OE1" <-> "OE2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C ASP 168": "OD1" <-> "OD2" Residue "C GLU 293": "OE1" <-> "OE2" Residue "C ASP 297": "OD1" <-> "OD2" Residue "C PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C GLU 386": "OE1" <-> "OE2" Residue "C PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "C GLU 419": "OE1" <-> "OE2" Residue "C GLU 445": "OE1" <-> "OE2" Residue "C ASP 449": "OD1" <-> "OD2" Residue "C GLU 457": "OE1" <-> "OE2" Residue "C TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 504": "OD1" <-> "OD2" Residue "C GLU 538": "OE1" <-> "OE2" Residue "C ASP 569": "OD1" <-> "OD2" Residue "D GLU 7": "OE1" <-> "OE2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D GLU 53": "OE1" <-> "OE2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D GLU 111": "OE1" <-> "OE2" Residue "D ASP 168": "OD1" <-> "OD2" Residue "D GLU 293": "OE1" <-> "OE2" Residue "D ASP 297": "OD1" <-> "OD2" Residue "D PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D GLU 386": "OE1" <-> "OE2" Residue "D PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 412": "OE1" <-> "OE2" Residue "D GLU 419": "OE1" <-> "OE2" Residue "D GLU 445": "OE1" <-> "OE2" Residue "D ASP 449": "OD1" <-> "OD2" Residue "D GLU 457": "OE1" <-> "OE2" Residue "D TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 504": "OD1" <-> "OD2" Residue "D ASP 569": "OD1" <-> "OD2" Residue "E GLU 7": "OE1" <-> "OE2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "E GLU 45": "OE1" <-> "OE2" Residue "E GLU 53": "OE1" <-> "OE2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "E ASP 168": "OD1" <-> "OD2" Residue "E GLU 293": "OE1" <-> "OE2" Residue "E ASP 297": "OD1" <-> "OD2" Residue "E PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E GLU 386": "OE1" <-> "OE2" Residue "E PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 412": "OE1" <-> "OE2" Residue "E GLU 419": "OE1" <-> "OE2" Residue "E GLU 445": "OE1" <-> "OE2" Residue "E ASP 449": "OD1" <-> "OD2" Residue "E GLU 457": "OE1" <-> "OE2" Residue "E TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 504": "OD1" <-> "OD2" Residue "E GLU 538": "OE1" <-> "OE2" Residue "E ASP 569": "OD1" <-> "OD2" Residue "F GLU 7": "OE1" <-> "OE2" Residue "F GLU 34": "OE1" <-> "OE2" Residue "F GLU 45": "OE1" <-> "OE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F GLU 60": "OE1" <-> "OE2" Residue "F GLU 111": "OE1" <-> "OE2" Residue "F ASP 168": "OD1" <-> "OD2" Residue "F GLU 293": "OE1" <-> "OE2" Residue "F ASP 297": "OD1" <-> "OD2" Residue "F PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F GLU 386": "OE1" <-> "OE2" Residue "F PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 412": "OE1" <-> "OE2" Residue "F GLU 419": "OE1" <-> "OE2" Residue "F GLU 445": "OE1" <-> "OE2" Residue "F ASP 449": "OD1" <-> "OD2" Residue "F GLU 457": "OE1" <-> "OE2" Residue "F TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 504": "OD1" <-> "OD2" Residue "F GLU 538": "OE1" <-> "OE2" Residue "F ASP 569": "OD1" <-> "OD2" Residue "G GLU 7": "OE1" <-> "OE2" Residue "G GLU 34": "OE1" <-> "OE2" Residue "G GLU 45": "OE1" <-> "OE2" Residue "G GLU 53": "OE1" <-> "OE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 111": "OE1" <-> "OE2" Residue "G ASP 168": "OD1" <-> "OD2" Residue "G GLU 293": "OE1" <-> "OE2" Residue "G ASP 297": "OD1" <-> "OD2" Residue "G PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 338": "OE1" <-> "OE2" Residue "G GLU 386": "OE1" <-> "OE2" Residue "G PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 412": "OE1" <-> "OE2" Residue "G GLU 419": "OE1" <-> "OE2" Residue "G GLU 445": "OE1" <-> "OE2" Residue "G ASP 449": "OD1" <-> "OD2" Residue "G GLU 457": "OE1" <-> "OE2" Residue "G TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 504": "OD1" <-> "OD2" Residue "G GLU 538": "OE1" <-> "OE2" Residue "G ASP 569": "OD1" <-> "OD2" Residue "H GLU 7": "OE1" <-> "OE2" Residue "H GLU 34": "OE1" <-> "OE2" Residue "H GLU 45": "OE1" <-> "OE2" Residue "H GLU 53": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H GLU 111": "OE1" <-> "OE2" Residue "H ASP 168": "OD1" <-> "OD2" Residue "H GLU 293": "OE1" <-> "OE2" Residue "H ASP 297": "OD1" <-> "OD2" Residue "H PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 338": "OE1" <-> "OE2" Residue "H GLU 386": "OE1" <-> "OE2" Residue "H PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 412": "OE1" <-> "OE2" Residue "H GLU 419": "OE1" <-> "OE2" Residue "H GLU 445": "OE1" <-> "OE2" Residue "H ASP 449": "OD1" <-> "OD2" Residue "H GLU 457": "OE1" <-> "OE2" Residue "H TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 504": "OD1" <-> "OD2" Residue "H GLU 538": "OE1" <-> "OE2" Residue "H ASP 569": "OD1" <-> "OD2" Residue "I GLU 7": "OE1" <-> "OE2" Residue "I GLU 34": "OE1" <-> "OE2" Residue "I GLU 45": "OE1" <-> "OE2" Residue "I GLU 53": "OE1" <-> "OE2" Residue "I GLU 60": "OE1" <-> "OE2" Residue "I GLU 111": "OE1" <-> "OE2" Residue "I ASP 168": "OD1" <-> "OD2" Residue "I GLU 293": "OE1" <-> "OE2" Residue "I ASP 297": "OD1" <-> "OD2" Residue "I PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 338": "OE1" <-> "OE2" Residue "I GLU 386": "OE1" <-> "OE2" Residue "I PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 412": "OE1" <-> "OE2" Residue "I GLU 419": "OE1" <-> "OE2" Residue "I GLU 445": "OE1" <-> "OE2" Residue "I ASP 449": "OD1" <-> "OD2" Residue "I GLU 457": "OE1" <-> "OE2" Residue "I TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 504": "OD1" <-> "OD2" Residue "I GLU 538": "OE1" <-> "OE2" Residue "I ASP 569": "OD1" <-> "OD2" Residue "J GLU 7": "OE1" <-> "OE2" Residue "J GLU 34": "OE1" <-> "OE2" Residue "J GLU 45": "OE1" <-> "OE2" Residue "J GLU 53": "OE1" <-> "OE2" Residue "J GLU 60": "OE1" <-> "OE2" Residue "J GLU 111": "OE1" <-> "OE2" Residue "J ASP 168": "OD1" <-> "OD2" Residue "J GLU 293": "OE1" <-> "OE2" Residue "J ASP 297": "OD1" <-> "OD2" Residue "J PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 338": "OE1" <-> "OE2" Residue "J GLU 386": "OE1" <-> "OE2" Residue "J PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 412": "OE1" <-> "OE2" Residue "J GLU 419": "OE1" <-> "OE2" Residue "J GLU 445": "OE1" <-> "OE2" Residue "J ASP 449": "OD1" <-> "OD2" Residue "J GLU 457": "OE1" <-> "OE2" Residue "J TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 504": "OD1" <-> "OD2" Residue "J GLU 538": "OE1" <-> "OE2" Residue "J ASP 569": "OD1" <-> "OD2" Residue "K GLU 7": "OE1" <-> "OE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K GLU 45": "OE1" <-> "OE2" Residue "K GLU 53": "OE1" <-> "OE2" Residue "K GLU 60": "OE1" <-> "OE2" Residue "K GLU 111": "OE1" <-> "OE2" Residue "K ASP 168": "OD1" <-> "OD2" Residue "K GLU 293": "OE1" <-> "OE2" Residue "K ASP 297": "OD1" <-> "OD2" Residue "K PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 338": "OE1" <-> "OE2" Residue "K GLU 386": "OE1" <-> "OE2" Residue "K PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 412": "OE1" <-> "OE2" Residue "K GLU 419": "OE1" <-> "OE2" Residue "K GLU 445": "OE1" <-> "OE2" Residue "K ASP 449": "OD1" <-> "OD2" Residue "K GLU 457": "OE1" <-> "OE2" Residue "K TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 504": "OD1" <-> "OD2" Residue "K GLU 538": "OE1" <-> "OE2" Residue "K ASP 569": "OD1" <-> "OD2" Residue "L GLU 7": "OE1" <-> "OE2" Residue "L GLU 34": "OE1" <-> "OE2" Residue "L GLU 45": "OE1" <-> "OE2" Residue "L GLU 53": "OE1" <-> "OE2" Residue "L GLU 60": "OE1" <-> "OE2" Residue "L GLU 111": "OE1" <-> "OE2" Residue "L ASP 168": "OD1" <-> "OD2" Residue "L GLU 293": "OE1" <-> "OE2" Residue "L ASP 297": "OD1" <-> "OD2" Residue "L PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 338": "OE1" <-> "OE2" Residue "L GLU 386": "OE1" <-> "OE2" Residue "L PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 412": "OE1" <-> "OE2" Residue "L GLU 419": "OE1" <-> "OE2" Residue "L GLU 445": "OE1" <-> "OE2" Residue "L ASP 449": "OD1" <-> "OD2" Residue "L GLU 457": "OE1" <-> "OE2" Residue "L TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 504": "OD1" <-> "OD2" Residue "L GLU 538": "OE1" <-> "OE2" Residue "L ASP 569": "OD1" <-> "OD2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 46368 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3862 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 11, 'TRANS': 466} Chain breaks: 2 Chain: "B" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3862 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 11, 'TRANS': 466} Chain breaks: 2 Chain: "C" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3862 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 11, 'TRANS': 466} Chain breaks: 2 Chain: "D" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3862 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 11, 'TRANS': 466} Chain breaks: 2 Chain: "E" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3862 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 11, 'TRANS': 466} Chain breaks: 2 Chain: "F" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3862 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 11, 'TRANS': 466} Chain breaks: 2 Chain: "G" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3862 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 11, 'TRANS': 466} Chain breaks: 2 Chain: "H" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3862 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 11, 'TRANS': 466} Chain breaks: 2 Chain: "I" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3862 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 11, 'TRANS': 466} Chain breaks: 2 Chain: "J" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3862 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 11, 'TRANS': 466} Chain breaks: 2 Chain: "K" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3862 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 11, 'TRANS': 466} Chain breaks: 2 Chain: "L" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3862 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 11, 'TRANS': 466} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 22.10, per 1000 atoms: 0.48 Number of scatterers: 46368 At special positions: 0 Unit cell: (162.24, 156, 150.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 24 29.99 S 252 16.00 O 8616 8.00 N 7848 7.00 C 29628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 26 " - pdb=" SG CYS A 58 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 58 " distance=2.03 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 58 " distance=2.03 Simple disulfide: pdb=" SG CYS D 26 " - pdb=" SG CYS D 58 " distance=2.03 Simple disulfide: pdb=" SG CYS E 26 " - pdb=" SG CYS E 58 " distance=2.03 Simple disulfide: pdb=" SG CYS F 26 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS G 26 " - pdb=" SG CYS G 58 " distance=2.03 Simple disulfide: pdb=" SG CYS H 26 " - pdb=" SG CYS H 58 " distance=2.03 Simple disulfide: pdb=" SG CYS I 26 " - pdb=" SG CYS I 58 " distance=2.03 Simple disulfide: pdb=" SG CYS J 26 " - pdb=" SG CYS J 58 " distance=2.03 Simple disulfide: pdb=" SG CYS K 26 " - pdb=" SG CYS K 58 " distance=2.03 Simple disulfide: pdb=" SG CYS L 26 " - pdb=" SG CYS L 58 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.30 Conformation dependent library (CDL) restraints added in 7.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1000 " pdb="ZN ZN A1000 " - pdb="ZN ZN A1001 " pdb="ZN ZN A1000 " - pdb=" NE2 HIS A 86 " pdb=" ZN B1000 " pdb="ZN ZN B1000 " - pdb="ZN ZN B1001 " pdb="ZN ZN B1000 " - pdb=" NE2 HIS B 86 " pdb=" ZN C1000 " pdb="ZN ZN C1000 " - pdb="ZN ZN C1001 " pdb="ZN ZN C1000 " - pdb=" NE2 HIS C 86 " pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb="ZN ZN D1001 " pdb="ZN ZN D1000 " - pdb=" NE2 HIS D 86 " pdb=" ZN E1000 " pdb="ZN ZN E1000 " - pdb="ZN ZN E1001 " pdb="ZN ZN E1000 " - pdb=" NE2 HIS E 86 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb="ZN ZN F1001 " pdb="ZN ZN F1000 " - pdb=" NE2 HIS F 86 " pdb=" ZN G1000 " pdb="ZN ZN G1000 " - pdb="ZN ZN G1001 " pdb="ZN ZN G1000 " - pdb=" NE2 HIS G 86 " pdb=" ZN H1000 " pdb="ZN ZN H1000 " - pdb="ZN ZN H1001 " pdb="ZN ZN H1000 " - pdb=" NE2 HIS H 86 " pdb=" ZN I1000 " pdb="ZN ZN I1000 " - pdb="ZN ZN I1001 " pdb="ZN ZN I1000 " - pdb=" NE2 HIS I 86 " pdb=" ZN J1000 " pdb="ZN ZN J1000 " - pdb="ZN ZN J1001 " pdb="ZN ZN J1000 " - pdb=" NE2 HIS J 86 " pdb=" ZN K1000 " pdb="ZN ZN K1000 " - pdb="ZN ZN K1001 " pdb="ZN ZN K1000 " - pdb=" NE2 HIS K 86 " pdb=" ZN L1000 " pdb="ZN ZN L1000 " - pdb="ZN ZN L1001 " pdb="ZN ZN L1000 " - pdb=" NE2 HIS L 86 " 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10824 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 48 sheets defined 35.2% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.59 Creating SS restraints... Processing helix chain 'A' and resid 1 through 16 Processing helix chain 'A' and resid 22 through 35 Processing helix chain 'A' and resid 166 through 171 removed outlier: 4.104A pdb=" N SER A 170 " --> pdb=" O TYR A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 277 through 289 Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 327 through 345 Processing helix chain 'A' and resid 378 through 382 removed outlier: 3.606A pdb=" N ILE A 381 " --> pdb=" O HIS A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 406 removed outlier: 3.539A pdb=" N SER A 403 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 414 removed outlier: 3.629A pdb=" N ILE A 410 " --> pdb=" O PHE A 406 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N HIS A 411 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU A 412 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS A 413 " --> pdb=" O GLU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 removed outlier: 4.112A pdb=" N ASN A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 491 removed outlier: 3.784A pdb=" N ILE A 479 " --> pdb=" O HIS A 475 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 520 Processing helix chain 'A' and resid 542 through 564 removed outlier: 3.516A pdb=" N TYR A 559 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASN A 560 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLN A 561 " --> pdb=" O THR A 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 16 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 166 through 171 removed outlier: 4.103A pdb=" N SER B 170 " --> pdb=" O TYR B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 277 through 289 Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 327 through 345 Processing helix chain 'B' and resid 378 through 382 removed outlier: 3.606A pdb=" N ILE B 381 " --> pdb=" O HIS B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 406 removed outlier: 3.540A pdb=" N SER B 403 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 414 removed outlier: 3.630A pdb=" N ILE B 410 " --> pdb=" O PHE B 406 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N HIS B 411 " --> pdb=" O LYS B 407 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU B 412 " --> pdb=" O LYS B 408 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B 413 " --> pdb=" O GLU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 426 removed outlier: 4.111A pdb=" N ASN B 426 " --> pdb=" O GLY B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 491 removed outlier: 3.784A pdb=" N ILE B 479 " --> pdb=" O HIS B 475 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 520 Processing helix chain 'B' and resid 542 through 564 removed outlier: 3.516A pdb=" N TYR B 559 " --> pdb=" O PHE B 555 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASN B 560 " --> pdb=" O TYR B 556 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLN B 561 " --> pdb=" O THR B 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 16 Processing helix chain 'C' and resid 22 through 35 Processing helix chain 'C' and resid 166 through 171 removed outlier: 4.103A pdb=" N SER C 170 " --> pdb=" O TYR C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 192 Processing helix chain 'C' and resid 277 through 289 Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 327 through 345 Processing helix chain 'C' and resid 378 through 382 removed outlier: 3.606A pdb=" N ILE C 381 " --> pdb=" O HIS C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 406 removed outlier: 3.539A pdb=" N SER C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 414 removed outlier: 3.630A pdb=" N ILE C 410 " --> pdb=" O PHE C 406 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N HIS C 411 " --> pdb=" O LYS C 407 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU C 412 " --> pdb=" O LYS C 408 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS C 413 " --> pdb=" O GLU C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 426 removed outlier: 4.111A pdb=" N ASN C 426 " --> pdb=" O GLY C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 491 removed outlier: 3.783A pdb=" N ILE C 479 " --> pdb=" O HIS C 475 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 489 " --> pdb=" O LEU C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 520 Processing helix chain 'C' and resid 542 through 564 removed outlier: 3.517A pdb=" N TYR C 559 " --> pdb=" O PHE C 555 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASN C 560 " --> pdb=" O TYR C 556 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLN C 561 " --> pdb=" O THR C 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 16 Processing helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 166 through 171 removed outlier: 4.103A pdb=" N SER D 170 " --> pdb=" O TYR D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 192 Processing helix chain 'D' and resid 277 through 289 Processing helix chain 'D' and resid 291 through 293 No H-bonds generated for 'chain 'D' and resid 291 through 293' Processing helix chain 'D' and resid 327 through 345 Processing helix chain 'D' and resid 378 through 382 removed outlier: 3.606A pdb=" N ILE D 381 " --> pdb=" O HIS D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 406 removed outlier: 3.539A pdb=" N SER D 403 " --> pdb=" O ASP D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 414 removed outlier: 3.629A pdb=" N ILE D 410 " --> pdb=" O PHE D 406 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N HIS D 411 " --> pdb=" O LYS D 407 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU D 412 " --> pdb=" O LYS D 408 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS D 413 " --> pdb=" O GLU D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 426 removed outlier: 4.111A pdb=" N ASN D 426 " --> pdb=" O GLY D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 491 removed outlier: 3.784A pdb=" N ILE D 479 " --> pdb=" O HIS D 475 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS D 489 " --> pdb=" O LEU D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 520 Processing helix chain 'D' and resid 542 through 564 removed outlier: 3.515A pdb=" N TYR D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASN D 560 " --> pdb=" O TYR D 556 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLN D 561 " --> pdb=" O THR D 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 16 Processing helix chain 'E' and resid 22 through 35 Processing helix chain 'E' and resid 166 through 171 removed outlier: 4.104A pdb=" N SER E 170 " --> pdb=" O TYR E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 192 Processing helix chain 'E' and resid 277 through 289 Processing helix chain 'E' and resid 291 through 293 No H-bonds generated for 'chain 'E' and resid 291 through 293' Processing helix chain 'E' and resid 327 through 345 Processing helix chain 'E' and resid 378 through 382 removed outlier: 3.606A pdb=" N ILE E 381 " --> pdb=" O HIS E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 406 removed outlier: 3.540A pdb=" N SER E 403 " --> pdb=" O ASP E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 414 removed outlier: 3.629A pdb=" N ILE E 410 " --> pdb=" O PHE E 406 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N HIS E 411 " --> pdb=" O LYS E 407 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU E 412 " --> pdb=" O LYS E 408 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS E 413 " --> pdb=" O GLU E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 426 removed outlier: 4.112A pdb=" N ASN E 426 " --> pdb=" O GLY E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 491 removed outlier: 3.783A pdb=" N ILE E 479 " --> pdb=" O HIS E 475 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS E 489 " --> pdb=" O LEU E 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 520 Processing helix chain 'E' and resid 542 through 564 removed outlier: 3.516A pdb=" N TYR E 559 " --> pdb=" O PHE E 555 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASN E 560 " --> pdb=" O TYR E 556 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLN E 561 " --> pdb=" O THR E 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 16 Processing helix chain 'F' and resid 22 through 35 Processing helix chain 'F' and resid 166 through 171 removed outlier: 4.104A pdb=" N SER F 170 " --> pdb=" O TYR F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 192 Processing helix chain 'F' and resid 277 through 289 Processing helix chain 'F' and resid 291 through 293 No H-bonds generated for 'chain 'F' and resid 291 through 293' Processing helix chain 'F' and resid 327 through 345 Processing helix chain 'F' and resid 378 through 382 removed outlier: 3.607A pdb=" N ILE F 381 " --> pdb=" O HIS F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 406 removed outlier: 3.540A pdb=" N SER F 403 " --> pdb=" O ASP F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 414 removed outlier: 3.629A pdb=" N ILE F 410 " --> pdb=" O PHE F 406 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N HIS F 411 " --> pdb=" O LYS F 407 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU F 412 " --> pdb=" O LYS F 408 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS F 413 " --> pdb=" O GLU F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 426 removed outlier: 4.111A pdb=" N ASN F 426 " --> pdb=" O GLY F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 491 removed outlier: 3.784A pdb=" N ILE F 479 " --> pdb=" O HIS F 475 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS F 489 " --> pdb=" O LEU F 485 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 520 Processing helix chain 'F' and resid 542 through 564 removed outlier: 3.516A pdb=" N TYR F 559 " --> pdb=" O PHE F 555 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASN F 560 " --> pdb=" O TYR F 556 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLN F 561 " --> pdb=" O THR F 557 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 16 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'G' and resid 166 through 171 removed outlier: 4.103A pdb=" N SER G 170 " --> pdb=" O TYR G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 192 Processing helix chain 'G' and resid 277 through 289 Processing helix chain 'G' and resid 291 through 293 No H-bonds generated for 'chain 'G' and resid 291 through 293' Processing helix chain 'G' and resid 327 through 345 Processing helix chain 'G' and resid 378 through 382 removed outlier: 3.606A pdb=" N ILE G 381 " --> pdb=" O HIS G 378 " (cutoff:3.500A) Processing helix chain 'G' and resid 392 through 406 removed outlier: 3.539A pdb=" N SER G 403 " --> pdb=" O ASP G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 414 removed outlier: 3.630A pdb=" N ILE G 410 " --> pdb=" O PHE G 406 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N HIS G 411 " --> pdb=" O LYS G 407 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU G 412 " --> pdb=" O LYS G 408 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS G 413 " --> pdb=" O GLU G 409 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 426 removed outlier: 4.112A pdb=" N ASN G 426 " --> pdb=" O GLY G 422 " (cutoff:3.500A) Processing helix chain 'G' and resid 474 through 491 removed outlier: 3.784A pdb=" N ILE G 479 " --> pdb=" O HIS G 475 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS G 489 " --> pdb=" O LEU G 485 " (cutoff:3.500A) Processing helix chain 'G' and resid 511 through 520 Processing helix chain 'G' and resid 542 through 564 removed outlier: 3.516A pdb=" N TYR G 559 " --> pdb=" O PHE G 555 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASN G 560 " --> pdb=" O TYR G 556 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLN G 561 " --> pdb=" O THR G 557 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 16 Processing helix chain 'H' and resid 22 through 35 Processing helix chain 'H' and resid 166 through 171 removed outlier: 4.103A pdb=" N SER H 170 " --> pdb=" O TYR H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 192 Processing helix chain 'H' and resid 277 through 289 Processing helix chain 'H' and resid 291 through 293 No H-bonds generated for 'chain 'H' and resid 291 through 293' Processing helix chain 'H' and resid 327 through 345 Processing helix chain 'H' and resid 378 through 382 removed outlier: 3.607A pdb=" N ILE H 381 " --> pdb=" O HIS H 378 " (cutoff:3.500A) Processing helix chain 'H' and resid 392 through 406 removed outlier: 3.539A pdb=" N SER H 403 " --> pdb=" O ASP H 399 " (cutoff:3.500A) Processing helix chain 'H' and resid 406 through 414 removed outlier: 3.629A pdb=" N ILE H 410 " --> pdb=" O PHE H 406 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N HIS H 411 " --> pdb=" O LYS H 407 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU H 412 " --> pdb=" O LYS H 408 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS H 413 " --> pdb=" O GLU H 409 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 426 removed outlier: 4.111A pdb=" N ASN H 426 " --> pdb=" O GLY H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 474 through 491 removed outlier: 3.784A pdb=" N ILE H 479 " --> pdb=" O HIS H 475 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS H 489 " --> pdb=" O LEU H 485 " (cutoff:3.500A) Processing helix chain 'H' and resid 511 through 520 Processing helix chain 'H' and resid 542 through 564 removed outlier: 3.516A pdb=" N TYR H 559 " --> pdb=" O PHE H 555 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASN H 560 " --> pdb=" O TYR H 556 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N GLN H 561 " --> pdb=" O THR H 557 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 16 Processing helix chain 'I' and resid 22 through 35 Processing helix chain 'I' and resid 166 through 171 removed outlier: 4.104A pdb=" N SER I 170 " --> pdb=" O TYR I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 192 Processing helix chain 'I' and resid 277 through 289 Processing helix chain 'I' and resid 291 through 293 No H-bonds generated for 'chain 'I' and resid 291 through 293' Processing helix chain 'I' and resid 327 through 345 Processing helix chain 'I' and resid 378 through 382 removed outlier: 3.606A pdb=" N ILE I 381 " --> pdb=" O HIS I 378 " (cutoff:3.500A) Processing helix chain 'I' and resid 392 through 406 removed outlier: 3.540A pdb=" N SER I 403 " --> pdb=" O ASP I 399 " (cutoff:3.500A) Processing helix chain 'I' and resid 406 through 414 removed outlier: 3.629A pdb=" N ILE I 410 " --> pdb=" O PHE I 406 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N HIS I 411 " --> pdb=" O LYS I 407 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU I 412 " --> pdb=" O LYS I 408 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS I 413 " --> pdb=" O GLU I 409 " (cutoff:3.500A) Processing helix chain 'I' and resid 416 through 426 removed outlier: 4.112A pdb=" N ASN I 426 " --> pdb=" O GLY I 422 " (cutoff:3.500A) Processing helix chain 'I' and resid 474 through 491 removed outlier: 3.784A pdb=" N ILE I 479 " --> pdb=" O HIS I 475 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS I 489 " --> pdb=" O LEU I 485 " (cutoff:3.500A) Processing helix chain 'I' and resid 511 through 520 Processing helix chain 'I' and resid 542 through 564 removed outlier: 3.516A pdb=" N TYR I 559 " --> pdb=" O PHE I 555 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASN I 560 " --> pdb=" O TYR I 556 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLN I 561 " --> pdb=" O THR I 557 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 16 Processing helix chain 'J' and resid 22 through 35 Processing helix chain 'J' and resid 166 through 171 removed outlier: 4.104A pdb=" N SER J 170 " --> pdb=" O TYR J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 186 through 192 Processing helix chain 'J' and resid 277 through 289 Processing helix chain 'J' and resid 291 through 293 No H-bonds generated for 'chain 'J' and resid 291 through 293' Processing helix chain 'J' and resid 327 through 345 Processing helix chain 'J' and resid 378 through 382 removed outlier: 3.606A pdb=" N ILE J 381 " --> pdb=" O HIS J 378 " (cutoff:3.500A) Processing helix chain 'J' and resid 392 through 406 removed outlier: 3.539A pdb=" N SER J 403 " --> pdb=" O ASP J 399 " (cutoff:3.500A) Processing helix chain 'J' and resid 406 through 414 removed outlier: 3.629A pdb=" N ILE J 410 " --> pdb=" O PHE J 406 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N HIS J 411 " --> pdb=" O LYS J 407 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU J 412 " --> pdb=" O LYS J 408 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS J 413 " --> pdb=" O GLU J 409 " (cutoff:3.500A) Processing helix chain 'J' and resid 416 through 426 removed outlier: 4.112A pdb=" N ASN J 426 " --> pdb=" O GLY J 422 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 491 removed outlier: 3.784A pdb=" N ILE J 479 " --> pdb=" O HIS J 475 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS J 489 " --> pdb=" O LEU J 485 " (cutoff:3.500A) Processing helix chain 'J' and resid 511 through 520 Processing helix chain 'J' and resid 542 through 564 removed outlier: 3.517A pdb=" N TYR J 559 " --> pdb=" O PHE J 555 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASN J 560 " --> pdb=" O TYR J 556 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLN J 561 " --> pdb=" O THR J 557 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 16 Processing helix chain 'K' and resid 22 through 35 Processing helix chain 'K' and resid 166 through 171 removed outlier: 4.103A pdb=" N SER K 170 " --> pdb=" O TYR K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 186 through 192 Processing helix chain 'K' and resid 277 through 289 Processing helix chain 'K' and resid 291 through 293 No H-bonds generated for 'chain 'K' and resid 291 through 293' Processing helix chain 'K' and resid 327 through 345 Processing helix chain 'K' and resid 378 through 382 removed outlier: 3.606A pdb=" N ILE K 381 " --> pdb=" O HIS K 378 " (cutoff:3.500A) Processing helix chain 'K' and resid 392 through 406 removed outlier: 3.539A pdb=" N SER K 403 " --> pdb=" O ASP K 399 " (cutoff:3.500A) Processing helix chain 'K' and resid 406 through 414 removed outlier: 3.629A pdb=" N ILE K 410 " --> pdb=" O PHE K 406 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N HIS K 411 " --> pdb=" O LYS K 407 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU K 412 " --> pdb=" O LYS K 408 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS K 413 " --> pdb=" O GLU K 409 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 426 removed outlier: 4.112A pdb=" N ASN K 426 " --> pdb=" O GLY K 422 " (cutoff:3.500A) Processing helix chain 'K' and resid 474 through 491 removed outlier: 3.783A pdb=" N ILE K 479 " --> pdb=" O HIS K 475 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS K 489 " --> pdb=" O LEU K 485 " (cutoff:3.500A) Processing helix chain 'K' and resid 511 through 520 Processing helix chain 'K' and resid 542 through 564 removed outlier: 3.516A pdb=" N TYR K 559 " --> pdb=" O PHE K 555 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASN K 560 " --> pdb=" O TYR K 556 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLN K 561 " --> pdb=" O THR K 557 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 16 Processing helix chain 'L' and resid 22 through 35 Processing helix chain 'L' and resid 166 through 171 removed outlier: 4.104A pdb=" N SER L 170 " --> pdb=" O TYR L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 192 Processing helix chain 'L' and resid 277 through 289 Processing helix chain 'L' and resid 291 through 293 No H-bonds generated for 'chain 'L' and resid 291 through 293' Processing helix chain 'L' and resid 327 through 345 Processing helix chain 'L' and resid 378 through 382 removed outlier: 3.606A pdb=" N ILE L 381 " --> pdb=" O HIS L 378 " (cutoff:3.500A) Processing helix chain 'L' and resid 392 through 406 removed outlier: 3.539A pdb=" N SER L 403 " --> pdb=" O ASP L 399 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 414 removed outlier: 3.630A pdb=" N ILE L 410 " --> pdb=" O PHE L 406 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N HIS L 411 " --> pdb=" O LYS L 407 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU L 412 " --> pdb=" O LYS L 408 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS L 413 " --> pdb=" O GLU L 409 " (cutoff:3.500A) Processing helix chain 'L' and resid 416 through 426 removed outlier: 4.111A pdb=" N ASN L 426 " --> pdb=" O GLY L 422 " (cutoff:3.500A) Processing helix chain 'L' and resid 474 through 491 removed outlier: 3.784A pdb=" N ILE L 479 " --> pdb=" O HIS L 475 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS L 489 " --> pdb=" O LEU L 485 " (cutoff:3.500A) Processing helix chain 'L' and resid 511 through 520 Processing helix chain 'L' and resid 542 through 564 removed outlier: 3.517A pdb=" N TYR L 559 " --> pdb=" O PHE L 555 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASN L 560 " --> pdb=" O TYR L 556 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLN L 561 " --> pdb=" O THR L 557 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 40 removed outlier: 6.707A pdb=" N SER A 79 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE A 372 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU A 81 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE A 374 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER A 83 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE A 80 " --> pdb=" O PHE A 429 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LEU A 431 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE A 82 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL A 433 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE A 84 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE A 430 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE A 526 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN A 432 " --> pdb=" O ILE A 526 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASP A 525 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 113 removed outlier: 4.298A pdb=" N LEU A 92 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU A 300 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE A 295 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS A 135 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A 297 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU A 126 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS A 149 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 139 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU A 140 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.820A pdb=" N HIS A 106 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 309 through 311 removed outlier: 4.447A pdb=" N ALA A 541 " --> pdb=" O PRO A 529 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ALA A 436 " --> pdb=" O GLN A 530 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 39 through 40 removed outlier: 6.707A pdb=" N SER B 79 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE B 372 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU B 81 " --> pdb=" O ILE B 372 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE B 374 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER B 83 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE B 80 " --> pdb=" O PHE B 429 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LEU B 431 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE B 82 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL B 433 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE B 84 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE B 430 " --> pdb=" O ILE B 524 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE B 526 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASN B 432 " --> pdb=" O ILE B 526 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASP B 525 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 113 removed outlier: 4.298A pdb=" N LEU B 92 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU B 300 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE B 295 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS B 135 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP B 297 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU B 126 " --> pdb=" O LYS B 149 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS B 149 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 139 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU B 140 " --> pdb=" O VAL C 567 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.821A pdb=" N HIS B 106 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 309 through 311 removed outlier: 4.447A pdb=" N ALA B 541 " --> pdb=" O PRO B 529 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ALA B 436 " --> pdb=" O GLN B 530 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.707A pdb=" N SER C 79 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE C 372 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU C 81 " --> pdb=" O ILE C 372 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE C 374 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER C 83 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE C 80 " --> pdb=" O PHE C 429 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU C 431 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE C 82 " --> pdb=" O LEU C 431 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL C 433 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE C 84 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE C 430 " --> pdb=" O ILE C 524 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE C 526 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN C 432 " --> pdb=" O ILE C 526 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASP C 525 " --> pdb=" O LYS C 462 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 110 through 113 removed outlier: 4.298A pdb=" N LEU C 92 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU C 300 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE C 295 " --> pdb=" O LYS C 135 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS C 135 " --> pdb=" O ILE C 295 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP C 297 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU C 126 " --> pdb=" O LYS C 149 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS C 149 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C 139 " --> pdb=" O LYS C 136 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.820A pdb=" N HIS C 106 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 309 through 311 removed outlier: 4.447A pdb=" N ALA C 541 " --> pdb=" O PRO C 529 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ALA C 436 " --> pdb=" O GLN C 530 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 39 through 40 removed outlier: 6.707A pdb=" N SER D 79 " --> pdb=" O LEU D 370 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE D 372 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU D 81 " --> pdb=" O ILE D 372 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE D 374 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER D 83 " --> pdb=" O ILE D 374 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE D 80 " --> pdb=" O PHE D 429 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LEU D 431 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE D 82 " --> pdb=" O LEU D 431 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL D 433 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE D 84 " --> pdb=" O VAL D 433 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE D 430 " --> pdb=" O ILE D 524 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE D 526 " --> pdb=" O ILE D 430 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASN D 432 " --> pdb=" O ILE D 526 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASP D 525 " --> pdb=" O LYS D 462 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 110 through 113 removed outlier: 4.298A pdb=" N LEU D 92 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LEU D 300 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE D 295 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS D 135 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP D 297 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU D 126 " --> pdb=" O LYS D 149 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS D 149 " --> pdb=" O LEU D 126 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS D 139 " --> pdb=" O LYS D 136 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU D 140 " --> pdb=" O VAL L 567 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 100 through 102 removed outlier: 6.820A pdb=" N HIS D 106 " --> pdb=" O ILE D 183 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 309 through 311 removed outlier: 4.447A pdb=" N ALA D 541 " --> pdb=" O PRO D 529 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ALA D 436 " --> pdb=" O GLN D 530 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 566 through 567 removed outlier: 3.587A pdb=" N LYS H 139 " --> pdb=" O LYS H 136 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS H 149 " --> pdb=" O LEU H 126 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU H 126 " --> pdb=" O LYS H 149 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP H 297 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS H 135 " --> pdb=" O ILE H 295 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE H 295 " --> pdb=" O LYS H 135 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU H 300 " --> pdb=" O ILE H 94 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU H 92 " --> pdb=" O LEU H 302 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 39 through 40 removed outlier: 6.707A pdb=" N SER E 79 " --> pdb=" O LEU E 370 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE E 372 " --> pdb=" O SER E 79 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU E 81 " --> pdb=" O ILE E 372 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE E 374 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER E 83 " --> pdb=" O ILE E 374 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE E 80 " --> pdb=" O PHE E 429 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LEU E 431 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE E 82 " --> pdb=" O LEU E 431 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL E 433 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE E 84 " --> pdb=" O VAL E 433 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE E 430 " --> pdb=" O ILE E 524 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE E 526 " --> pdb=" O ILE E 430 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN E 432 " --> pdb=" O ILE E 526 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASP E 525 " --> pdb=" O LYS E 462 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 110 through 113 removed outlier: 4.297A pdb=" N LEU E 92 " --> pdb=" O LEU E 302 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU E 300 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE E 295 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS E 135 " --> pdb=" O ILE E 295 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP E 297 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU E 126 " --> pdb=" O LYS E 149 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS E 149 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS E 139 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU E 140 " --> pdb=" O VAL F 567 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 100 through 102 removed outlier: 6.821A pdb=" N HIS E 106 " --> pdb=" O ILE E 183 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 309 through 311 removed outlier: 4.447A pdb=" N ALA E 541 " --> pdb=" O PRO E 529 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ALA E 436 " --> pdb=" O GLN E 530 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 39 through 40 removed outlier: 6.706A pdb=" N SER F 79 " --> pdb=" O LEU F 370 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE F 372 " --> pdb=" O SER F 79 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU F 81 " --> pdb=" O ILE F 372 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE F 374 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER F 83 " --> pdb=" O ILE F 374 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE F 80 " --> pdb=" O PHE F 429 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU F 431 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE F 82 " --> pdb=" O LEU F 431 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL F 433 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE F 84 " --> pdb=" O VAL F 433 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE F 430 " --> pdb=" O ILE F 524 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE F 526 " --> pdb=" O ILE F 430 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN F 432 " --> pdb=" O ILE F 526 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASP F 525 " --> pdb=" O LYS F 462 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 110 through 113 removed outlier: 4.298A pdb=" N LEU F 92 " --> pdb=" O LEU F 302 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU F 300 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE F 295 " --> pdb=" O LYS F 135 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS F 135 " --> pdb=" O ILE F 295 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP F 297 " --> pdb=" O LEU F 133 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU F 126 " --> pdb=" O LYS F 149 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS F 149 " --> pdb=" O LEU F 126 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS F 139 " --> pdb=" O LYS F 136 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU F 140 " --> pdb=" O VAL G 567 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 100 through 102 removed outlier: 6.821A pdb=" N HIS F 106 " --> pdb=" O ILE F 183 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 309 through 311 removed outlier: 4.446A pdb=" N ALA F 541 " --> pdb=" O PRO F 529 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ALA F 436 " --> pdb=" O GLN F 530 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 39 through 40 removed outlier: 6.707A pdb=" N SER G 79 " --> pdb=" O LEU G 370 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE G 372 " --> pdb=" O SER G 79 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU G 81 " --> pdb=" O ILE G 372 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE G 374 " --> pdb=" O LEU G 81 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER G 83 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE G 80 " --> pdb=" O PHE G 429 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LEU G 431 " --> pdb=" O ILE G 80 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE G 82 " --> pdb=" O LEU G 431 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL G 433 " --> pdb=" O ILE G 82 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE G 84 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE G 430 " --> pdb=" O ILE G 524 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE G 526 " --> pdb=" O ILE G 430 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN G 432 " --> pdb=" O ILE G 526 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASP G 525 " --> pdb=" O LYS G 462 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 110 through 113 removed outlier: 4.298A pdb=" N LEU G 92 " --> pdb=" O LEU G 302 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU G 300 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE G 295 " --> pdb=" O LYS G 135 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS G 135 " --> pdb=" O ILE G 295 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP G 297 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU G 126 " --> pdb=" O LYS G 149 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS G 149 " --> pdb=" O LEU G 126 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS G 139 " --> pdb=" O LYS G 136 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 100 through 102 removed outlier: 6.820A pdb=" N HIS G 106 " --> pdb=" O ILE G 183 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 309 through 311 removed outlier: 4.447A pdb=" N ALA G 541 " --> pdb=" O PRO G 529 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ALA G 436 " --> pdb=" O GLN G 530 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 39 through 40 removed outlier: 6.707A pdb=" N SER H 79 " --> pdb=" O LEU H 370 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE H 372 " --> pdb=" O SER H 79 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU H 81 " --> pdb=" O ILE H 372 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE H 374 " --> pdb=" O LEU H 81 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER H 83 " --> pdb=" O ILE H 374 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE H 80 " --> pdb=" O PHE H 429 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LEU H 431 " --> pdb=" O ILE H 80 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE H 82 " --> pdb=" O LEU H 431 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL H 433 " --> pdb=" O ILE H 82 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE H 84 " --> pdb=" O VAL H 433 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE H 430 " --> pdb=" O ILE H 524 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE H 526 " --> pdb=" O ILE H 430 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN H 432 " --> pdb=" O ILE H 526 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASP H 525 " --> pdb=" O LYS H 462 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 100 through 102 removed outlier: 6.821A pdb=" N HIS H 106 " --> pdb=" O ILE H 183 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 309 through 311 removed outlier: 4.446A pdb=" N ALA H 541 " --> pdb=" O PRO H 529 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ALA H 436 " --> pdb=" O GLN H 530 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 39 through 40 removed outlier: 6.707A pdb=" N SER I 79 " --> pdb=" O LEU I 370 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE I 372 " --> pdb=" O SER I 79 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU I 81 " --> pdb=" O ILE I 372 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE I 374 " --> pdb=" O LEU I 81 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER I 83 " --> pdb=" O ILE I 374 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE I 80 " --> pdb=" O PHE I 429 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU I 431 " --> pdb=" O ILE I 80 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE I 82 " --> pdb=" O LEU I 431 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL I 433 " --> pdb=" O ILE I 82 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE I 84 " --> pdb=" O VAL I 433 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE I 430 " --> pdb=" O ILE I 524 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ILE I 526 " --> pdb=" O ILE I 430 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN I 432 " --> pdb=" O ILE I 526 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASP I 525 " --> pdb=" O LYS I 462 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 110 through 113 removed outlier: 4.297A pdb=" N LEU I 92 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU I 300 " --> pdb=" O ILE I 94 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE I 295 " --> pdb=" O LYS I 135 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS I 135 " --> pdb=" O ILE I 295 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP I 297 " --> pdb=" O LEU I 133 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU I 126 " --> pdb=" O LYS I 149 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS I 149 " --> pdb=" O LEU I 126 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS I 139 " --> pdb=" O LYS I 136 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU I 140 " --> pdb=" O VAL J 567 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 100 through 102 removed outlier: 6.821A pdb=" N HIS I 106 " --> pdb=" O ILE I 183 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 309 through 311 removed outlier: 4.446A pdb=" N ALA I 541 " --> pdb=" O PRO I 529 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ALA I 436 " --> pdb=" O GLN I 530 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 566 through 567 removed outlier: 3.570A pdb=" N GLU K 142 " --> pdb=" O VAL I 567 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS K 139 " --> pdb=" O LYS K 136 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS K 149 " --> pdb=" O LEU K 126 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU K 126 " --> pdb=" O LYS K 149 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP K 297 " --> pdb=" O LEU K 133 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS K 135 " --> pdb=" O ILE K 295 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE K 295 " --> pdb=" O LYS K 135 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU K 300 " --> pdb=" O ILE K 94 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU K 92 " --> pdb=" O LEU K 302 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 39 through 40 removed outlier: 6.707A pdb=" N SER J 79 " --> pdb=" O LEU J 370 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE J 372 " --> pdb=" O SER J 79 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU J 81 " --> pdb=" O ILE J 372 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE J 374 " --> pdb=" O LEU J 81 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER J 83 " --> pdb=" O ILE J 374 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE J 80 " --> pdb=" O PHE J 429 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LEU J 431 " --> pdb=" O ILE J 80 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE J 82 " --> pdb=" O LEU J 431 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL J 433 " --> pdb=" O ILE J 82 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE J 84 " --> pdb=" O VAL J 433 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE J 430 " --> pdb=" O ILE J 524 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE J 526 " --> pdb=" O ILE J 430 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN J 432 " --> pdb=" O ILE J 526 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASP J 525 " --> pdb=" O LYS J 462 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 110 through 113 removed outlier: 4.297A pdb=" N LEU J 92 " --> pdb=" O LEU J 302 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LEU J 300 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE J 295 " --> pdb=" O LYS J 135 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS J 135 " --> pdb=" O ILE J 295 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP J 297 " --> pdb=" O LEU J 133 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU J 126 " --> pdb=" O LYS J 149 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS J 149 " --> pdb=" O LEU J 126 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS J 139 " --> pdb=" O LYS J 136 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU J 140 " --> pdb=" O VAL K 567 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 100 through 102 removed outlier: 6.820A pdb=" N HIS J 106 " --> pdb=" O ILE J 183 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 309 through 311 removed outlier: 4.447A pdb=" N ALA J 541 " --> pdb=" O PRO J 529 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ALA J 436 " --> pdb=" O GLN J 530 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 39 through 40 removed outlier: 6.707A pdb=" N SER K 79 " --> pdb=" O LEU K 370 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE K 372 " --> pdb=" O SER K 79 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU K 81 " --> pdb=" O ILE K 372 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE K 374 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER K 83 " --> pdb=" O ILE K 374 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE K 80 " --> pdb=" O PHE K 429 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU K 431 " --> pdb=" O ILE K 80 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE K 82 " --> pdb=" O LEU K 431 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL K 433 " --> pdb=" O ILE K 82 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE K 84 " --> pdb=" O VAL K 433 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE K 430 " --> pdb=" O ILE K 524 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE K 526 " --> pdb=" O ILE K 430 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASN K 432 " --> pdb=" O ILE K 526 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASP K 525 " --> pdb=" O LYS K 462 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 100 through 102 removed outlier: 6.820A pdb=" N HIS K 106 " --> pdb=" O ILE K 183 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 309 through 311 removed outlier: 4.447A pdb=" N ALA K 541 " --> pdb=" O PRO K 529 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ALA K 436 " --> pdb=" O GLN K 530 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 39 through 40 removed outlier: 6.707A pdb=" N SER L 79 " --> pdb=" O LEU L 370 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE L 372 " --> pdb=" O SER L 79 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU L 81 " --> pdb=" O ILE L 372 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE L 374 " --> pdb=" O LEU L 81 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER L 83 " --> pdb=" O ILE L 374 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE L 80 " --> pdb=" O PHE L 429 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU L 431 " --> pdb=" O ILE L 80 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE L 82 " --> pdb=" O LEU L 431 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL L 433 " --> pdb=" O ILE L 82 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE L 84 " --> pdb=" O VAL L 433 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE L 430 " --> pdb=" O ILE L 524 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE L 526 " --> pdb=" O ILE L 430 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN L 432 " --> pdb=" O ILE L 526 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASP L 525 " --> pdb=" O LYS L 462 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 110 through 113 removed outlier: 4.297A pdb=" N LEU L 92 " --> pdb=" O LEU L 302 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU L 300 " --> pdb=" O ILE L 94 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE L 295 " --> pdb=" O LYS L 135 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS L 135 " --> pdb=" O ILE L 295 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP L 297 " --> pdb=" O LEU L 133 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU L 126 " --> pdb=" O LYS L 149 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS L 149 " --> pdb=" O LEU L 126 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS L 139 " --> pdb=" O LYS L 136 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 100 through 102 removed outlier: 6.820A pdb=" N HIS L 106 " --> pdb=" O ILE L 183 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 309 through 311 removed outlier: 4.447A pdb=" N ALA L 541 " --> pdb=" O PRO L 529 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ALA L 436 " --> pdb=" O GLN L 530 " (cutoff:3.500A) 1900 hydrogen bonds defined for protein. 5304 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: 19.40 Time building geometry restraints manager: 18.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14926 1.34 - 1.46: 11228 1.46 - 1.59: 20838 1.59 - 1.71: 0 1.71 - 1.84: 336 Bond restraints: 47328 Sorted by residual: bond pdb=" N THR E 165 " pdb=" CA THR E 165 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.15e-02 7.56e+03 3.82e+00 bond pdb=" N THR K 165 " pdb=" CA THR K 165 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.15e-02 7.56e+03 3.68e+00 bond pdb=" N THR G 165 " pdb=" CA THR G 165 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.15e-02 7.56e+03 3.60e+00 bond pdb=" N THR I 165 " pdb=" CA THR I 165 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.15e-02 7.56e+03 3.57e+00 bond pdb=" N THR J 165 " pdb=" CA THR J 165 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.15e-02 7.56e+03 3.56e+00 ... (remaining 47323 not shown) Histogram of bond angle deviations from ideal: 98.06 - 105.30: 528 105.30 - 112.54: 24079 112.54 - 119.78: 16096 119.78 - 127.02: 22695 127.02 - 134.26: 490 Bond angle restraints: 63888 Sorted by residual: angle pdb=" C GLU F 319 " pdb=" N GLY F 320 " pdb=" CA GLY F 320 " ideal model delta sigma weight residual 121.41 113.54 7.87 1.96e+00 2.60e-01 1.61e+01 angle pdb=" C GLU L 319 " pdb=" N GLY L 320 " pdb=" CA GLY L 320 " ideal model delta sigma weight residual 121.41 113.54 7.87 1.96e+00 2.60e-01 1.61e+01 angle pdb=" C GLU E 319 " pdb=" N GLY E 320 " pdb=" CA GLY E 320 " ideal model delta sigma weight residual 121.41 113.54 7.87 1.96e+00 2.60e-01 1.61e+01 angle pdb=" C GLU J 319 " pdb=" N GLY J 320 " pdb=" CA GLY J 320 " ideal model delta sigma weight residual 121.41 113.55 7.86 1.96e+00 2.60e-01 1.61e+01 angle pdb=" C GLU H 319 " pdb=" N GLY H 320 " pdb=" CA GLY H 320 " ideal model delta sigma weight residual 121.41 113.56 7.85 1.96e+00 2.60e-01 1.60e+01 ... (remaining 63883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 24671 18.10 - 36.19: 2763 36.19 - 54.29: 562 54.29 - 72.39: 149 72.39 - 90.48: 91 Dihedral angle restraints: 28236 sinusoidal: 11436 harmonic: 16800 Sorted by residual: dihedral pdb=" CA GLU J 319 " pdb=" C GLU J 319 " pdb=" N GLY J 320 " pdb=" CA GLY J 320 " ideal model delta harmonic sigma weight residual 180.00 147.64 32.36 0 5.00e+00 4.00e-02 4.19e+01 dihedral pdb=" CA GLU E 319 " pdb=" C GLU E 319 " pdb=" N GLY E 320 " pdb=" CA GLY E 320 " ideal model delta harmonic sigma weight residual 180.00 147.64 32.36 0 5.00e+00 4.00e-02 4.19e+01 dihedral pdb=" CA GLU H 319 " pdb=" C GLU H 319 " pdb=" N GLY H 320 " pdb=" CA GLY H 320 " ideal model delta harmonic sigma weight residual 180.00 147.65 32.35 0 5.00e+00 4.00e-02 4.19e+01 ... (remaining 28233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4880 0.054 - 0.108: 1604 0.108 - 0.163: 440 0.163 - 0.217: 84 0.217 - 0.271: 12 Chirality restraints: 7020 Sorted by residual: chirality pdb=" CB VAL B 470 " pdb=" CA VAL B 470 " pdb=" CG1 VAL B 470 " pdb=" CG2 VAL B 470 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB VAL C 470 " pdb=" CA VAL C 470 " pdb=" CG1 VAL C 470 " pdb=" CG2 VAL C 470 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB VAL G 470 " pdb=" CA VAL G 470 " pdb=" CG1 VAL G 470 " pdb=" CG2 VAL G 470 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 7017 not shown) Planarity restraints: 8208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR I 278 " 0.043 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO I 279 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO I 279 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO I 279 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 278 " 0.043 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO F 279 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO F 279 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 279 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 278 " -0.043 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO E 279 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO E 279 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 279 " -0.036 5.00e-02 4.00e+02 ... (remaining 8205 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 1187 2.66 - 3.22: 41854 3.22 - 3.78: 77168 3.78 - 4.34: 112422 4.34 - 4.90: 184553 Nonbonded interactions: 417184 Sorted by model distance: nonbonded pdb=" OD1 ASP B 324 " pdb="ZN ZN B1000 " model vdw 2.103 2.230 nonbonded pdb=" OD1 ASP G 324 " pdb="ZN ZN G1000 " model vdw 2.103 2.230 nonbonded pdb=" OD1 ASP K 324 " pdb="ZN ZN K1000 " model vdw 2.103 2.230 nonbonded pdb=" OD1 ASP H 324 " pdb="ZN ZN H1000 " model vdw 2.103 2.230 nonbonded pdb=" OD1 ASP A 324 " pdb="ZN ZN A1000 " model vdw 2.104 2.230 ... (remaining 417179 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.500 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: 0.040 Extract box with map and model: 9.400 Check model and map are aligned: 0.670 Set scattering table: 0.380 Process input model: 123.500 Find NCS groups from input model: 2.710 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 47328 Z= 0.491 Angle : 0.992 9.036 63888 Z= 0.565 Chirality : 0.058 0.271 7020 Planarity : 0.006 0.064 8208 Dihedral : 16.571 90.485 17376 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.87 % Favored : 94.92 % Rotamer: Outliers : 1.84 % Allowed : 9.79 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.08), residues: 5664 helix: -4.09 (0.05), residues: 1836 sheet: -1.33 (0.15), residues: 1056 loop : -2.28 (0.09), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP L 47 HIS 0.008 0.002 HIS K 543 PHE 0.031 0.003 PHE B 188 TYR 0.025 0.003 TYR J 167 ARG 0.004 0.001 ARG D 164 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1121 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 1025 time to evaluate : 4.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ASP cc_start: 0.6980 (OUTLIER) cc_final: 0.6768 (m-30) REVERT: A 19 SER cc_start: 0.8677 (t) cc_final: 0.8335 (t) REVERT: A 338 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7507 (mt-10) REVERT: A 408 LYS cc_start: 0.7350 (ptmm) cc_final: 0.6173 (ptmt) REVERT: A 535 SER cc_start: 0.8706 (OUTLIER) cc_final: 0.8133 (p) REVERT: B 338 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7111 (mt-10) REVERT: C 2 ASP cc_start: 0.7091 (OUTLIER) cc_final: 0.6829 (t70) REVERT: C 135 LYS cc_start: 0.8118 (mtmt) cc_final: 0.7844 (mtpt) REVERT: C 439 SER cc_start: 0.8457 (t) cc_final: 0.8063 (m) REVERT: D 2 ASP cc_start: 0.6596 (OUTLIER) cc_final: 0.6378 (t70) REVERT: D 19 SER cc_start: 0.8639 (t) cc_final: 0.8425 (t) REVERT: D 102 LYS cc_start: 0.8571 (mtmt) cc_final: 0.8304 (mtmm) REVERT: D 338 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6822 (mt-10) REVERT: D 386 GLU cc_start: 0.7504 (pm20) cc_final: 0.7262 (pm20) REVERT: D 427 ARG cc_start: 0.8624 (mpp80) cc_final: 0.8368 (mpp-170) REVERT: D 435 MET cc_start: 0.8391 (mmm) cc_final: 0.8085 (mmm) REVERT: E 2 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6876 (t70) REVERT: E 19 SER cc_start: 0.8725 (t) cc_final: 0.8396 (t) REVERT: E 386 GLU cc_start: 0.7397 (pm20) cc_final: 0.7116 (pm20) REVERT: E 425 VAL cc_start: 0.8938 (OUTLIER) cc_final: 0.8628 (t) REVERT: F 60 GLU cc_start: 0.7955 (pt0) cc_final: 0.7744 (pt0) REVERT: F 172 LYS cc_start: 0.6942 (mmtm) cc_final: 0.6495 (tptp) REVERT: F 481 ARG cc_start: 0.8197 (mmm-85) cc_final: 0.7944 (mmm-85) REVERT: G 60 GLU cc_start: 0.7979 (pt0) cc_final: 0.7573 (pt0) REVERT: G 98 ASN cc_start: 0.7574 (p0) cc_final: 0.7145 (p0) REVERT: G 338 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7454 (mt-10) REVERT: H 19 SER cc_start: 0.8728 (t) cc_final: 0.8372 (t) REVERT: H 102 LYS cc_start: 0.8463 (mtmt) cc_final: 0.8226 (mtmt) REVERT: H 172 LYS cc_start: 0.7304 (mmtm) cc_final: 0.6802 (tptp) REVERT: H 426 ASN cc_start: 0.8426 (t0) cc_final: 0.8162 (t0) REVERT: H 428 SER cc_start: 0.8211 (OUTLIER) cc_final: 0.7921 (t) REVERT: H 521 MET cc_start: 0.8768 (mtt) cc_final: 0.8504 (mtt) REVERT: I 338 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6974 (mt-10) REVERT: I 428 SER cc_start: 0.8660 (OUTLIER) cc_final: 0.8372 (t) REVERT: J 19 SER cc_start: 0.8721 (t) cc_final: 0.8356 (t) REVERT: J 338 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6537 (mt-10) REVERT: K 408 LYS cc_start: 0.7319 (ptmm) cc_final: 0.6386 (ptmm) REVERT: K 428 SER cc_start: 0.8289 (OUTLIER) cc_final: 0.7531 (t) REVERT: K 500 MET cc_start: 0.8583 (ttp) cc_final: 0.8312 (ttp) REVERT: L 19 SER cc_start: 0.8730 (t) cc_final: 0.8382 (t) REVERT: L 172 LYS cc_start: 0.7264 (mmtm) cc_final: 0.6824 (tptp) REVERT: L 289 ASN cc_start: 0.7171 (t0) cc_final: 0.6953 (t0) REVERT: L 428 SER cc_start: 0.8150 (OUTLIER) cc_final: 0.7843 (t) REVERT: L 439 SER cc_start: 0.8660 (t) cc_final: 0.8312 (m) REVERT: L 535 SER cc_start: 0.8875 (OUTLIER) cc_final: 0.8662 (p) outliers start: 96 outliers final: 14 residues processed: 1090 average time/residue: 0.6830 time to fit residues: 1187.4690 Evaluate side-chains 637 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 612 time to evaluate : 5.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 535 SER Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain D residue 2 ASP Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 412 GLU Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 535 SER Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain G residue 412 GLU Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain H residue 428 SER Chi-restraints excluded: chain H residue 542 VAL Chi-restraints excluded: chain I residue 428 SER Chi-restraints excluded: chain J residue 535 SER Chi-restraints excluded: chain K residue 428 SER Chi-restraints excluded: chain L residue 428 SER Chi-restraints excluded: chain L residue 535 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 476 optimal weight: 0.9990 chunk 427 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 288 optimal weight: 0.9990 chunk 228 optimal weight: 1.9990 chunk 442 optimal weight: 10.0000 chunk 171 optimal weight: 0.7980 chunk 268 optimal weight: 2.9990 chunk 329 optimal weight: 0.7980 chunk 512 optimal weight: 0.0870 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 36 ASN A 119 HIS ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 ASN A 411 HIS A 432 ASN A 437 HIS A 498 ASN A 518 ASN B 36 ASN B 119 HIS ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 ASN B 426 ASN ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 ASN B 518 ASN C 22 ASN C 35 ASN C 119 HIS ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 ASN ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 ASN C 498 ASN C 518 ASN D 36 ASN D 72 ASN D 119 HIS D 276 ASN D 289 ASN ** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN D 426 ASN D 432 ASN D 498 ASN D 518 ASN E 35 ASN E 36 ASN E 119 HIS ** E 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 ASN E 498 ASN E 518 ASN E 543 HIS F 10 GLN F 35 ASN F 119 HIS F 131 GLN F 160 HIS ** F 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 363 ASN F 414 ASN F 498 ASN F 518 ASN G 28 ASN G 35 ASN G 36 ASN G 119 HIS G 131 GLN G 276 ASN G 363 ASN G 426 ASN G 498 ASN ** G 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 560 ASN H 10 GLN H 119 HIS H 276 ASN ** H 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 363 ASN H 432 ASN ** H 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 498 ASN H 518 ASN H 560 ASN I 28 ASN I 36 ASN I 119 HIS I 131 GLN I 276 ASN ** I 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 363 ASN I 411 HIS I 498 ASN I 518 ASN J 36 ASN J 72 ASN J 119 HIS ** J 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 363 ASN ** J 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 498 ASN J 518 ASN J 560 ASN K 35 ASN K 119 HIS ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 363 ASN K 396 ASN K 426 ASN ** K 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 498 ASN K 518 ASN L 22 ASN L 35 ASN L 36 ASN L 119 HIS L 131 GLN ** L 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 363 ASN L 396 ASN L 414 ASN L 437 HIS ** L 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 498 ASN L 518 ASN ** L 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 543 HIS L 560 ASN Total number of N/Q/H flips: 103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 47328 Z= 0.185 Angle : 0.588 6.794 63888 Z= 0.323 Chirality : 0.045 0.178 7020 Planarity : 0.004 0.048 8208 Dihedral : 6.122 59.781 6165 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.04 % Allowed : 13.27 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.09), residues: 5664 helix: -1.87 (0.09), residues: 1956 sheet: -1.15 (0.15), residues: 1164 loop : -1.83 (0.10), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 118 HIS 0.005 0.001 HIS D 475 PHE 0.017 0.001 PHE K 330 TYR 0.019 0.001 TYR F 167 ARG 0.006 0.000 ARG L 6 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 745 time to evaluate : 4.225 Fit side-chains revert: symmetry clash REVERT: A 2 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.7127 (t70) REVERT: A 395 LYS cc_start: 0.8553 (tptp) cc_final: 0.8347 (tptp) REVERT: B 19 SER cc_start: 0.8607 (t) cc_final: 0.8349 (t) REVERT: C 72 ASN cc_start: 0.7377 (OUTLIER) cc_final: 0.7096 (p0) REVERT: C 135 LYS cc_start: 0.8392 (mtmt) cc_final: 0.7853 (mtpt) REVERT: C 439 SER cc_start: 0.8428 (t) cc_final: 0.7943 (m) REVERT: C 457 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7322 (mt-10) REVERT: D 386 GLU cc_start: 0.7677 (pm20) cc_final: 0.7354 (pm20) REVERT: D 446 THR cc_start: 0.8874 (p) cc_final: 0.8665 (p) REVERT: E 2 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7178 (t70) REVERT: E 19 SER cc_start: 0.8741 (t) cc_final: 0.8507 (t) REVERT: E 386 GLU cc_start: 0.7555 (pm20) cc_final: 0.7198 (pm20) REVERT: E 535 SER cc_start: 0.8421 (OUTLIER) cc_final: 0.8214 (t) REVERT: F 286 LYS cc_start: 0.7985 (tppt) cc_final: 0.7668 (tptp) REVERT: G 338 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7429 (mt-10) REVERT: G 514 MET cc_start: 0.8262 (mtm) cc_final: 0.7909 (mtt) REVERT: H 19 SER cc_start: 0.8735 (t) cc_final: 0.8466 (t) REVERT: H 55 TYR cc_start: 0.8785 (m-80) cc_final: 0.8375 (m-80) REVERT: H 102 LYS cc_start: 0.8670 (mtmt) cc_final: 0.8447 (mtmt) REVERT: H 131 GLN cc_start: 0.8059 (tt0) cc_final: 0.7850 (tt0) REVERT: H 457 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7135 (mt-10) REVERT: H 530 GLN cc_start: 0.8656 (pt0) cc_final: 0.8423 (pt0) REVERT: I 172 LYS cc_start: 0.7224 (mmtm) cc_final: 0.6980 (tptp) REVERT: I 338 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7065 (mt-10) REVERT: I 428 SER cc_start: 0.8704 (t) cc_final: 0.8271 (t) REVERT: J 19 SER cc_start: 0.8696 (t) cc_final: 0.8478 (t) REVERT: J 280 LEU cc_start: 0.9003 (tp) cc_final: 0.8773 (tp) REVERT: J 390 ARG cc_start: 0.7477 (mtt180) cc_final: 0.7216 (mtt180) REVERT: J 435 MET cc_start: 0.8418 (mmm) cc_final: 0.7949 (mmm) REVERT: K 428 SER cc_start: 0.8267 (t) cc_final: 0.7907 (t) REVERT: K 500 MET cc_start: 0.8532 (ttp) cc_final: 0.8226 (ttp) REVERT: L 439 SER cc_start: 0.8700 (t) cc_final: 0.8345 (m) outliers start: 106 outliers final: 29 residues processed: 820 average time/residue: 0.6210 time to fit residues: 830.7898 Evaluate side-chains 590 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 557 time to evaluate : 5.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 535 SER Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 535 SER Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 135 LYS Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 567 VAL Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 276 ASN Chi-restraints excluded: chain G residue 363 ASN Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain H residue 72 ASN Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain I residue 381 ILE Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 73 PHE Chi-restraints excluded: chain L residue 72 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 284 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 chunk 426 optimal weight: 0.9980 chunk 348 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 513 optimal weight: 2.9990 chunk 554 optimal weight: 1.9990 chunk 456 optimal weight: 4.9990 chunk 508 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 411 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 HIS A 414 ASN B 22 ASN B 119 HIS ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 ASN B 437 HIS C 36 ASN ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 ASN C 426 ASN C 432 ASN C 437 HIS D 28 ASN D 72 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 HIS E 174 ASN ** E 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 432 ASN F 36 ASN F 174 ASN ** F 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 426 ASN F 432 ASN ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 432 ASN ** G 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 518 ASN H 36 ASN H 74 ASN ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 174 ASN H 396 ASN H 432 ASN H 437 HIS ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 432 ASN I 437 HIS J 35 ASN J 72 ASN ** J 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 432 ASN ** J 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 ASN K 190 GLN ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 426 ASN K 432 ASN K 437 HIS L 22 ASN L 72 ASN ** L 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 289 ASN L 432 ASN ** L 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 47328 Z= 0.289 Angle : 0.614 11.352 63888 Z= 0.331 Chirality : 0.047 0.185 7020 Planarity : 0.004 0.044 8208 Dihedral : 5.520 57.794 6141 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.88 % Allowed : 15.99 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.10), residues: 5664 helix: -0.54 (0.10), residues: 1992 sheet: -1.00 (0.15), residues: 1104 loop : -1.63 (0.10), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 118 HIS 0.005 0.001 HIS J 543 PHE 0.015 0.001 PHE A 330 TYR 0.020 0.002 TYR G 278 ARG 0.004 0.000 ARG L 6 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 621 time to evaluate : 5.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 SER cc_start: 0.8731 (t) cc_final: 0.8460 (t) REVERT: C 135 LYS cc_start: 0.8602 (mtmt) cc_final: 0.8217 (mtpt) REVERT: C 435 MET cc_start: 0.8805 (mmm) cc_final: 0.8007 (mmm) REVERT: C 439 SER cc_start: 0.8684 (t) cc_final: 0.8169 (m) REVERT: D 386 GLU cc_start: 0.7807 (pm20) cc_final: 0.7030 (pm20) REVERT: E 19 SER cc_start: 0.8862 (t) cc_final: 0.8605 (t) REVERT: E 172 LYS cc_start: 0.7427 (mmtm) cc_final: 0.6790 (tptp) REVERT: E 457 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7298 (mt-10) REVERT: F 32 ARG cc_start: 0.7384 (ttm-80) cc_final: 0.6989 (ttm-80) REVERT: F 286 LYS cc_start: 0.8263 (tppt) cc_final: 0.7944 (tptp) REVERT: F 425 VAL cc_start: 0.9256 (OUTLIER) cc_final: 0.8988 (t) REVERT: F 481 ARG cc_start: 0.8226 (mmm-85) cc_final: 0.7966 (mmm160) REVERT: G 32 ARG cc_start: 0.7349 (ttm-80) cc_final: 0.7135 (ttm-80) REVERT: H 19 SER cc_start: 0.8822 (t) cc_final: 0.8548 (t) REVERT: H 435 MET cc_start: 0.8565 (mmm) cc_final: 0.8118 (mmm) REVERT: H 457 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7222 (mt-10) REVERT: I 303 MET cc_start: 0.8890 (ptm) cc_final: 0.8633 (ptt) REVERT: J 19 SER cc_start: 0.8805 (t) cc_final: 0.8567 (t) REVERT: J 280 LEU cc_start: 0.9142 (tp) cc_final: 0.8913 (tp) REVERT: J 390 ARG cc_start: 0.7505 (mtt180) cc_final: 0.7252 (mtt180) REVERT: K 428 SER cc_start: 0.8336 (t) cc_final: 0.8046 (t) REVERT: K 500 MET cc_start: 0.8651 (ttp) cc_final: 0.8444 (ttp) REVERT: L 439 SER cc_start: 0.8841 (t) cc_final: 0.8457 (m) outliers start: 98 outliers final: 56 residues processed: 688 average time/residue: 0.6177 time to fit residues: 689.7735 Evaluate side-chains 596 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 539 time to evaluate : 5.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 567 VAL Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain H residue 391 SER Chi-restraints excluded: chain H residue 425 VAL Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 89 SER Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 293 GLU Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 524 ILE Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 58 CYS Chi-restraints excluded: chain K residue 73 PHE Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 391 SER Chi-restraints excluded: chain K residue 525 ASP Chi-restraints excluded: chain K residue 538 GLU Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 293 GLU Chi-restraints excluded: chain L residue 383 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 506 optimal weight: 3.9990 chunk 385 optimal weight: 3.9990 chunk 266 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 344 optimal weight: 0.6980 chunk 514 optimal weight: 1.9990 chunk 545 optimal weight: 3.9990 chunk 269 optimal weight: 4.9990 chunk 488 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN B 119 HIS ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 HIS ** B 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN C 131 GLN ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 ASN D 72 ASN D 131 GLN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 ASN ** E 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 HIS E 568 HIS ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 ASN ** F 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN ** I 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 426 ASN J 72 ASN ** J 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 432 ASN ** J 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 47328 Z= 0.340 Angle : 0.622 8.030 63888 Z= 0.333 Chirality : 0.047 0.180 7020 Planarity : 0.004 0.047 8208 Dihedral : 5.527 57.366 6139 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.71 % Allowed : 17.28 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.10), residues: 5664 helix: -0.02 (0.11), residues: 1992 sheet: -1.27 (0.15), residues: 1164 loop : -1.36 (0.11), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.005 0.001 HIS L 367 PHE 0.030 0.001 PHE L 73 TYR 0.019 0.002 TYR G 278 ARG 0.005 0.000 ARG F 390 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 580 time to evaluate : 4.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 LYS cc_start: 0.8608 (tptp) cc_final: 0.8403 (tptp) REVERT: B 19 SER cc_start: 0.8684 (t) cc_final: 0.8446 (t) REVERT: C 435 MET cc_start: 0.8844 (mmm) cc_final: 0.8031 (mmm) REVERT: C 439 SER cc_start: 0.8670 (t) cc_final: 0.8135 (m) REVERT: E 19 SER cc_start: 0.8803 (t) cc_final: 0.8559 (t) REVERT: E 172 LYS cc_start: 0.7510 (mmtm) cc_final: 0.6945 (tptp) REVERT: E 390 ARG cc_start: 0.7592 (mtt180) cc_final: 0.7231 (mtt180) REVERT: E 457 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7308 (mt-10) REVERT: F 286 LYS cc_start: 0.8264 (tppt) cc_final: 0.7991 (tptp) REVERT: F 425 VAL cc_start: 0.9276 (OUTLIER) cc_final: 0.9051 (t) REVERT: F 457 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7393 (mt-10) REVERT: F 481 ARG cc_start: 0.8245 (mmm-85) cc_final: 0.7985 (mmm160) REVERT: H 19 SER cc_start: 0.8871 (t) cc_final: 0.8643 (t) REVERT: H 338 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7543 (mt-10) REVERT: H 435 MET cc_start: 0.8766 (mmm) cc_final: 0.8056 (mmm) REVERT: H 457 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7255 (mt-10) REVERT: I 73 PHE cc_start: 0.5885 (OUTLIER) cc_final: 0.5369 (m-80) REVERT: I 303 MET cc_start: 0.8859 (ptm) cc_final: 0.8541 (ptt) REVERT: J 280 LEU cc_start: 0.9141 (tp) cc_final: 0.8928 (tp) REVERT: J 390 ARG cc_start: 0.7540 (mtt180) cc_final: 0.7277 (mtt180) REVERT: K 172 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.7110 (tptt) REVERT: L 172 LYS cc_start: 0.7155 (tppt) cc_final: 0.6685 (tptp) REVERT: L 439 SER cc_start: 0.8916 (t) cc_final: 0.8521 (m) outliers start: 141 outliers final: 90 residues processed: 680 average time/residue: 0.5957 time to fit residues: 659.8884 Evaluate side-chains 613 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 520 time to evaluate : 5.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 409 GLU Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 525 ASP Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 391 SER Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 501 VAL Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 567 VAL Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 524 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain H residue 381 ILE Chi-restraints excluded: chain H residue 391 SER Chi-restraints excluded: chain H residue 409 GLU Chi-restraints excluded: chain H residue 425 VAL Chi-restraints excluded: chain H residue 428 SER Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 409 GLU Chi-restraints excluded: chain I residue 525 ASP Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain I residue 567 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 73 PHE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 293 GLU Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 409 GLU Chi-restraints excluded: chain J residue 524 ILE Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 73 PHE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 172 LYS Chi-restraints excluded: chain K residue 293 GLU Chi-restraints excluded: chain K residue 381 ILE Chi-restraints excluded: chain K residue 391 SER Chi-restraints excluded: chain K residue 409 GLU Chi-restraints excluded: chain K residue 525 ASP Chi-restraints excluded: chain K residue 538 GLU Chi-restraints excluded: chain L residue 73 PHE Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 293 GLU Chi-restraints excluded: chain L residue 383 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 454 optimal weight: 0.7980 chunk 309 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 405 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 465 optimal weight: 3.9990 chunk 376 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 278 optimal weight: 5.9990 chunk 489 optimal weight: 0.0980 chunk 137 optimal weight: 0.8980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 HIS ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN ** B 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 HIS D 72 ASN D 74 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN ** E 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 ASN E 568 HIS F 119 HIS F 192 ASN ** F 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 568 HIS ** G 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 GLN ** I 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 568 HIS J 28 ASN J 72 ASN ** J 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 568 HIS K 22 ASN ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 74 ASN ** L 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 47328 Z= 0.343 Angle : 0.625 11.668 63888 Z= 0.335 Chirality : 0.047 0.178 7020 Planarity : 0.004 0.046 8208 Dihedral : 5.508 50.262 6139 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.42 % Allowed : 17.51 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.10), residues: 5664 helix: 0.20 (0.11), residues: 2016 sheet: -1.19 (0.16), residues: 1080 loop : -1.41 (0.11), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.004 0.001 HIS J 456 PHE 0.016 0.001 PHE D 73 TYR 0.019 0.001 TYR I 278 ARG 0.011 0.000 ARG F 390 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 559 time to evaluate : 5.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7860 (mttm) REVERT: A 395 LYS cc_start: 0.8609 (tptp) cc_final: 0.8394 (tptp) REVERT: B 14 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7812 (mttp) REVERT: B 19 SER cc_start: 0.8681 (t) cc_final: 0.8458 (t) REVERT: B 136 LYS cc_start: 0.8380 (ttpp) cc_final: 0.8154 (ptmm) REVERT: C 73 PHE cc_start: 0.6111 (OUTLIER) cc_final: 0.5657 (m-80) REVERT: C 136 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7953 (ptmt) REVERT: C 435 MET cc_start: 0.8837 (mmm) cc_final: 0.8024 (mmm) REVERT: C 439 SER cc_start: 0.8659 (t) cc_final: 0.8152 (m) REVERT: D 390 ARG cc_start: 0.7434 (mtt180) cc_final: 0.7187 (mtt180) REVERT: E 14 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7981 (mttp) REVERT: E 19 SER cc_start: 0.8878 (t) cc_final: 0.8663 (t) REVERT: E 172 LYS cc_start: 0.7652 (mmtm) cc_final: 0.7235 (tptp) REVERT: E 390 ARG cc_start: 0.7555 (mtt180) cc_final: 0.7325 (mtt180) REVERT: E 457 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7308 (mt-10) REVERT: E 521 MET cc_start: 0.8673 (mtp) cc_final: 0.8409 (mtp) REVERT: F 286 LYS cc_start: 0.8318 (tppt) cc_final: 0.8063 (tptp) REVERT: F 425 VAL cc_start: 0.9277 (OUTLIER) cc_final: 0.9065 (t) REVERT: F 457 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7445 (mt-10) REVERT: F 481 ARG cc_start: 0.8171 (mmm-85) cc_final: 0.7898 (mmm160) REVERT: G 133 LEU cc_start: 0.8602 (tt) cc_final: 0.8357 (mp) REVERT: H 24 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8831 (mp) REVERT: H 435 MET cc_start: 0.8789 (mmm) cc_final: 0.8080 (mmm) REVERT: H 457 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7328 (mt-10) REVERT: I 73 PHE cc_start: 0.6039 (OUTLIER) cc_final: 0.5425 (m-80) REVERT: I 303 MET cc_start: 0.8902 (ptm) cc_final: 0.8568 (ptt) REVERT: J 280 LEU cc_start: 0.9153 (tp) cc_final: 0.8950 (tp) REVERT: J 390 ARG cc_start: 0.7526 (mtt180) cc_final: 0.7288 (mtt180) REVERT: K 481 ARG cc_start: 0.8227 (mmm-85) cc_final: 0.8027 (mmm-85) REVERT: L 14 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8095 (mttp) REVERT: L 17 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7715 (pp30) REVERT: L 172 LYS cc_start: 0.7249 (tppt) cc_final: 0.6831 (tptp) REVERT: L 439 SER cc_start: 0.8920 (t) cc_final: 0.8525 (m) outliers start: 178 outliers final: 110 residues processed: 691 average time/residue: 0.6038 time to fit residues: 679.4323 Evaluate side-chains 638 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 518 time to evaluate : 5.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 525 ASP Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 58 CYS Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 391 SER Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 501 VAL Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 528 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 524 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain H residue 391 SER Chi-restraints excluded: chain H residue 409 GLU Chi-restraints excluded: chain H residue 428 SER Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain H residue 567 VAL Chi-restraints excluded: chain I residue 58 CYS Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 409 GLU Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 73 PHE Chi-restraints excluded: chain J residue 89 SER Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 293 GLU Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 524 ILE Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 58 CYS Chi-restraints excluded: chain K residue 73 PHE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 293 GLU Chi-restraints excluded: chain K residue 381 ILE Chi-restraints excluded: chain K residue 391 SER Chi-restraints excluded: chain K residue 409 GLU Chi-restraints excluded: chain K residue 525 ASP Chi-restraints excluded: chain K residue 538 GLU Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 17 GLN Chi-restraints excluded: chain L residue 73 PHE Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 293 GLU Chi-restraints excluded: chain L residue 383 SER Chi-restraints excluded: chain L residue 524 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 183 optimal weight: 0.6980 chunk 490 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 320 optimal weight: 8.9990 chunk 134 optimal weight: 0.9990 chunk 545 optimal weight: 0.8980 chunk 452 optimal weight: 4.9990 chunk 252 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 180 optimal weight: 0.7980 chunk 286 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 ASN A 568 HIS ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 HIS ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN ** E 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 HIS ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 568 HIS G 28 ASN G 426 ASN ** G 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 ASN ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 568 HIS ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 432 ASN L 466 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 47328 Z= 0.197 Angle : 0.556 10.531 63888 Z= 0.299 Chirality : 0.045 0.184 7020 Planarity : 0.003 0.057 8208 Dihedral : 5.228 36.461 6136 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.63 % Allowed : 18.22 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.11), residues: 5664 helix: 0.60 (0.11), residues: 2016 sheet: -0.99 (0.16), residues: 1056 loop : -1.37 (0.11), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 47 HIS 0.003 0.001 HIS G 475 PHE 0.016 0.001 PHE A 73 TYR 0.016 0.001 TYR E 278 ARG 0.013 0.000 ARG F 390 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 583 time to evaluate : 5.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 LYS cc_start: 0.8541 (tptp) cc_final: 0.8240 (tptp) REVERT: A 448 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7490 (tm-30) REVERT: B 17 GLN cc_start: 0.7326 (tm-30) cc_final: 0.7089 (pt0) REVERT: C 14 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8072 (mttt) REVERT: C 73 PHE cc_start: 0.6024 (OUTLIER) cc_final: 0.5644 (m-80) REVERT: C 136 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7776 (ptmt) REVERT: C 435 MET cc_start: 0.8807 (mmm) cc_final: 0.8061 (mmm) REVERT: C 439 SER cc_start: 0.8666 (t) cc_final: 0.8159 (m) REVERT: D 14 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7985 (mttm) REVERT: D 390 ARG cc_start: 0.7319 (mtt180) cc_final: 0.7075 (mtt180) REVERT: E 14 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7908 (mttp) REVERT: E 457 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7147 (mt-10) REVERT: F 286 LYS cc_start: 0.8175 (tppt) cc_final: 0.7914 (tptp) REVERT: F 457 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7452 (mt-10) REVERT: F 481 ARG cc_start: 0.8137 (mmm-85) cc_final: 0.7854 (mmm160) REVERT: G 133 LEU cc_start: 0.8570 (tt) cc_final: 0.8363 (mp) REVERT: G 339 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7655 (tp) REVERT: H 435 MET cc_start: 0.8658 (mmm) cc_final: 0.8006 (mmm) REVERT: H 439 SER cc_start: 0.8968 (t) cc_final: 0.8667 (p) REVERT: H 457 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7323 (mt-10) REVERT: I 73 PHE cc_start: 0.5720 (OUTLIER) cc_final: 0.5192 (m-80) REVERT: I 303 MET cc_start: 0.8916 (ptm) cc_final: 0.8611 (ptt) REVERT: J 14 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7784 (mttm) REVERT: J 185 THR cc_start: 0.9284 (p) cc_final: 0.9059 (t) REVERT: J 280 LEU cc_start: 0.9126 (tp) cc_final: 0.8869 (tp) REVERT: J 297 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7627 (t0) REVERT: K 172 LYS cc_start: 0.7379 (tppt) cc_final: 0.7092 (tptt) REVERT: L 172 LYS cc_start: 0.7176 (tppt) cc_final: 0.6780 (tptp) REVERT: L 190 GLN cc_start: 0.7649 (mm-40) cc_final: 0.7374 (mm-40) REVERT: L 439 SER cc_start: 0.8861 (t) cc_final: 0.8509 (m) outliers start: 137 outliers final: 76 residues processed: 695 average time/residue: 0.5964 time to fit residues: 679.7275 Evaluate side-chains 616 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 530 time to evaluate : 4.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 58 CYS Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 501 VAL Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 528 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 524 ILE Chi-restraints excluded: chain H residue 58 CYS Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 394 THR Chi-restraints excluded: chain H residue 409 GLU Chi-restraints excluded: chain H residue 425 VAL Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain I residue 58 CYS Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 409 GLU Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 73 PHE Chi-restraints excluded: chain J residue 89 SER Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 297 ASP Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 524 ILE Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 58 CYS Chi-restraints excluded: chain K residue 73 PHE Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 381 ILE Chi-restraints excluded: chain K residue 409 GLU Chi-restraints excluded: chain K residue 525 ASP Chi-restraints excluded: chain L residue 58 CYS Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 339 LEU Chi-restraints excluded: chain L residue 383 SER Chi-restraints excluded: chain L residue 524 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 526 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 310 optimal weight: 2.9990 chunk 398 optimal weight: 0.9980 chunk 308 optimal weight: 3.9990 chunk 459 optimal weight: 0.8980 chunk 304 optimal weight: 2.9990 chunk 543 optimal weight: 4.9990 chunk 340 optimal weight: 0.5980 chunk 331 optimal weight: 0.7980 chunk 250 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 ASN A 432 ASN A 568 HIS B 28 ASN ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 HIS C 61 ASN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 HIS ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN E 74 ASN ** E 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 HIS F 28 ASN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 HIS ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 131 GLN ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 414 ASN ** L 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 47328 Z= 0.198 Angle : 0.554 10.234 63888 Z= 0.297 Chirality : 0.045 0.170 7020 Planarity : 0.003 0.065 8208 Dihedral : 5.110 38.082 6134 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.38 % Allowed : 18.78 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.11), residues: 5664 helix: 0.84 (0.12), residues: 2016 sheet: -0.95 (0.16), residues: 1056 loop : -1.28 (0.11), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 47 HIS 0.003 0.001 HIS D 475 PHE 0.015 0.001 PHE D 73 TYR 0.015 0.001 TYR I 278 ARG 0.013 0.000 ARG F 390 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 553 time to evaluate : 5.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7858 (mttm) REVERT: A 136 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8000 (ptpt) REVERT: A 448 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7491 (tm-30) REVERT: B 395 LYS cc_start: 0.8436 (tptp) cc_final: 0.8197 (tptp) REVERT: C 14 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8094 (mttt) REVERT: C 131 GLN cc_start: 0.8300 (tt0) cc_final: 0.7699 (tt0) REVERT: C 435 MET cc_start: 0.8793 (mmm) cc_final: 0.8059 (mmm) REVERT: C 439 SER cc_start: 0.8711 (t) cc_final: 0.8272 (m) REVERT: D 14 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.8032 (mttm) REVERT: D 390 ARG cc_start: 0.7340 (mtt180) cc_final: 0.7065 (mtt180) REVERT: E 457 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7147 (mt-10) REVERT: F 286 LYS cc_start: 0.8159 (tppt) cc_final: 0.7918 (tptp) REVERT: F 425 VAL cc_start: 0.9224 (OUTLIER) cc_final: 0.9010 (t) REVERT: F 457 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7474 (mt-10) REVERT: F 481 ARG cc_start: 0.8177 (mmm-85) cc_final: 0.7883 (mmm160) REVERT: H 24 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8898 (mt) REVERT: H 435 MET cc_start: 0.8650 (mmm) cc_final: 0.7984 (mmm) REVERT: H 439 SER cc_start: 0.8958 (t) cc_final: 0.8668 (p) REVERT: H 457 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7310 (mt-10) REVERT: I 73 PHE cc_start: 0.5528 (OUTLIER) cc_final: 0.5008 (m-80) REVERT: I 303 MET cc_start: 0.8899 (ptm) cc_final: 0.8584 (ptt) REVERT: J 14 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7686 (mttm) REVERT: J 185 THR cc_start: 0.9293 (p) cc_final: 0.9068 (t) REVERT: J 280 LEU cc_start: 0.9134 (tp) cc_final: 0.8879 (tp) REVERT: J 297 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7670 (t0) REVERT: J 390 ARG cc_start: 0.7479 (mtt180) cc_final: 0.7143 (mtt180) REVERT: K 131 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7688 (tt0) REVERT: K 142 GLU cc_start: 0.6276 (tp30) cc_final: 0.5827 (tp30) REVERT: L 172 LYS cc_start: 0.7148 (tppt) cc_final: 0.6809 (tptp) REVERT: L 439 SER cc_start: 0.8871 (t) cc_final: 0.8537 (m) outliers start: 124 outliers final: 87 residues processed: 655 average time/residue: 0.6180 time to fit residues: 659.7489 Evaluate side-chains 631 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 533 time to evaluate : 5.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 58 CYS Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 501 VAL Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 528 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 524 ILE Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 58 CYS Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 409 GLU Chi-restraints excluded: chain H residue 425 VAL Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 524 ILE Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain I residue 58 CYS Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 387 VAL Chi-restraints excluded: chain I residue 409 GLU Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 73 PHE Chi-restraints excluded: chain J residue 89 SER Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 297 ASP Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 425 VAL Chi-restraints excluded: chain J residue 524 ILE Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 58 CYS Chi-restraints excluded: chain K residue 73 PHE Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 131 GLN Chi-restraints excluded: chain K residue 172 LYS Chi-restraints excluded: chain K residue 293 GLU Chi-restraints excluded: chain K residue 381 ILE Chi-restraints excluded: chain K residue 409 GLU Chi-restraints excluded: chain K residue 538 GLU Chi-restraints excluded: chain L residue 58 CYS Chi-restraints excluded: chain L residue 73 PHE Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 293 GLU Chi-restraints excluded: chain L residue 339 LEU Chi-restraints excluded: chain L residue 383 SER Chi-restraints excluded: chain L residue 524 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 336 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 324 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 345 optimal weight: 0.9980 chunk 370 optimal weight: 9.9990 chunk 268 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 427 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 HIS C 131 GLN ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 HIS ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 432 ASN ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 568 HIS G 131 GLN ** G 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 432 ASN I 568 HIS ** J 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 426 ASN ** J 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 568 HIS ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 47328 Z= 0.348 Angle : 0.627 13.376 63888 Z= 0.334 Chirality : 0.048 0.188 7020 Planarity : 0.004 0.064 8208 Dihedral : 5.313 39.820 6134 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.50 % Allowed : 18.80 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.11), residues: 5664 helix: 0.67 (0.11), residues: 2028 sheet: -1.34 (0.17), residues: 960 loop : -1.19 (0.11), residues: 2676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 47 HIS 0.005 0.001 HIS A 160 PHE 0.016 0.001 PHE D 73 TYR 0.022 0.001 TYR I 278 ARG 0.011 0.000 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 525 time to evaluate : 5.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7893 (mttm) REVERT: A 448 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7513 (tm-30) REVERT: B 17 GLN cc_start: 0.7517 (tm-30) cc_final: 0.7251 (pt0) REVERT: B 395 LYS cc_start: 0.8568 (tptp) cc_final: 0.8306 (tptp) REVERT: C 14 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8010 (mttt) REVERT: C 73 PHE cc_start: 0.5941 (OUTLIER) cc_final: 0.5522 (m-80) REVERT: C 435 MET cc_start: 0.8853 (mmm) cc_final: 0.8055 (mmm) REVERT: C 439 SER cc_start: 0.8742 (t) cc_final: 0.8281 (m) REVERT: D 14 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7965 (mttm) REVERT: D 172 LYS cc_start: 0.7109 (OUTLIER) cc_final: 0.6718 (tptt) REVERT: D 297 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7443 (t0) REVERT: F 286 LYS cc_start: 0.8267 (tppt) cc_final: 0.8039 (tptp) REVERT: F 425 VAL cc_start: 0.9286 (OUTLIER) cc_final: 0.9067 (t) REVERT: F 457 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7459 (mt-10) REVERT: H 24 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8925 (mp) REVERT: H 77 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8570 (p) REVERT: H 435 MET cc_start: 0.8775 (mmm) cc_final: 0.8038 (mmm) REVERT: H 439 SER cc_start: 0.9013 (t) cc_final: 0.8675 (p) REVERT: H 457 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7362 (mt-10) REVERT: I 73 PHE cc_start: 0.5869 (OUTLIER) cc_final: 0.5263 (m-80) REVERT: I 303 MET cc_start: 0.8950 (ptm) cc_final: 0.8583 (ptt) REVERT: J 14 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7646 (mttm) REVERT: J 280 LEU cc_start: 0.9175 (tp) cc_final: 0.8922 (tp) REVERT: J 297 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7716 (t0) REVERT: L 1 MET cc_start: 0.7043 (ttp) cc_final: 0.6639 (ttp) REVERT: L 172 LYS cc_start: 0.7324 (tppt) cc_final: 0.6974 (tptp) REVERT: L 190 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7417 (mm-40) REVERT: L 439 SER cc_start: 0.8904 (t) cc_final: 0.8560 (m) outliers start: 130 outliers final: 100 residues processed: 632 average time/residue: 0.6251 time to fit residues: 646.1019 Evaluate side-chains 618 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 505 time to evaluate : 5.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 58 CYS Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 501 VAL Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 528 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 524 ILE Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain H residue 394 THR Chi-restraints excluded: chain H residue 409 GLU Chi-restraints excluded: chain H residue 425 VAL Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 524 ILE Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain H residue 567 VAL Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 409 GLU Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 73 PHE Chi-restraints excluded: chain J residue 89 SER Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 297 ASP Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 425 VAL Chi-restraints excluded: chain J residue 524 ILE Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 58 CYS Chi-restraints excluded: chain K residue 73 PHE Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 131 GLN Chi-restraints excluded: chain K residue 293 GLU Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 381 ILE Chi-restraints excluded: chain K residue 391 SER Chi-restraints excluded: chain K residue 409 GLU Chi-restraints excluded: chain K residue 538 GLU Chi-restraints excluded: chain L residue 58 CYS Chi-restraints excluded: chain L residue 73 PHE Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 293 GLU Chi-restraints excluded: chain L residue 339 LEU Chi-restraints excluded: chain L residue 383 SER Chi-restraints excluded: chain L residue 417 VAL Chi-restraints excluded: chain L residue 524 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 494 optimal weight: 0.9980 chunk 520 optimal weight: 4.9990 chunk 475 optimal weight: 2.9990 chunk 506 optimal weight: 2.9990 chunk 304 optimal weight: 1.9990 chunk 220 optimal weight: 0.8980 chunk 397 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 457 optimal weight: 0.9990 chunk 479 optimal weight: 0.3980 chunk 504 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN B 568 HIS ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 411 HIS ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 131 GLN ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 432 ASN ** L 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 289 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 47328 Z= 0.199 Angle : 0.565 12.246 63888 Z= 0.302 Chirality : 0.045 0.185 7020 Planarity : 0.003 0.079 8208 Dihedral : 5.156 39.430 6134 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.42 % Allowed : 19.05 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.11), residues: 5664 helix: 0.95 (0.12), residues: 2016 sheet: -1.07 (0.17), residues: 924 loop : -1.21 (0.10), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 47 HIS 0.004 0.001 HIS D 475 PHE 0.014 0.001 PHE D 73 TYR 0.019 0.001 TYR I 278 ARG 0.015 0.000 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 534 time to evaluate : 5.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7889 (mttm) REVERT: A 448 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7477 (tm-30) REVERT: B 395 LYS cc_start: 0.8476 (tptp) cc_final: 0.8225 (tptp) REVERT: C 19 SER cc_start: 0.8863 (OUTLIER) cc_final: 0.8590 (p) REVERT: C 71 LYS cc_start: 0.8234 (ttpt) cc_final: 0.8003 (tttm) REVERT: C 435 MET cc_start: 0.8802 (mmm) cc_final: 0.8074 (mmm) REVERT: C 439 SER cc_start: 0.8733 (t) cc_final: 0.8276 (m) REVERT: D 14 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7949 (mttm) REVERT: D 172 LYS cc_start: 0.6942 (OUTLIER) cc_final: 0.6529 (tptt) REVERT: D 297 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7375 (t0) REVERT: D 390 ARG cc_start: 0.7327 (mtt180) cc_final: 0.7038 (mtt180) REVERT: E 439 SER cc_start: 0.8707 (t) cc_final: 0.8224 (m) REVERT: E 457 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7243 (mt-10) REVERT: F 286 LYS cc_start: 0.8213 (tppt) cc_final: 0.7984 (tptp) REVERT: F 457 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7476 (mt-10) REVERT: G 275 ASP cc_start: 0.7516 (m-30) cc_final: 0.7280 (m-30) REVERT: H 24 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8892 (mt) REVERT: H 435 MET cc_start: 0.8674 (mmm) cc_final: 0.8025 (mmm) REVERT: H 439 SER cc_start: 0.8960 (t) cc_final: 0.8665 (p) REVERT: H 457 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7319 (mt-10) REVERT: I 73 PHE cc_start: 0.5558 (OUTLIER) cc_final: 0.4967 (m-80) REVERT: I 303 MET cc_start: 0.8930 (ptm) cc_final: 0.8606 (ptt) REVERT: J 14 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7599 (mttm) REVERT: J 280 LEU cc_start: 0.9141 (tp) cc_final: 0.8888 (tp) REVERT: J 297 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7630 (t0) REVERT: J 390 ARG cc_start: 0.7487 (mtt180) cc_final: 0.7234 (mtt180) REVERT: L 172 LYS cc_start: 0.7071 (tppt) cc_final: 0.6822 (tptp) REVERT: L 190 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7411 (mm-40) REVERT: L 439 SER cc_start: 0.8882 (t) cc_final: 0.8542 (m) outliers start: 126 outliers final: 89 residues processed: 640 average time/residue: 0.6141 time to fit residues: 645.5362 Evaluate side-chains 619 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 520 time to evaluate : 5.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 58 CYS Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 501 VAL Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 528 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 524 ILE Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain H residue 409 GLU Chi-restraints excluded: chain H residue 425 VAL Chi-restraints excluded: chain H residue 524 ILE Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain H residue 567 VAL Chi-restraints excluded: chain I residue 26 CYS Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 409 GLU Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 58 CYS Chi-restraints excluded: chain J residue 73 PHE Chi-restraints excluded: chain J residue 89 SER Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 297 ASP Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 524 ILE Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 58 CYS Chi-restraints excluded: chain K residue 73 PHE Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 131 GLN Chi-restraints excluded: chain K residue 293 GLU Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 381 ILE Chi-restraints excluded: chain K residue 409 GLU Chi-restraints excluded: chain K residue 538 GLU Chi-restraints excluded: chain L residue 58 CYS Chi-restraints excluded: chain L residue 73 PHE Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 339 LEU Chi-restraints excluded: chain L residue 383 SER Chi-restraints excluded: chain L residue 524 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 332 optimal weight: 4.9990 chunk 535 optimal weight: 1.9990 chunk 326 optimal weight: 1.9990 chunk 254 optimal weight: 10.0000 chunk 372 optimal weight: 2.9990 chunk 561 optimal weight: 0.5980 chunk 517 optimal weight: 7.9990 chunk 447 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 345 optimal weight: 1.9990 chunk 274 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN B 568 HIS ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 HIS ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 411 HIS ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 ASN ** I 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 131 GLN ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 289 ASN ** L 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 568 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 47328 Z= 0.289 Angle : 0.605 13.045 63888 Z= 0.322 Chirality : 0.047 0.200 7020 Planarity : 0.004 0.051 8208 Dihedral : 5.229 41.132 6134 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.09 % Allowed : 19.37 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.11), residues: 5664 helix: 0.86 (0.11), residues: 2028 sheet: -1.17 (0.17), residues: 936 loop : -1.15 (0.11), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 118 HIS 0.004 0.001 HIS J 475 PHE 0.016 0.001 PHE D 73 TYR 0.019 0.001 TYR I 278 ARG 0.011 0.000 ARG A 390 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 506 time to evaluate : 5.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7921 (mttm) REVERT: A 448 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7505 (tm-30) REVERT: B 395 LYS cc_start: 0.8536 (tptp) cc_final: 0.8296 (tptp) REVERT: C 435 MET cc_start: 0.8842 (mmm) cc_final: 0.8059 (mmm) REVERT: C 439 SER cc_start: 0.8757 (t) cc_final: 0.8284 (m) REVERT: D 14 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7988 (mttm) REVERT: D 172 LYS cc_start: 0.7000 (OUTLIER) cc_final: 0.6618 (tptt) REVERT: D 297 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7452 (t0) REVERT: D 395 LYS cc_start: 0.8607 (mmmt) cc_final: 0.8357 (mmmt) REVERT: F 286 LYS cc_start: 0.8236 (tppt) cc_final: 0.8013 (tptp) REVERT: F 457 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7467 (mt-10) REVERT: G 275 ASP cc_start: 0.7544 (m-30) cc_final: 0.7309 (m-30) REVERT: H 192 ASN cc_start: 0.7670 (t0) cc_final: 0.7445 (t0) REVERT: H 435 MET cc_start: 0.8731 (mmm) cc_final: 0.8006 (mmm) REVERT: H 439 SER cc_start: 0.8978 (t) cc_final: 0.8667 (p) REVERT: H 457 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7358 (mt-10) REVERT: I 73 PHE cc_start: 0.5628 (OUTLIER) cc_final: 0.5027 (m-80) REVERT: I 303 MET cc_start: 0.8951 (ptm) cc_final: 0.8609 (ptt) REVERT: J 14 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7634 (mttm) REVERT: J 172 LYS cc_start: 0.6993 (tppt) cc_final: 0.6419 (tptt) REVERT: J 280 LEU cc_start: 0.9157 (tp) cc_final: 0.8884 (tp) REVERT: J 297 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7680 (t0) REVERT: J 390 ARG cc_start: 0.7513 (mtt180) cc_final: 0.7276 (mtt180) REVERT: K 421 TYR cc_start: 0.8994 (t80) cc_final: 0.8755 (t80) REVERT: L 172 LYS cc_start: 0.7197 (tppt) cc_final: 0.6806 (tptp) REVERT: L 190 GLN cc_start: 0.7728 (mm-40) cc_final: 0.7485 (mm-40) REVERT: L 439 SER cc_start: 0.8890 (t) cc_final: 0.8560 (m) outliers start: 109 outliers final: 94 residues processed: 599 average time/residue: 0.6131 time to fit residues: 598.5886 Evaluate side-chains 601 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 499 time to evaluate : 5.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 58 CYS Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 501 VAL Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 528 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 524 ILE Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain H residue 58 CYS Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain H residue 394 THR Chi-restraints excluded: chain H residue 409 GLU Chi-restraints excluded: chain H residue 425 VAL Chi-restraints excluded: chain H residue 524 ILE Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain H residue 567 VAL Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 409 GLU Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 58 CYS Chi-restraints excluded: chain J residue 73 PHE Chi-restraints excluded: chain J residue 89 SER Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 297 ASP Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 524 ILE Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 58 CYS Chi-restraints excluded: chain K residue 73 PHE Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 172 LYS Chi-restraints excluded: chain K residue 293 GLU Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 381 ILE Chi-restraints excluded: chain K residue 409 GLU Chi-restraints excluded: chain K residue 538 GLU Chi-restraints excluded: chain L residue 58 CYS Chi-restraints excluded: chain L residue 73 PHE Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 339 LEU Chi-restraints excluded: chain L residue 381 ILE Chi-restraints excluded: chain L residue 383 SER Chi-restraints excluded: chain L residue 524 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 355 optimal weight: 3.9990 chunk 476 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 412 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 124 optimal weight: 0.9990 chunk 448 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 460 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN B 568 HIS ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 ASN ** I 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 131 GLN ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.121455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.105453 restraints weight = 56032.100| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.47 r_work: 0.3015 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 47328 Z= 0.229 Angle : 0.578 12.916 63888 Z= 0.308 Chirality : 0.045 0.231 7020 Planarity : 0.003 0.035 8208 Dihedral : 5.159 41.735 6134 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.17 % Allowed : 19.28 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.11), residues: 5664 helix: 1.01 (0.12), residues: 2028 sheet: -0.95 (0.17), residues: 900 loop : -1.20 (0.10), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 118 HIS 0.004 0.001 HIS G 475 PHE 0.015 0.001 PHE D 73 TYR 0.018 0.001 TYR G 278 ARG 0.009 0.000 ARG L 6 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12203.01 seconds wall clock time: 221 minutes 57.93 seconds (13317.93 seconds total)