Starting phenix.real_space_refine on Tue Apr 16 22:01:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rff_24440/04_2024/7rff_24440.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rff_24440/04_2024/7rff_24440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rff_24440/04_2024/7rff_24440.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rff_24440/04_2024/7rff_24440.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rff_24440/04_2024/7rff_24440.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rff_24440/04_2024/7rff_24440.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.240 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 S 136 5.16 5 C 12896 2.51 5 N 3504 2.21 5 O 3864 1.98 5 H 20600 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 232": "OD1" <-> "OD2" Residue "A ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 256": "OD1" <-> "OD2" Residue "A TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 319": "OD1" <-> "OD2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 470": "OD1" <-> "OD2" Residue "A ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 500": "OE1" <-> "OE2" Residue "B TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 28": "OD1" <-> "OD2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 232": "OD1" <-> "OD2" Residue "B ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 256": "OD1" <-> "OD2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 319": "OD1" <-> "OD2" Residue "B ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 470": "OD1" <-> "OD2" Residue "B ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 500": "OE1" <-> "OE2" Residue "C TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 232": "OD1" <-> "OD2" Residue "C ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 256": "OD1" <-> "OD2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "C ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 470": "OD1" <-> "OD2" Residue "C ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 500": "OE1" <-> "OE2" Residue "D TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 47": "OD1" <-> "OD2" Residue "D ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 232": "OD1" <-> "OD2" Residue "D ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 256": "OD1" <-> "OD2" Residue "D ASP 261": "OD1" <-> "OD2" Residue "D TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 352": "OE1" <-> "OE2" Residue "D ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 470": "OD1" <-> "OD2" Residue "D ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 500": "OE1" <-> "OE2" Residue "E GLU -19": "OE1" <-> "OE2" Residue "E TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 75": "OE1" <-> "OE2" Residue "E PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 232": "OD1" <-> "OD2" Residue "E ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 256": "OD1" <-> "OD2" Residue "E TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 319": "OD1" <-> "OD2" Residue "E GLU 352": "OE1" <-> "OE2" Residue "E ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 470": "OD1" <-> "OD2" Residue "E ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 500": "OE1" <-> "OE2" Residue "F TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 47": "OD1" <-> "OD2" Residue "F ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 232": "OD1" <-> "OD2" Residue "F ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 256": "OD1" <-> "OD2" Residue "F TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 319": "OD1" <-> "OD2" Residue "F GLU 335": "OE1" <-> "OE2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "F ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 470": "OD1" <-> "OD2" Residue "F ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU -19": "OE1" <-> "OE2" Residue "G TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 47": "OD1" <-> "OD2" Residue "G ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 75": "OE1" <-> "OE2" Residue "G PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 232": "OD1" <-> "OD2" Residue "G TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 256": "OD1" <-> "OD2" Residue "G TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 319": "OD1" <-> "OD2" Residue "G GLU 335": "OE1" <-> "OE2" Residue "G ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 500": "OE1" <-> "OE2" Residue "H TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 47": "OD1" <-> "OD2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 71": "OD1" <-> "OD2" Residue "H GLU 75": "OE1" <-> "OE2" Residue "H PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 232": "OD1" <-> "OD2" Residue "H ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 256": "OD1" <-> "OD2" Residue "H ASP 261": "OD1" <-> "OD2" Residue "H TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 470": "OD1" <-> "OD2" Residue "H ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 500": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 41000 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5125 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 4 Chain: "B" Number of atoms: 5125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5125 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 4 Chain: "C" Number of atoms: 5125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5125 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 4 Chain: "D" Number of atoms: 5125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5125 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 4 Chain: "E" Number of atoms: 5125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5125 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 4 Chain: "F" Number of atoms: 5125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5125 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 4 Chain: "G" Number of atoms: 5125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5125 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 4 Chain: "H" Number of atoms: 5125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5125 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 4 Time building chain proxies: 18.08, per 1000 atoms: 0.44 Number of scatterers: 41000 At special positions: 0 Unit cell: (126, 124.95, 101.85, 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) S 136 16.00 O 3864 8.00 N 3504 7.00 C 12896 6.00 H 20600 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 34.77 Conformation dependent library (CDL) restraints added in 4.0 seconds 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4880 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 24 sheets defined 49.1% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.67 Creating SS restraints... Processing helix chain 'A' and resid -18 through -9 Processing helix chain 'A' and resid -8 through -6 No H-bonds generated for 'chain 'A' and resid -8 through -6' Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 19 through 25 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 75 through 85 Processing helix chain 'A' and resid 96 through 110 removed outlier: 3.525A pdb=" N PHE A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 266 removed outlier: 3.670A pdb=" N ASP A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 342 through 356 removed outlier: 3.929A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 452 through 472 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'B' and resid -18 through -8 removed outlier: 3.534A pdb=" N LEU B -8 " --> pdb=" O SER B -12 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 8 Processing helix chain 'B' and resid 19 through 25 Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 75 through 85 Processing helix chain 'B' and resid 96 through 110 Processing helix chain 'B' and resid 255 through 266 removed outlier: 3.654A pdb=" N ASP B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 317 Processing helix chain 'B' and resid 342 through 356 removed outlier: 3.880A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 452 through 472 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 502 Processing helix chain 'C' and resid -18 through -9 Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 19 through 25 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 96 through 110 removed outlier: 3.583A pdb=" N PHE C 110 " --> pdb=" O LYS C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 266 removed outlier: 3.753A pdb=" N ASP C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 317 Processing helix chain 'C' and resid 342 through 356 removed outlier: 3.926A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 Processing helix chain 'C' and resid 452 through 472 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 494 through 502 Processing helix chain 'D' and resid -18 through -9 Processing helix chain 'D' and resid -8 through -6 No H-bonds generated for 'chain 'D' and resid -8 through -6' Processing helix chain 'D' and resid 2 through 8 Processing helix chain 'D' and resid 19 through 25 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 75 through 85 Processing helix chain 'D' and resid 96 through 110 Processing helix chain 'D' and resid 255 through 266 removed outlier: 3.690A pdb=" N ASP D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 306 through 317 Processing helix chain 'D' and resid 342 through 356 removed outlier: 3.909A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 Processing helix chain 'D' and resid 452 through 472 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 502 Processing helix chain 'E' and resid -18 through -9 Processing helix chain 'E' and resid -8 through -6 No H-bonds generated for 'chain 'E' and resid -8 through -6' Processing helix chain 'E' and resid 2 through 8 Processing helix chain 'E' and resid 19 through 25 Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 75 through 85 Processing helix chain 'E' and resid 96 through 110 removed outlier: 3.551A pdb=" N PHE E 110 " --> pdb=" O LYS E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 266 removed outlier: 3.512A pdb=" N ARG E 259 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP E 261 " --> pdb=" O LYS E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 317 Processing helix chain 'E' and resid 342 through 356 removed outlier: 3.911A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 Processing helix chain 'E' and resid 452 through 472 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 494 through 502 Processing helix chain 'F' and resid -18 through -9 Processing helix chain 'F' and resid -8 through -6 No H-bonds generated for 'chain 'F' and resid -8 through -6' Processing helix chain 'F' and resid 2 through 8 Processing helix chain 'F' and resid 19 through 25 Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 45 through 49 Processing helix chain 'F' and resid 75 through 86 Processing helix chain 'F' and resid 96 through 110 removed outlier: 3.559A pdb=" N PHE F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 266 removed outlier: 3.714A pdb=" N ASP F 261 " --> pdb=" O LYS F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 317 Processing helix chain 'F' and resid 342 through 356 removed outlier: 3.904A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 379 Processing helix chain 'F' and resid 452 through 472 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 494 through 502 Processing helix chain 'G' and resid -18 through -9 Processing helix chain 'G' and resid -8 through -6 No H-bonds generated for 'chain 'G' and resid -8 through -6' Processing helix chain 'G' and resid 2 through 8 Processing helix chain 'G' and resid 19 through 25 Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 45 through 49 Processing helix chain 'G' and resid 75 through 85 Processing helix chain 'G' and resid 96 through 110 Processing helix chain 'G' and resid 255 through 266 removed outlier: 3.737A pdb=" N ASP G 261 " --> pdb=" O LYS G 257 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 317 Processing helix chain 'G' and resid 342 through 356 removed outlier: 3.864A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 379 Processing helix chain 'G' and resid 452 through 472 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 475 through 485 Processing helix chain 'G' and resid 494 through 502 Processing helix chain 'H' and resid -18 through -9 Processing helix chain 'H' and resid -8 through -6 No H-bonds generated for 'chain 'H' and resid -8 through -6' Processing helix chain 'H' and resid 2 through 8 Processing helix chain 'H' and resid 19 through 25 Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 45 through 49 Processing helix chain 'H' and resid 75 through 85 Processing helix chain 'H' and resid 96 through 110 removed outlier: 3.530A pdb=" N PHE H 110 " --> pdb=" O LYS H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 266 removed outlier: 3.672A pdb=" N ASP H 261 " --> pdb=" O LYS H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 317 Processing helix chain 'H' and resid 342 through 356 removed outlier: 3.871A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 Processing helix chain 'H' and resid 452 through 472 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 494 through 502 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 37 removed outlier: 7.989A pdb=" N GLY B 29 " --> pdb=" O PHE A 490 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LYS A 492 " --> pdb=" O GLY B 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.599A pdb=" N ALA A 248 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N MET A 385 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE A 66 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 35 through 37 removed outlier: 7.992A pdb=" N GLY C 29 " --> pdb=" O PHE B 490 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS B 492 " --> pdb=" O GLY C 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA7, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.600A pdb=" N ALA B 248 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG B 322 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N MET B 385 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE B 66 " --> pdb=" O MET B 386 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 35 through 37 removed outlier: 7.987A pdb=" N GLY D 29 " --> pdb=" O PHE C 490 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS C 492 " --> pdb=" O GLY D 29 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.609A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG C 322 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN C 303 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N MET C 385 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.613A pdb=" N ALA D 248 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG D 322 " --> pdb=" O GLY D 301 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN D 303 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N MET D 385 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 28 through 29 Processing sheet with id=AB5, first strand: chain 'E' and resid 35 through 37 removed outlier: 7.969A pdb=" N GLY F 29 " --> pdb=" O PHE E 490 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS E 492 " --> pdb=" O GLY F 29 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.592A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG E 322 " --> pdb=" O GLY E 301 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N MET E 385 " --> pdb=" O ILE E 361 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 35 through 37 removed outlier: 7.961A pdb=" N GLY G 29 " --> pdb=" O PHE F 490 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS F 492 " --> pdb=" O GLY G 29 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.507A pdb=" N ILE F 88 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA F 248 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG F 322 " --> pdb=" O GLY F 301 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N MET F 385 " --> pdb=" O ILE F 361 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE F 66 " --> pdb=" O MET F 386 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 35 through 37 removed outlier: 7.957A pdb=" N GLY H 29 " --> pdb=" O PHE G 490 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS G 492 " --> pdb=" O GLY H 29 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AC4, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.607A pdb=" N ALA G 248 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG G 322 " --> pdb=" O GLY G 301 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASN G 303 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N MET G 385 " --> pdb=" O ILE G 361 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE G 66 " --> pdb=" O MET G 386 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AC6, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.588A pdb=" N ALA H 248 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG H 322 " --> pdb=" O GLY H 301 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN H 303 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N MET H 385 " --> pdb=" O ILE H 361 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE H 66 " --> pdb=" O MET H 386 " (cutoff:3.500A) 962 hydrogen bonds defined for protein. 2745 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: 16.92 Time building geometry restraints manager: 36.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 20568 1.12 - 1.30: 3642 1.30 - 1.48: 7708 1.48 - 1.65: 9146 1.65 - 1.83: 240 Bond restraints: 41304 Sorted by residual: bond pdb=" N HIS F 296 " pdb=" H HIS F 296 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N GLY G 251 " pdb=" H GLY G 251 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N GLU B 15 " pdb=" H GLU B 15 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CD2 TYR B 348 " pdb=" HD2 TYR B 348 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NH2 ARG C 474 " pdb="HH21 ARG C 474 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 41299 not shown) Histogram of bond angle deviations from ideal: 95.95 - 102.68: 216 102.68 - 109.42: 28628 109.42 - 116.16: 22545 116.16 - 122.89: 20537 122.89 - 129.63: 2722 Bond angle restraints: 74648 Sorted by residual: angle pdb=" CA GLY H 324 " pdb=" C GLY H 324 " pdb=" N MET H 325 " ideal model delta sigma weight residual 115.34 120.84 -5.50 8.10e-01 1.52e+00 4.61e+01 angle pdb=" OE1 GLN B 277 " pdb=" CD GLN B 277 " pdb=" NE2 GLN B 277 " ideal model delta sigma weight residual 122.60 116.29 6.31 1.00e+00 1.00e+00 3.98e+01 angle pdb=" CA ASP D 28 " pdb=" CB ASP D 28 " pdb=" CG ASP D 28 " ideal model delta sigma weight residual 112.60 118.67 -6.07 1.00e+00 1.00e+00 3.68e+01 angle pdb=" CA GLY C 324 " pdb=" C GLY C 324 " pdb=" N MET C 325 " ideal model delta sigma weight residual 115.74 120.04 -4.30 7.30e-01 1.88e+00 3.47e+01 angle pdb=" CA GLY B 324 " pdb=" C GLY B 324 " pdb=" N MET B 325 " ideal model delta sigma weight residual 115.34 120.11 -4.77 8.10e-01 1.52e+00 3.46e+01 ... (remaining 74643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 17383 17.98 - 35.96: 1145 35.96 - 53.94: 430 53.94 - 71.92: 359 71.92 - 89.90: 43 Dihedral angle restraints: 19360 sinusoidal: 10656 harmonic: 8704 Sorted by residual: dihedral pdb=" CA GLU F 335 " pdb=" C GLU F 335 " pdb=" N VAL F 336 " pdb=" CA VAL F 336 " ideal model delta harmonic sigma weight residual 180.00 150.17 29.83 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" C VAL B 457 " pdb=" N VAL B 457 " pdb=" CA VAL B 457 " pdb=" CB VAL B 457 " ideal model delta harmonic sigma weight residual -122.00 -136.69 14.69 0 2.50e+00 1.60e-01 3.45e+01 dihedral pdb=" C VAL G 457 " pdb=" N VAL G 457 " pdb=" CA VAL G 457 " pdb=" CB VAL G 457 " ideal model delta harmonic sigma weight residual -122.00 -136.39 14.39 0 2.50e+00 1.60e-01 3.31e+01 ... (remaining 19357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2322 0.094 - 0.188: 772 0.188 - 0.282: 121 0.282 - 0.376: 20 0.376 - 0.470: 5 Chirality restraints: 3240 Sorted by residual: chirality pdb=" CA VAL G 457 " pdb=" N VAL G 457 " pdb=" C VAL G 457 " pdb=" CB VAL G 457 " both_signs ideal model delta sigma weight residual False 2.44 1.97 0.47 2.00e-01 2.50e+01 5.53e+00 chirality pdb=" CA VAL B 457 " pdb=" N VAL B 457 " pdb=" C VAL B 457 " pdb=" CB VAL B 457 " both_signs ideal model delta sigma weight residual False 2.44 1.97 0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" CA VAL E 457 " pdb=" N VAL E 457 " pdb=" C VAL E 457 " pdb=" CB VAL E 457 " both_signs ideal model delta sigma weight residual False 2.44 1.99 0.46 2.00e-01 2.50e+01 5.18e+00 ... (remaining 3237 not shown) Planarity restraints: 6176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 259 " -0.015 9.50e-02 1.11e+02 7.36e-02 1.21e+02 pdb=" NE ARG E 259 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG E 259 " -0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG E 259 " -0.054 2.00e-02 2.50e+03 pdb=" NH2 ARG E 259 " -0.037 2.00e-02 2.50e+03 pdb="HH11 ARG E 259 " 0.144 2.00e-02 2.50e+03 pdb="HH12 ARG E 259 " -0.042 2.00e-02 2.50e+03 pdb="HH21 ARG E 259 " 0.120 2.00e-02 2.50e+03 pdb="HH22 ARG E 259 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 259 " 0.026 9.50e-02 1.11e+02 7.01e-02 1.09e+02 pdb=" NE ARG F 259 " 0.062 2.00e-02 2.50e+03 pdb=" CZ ARG F 259 " 0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG F 259 " 0.053 2.00e-02 2.50e+03 pdb=" NH2 ARG F 259 " 0.035 2.00e-02 2.50e+03 pdb="HH11 ARG F 259 " -0.138 2.00e-02 2.50e+03 pdb="HH12 ARG F 259 " 0.039 2.00e-02 2.50e+03 pdb="HH21 ARG F 259 " -0.113 2.00e-02 2.50e+03 pdb="HH22 ARG F 259 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 259 " 0.031 9.50e-02 1.11e+02 6.89e-02 1.04e+02 pdb=" NE ARG B 259 " -0.062 2.00e-02 2.50e+03 pdb=" CZ ARG B 259 " -0.049 2.00e-02 2.50e+03 pdb=" NH1 ARG B 259 " -0.046 2.00e-02 2.50e+03 pdb=" NH2 ARG B 259 " -0.044 2.00e-02 2.50e+03 pdb="HH11 ARG B 259 " 0.127 2.00e-02 2.50e+03 pdb="HH12 ARG B 259 " -0.032 2.00e-02 2.50e+03 pdb="HH21 ARG B 259 " 0.118 2.00e-02 2.50e+03 pdb="HH22 ARG B 259 " -0.015 2.00e-02 2.50e+03 ... (remaining 6173 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 2967 2.20 - 2.80: 76957 2.80 - 3.40: 119226 3.40 - 4.00: 164099 4.00 - 4.60: 239861 Nonbonded interactions: 603110 Sorted by model distance: nonbonded pdb=" HG SER G 26 " pdb=" OD1 ASP G 28 " model vdw 1.602 1.850 nonbonded pdb=" HG SER H 26 " pdb=" OD1 ASP H 28 " model vdw 1.604 1.850 nonbonded pdb=" HG SER C 26 " pdb=" OD1 ASP C 28 " model vdw 1.604 1.850 nonbonded pdb=" HB2 LEU H 321 " pdb="HD11 ILE H 361 " model vdw 1.605 2.440 nonbonded pdb=" HG SER D 26 " pdb=" OD1 ASP D 28 " model vdw 1.607 1.850 ... (remaining 603105 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' } 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: 2.280 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: 0.720 Extract box with map and model: 8.780 Check model and map are aligned: 0.600 Set scattering table: 0.360 Process input model: 132.160 Find NCS groups from input model: 2.330 Set up NCS constraints: 0.230 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:13.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 161.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 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 : 0.012 0.073 20704 Z= 0.778 Angle : 1.833 7.915 27952 Z= 1.233 Chirality : 0.093 0.470 3240 Planarity : 0.013 0.125 3592 Dihedral : 14.113 89.895 7536 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.80 % Favored : 95.90 % Rotamer: Outliers : 1.97 % Allowed : 6.37 % Favored : 91.67 % Cbeta Deviations : 0.20 % 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: -1.34 (0.14), residues: 2632 helix: -0.89 (0.12), residues: 1208 sheet: -0.31 (0.27), residues: 216 loop : -0.85 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.003 HIS G 288 PHE 0.061 0.011 PHE E 44 TYR 0.098 0.018 TYR B 353 ARG 0.008 0.001 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 635 time to evaluate : 3.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.6634 (pp20) cc_final: 0.6400 (pp20) REVERT: A 21 GLN cc_start: 0.8289 (tt0) cc_final: 0.7913 (tt0) REVERT: A 60 THR cc_start: 0.8875 (t) cc_final: 0.8431 (m) REVERT: A 62 LYS cc_start: 0.8259 (mttt) cc_final: 0.7469 (mtpt) REVERT: A 75 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7212 (mt-10) REVERT: A 78 MET cc_start: 0.8595 (tpp) cc_final: 0.8117 (tpp) REVERT: A 82 MET cc_start: 0.7846 (mmm) cc_final: 0.7615 (mmm) REVERT: A 106 LYS cc_start: 0.7816 (ttmt) cc_final: 0.7535 (ttmm) REVERT: A 233 TYR cc_start: 0.8074 (m-80) cc_final: 0.7727 (m-80) REVERT: A 242 LYS cc_start: 0.7482 (mttt) cc_final: 0.6965 (mmmt) REVERT: A 255 ASP cc_start: 0.8409 (p0) cc_final: 0.8111 (p0) REVERT: A 293 LYS cc_start: 0.7812 (tttp) cc_final: 0.7572 (tttt) REVERT: A 311 LYS cc_start: 0.8352 (tttp) cc_final: 0.8004 (tttt) REVERT: A 349 LYS cc_start: 0.8298 (mmtp) cc_final: 0.7977 (mmtp) REVERT: A 394 THR cc_start: 0.8685 (m) cc_final: 0.8320 (t) REVERT: A 471 ILE cc_start: 0.8494 (mt) cc_final: 0.8284 (mm) REVERT: B 15 GLU cc_start: 0.6686 (pp20) cc_final: 0.6412 (pp20) REVERT: B 21 GLN cc_start: 0.8190 (tt0) cc_final: 0.7594 (tt0) REVERT: B 75 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7158 (mt-10) REVERT: B 78 MET cc_start: 0.8639 (tpp) cc_final: 0.8116 (tpp) REVERT: B 106 LYS cc_start: 0.7691 (ttmt) cc_final: 0.7484 (ttmm) REVERT: B 242 LYS cc_start: 0.7408 (mttt) cc_final: 0.7026 (mmtt) REVERT: B 255 ASP cc_start: 0.8324 (p0) cc_final: 0.8112 (p0) REVERT: B 293 LYS cc_start: 0.7831 (tttp) cc_final: 0.7594 (tttt) REVERT: B 311 LYS cc_start: 0.8347 (tttp) cc_final: 0.7914 (tttt) REVERT: B 394 THR cc_start: 0.8126 (m) cc_final: 0.7837 (t) REVERT: C 78 MET cc_start: 0.8468 (tpp) cc_final: 0.7986 (tpp) REVERT: C 82 MET cc_start: 0.7797 (mmm) cc_final: 0.7588 (mmm) REVERT: C 106 LYS cc_start: 0.7715 (ttmt) cc_final: 0.7478 (ttmm) REVERT: C 242 LYS cc_start: 0.7384 (mttt) cc_final: 0.7040 (mmmt) REVERT: C 255 ASP cc_start: 0.8328 (p0) cc_final: 0.8061 (p0) REVERT: C 277 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8572 (tm-30) REVERT: C 349 LYS cc_start: 0.8269 (mmtp) cc_final: 0.7966 (mmtt) REVERT: C 454 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7774 (mm-40) REVERT: D 60 THR cc_start: 0.8798 (t) cc_final: 0.8351 (m) REVERT: D 62 LYS cc_start: 0.8275 (mttt) cc_final: 0.7597 (mtpt) REVERT: D 75 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7256 (mt-10) REVERT: D 78 MET cc_start: 0.8454 (tpp) cc_final: 0.7975 (tpp) REVERT: D 82 MET cc_start: 0.7801 (mmm) cc_final: 0.7596 (mmm) REVERT: D 85 MET cc_start: 0.7415 (mmm) cc_final: 0.7148 (mmm) REVERT: D 106 LYS cc_start: 0.7649 (ttmt) cc_final: 0.7421 (ttmm) REVERT: D 233 TYR cc_start: 0.8160 (m-80) cc_final: 0.7767 (m-80) REVERT: D 242 LYS cc_start: 0.7471 (mttt) cc_final: 0.7031 (mmtt) REVERT: D 255 ASP cc_start: 0.8221 (p0) cc_final: 0.7988 (p0) REVERT: D 293 LYS cc_start: 0.7876 (tttp) cc_final: 0.7668 (tttt) REVERT: D 349 LYS cc_start: 0.8279 (mmtp) cc_final: 0.7933 (mmtt) REVERT: D 454 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7571 (mm-40) REVERT: D 500 GLU cc_start: 0.6167 (tt0) cc_final: 0.5951 (tt0) REVERT: E 15 GLU cc_start: 0.6585 (pp20) cc_final: 0.6327 (pp20) REVERT: E 21 GLN cc_start: 0.8240 (tt0) cc_final: 0.8034 (tt0) REVERT: E 62 LYS cc_start: 0.8170 (mttt) cc_final: 0.7531 (mtpt) REVERT: E 78 MET cc_start: 0.8593 (tpp) cc_final: 0.7972 (tpp) REVERT: E 82 MET cc_start: 0.7818 (mmm) cc_final: 0.7595 (mmm) REVERT: E 106 LYS cc_start: 0.7760 (ttmt) cc_final: 0.7454 (ttmm) REVERT: E 238 LYS cc_start: 0.8240 (mttm) cc_final: 0.8038 (mtmm) REVERT: E 242 LYS cc_start: 0.7517 (mttt) cc_final: 0.6974 (mmmt) REVERT: E 255 ASP cc_start: 0.8357 (p0) cc_final: 0.8082 (p0) REVERT: E 293 LYS cc_start: 0.7769 (tttp) cc_final: 0.7489 (tttt) REVERT: E 349 LYS cc_start: 0.8236 (mmtp) cc_final: 0.7887 (mmtp) REVERT: E 394 THR cc_start: 0.8661 (m) cc_final: 0.8290 (t) REVERT: E 470 ASP cc_start: 0.7738 (m-30) cc_final: 0.7438 (m-30) REVERT: F 28 ASP cc_start: 0.7352 (p0) cc_final: 0.6755 (p0) REVERT: F 62 LYS cc_start: 0.8263 (mttt) cc_final: 0.7505 (mtpt) REVERT: F 75 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7165 (mt-10) REVERT: F 78 MET cc_start: 0.8571 (tpp) cc_final: 0.8049 (tpp) REVERT: F 82 MET cc_start: 0.7912 (mmm) cc_final: 0.7675 (mmm) REVERT: F 85 MET cc_start: 0.7717 (mmm) cc_final: 0.7434 (mmm) REVERT: F 242 LYS cc_start: 0.7514 (mttt) cc_final: 0.6991 (mmmt) REVERT: F 277 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8555 (tm-30) REVERT: F 293 LYS cc_start: 0.7779 (tttp) cc_final: 0.7516 (tttt) REVERT: F 311 LYS cc_start: 0.8335 (tttp) cc_final: 0.7882 (tttt) REVERT: F 349 LYS cc_start: 0.8301 (mmtp) cc_final: 0.7983 (mmtp) REVERT: F 394 THR cc_start: 0.8596 (m) cc_final: 0.8228 (t) REVERT: F 454 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7651 (mm-40) REVERT: F 495 MET cc_start: 0.7190 (mmm) cc_final: 0.6861 (mmm) REVERT: G 60 THR cc_start: 0.8859 (t) cc_final: 0.8350 (m) REVERT: G 78 MET cc_start: 0.8570 (tpp) cc_final: 0.8074 (tpp) REVERT: G 82 MET cc_start: 0.7813 (mmm) cc_final: 0.7596 (mmm) REVERT: G 85 MET cc_start: 0.7628 (mmm) cc_final: 0.7301 (mmm) REVERT: G 106 LYS cc_start: 0.7696 (ttmt) cc_final: 0.7468 (ttmm) REVERT: G 109 LYS cc_start: 0.7732 (mttm) cc_final: 0.7523 (mmtt) REVERT: G 233 TYR cc_start: 0.7843 (m-80) cc_final: 0.7642 (m-80) REVERT: G 242 LYS cc_start: 0.7377 (mttt) cc_final: 0.6959 (mmtt) REVERT: G 293 LYS cc_start: 0.7852 (tttp) cc_final: 0.7637 (tttt) REVERT: G 311 LYS cc_start: 0.8346 (tttp) cc_final: 0.8107 (tttm) REVERT: G 394 THR cc_start: 0.8597 (m) cc_final: 0.8289 (t) REVERT: G 454 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7439 (mm-40) REVERT: G 470 ASP cc_start: 0.7785 (m-30) cc_final: 0.7511 (m-30) REVERT: H 21 GLN cc_start: 0.8159 (tt0) cc_final: 0.7774 (tt0) REVERT: H 62 LYS cc_start: 0.8304 (mttt) cc_final: 0.7618 (mtpt) REVERT: H 78 MET cc_start: 0.8569 (tpp) cc_final: 0.8003 (tpp) REVERT: H 82 MET cc_start: 0.7752 (mmm) cc_final: 0.7519 (mmm) REVERT: H 106 LYS cc_start: 0.7763 (ttmt) cc_final: 0.7521 (ttmm) REVERT: H 109 LYS cc_start: 0.7805 (mttm) cc_final: 0.7579 (mmtt) REVERT: H 242 LYS cc_start: 0.7463 (mttt) cc_final: 0.6978 (mmmt) REVERT: H 349 LYS cc_start: 0.8295 (mmtp) cc_final: 0.7966 (mmtt) REVERT: H 454 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7655 (mm-40) REVERT: H 470 ASP cc_start: 0.7857 (m-30) cc_final: 0.7557 (m-30) outliers start: 42 outliers final: 16 residues processed: 676 average time/residue: 2.6280 time to fit residues: 2042.9363 Evaluate side-chains 594 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 576 time to evaluate : 3.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain G residue 388 SER Chi-restraints excluded: chain H residue 377 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.6980 chunk 200 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 206 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 154 optimal weight: 0.9990 chunk 239 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN B 100 GLN C 100 GLN C 312 ASN D 100 GLN D 312 ASN E 100 GLN F 100 GLN F 312 ASN G 100 GLN H 100 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20704 Z= 0.224 Angle : 0.610 5.758 27952 Z= 0.330 Chirality : 0.043 0.185 3240 Planarity : 0.004 0.035 3592 Dihedral : 6.273 43.720 2924 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.53 % Favored : 96.16 % Rotamer: Outliers : 2.15 % Allowed : 13.06 % Favored : 84.78 % 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: 0.16 (0.16), residues: 2632 helix: 1.12 (0.15), residues: 1176 sheet: -0.17 (0.29), residues: 216 loop : -0.81 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 92 PHE 0.011 0.001 PHE G 24 TYR 0.013 0.002 TYR H 353 ARG 0.003 0.000 ARG G 253 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 584 time to evaluate : 3.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 THR cc_start: 0.8804 (t) cc_final: 0.8357 (m) REVERT: A 62 LYS cc_start: 0.8272 (mttt) cc_final: 0.7582 (mtpt) REVERT: A 75 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6824 (mt-10) REVERT: A 78 MET cc_start: 0.8195 (tpp) cc_final: 0.7660 (tpp) REVERT: A 82 MET cc_start: 0.7646 (mmm) cc_final: 0.7209 (mmm) REVERT: A 94 ASN cc_start: 0.8106 (m110) cc_final: 0.7727 (t0) REVERT: A 106 LYS cc_start: 0.7453 (ttmt) cc_final: 0.7227 (ttmm) REVERT: A 242 LYS cc_start: 0.7095 (mttt) cc_final: 0.6721 (mmtt) REVERT: A 255 ASP cc_start: 0.8307 (p0) cc_final: 0.8028 (p0) REVERT: A 291 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7381 (mptt) REVERT: A 349 LYS cc_start: 0.7948 (mmtp) cc_final: 0.7654 (mmtt) REVERT: B 1 MET cc_start: 0.6484 (OUTLIER) cc_final: 0.6138 (tpp) REVERT: B 15 GLU cc_start: 0.6350 (pp20) cc_final: 0.6133 (pp20) REVERT: B 66 ILE cc_start: 0.8535 (mt) cc_final: 0.8124 (mm) REVERT: B 75 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6756 (mt-10) REVERT: B 78 MET cc_start: 0.8278 (tpp) cc_final: 0.7814 (tpp) REVERT: B 94 ASN cc_start: 0.8013 (m110) cc_final: 0.7596 (t0) REVERT: B 242 LYS cc_start: 0.7176 (mttt) cc_final: 0.6859 (mmtt) REVERT: B 255 ASP cc_start: 0.8317 (p0) cc_final: 0.8034 (p0) REVERT: B 291 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7316 (mptt) REVERT: B 349 LYS cc_start: 0.7902 (mmtp) cc_final: 0.7663 (mmtp) REVERT: B 394 THR cc_start: 0.8068 (m) cc_final: 0.7773 (t) REVERT: B 470 ASP cc_start: 0.7780 (m-30) cc_final: 0.7518 (m-30) REVERT: C 1 MET cc_start: 0.6355 (OUTLIER) cc_final: 0.6117 (tpp) REVERT: C 66 ILE cc_start: 0.8480 (mt) cc_final: 0.8110 (mm) REVERT: C 78 MET cc_start: 0.8219 (tpp) cc_final: 0.7649 (tpp) REVERT: C 82 MET cc_start: 0.7587 (mmm) cc_final: 0.7207 (mmm) REVERT: C 106 LYS cc_start: 0.7401 (ttmt) cc_final: 0.7194 (ttmm) REVERT: C 242 LYS cc_start: 0.7145 (mttt) cc_final: 0.6829 (mmtt) REVERT: C 255 ASP cc_start: 0.8268 (p0) cc_final: 0.7949 (p0) REVERT: D 62 LYS cc_start: 0.8313 (mttt) cc_final: 0.7700 (mtpt) REVERT: D 66 ILE cc_start: 0.8491 (mt) cc_final: 0.8116 (mm) REVERT: D 75 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6822 (mt-10) REVERT: D 78 MET cc_start: 0.8201 (tpp) cc_final: 0.7658 (tpp) REVERT: D 82 MET cc_start: 0.7614 (mmm) cc_final: 0.7205 (mmm) REVERT: D 106 LYS cc_start: 0.7297 (ttmt) cc_final: 0.7097 (ttmm) REVERT: D 233 TYR cc_start: 0.8339 (m-80) cc_final: 0.8033 (m-80) REVERT: D 242 LYS cc_start: 0.7179 (mttt) cc_final: 0.6792 (mmmt) REVERT: D 255 ASP cc_start: 0.8256 (p0) cc_final: 0.8028 (p0) REVERT: D 293 LYS cc_start: 0.7809 (tttp) cc_final: 0.7525 (tttt) REVERT: D 349 LYS cc_start: 0.8064 (mmtp) cc_final: 0.7805 (mmtp) REVERT: D 454 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7528 (mm-40) REVERT: D 470 ASP cc_start: 0.7794 (m-30) cc_final: 0.7492 (m-30) REVERT: D 495 MET cc_start: 0.7114 (tpt) cc_final: 0.6907 (tpt) REVERT: E 21 GLN cc_start: 0.8050 (tt0) cc_final: 0.7850 (tt0) REVERT: E 66 ILE cc_start: 0.8504 (mt) cc_final: 0.8122 (mm) REVERT: E 78 MET cc_start: 0.8229 (tpp) cc_final: 0.7775 (tpp) REVERT: E 242 LYS cc_start: 0.7150 (mttt) cc_final: 0.6734 (mmtt) REVERT: E 349 LYS cc_start: 0.7874 (mmtp) cc_final: 0.7525 (mmtt) REVERT: E 470 ASP cc_start: 0.7742 (m-30) cc_final: 0.7451 (m-30) REVERT: F 28 ASP cc_start: 0.7439 (p0) cc_final: 0.7014 (p0) REVERT: F 62 LYS cc_start: 0.8314 (mttt) cc_final: 0.7634 (mtpt) REVERT: F 75 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6764 (mt-10) REVERT: F 78 MET cc_start: 0.8208 (tpp) cc_final: 0.7693 (tpp) REVERT: F 82 MET cc_start: 0.7513 (mmm) cc_final: 0.7221 (mmm) REVERT: F 85 MET cc_start: 0.7548 (mmm) cc_final: 0.7273 (mmm) REVERT: F 94 ASN cc_start: 0.7905 (m-40) cc_final: 0.7582 (t0) REVERT: F 98 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6866 (mm-30) REVERT: F 242 LYS cc_start: 0.7115 (mttt) cc_final: 0.6725 (mmtt) REVERT: F 318 VAL cc_start: 0.8253 (OUTLIER) cc_final: 0.8036 (m) REVERT: F 349 LYS cc_start: 0.7896 (mmtp) cc_final: 0.7657 (mmtp) REVERT: F 454 GLN cc_start: 0.7471 (mm-40) cc_final: 0.7216 (mm-40) REVERT: F 470 ASP cc_start: 0.7760 (m-30) cc_final: 0.7354 (m-30) REVERT: G 45 ILE cc_start: 0.7133 (OUTLIER) cc_final: 0.6922 (pt) REVERT: G 60 THR cc_start: 0.8779 (t) cc_final: 0.8305 (m) REVERT: G 78 MET cc_start: 0.8200 (tpp) cc_final: 0.7665 (tpp) REVERT: G 82 MET cc_start: 0.7667 (mmm) cc_final: 0.7211 (mmm) REVERT: G 242 LYS cc_start: 0.7107 (mttt) cc_final: 0.6738 (mmtt) REVERT: G 291 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7387 (mptt) REVERT: G 293 LYS cc_start: 0.7671 (tttp) cc_final: 0.7407 (tttt) REVERT: G 349 LYS cc_start: 0.7971 (mmtp) cc_final: 0.7719 (mmtp) REVERT: G 454 GLN cc_start: 0.7438 (mm-40) cc_final: 0.7156 (mm-40) REVERT: G 470 ASP cc_start: 0.7752 (m-30) cc_final: 0.7486 (m-30) REVERT: G 492 LYS cc_start: 0.8394 (mtmt) cc_final: 0.8183 (mtmt) REVERT: H 62 LYS cc_start: 0.8298 (mttt) cc_final: 0.7637 (mtpt) REVERT: H 66 ILE cc_start: 0.8506 (mt) cc_final: 0.8125 (mm) REVERT: H 78 MET cc_start: 0.8231 (tpp) cc_final: 0.7785 (tpp) REVERT: H 98 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6993 (mm-30) REVERT: H 242 LYS cc_start: 0.7098 (mttt) cc_final: 0.6718 (mmtt) REVERT: H 337 MET cc_start: 0.5348 (pmt) cc_final: 0.5109 (pmt) REVERT: H 349 LYS cc_start: 0.8030 (mmtp) cc_final: 0.7786 (mmtp) REVERT: H 454 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7578 (mm-40) REVERT: H 470 ASP cc_start: 0.7780 (m-30) cc_final: 0.7504 (m-30) outliers start: 46 outliers final: 20 residues processed: 620 average time/residue: 2.6381 time to fit residues: 1880.0827 Evaluate side-chains 572 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 545 time to evaluate : 3.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 291 LYS Chi-restraints excluded: chain G residue 337 MET Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 377 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 199 optimal weight: 8.9990 chunk 163 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 240 optimal weight: 3.9990 chunk 259 optimal weight: 0.9980 chunk 213 optimal weight: 0.8980 chunk 238 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 192 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN B 454 GLN E 454 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20704 Z= 0.209 Angle : 0.541 6.059 27952 Z= 0.288 Chirality : 0.041 0.140 3240 Planarity : 0.004 0.037 3592 Dihedral : 5.145 39.137 2903 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.19 % Favored : 96.50 % Rotamer: Outliers : 3.28 % Allowed : 12.87 % Favored : 83.85 % 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: 0.70 (0.17), residues: 2632 helix: 1.85 (0.16), residues: 1176 sheet: -0.90 (0.28), residues: 264 loop : -0.61 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 92 PHE 0.010 0.001 PHE E 24 TYR 0.012 0.001 TYR H 353 ARG 0.003 0.000 ARG F 253 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 539 time to evaluate : 3.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 THR cc_start: 0.8858 (t) cc_final: 0.8444 (m) REVERT: A 75 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6625 (mt-10) REVERT: A 78 MET cc_start: 0.8191 (tpp) cc_final: 0.7688 (tpp) REVERT: A 82 MET cc_start: 0.7536 (mmm) cc_final: 0.7176 (mmm) REVERT: A 94 ASN cc_start: 0.8110 (m110) cc_final: 0.7722 (t0) REVERT: A 233 TYR cc_start: 0.8309 (m-80) cc_final: 0.7941 (m-80) REVERT: A 242 LYS cc_start: 0.7129 (mttt) cc_final: 0.6784 (mmtt) REVERT: A 255 ASP cc_start: 0.8228 (p0) cc_final: 0.7947 (p0) REVERT: A 274 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7246 (m-30) REVERT: A 349 LYS cc_start: 0.8047 (mmtp) cc_final: 0.7739 (mmtt) REVERT: A 454 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.6471 (mm-40) REVERT: A 495 MET cc_start: 0.7526 (tpt) cc_final: 0.7104 (mmt) REVERT: B 1 MET cc_start: 0.6352 (OUTLIER) cc_final: 0.5888 (tpp) REVERT: B 60 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8388 (m) REVERT: B 66 ILE cc_start: 0.8529 (mt) cc_final: 0.8153 (mm) REVERT: B 75 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6541 (mt-10) REVERT: B 78 MET cc_start: 0.8215 (tpp) cc_final: 0.7802 (tpp) REVERT: B 94 ASN cc_start: 0.8035 (m110) cc_final: 0.7688 (t0) REVERT: B 242 LYS cc_start: 0.7215 (mttt) cc_final: 0.6908 (mmtt) REVERT: B 349 LYS cc_start: 0.8049 (mmtp) cc_final: 0.7791 (mmtp) REVERT: C 1 MET cc_start: 0.6311 (OUTLIER) cc_final: 0.5845 (tpp) REVERT: C 66 ILE cc_start: 0.8519 (mt) cc_final: 0.8203 (mm) REVERT: C 78 MET cc_start: 0.8151 (tpp) cc_final: 0.7774 (tpp) REVERT: C 242 LYS cc_start: 0.7253 (mttt) cc_final: 0.6942 (mmtt) REVERT: C 255 ASP cc_start: 0.8202 (p0) cc_final: 0.7883 (p0) REVERT: C 319 ASP cc_start: 0.7897 (m-30) cc_final: 0.7617 (m-30) REVERT: C 500 GLU cc_start: 0.6777 (tp30) cc_final: 0.6512 (tt0) REVERT: D 21 GLN cc_start: 0.8067 (tt0) cc_final: 0.7860 (tt0) REVERT: D 48 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7189 (mt-10) REVERT: D 60 THR cc_start: 0.8869 (OUTLIER) cc_final: 0.8379 (m) REVERT: D 62 LYS cc_start: 0.8312 (mttt) cc_final: 0.7662 (mtpt) REVERT: D 66 ILE cc_start: 0.8524 (mt) cc_final: 0.8183 (mm) REVERT: D 78 MET cc_start: 0.8146 (tpp) cc_final: 0.7698 (tpp) REVERT: D 82 MET cc_start: 0.7588 (mmm) cc_final: 0.7202 (mmm) REVERT: D 233 TYR cc_start: 0.8322 (m-80) cc_final: 0.8066 (m-80) REVERT: D 242 LYS cc_start: 0.7247 (mttt) cc_final: 0.6859 (mmmt) REVERT: D 322 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.7242 (ttm170) REVERT: D 349 LYS cc_start: 0.8023 (mmtp) cc_final: 0.7773 (mmtp) REVERT: E 66 ILE cc_start: 0.8530 (mt) cc_final: 0.8196 (mm) REVERT: E 78 MET cc_start: 0.8182 (tpp) cc_final: 0.7807 (tpp) REVERT: E 242 LYS cc_start: 0.7227 (mttt) cc_final: 0.6852 (mmtt) REVERT: E 322 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.7259 (ttm170) REVERT: E 349 LYS cc_start: 0.7994 (mmtp) cc_final: 0.7745 (mmtp) REVERT: F 60 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8401 (m) REVERT: F 62 LYS cc_start: 0.8271 (mttt) cc_final: 0.7981 (mtpt) REVERT: F 78 MET cc_start: 0.8174 (tpp) cc_final: 0.7624 (tpp) REVERT: F 82 MET cc_start: 0.7517 (mmm) cc_final: 0.7291 (mmm) REVERT: F 85 MET cc_start: 0.7348 (mmm) cc_final: 0.7039 (mmm) REVERT: F 98 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6964 (mm-30) REVERT: F 242 LYS cc_start: 0.7200 (mttt) cc_final: 0.6816 (mmtt) REVERT: F 291 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7372 (mptt) REVERT: F 349 LYS cc_start: 0.8036 (mmtp) cc_final: 0.7705 (mmtt) REVERT: F 470 ASP cc_start: 0.7730 (m-30) cc_final: 0.7428 (m-30) REVERT: G 45 ILE cc_start: 0.7179 (OUTLIER) cc_final: 0.6920 (pt) REVERT: G 60 THR cc_start: 0.8884 (t) cc_final: 0.8452 (m) REVERT: G 66 ILE cc_start: 0.8534 (mt) cc_final: 0.8229 (mm) REVERT: G 78 MET cc_start: 0.8197 (tpp) cc_final: 0.7707 (tpp) REVERT: G 82 MET cc_start: 0.7556 (mmm) cc_final: 0.7205 (mmm) REVERT: G 85 MET cc_start: 0.7472 (mmm) cc_final: 0.7256 (mmm) REVERT: G 242 LYS cc_start: 0.7157 (mttt) cc_final: 0.6815 (mmtt) REVERT: G 335 GLU cc_start: 0.5306 (OUTLIER) cc_final: 0.4457 (mp0) REVERT: G 349 LYS cc_start: 0.8105 (mmtp) cc_final: 0.7824 (mmtp) REVERT: G 454 GLN cc_start: 0.7372 (mm-40) cc_final: 0.7160 (mm-40) REVERT: G 470 ASP cc_start: 0.7768 (m-30) cc_final: 0.7471 (m-30) REVERT: H 66 ILE cc_start: 0.8493 (mt) cc_final: 0.8117 (mm) REVERT: H 78 MET cc_start: 0.8113 (tpp) cc_final: 0.7725 (tpp) REVERT: H 98 GLU cc_start: 0.7282 (mm-30) cc_final: 0.7050 (mm-30) REVERT: H 242 LYS cc_start: 0.7077 (mttt) cc_final: 0.6741 (mmtt) REVERT: H 322 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7250 (ttm170) REVERT: H 337 MET cc_start: 0.5350 (pmt) cc_final: 0.5147 (pmt) REVERT: H 349 LYS cc_start: 0.7988 (mmtp) cc_final: 0.7653 (mmtt) outliers start: 70 outliers final: 23 residues processed: 582 average time/residue: 2.7743 time to fit residues: 1845.6975 Evaluate side-chains 547 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 511 time to evaluate : 3.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -9 LEU Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue -9 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain E residue -9 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 274 ASP Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 454 GLN Chi-restraints excluded: chain F residue -9 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 322 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 1.9990 chunk 180 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 241 optimal weight: 1.9990 chunk 255 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 228 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN A 343 GLN B 312 ASN C 241 GLN C 343 GLN C 454 GLN E 283 GLN F 454 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 ASN G 343 GLN H 312 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20704 Z= 0.277 Angle : 0.548 6.633 27952 Z= 0.292 Chirality : 0.042 0.143 3240 Planarity : 0.004 0.032 3592 Dihedral : 4.860 30.787 2897 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.31 % Favored : 96.39 % Rotamer: Outliers : 3.23 % Allowed : 14.19 % Favored : 82.58 % 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: 0.75 (0.17), residues: 2632 helix: 1.90 (0.16), residues: 1184 sheet: -0.96 (0.28), residues: 264 loop : -0.57 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H -20 PHE 0.011 0.002 PHE H 110 TYR 0.013 0.001 TYR G 353 ARG 0.003 0.000 ARG F 253 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 528 time to evaluate : 3.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 THR cc_start: 0.8845 (t) cc_final: 0.8443 (m) REVERT: A 66 ILE cc_start: 0.8614 (mt) cc_final: 0.8274 (mm) REVERT: A 75 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6645 (mt-10) REVERT: A 78 MET cc_start: 0.8167 (tpp) cc_final: 0.7570 (tpp) REVERT: A 82 MET cc_start: 0.7522 (mmm) cc_final: 0.7180 (mmm) REVERT: A 94 ASN cc_start: 0.8120 (m110) cc_final: 0.7763 (t0) REVERT: A 233 TYR cc_start: 0.8341 (m-80) cc_final: 0.8079 (m-80) REVERT: A 242 LYS cc_start: 0.7176 (mttt) cc_final: 0.6833 (mmtt) REVERT: A 255 ASP cc_start: 0.8137 (p0) cc_final: 0.7882 (p0) REVERT: A 274 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7312 (m-30) REVERT: A 349 LYS cc_start: 0.8096 (mmtp) cc_final: 0.7800 (mmtt) REVERT: B 1 MET cc_start: 0.6273 (OUTLIER) cc_final: 0.5675 (tpp) REVERT: B 60 THR cc_start: 0.8900 (OUTLIER) cc_final: 0.8429 (m) REVERT: B 66 ILE cc_start: 0.8622 (mt) cc_final: 0.8230 (mm) REVERT: B 75 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6540 (mt-10) REVERT: B 78 MET cc_start: 0.8193 (tpp) cc_final: 0.7724 (tpp) REVERT: B 94 ASN cc_start: 0.8082 (m110) cc_final: 0.7722 (t0) REVERT: B 242 LYS cc_start: 0.7265 (mttt) cc_final: 0.6978 (mmtt) REVERT: B 277 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.5873 (tm-30) REVERT: B 349 LYS cc_start: 0.8079 (mmtp) cc_final: 0.7769 (mmtt) REVERT: C 1 MET cc_start: 0.6188 (OUTLIER) cc_final: 0.5694 (tpp) REVERT: C 28 ASP cc_start: 0.7429 (p0) cc_final: 0.7185 (p0) REVERT: C 60 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8399 (m) REVERT: C 66 ILE cc_start: 0.8558 (mt) cc_final: 0.8236 (mm) REVERT: C 78 MET cc_start: 0.8117 (tpp) cc_final: 0.7827 (tpp) REVERT: C 233 TYR cc_start: 0.8272 (m-80) cc_final: 0.7696 (m-80) REVERT: C 242 LYS cc_start: 0.7302 (mttt) cc_final: 0.6982 (mmtt) REVERT: C 255 ASP cc_start: 0.8119 (p0) cc_final: 0.7872 (p0) REVERT: C 277 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.5895 (tm-30) REVERT: C 319 ASP cc_start: 0.7958 (m-30) cc_final: 0.7711 (m-30) REVERT: C 322 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.7417 (ttm170) REVERT: C 454 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.6408 (mm-40) REVERT: C 495 MET cc_start: 0.7086 (mmm) cc_final: 0.6812 (mmm) REVERT: C 500 GLU cc_start: 0.6782 (tp30) cc_final: 0.6528 (tt0) REVERT: D 21 GLN cc_start: 0.8049 (tt0) cc_final: 0.7846 (tt0) REVERT: D 48 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7242 (mt-10) REVERT: D 60 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8400 (m) REVERT: D 66 ILE cc_start: 0.8547 (mt) cc_final: 0.8224 (mm) REVERT: D 78 MET cc_start: 0.8108 (tpp) cc_final: 0.7664 (tpp) REVERT: D 242 LYS cc_start: 0.7280 (mttt) cc_final: 0.6891 (mmmt) REVERT: D 322 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7318 (ttm170) REVERT: D 349 LYS cc_start: 0.8025 (mmtp) cc_final: 0.7680 (mmtt) REVERT: E 60 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8428 (m) REVERT: E 66 ILE cc_start: 0.8563 (mt) cc_final: 0.8245 (mm) REVERT: E 78 MET cc_start: 0.8216 (tpp) cc_final: 0.7911 (tpp) REVERT: E 242 LYS cc_start: 0.7295 (mttt) cc_final: 0.6920 (mmtt) REVERT: E 277 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.6109 (tm-30) REVERT: E 322 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.7373 (ttm170) REVERT: E 349 LYS cc_start: 0.8006 (mmtp) cc_final: 0.7637 (mmtt) REVERT: F 60 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8408 (m) REVERT: F 62 LYS cc_start: 0.8259 (mttt) cc_final: 0.8013 (mtpt) REVERT: F 75 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6561 (mt-10) REVERT: F 78 MET cc_start: 0.8174 (tpp) cc_final: 0.7755 (tpp) REVERT: F 85 MET cc_start: 0.7409 (mmm) cc_final: 0.6987 (mmm) REVERT: F 98 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7030 (mm-30) REVERT: F 242 LYS cc_start: 0.7253 (mttt) cc_final: 0.6864 (mmtt) REVERT: F 277 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.5943 (tm-30) REVERT: F 349 LYS cc_start: 0.8092 (mmtp) cc_final: 0.7783 (mmtt) REVERT: F 470 ASP cc_start: 0.7808 (m-30) cc_final: 0.7435 (m-30) REVERT: G 45 ILE cc_start: 0.7202 (OUTLIER) cc_final: 0.6933 (pt) REVERT: G 60 THR cc_start: 0.8890 (t) cc_final: 0.8465 (m) REVERT: G 66 ILE cc_start: 0.8623 (mt) cc_final: 0.8295 (mm) REVERT: G 78 MET cc_start: 0.8198 (tpp) cc_final: 0.7634 (tpp) REVERT: G 82 MET cc_start: 0.7562 (mmm) cc_final: 0.7229 (mmm) REVERT: G 242 LYS cc_start: 0.7274 (mttt) cc_final: 0.6900 (mmmt) REVERT: G 277 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.5947 (tm-30) REVERT: G 335 GLU cc_start: 0.5382 (OUTLIER) cc_final: 0.4628 (mp0) REVERT: G 349 LYS cc_start: 0.8102 (mmtp) cc_final: 0.7757 (mmtt) REVERT: G 454 GLN cc_start: 0.7381 (mm-40) cc_final: 0.7162 (mm-40) REVERT: G 470 ASP cc_start: 0.7784 (m-30) cc_final: 0.7525 (m-30) REVERT: H 60 THR cc_start: 0.8885 (OUTLIER) cc_final: 0.8402 (m) REVERT: H 66 ILE cc_start: 0.8608 (mt) cc_final: 0.8209 (mm) REVERT: H 98 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7069 (mm-30) REVERT: H 242 LYS cc_start: 0.7160 (mttt) cc_final: 0.6824 (mmtt) REVERT: H 322 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7292 (ttm170) REVERT: H 349 LYS cc_start: 0.8007 (mmtp) cc_final: 0.7668 (mmtt) outliers start: 69 outliers final: 39 residues processed: 574 average time/residue: 2.8321 time to fit residues: 1856.1505 Evaluate side-chains 574 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 514 time to evaluate : 3.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -9 LEU Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue -9 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 454 GLN Chi-restraints excluded: chain D residue -9 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue -9 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 274 ASP Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain F residue -9 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 454 GLN Chi-restraints excluded: chain G residue -9 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 337 MET Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 322 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 217 optimal weight: 0.9980 chunk 176 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 130 optimal weight: 0.5980 chunk 229 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 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 343 GLN A 454 GLN C 343 GLN D 343 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 ASN E 343 GLN F 283 GLN F 343 GLN G 283 GLN G 343 GLN H 343 GLN H 454 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20704 Z= 0.235 Angle : 0.527 6.361 27952 Z= 0.279 Chirality : 0.041 0.140 3240 Planarity : 0.004 0.032 3592 Dihedral : 4.723 21.628 2896 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.27 % Favored : 96.43 % Rotamer: Outliers : 3.46 % Allowed : 15.22 % Favored : 81.32 % 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: 0.89 (0.17), residues: 2632 helix: 2.06 (0.16), residues: 1184 sheet: -0.89 (0.27), residues: 264 loop : -0.56 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H -20 PHE 0.008 0.001 PHE H 110 TYR 0.012 0.001 TYR G 353 ARG 0.002 0.000 ARG F 253 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 529 time to evaluate : 3.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 THR cc_start: 0.8868 (t) cc_final: 0.8467 (m) REVERT: A 66 ILE cc_start: 0.8593 (mt) cc_final: 0.8257 (mm) REVERT: A 75 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6599 (mt-10) REVERT: A 78 MET cc_start: 0.8175 (tpp) cc_final: 0.7766 (tpp) REVERT: A 94 ASN cc_start: 0.8127 (m110) cc_final: 0.7793 (t0) REVERT: A 233 TYR cc_start: 0.8335 (m-80) cc_final: 0.8117 (m-80) REVERT: A 242 LYS cc_start: 0.7191 (mttt) cc_final: 0.6861 (mmtt) REVERT: A 255 ASP cc_start: 0.8122 (p0) cc_final: 0.7902 (p0) REVERT: A 274 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7311 (m-30) REVERT: A 349 LYS cc_start: 0.8072 (mmtp) cc_final: 0.7776 (mmtt) REVERT: B 1 MET cc_start: 0.6065 (OUTLIER) cc_final: 0.5417 (tmm) REVERT: B 60 THR cc_start: 0.8900 (OUTLIER) cc_final: 0.8437 (m) REVERT: B 62 LYS cc_start: 0.8275 (mmtp) cc_final: 0.7692 (mmmm) REVERT: B 66 ILE cc_start: 0.8581 (mt) cc_final: 0.8192 (mm) REVERT: B 75 GLU cc_start: 0.6739 (mt-10) cc_final: 0.6424 (mt-10) REVERT: B 78 MET cc_start: 0.8174 (tpp) cc_final: 0.7892 (tpp) REVERT: B 94 ASN cc_start: 0.8076 (m110) cc_final: 0.7722 (t0) REVERT: B 277 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.5825 (tm-30) REVERT: B 349 LYS cc_start: 0.8050 (mmtp) cc_final: 0.7738 (mmtt) REVERT: C 1 MET cc_start: 0.6153 (OUTLIER) cc_final: 0.5556 (tpp) REVERT: C 28 ASP cc_start: 0.7424 (p0) cc_final: 0.7069 (p0) REVERT: C 60 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8405 (m) REVERT: C 62 LYS cc_start: 0.8190 (mmtp) cc_final: 0.7591 (mmmm) REVERT: C 66 ILE cc_start: 0.8557 (mt) cc_final: 0.8237 (mm) REVERT: C 78 MET cc_start: 0.8115 (tpp) cc_final: 0.7699 (tpp) REVERT: C 233 TYR cc_start: 0.8202 (m-80) cc_final: 0.7946 (m-80) REVERT: C 242 LYS cc_start: 0.7316 (mttt) cc_final: 0.7017 (mmtt) REVERT: C 255 ASP cc_start: 0.8095 (p0) cc_final: 0.7870 (p0) REVERT: C 319 ASP cc_start: 0.7970 (m-30) cc_final: 0.7704 (m-30) REVERT: C 322 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.7402 (ttm170) REVERT: C 500 GLU cc_start: 0.6784 (tp30) cc_final: 0.6539 (tt0) REVERT: D 21 GLN cc_start: 0.8037 (tt0) cc_final: 0.7836 (tt0) REVERT: D 48 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7183 (mt-10) REVERT: D 60 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8409 (m) REVERT: D 66 ILE cc_start: 0.8554 (mt) cc_final: 0.8237 (mm) REVERT: D 78 MET cc_start: 0.8010 (tpp) cc_final: 0.7692 (tpp) REVERT: D 242 LYS cc_start: 0.7337 (mttt) cc_final: 0.6953 (mmmt) REVERT: D 277 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.5772 (tm-30) REVERT: D 322 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7348 (ttm170) REVERT: D 349 LYS cc_start: 0.8054 (mmtp) cc_final: 0.7718 (mmtt) REVERT: E 60 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8441 (m) REVERT: E 62 LYS cc_start: 0.8272 (mmtm) cc_final: 0.7664 (mmmt) REVERT: E 66 ILE cc_start: 0.8562 (mt) cc_final: 0.8253 (mm) REVERT: E 78 MET cc_start: 0.8181 (tpp) cc_final: 0.7811 (tpp) REVERT: E 242 LYS cc_start: 0.7331 (mttt) cc_final: 0.6963 (mmtt) REVERT: E 322 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.7351 (ttm170) REVERT: E 349 LYS cc_start: 0.8007 (mmtp) cc_final: 0.7675 (mmtt) REVERT: F 60 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8414 (m) REVERT: F 62 LYS cc_start: 0.8248 (mttt) cc_final: 0.8003 (mtpt) REVERT: F 78 MET cc_start: 0.8161 (tpp) cc_final: 0.7728 (tpp) REVERT: F 98 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7048 (mm-30) REVERT: F 242 LYS cc_start: 0.7263 (mttt) cc_final: 0.6849 (mmmt) REVERT: F 277 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.5810 (tm-30) REVERT: F 349 LYS cc_start: 0.8044 (mmtp) cc_final: 0.7742 (mmtt) REVERT: G 45 ILE cc_start: 0.7180 (OUTLIER) cc_final: 0.6906 (pt) REVERT: G 60 THR cc_start: 0.8894 (t) cc_final: 0.8471 (m) REVERT: G 62 LYS cc_start: 0.8203 (mmtp) cc_final: 0.7559 (mmmt) REVERT: G 66 ILE cc_start: 0.8579 (mt) cc_final: 0.8252 (mm) REVERT: G 78 MET cc_start: 0.8156 (tpp) cc_final: 0.7528 (tpp) REVERT: G 82 MET cc_start: 0.7539 (mmm) cc_final: 0.7215 (mmm) REVERT: G 242 LYS cc_start: 0.7284 (mttt) cc_final: 0.6915 (mmmt) REVERT: G 277 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.5778 (tm-30) REVERT: G 335 GLU cc_start: 0.5421 (OUTLIER) cc_final: 0.4778 (mp0) REVERT: G 349 LYS cc_start: 0.8089 (mmtp) cc_final: 0.7750 (mmtt) REVERT: H 60 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8410 (m) REVERT: H 66 ILE cc_start: 0.8622 (mt) cc_final: 0.8240 (mm) REVERT: H 98 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7110 (mm-30) REVERT: H 242 LYS cc_start: 0.7221 (mttt) cc_final: 0.6875 (mmtt) REVERT: H 322 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.7351 (ttm170) REVERT: H 349 LYS cc_start: 0.8044 (mmtp) cc_final: 0.7730 (mmtt) REVERT: H 454 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.6156 (mm-40) outliers start: 74 outliers final: 37 residues processed: 580 average time/residue: 2.8495 time to fit residues: 1891.3754 Evaluate side-chains 581 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 524 time to evaluate : 3.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -9 LEU Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue -9 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain D residue -9 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain E residue -9 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 274 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue -9 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain G residue -9 LEU Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 454 GLN Chi-restraints excluded: chain H residue 496 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 50 optimal weight: 0.0570 chunk 149 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 255 optimal weight: 0.0570 chunk 212 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 overall best weight: 0.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN A 454 GLN B 21 GLN B 454 GLN C 343 GLN C 454 GLN D 343 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 GLN G 454 GLN H 454 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20704 Z= 0.200 Angle : 0.514 6.198 27952 Z= 0.270 Chirality : 0.040 0.136 3240 Planarity : 0.003 0.032 3592 Dihedral : 4.607 21.833 2896 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.04 % Favored : 96.66 % Rotamer: Outliers : 3.46 % Allowed : 15.50 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.17), residues: 2632 helix: 2.23 (0.16), residues: 1184 sheet: -0.78 (0.27), residues: 264 loop : -0.51 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H -20 PHE 0.007 0.001 PHE G 24 TYR 0.012 0.001 TYR A 353 ARG 0.002 0.000 ARG F 253 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 543 time to evaluate : 3.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 THR cc_start: 0.8876 (t) cc_final: 0.8471 (m) REVERT: A 66 ILE cc_start: 0.8603 (mt) cc_final: 0.8267 (mm) REVERT: A 75 GLU cc_start: 0.6731 (mt-10) cc_final: 0.6438 (mt-10) REVERT: A 78 MET cc_start: 0.8173 (tpp) cc_final: 0.7758 (tpp) REVERT: A 94 ASN cc_start: 0.8138 (m110) cc_final: 0.7815 (t0) REVERT: A 255 ASP cc_start: 0.8084 (p0) cc_final: 0.7880 (p0) REVERT: A 274 ASP cc_start: 0.7648 (OUTLIER) cc_final: 0.7216 (m-30) REVERT: A 277 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.5788 (tm-30) REVERT: A 349 LYS cc_start: 0.8006 (mmtp) cc_final: 0.7716 (mmtt) REVERT: B 1 MET cc_start: 0.6005 (OUTLIER) cc_final: 0.5373 (tmm) REVERT: B 60 THR cc_start: 0.8901 (OUTLIER) cc_final: 0.8445 (m) REVERT: B 62 LYS cc_start: 0.8286 (mmtp) cc_final: 0.7684 (mmmm) REVERT: B 66 ILE cc_start: 0.8579 (mt) cc_final: 0.8196 (mm) REVERT: B 75 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6320 (mm-30) REVERT: B 94 ASN cc_start: 0.8078 (m110) cc_final: 0.7733 (t0) REVERT: B 349 LYS cc_start: 0.8040 (mmtp) cc_final: 0.7814 (mmtp) REVERT: B 454 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7022 (mt0) REVERT: C 1 MET cc_start: 0.5959 (OUTLIER) cc_final: 0.5217 (tpp) REVERT: C 28 ASP cc_start: 0.7144 (p0) cc_final: 0.6864 (p0) REVERT: C 60 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8420 (m) REVERT: C 62 LYS cc_start: 0.8195 (mmtp) cc_final: 0.7590 (mmmm) REVERT: C 66 ILE cc_start: 0.8552 (mt) cc_final: 0.8251 (mm) REVERT: C 242 LYS cc_start: 0.7308 (mttt) cc_final: 0.6992 (mmmt) REVERT: C 255 ASP cc_start: 0.8107 (p0) cc_final: 0.7900 (p0) REVERT: C 277 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.5816 (tm-30) REVERT: C 322 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7395 (ttm170) REVERT: C 454 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7198 (mt0) REVERT: C 500 GLU cc_start: 0.6757 (tp30) cc_final: 0.6553 (tt0) REVERT: D 48 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7200 (mt-10) REVERT: D 60 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8414 (m) REVERT: D 66 ILE cc_start: 0.8552 (mt) cc_final: 0.8246 (mm) REVERT: D 75 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6410 (mt-10) REVERT: D 242 LYS cc_start: 0.7325 (mttt) cc_final: 0.6952 (mmmt) REVERT: D 255 ASP cc_start: 0.8114 (p0) cc_final: 0.7904 (p0) REVERT: D 277 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.5731 (tm-30) REVERT: D 322 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.7351 (ttm170) REVERT: D 349 LYS cc_start: 0.8051 (mmtp) cc_final: 0.7812 (mmtp) REVERT: D 500 GLU cc_start: 0.6068 (tt0) cc_final: 0.5664 (pt0) REVERT: E 60 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8447 (m) REVERT: E 62 LYS cc_start: 0.8275 (mmtm) cc_final: 0.7709 (mmmm) REVERT: E 66 ILE cc_start: 0.8553 (mt) cc_final: 0.8251 (mm) REVERT: E 78 MET cc_start: 0.8120 (tpp) cc_final: 0.7722 (tpp) REVERT: E 242 LYS cc_start: 0.7327 (mttt) cc_final: 0.6982 (mmtt) REVERT: E 322 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.7346 (ttm170) REVERT: E 349 LYS cc_start: 0.7996 (mmtp) cc_final: 0.7770 (mmtp) REVERT: F 60 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8428 (m) REVERT: F 62 LYS cc_start: 0.8231 (mttt) cc_final: 0.7993 (mtpt) REVERT: F 78 MET cc_start: 0.8141 (tpp) cc_final: 0.7686 (tpp) REVERT: F 98 GLU cc_start: 0.7318 (mm-30) cc_final: 0.7050 (mm-30) REVERT: F 242 LYS cc_start: 0.7238 (mttt) cc_final: 0.6848 (mmmt) REVERT: F 277 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.5790 (tm-30) REVERT: F 349 LYS cc_start: 0.8038 (mmtp) cc_final: 0.7744 (mmtt) REVERT: G 45 ILE cc_start: 0.7152 (OUTLIER) cc_final: 0.6865 (pt) REVERT: G 60 THR cc_start: 0.8899 (t) cc_final: 0.8478 (m) REVERT: G 62 LYS cc_start: 0.8205 (mmtp) cc_final: 0.7586 (mmmm) REVERT: G 66 ILE cc_start: 0.8616 (mt) cc_final: 0.8293 (mm) REVERT: G 78 MET cc_start: 0.8120 (tpp) cc_final: 0.7803 (tpp) REVERT: G 85 MET cc_start: 0.7158 (mmm) cc_final: 0.6935 (mmm) REVERT: G 242 LYS cc_start: 0.7338 (mttt) cc_final: 0.6952 (mmmt) REVERT: G 277 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.5730 (tm-30) REVERT: G 335 GLU cc_start: 0.5358 (OUTLIER) cc_final: 0.4779 (mp0) REVERT: G 349 LYS cc_start: 0.8063 (mmtp) cc_final: 0.7803 (mmtp) REVERT: H 60 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8417 (m) REVERT: H 66 ILE cc_start: 0.8581 (mt) cc_final: 0.8183 (mm) REVERT: H 98 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7125 (mm-30) REVERT: H 242 LYS cc_start: 0.7209 (mttt) cc_final: 0.6878 (mmtt) REVERT: H 254 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7506 (tp30) REVERT: H 349 LYS cc_start: 0.8050 (mmtp) cc_final: 0.7740 (mmtt) outliers start: 74 outliers final: 40 residues processed: 591 average time/residue: 2.7869 time to fit residues: 1884.0769 Evaluate side-chains 580 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 518 time to evaluate : 3.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -9 LEU Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain B residue -9 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 454 GLN Chi-restraints excluded: chain D residue -9 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain E residue -9 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue -9 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue -9 LEU Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 454 GLN Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 496 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 254 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN A 454 GLN B 21 GLN B 343 GLN B 454 GLN C 241 GLN C 343 GLN D 343 GLN D 454 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN F 241 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 GLN G 454 GLN H 343 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20704 Z= 0.325 Angle : 0.561 6.347 27952 Z= 0.298 Chirality : 0.042 0.146 3240 Planarity : 0.004 0.032 3592 Dihedral : 4.736 21.913 2896 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.38 % Favored : 96.31 % Rotamer: Outliers : 3.84 % Allowed : 15.54 % Favored : 80.62 % 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: 0.88 (0.17), residues: 2632 helix: 2.03 (0.15), residues: 1168 sheet: -0.79 (0.26), residues: 264 loop : -0.53 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 296 PHE 0.014 0.002 PHE C 110 TYR 0.013 0.002 TYR C 233 ARG 0.005 0.001 ARG G 253 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 517 time to evaluate : 3.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 THR cc_start: 0.8887 (t) cc_final: 0.8486 (m) REVERT: A 62 LYS cc_start: 0.8177 (mmtp) cc_final: 0.7511 (mmmt) REVERT: A 78 MET cc_start: 0.8130 (tpp) cc_final: 0.7723 (tpp) REVERT: A 94 ASN cc_start: 0.8137 (m110) cc_final: 0.7810 (t0) REVERT: A 274 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7295 (m-30) REVERT: A 277 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.5811 (tm-30) REVERT: A 349 LYS cc_start: 0.8059 (mmtp) cc_final: 0.7774 (mmtt) REVERT: A 470 ASP cc_start: 0.7680 (m-30) cc_final: 0.7165 (m-30) REVERT: B 60 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8518 (m) REVERT: B 62 LYS cc_start: 0.8264 (mmtp) cc_final: 0.7670 (mmmm) REVERT: B 66 ILE cc_start: 0.8626 (mt) cc_final: 0.8224 (mm) REVERT: B 75 GLU cc_start: 0.6720 (mt-10) cc_final: 0.6370 (mt-10) REVERT: B 94 ASN cc_start: 0.8068 (m110) cc_final: 0.7706 (t0) REVERT: B 277 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.5799 (tm-30) REVERT: B 349 LYS cc_start: 0.8054 (mmtp) cc_final: 0.7746 (mmtt) REVERT: B 394 THR cc_start: 0.8377 (m) cc_final: 0.7977 (t) REVERT: C 28 ASP cc_start: 0.7183 (p0) cc_final: 0.6909 (p0) REVERT: C 60 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8492 (m) REVERT: C 62 LYS cc_start: 0.8228 (mmtp) cc_final: 0.7602 (mmmm) REVERT: C 66 ILE cc_start: 0.8569 (mt) cc_final: 0.8264 (mm) REVERT: C 78 MET cc_start: 0.7807 (tpp) cc_final: 0.7585 (tpp) REVERT: C 242 LYS cc_start: 0.7343 (mttt) cc_final: 0.6992 (mmmt) REVERT: C 277 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.5809 (tm-30) REVERT: C 322 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.7432 (ttm170) REVERT: C 500 GLU cc_start: 0.6813 (tp30) cc_final: 0.6576 (tt0) REVERT: D 48 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7210 (mt-10) REVERT: D 60 THR cc_start: 0.8899 (OUTLIER) cc_final: 0.8442 (m) REVERT: D 66 ILE cc_start: 0.8560 (mt) cc_final: 0.8242 (mm) REVERT: D 242 LYS cc_start: 0.7387 (mttt) cc_final: 0.7025 (mmmt) REVERT: D 274 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7193 (m-30) REVERT: D 277 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.5860 (tm-30) REVERT: D 322 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7335 (ttm170) REVERT: D 349 LYS cc_start: 0.8095 (mmtp) cc_final: 0.7786 (mmtt) REVERT: D 500 GLU cc_start: 0.6060 (tt0) cc_final: 0.5396 (pt0) REVERT: E 21 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7879 (mt0) REVERT: E 60 THR cc_start: 0.8915 (OUTLIER) cc_final: 0.8464 (m) REVERT: E 62 LYS cc_start: 0.8264 (mmtm) cc_final: 0.7695 (mmmm) REVERT: E 66 ILE cc_start: 0.8572 (mt) cc_final: 0.8263 (mm) REVERT: E 78 MET cc_start: 0.8096 (tpp) cc_final: 0.7719 (tpp) REVERT: E 242 LYS cc_start: 0.7316 (mttt) cc_final: 0.6967 (mmtt) REVERT: E 274 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7296 (m-30) REVERT: E 277 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.5825 (tm-30) REVERT: E 322 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7333 (ttm170) REVERT: E 349 LYS cc_start: 0.8023 (mmtp) cc_final: 0.7698 (mmtt) REVERT: F 60 THR cc_start: 0.8898 (OUTLIER) cc_final: 0.8449 (m) REVERT: F 62 LYS cc_start: 0.8224 (mttt) cc_final: 0.7987 (mtpt) REVERT: F 75 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6511 (mt-10) REVERT: F 78 MET cc_start: 0.8112 (tpp) cc_final: 0.7775 (tpp) REVERT: F 98 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7135 (mm-30) REVERT: F 233 TYR cc_start: 0.8087 (m-10) cc_final: 0.7777 (m-80) REVERT: F 242 LYS cc_start: 0.7313 (mttt) cc_final: 0.6906 (mmmt) REVERT: F 277 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.6097 (tm-30) REVERT: F 349 LYS cc_start: 0.8052 (mmtp) cc_final: 0.7756 (mmtt) REVERT: F 496 SER cc_start: 0.7421 (OUTLIER) cc_final: 0.7095 (m) REVERT: G 45 ILE cc_start: 0.7168 (OUTLIER) cc_final: 0.6862 (pt) REVERT: G 60 THR cc_start: 0.8878 (t) cc_final: 0.8471 (m) REVERT: G 62 LYS cc_start: 0.8197 (mmtp) cc_final: 0.7574 (mmmm) REVERT: G 78 MET cc_start: 0.8103 (tpp) cc_final: 0.7703 (tpp) REVERT: G 242 LYS cc_start: 0.7412 (mttt) cc_final: 0.7013 (mmmt) REVERT: G 277 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.5805 (tm-30) REVERT: G 335 GLU cc_start: 0.5271 (OUTLIER) cc_final: 0.4663 (mp0) REVERT: G 349 LYS cc_start: 0.8066 (mmtp) cc_final: 0.7764 (mmtt) REVERT: H 60 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8445 (m) REVERT: H 66 ILE cc_start: 0.8654 (mt) cc_final: 0.8256 (mm) REVERT: H 94 ASN cc_start: 0.7977 (m-40) cc_final: 0.7719 (t0) REVERT: H 98 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7126 (mm-30) REVERT: H 242 LYS cc_start: 0.7224 (mttt) cc_final: 0.6868 (mmtt) REVERT: H 274 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7254 (m-30) REVERT: H 277 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.5817 (tm-30) REVERT: H 349 LYS cc_start: 0.8067 (mmtp) cc_final: 0.7763 (mmtt) outliers start: 82 outliers final: 47 residues processed: 571 average time/residue: 2.8427 time to fit residues: 1857.5090 Evaluate side-chains 592 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 520 time to evaluate : 3.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -9 LEU Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain B residue -9 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain D residue -9 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 454 GLN Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue -9 LEU Chi-restraints excluded: chain E residue 21 GLN Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 274 ASP Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue -9 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue -9 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 496 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 161 optimal weight: 0.1980 chunk 173 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 200 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN A 454 GLN B 21 GLN C 343 GLN D 343 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20704 Z= 0.199 Angle : 0.518 6.271 27952 Z= 0.272 Chirality : 0.040 0.135 3240 Planarity : 0.003 0.032 3592 Dihedral : 4.591 22.283 2896 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.93 % Favored : 96.77 % Rotamer: Outliers : 3.00 % Allowed : 16.48 % Favored : 80.52 % 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: 1.22 (0.17), residues: 2632 helix: 2.35 (0.16), residues: 1168 sheet: -0.64 (0.27), residues: 264 loop : -0.39 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 296 PHE 0.007 0.001 PHE E 24 TYR 0.012 0.001 TYR A 353 ARG 0.005 0.000 ARG G 253 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 543 time to evaluate : 3.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 THR cc_start: 0.8880 (t) cc_final: 0.8475 (m) REVERT: A 62 LYS cc_start: 0.8170 (mmtp) cc_final: 0.7511 (mmmt) REVERT: A 66 ILE cc_start: 0.8574 (mt) cc_final: 0.8270 (mm) REVERT: A 78 MET cc_start: 0.8087 (tpp) cc_final: 0.7681 (tpp) REVERT: A 274 ASP cc_start: 0.7747 (t0) cc_final: 0.7320 (m-30) REVERT: A 277 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.5419 (tm-30) REVERT: A 349 LYS cc_start: 0.8040 (mmtp) cc_final: 0.7756 (mmtt) REVERT: B 1 MET cc_start: 0.5824 (OUTLIER) cc_final: 0.5140 (tmm) REVERT: B 60 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8502 (m) REVERT: B 62 LYS cc_start: 0.8257 (mmtp) cc_final: 0.7657 (mmmm) REVERT: B 66 ILE cc_start: 0.8595 (mt) cc_final: 0.8199 (mm) REVERT: B 75 GLU cc_start: 0.6786 (mt-10) cc_final: 0.6287 (mm-30) REVERT: B 94 ASN cc_start: 0.8053 (m110) cc_final: 0.7685 (t0) REVERT: B 254 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7579 (tp30) REVERT: B 277 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.5741 (tm-30) REVERT: B 349 LYS cc_start: 0.8031 (mmtp) cc_final: 0.7725 (mmtt) REVERT: C 28 ASP cc_start: 0.7143 (p0) cc_final: 0.6912 (p0) REVERT: C 60 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8451 (m) REVERT: C 62 LYS cc_start: 0.8248 (mmtp) cc_final: 0.7614 (mmmm) REVERT: C 66 ILE cc_start: 0.8546 (mt) cc_final: 0.8259 (mm) REVERT: C 78 MET cc_start: 0.7796 (tpp) cc_final: 0.7564 (tpp) REVERT: C 233 TYR cc_start: 0.8049 (m-10) cc_final: 0.7827 (m-80) REVERT: C 242 LYS cc_start: 0.7365 (mttt) cc_final: 0.7024 (mmmt) REVERT: C 277 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.5813 (tm-30) REVERT: C 322 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.7383 (ttm170) REVERT: C 500 GLU cc_start: 0.6794 (tp30) cc_final: 0.6584 (tt0) REVERT: D 48 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7216 (mt-10) REVERT: D 60 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8425 (m) REVERT: D 62 LYS cc_start: 0.8224 (mttp) cc_final: 0.7554 (mmmt) REVERT: D 66 ILE cc_start: 0.8552 (mt) cc_final: 0.8250 (mm) REVERT: D 242 LYS cc_start: 0.7380 (mttt) cc_final: 0.7015 (mmmt) REVERT: D 274 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7122 (m-30) REVERT: D 277 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.5700 (tm-30) REVERT: D 322 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7291 (ttm170) REVERT: D 349 LYS cc_start: 0.8076 (mmtp) cc_final: 0.7774 (mmtt) REVERT: D 500 GLU cc_start: 0.6056 (tt0) cc_final: 0.5659 (pt0) REVERT: E 60 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8455 (m) REVERT: E 62 LYS cc_start: 0.8268 (mmtm) cc_final: 0.7699 (mmmm) REVERT: E 66 ILE cc_start: 0.8552 (mt) cc_final: 0.8249 (mm) REVERT: E 78 MET cc_start: 0.8087 (tpp) cc_final: 0.7709 (tpp) REVERT: E 242 LYS cc_start: 0.7295 (mttt) cc_final: 0.6929 (mmmt) REVERT: E 274 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.7308 (m-30) REVERT: E 322 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.7274 (ttm170) REVERT: E 349 LYS cc_start: 0.8006 (mmtp) cc_final: 0.7687 (mmtt) REVERT: E 500 GLU cc_start: 0.6090 (tt0) cc_final: 0.5769 (pt0) REVERT: F 21 GLN cc_start: 0.7791 (mt0) cc_final: 0.7547 (mt0) REVERT: F 60 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8433 (m) REVERT: F 62 LYS cc_start: 0.8240 (mttt) cc_final: 0.8009 (mtpt) REVERT: F 78 MET cc_start: 0.8120 (tpp) cc_final: 0.7784 (tpp) REVERT: F 98 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7113 (mm-30) REVERT: F 233 TYR cc_start: 0.8059 (m-10) cc_final: 0.7733 (m-80) REVERT: F 242 LYS cc_start: 0.7289 (mttt) cc_final: 0.6895 (mmmt) REVERT: F 277 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.5843 (tm-30) REVERT: F 349 LYS cc_start: 0.8034 (mmtp) cc_final: 0.7735 (mmtt) REVERT: F 496 SER cc_start: 0.7329 (OUTLIER) cc_final: 0.7011 (m) REVERT: G 45 ILE cc_start: 0.7155 (OUTLIER) cc_final: 0.6850 (pt) REVERT: G 60 THR cc_start: 0.8897 (t) cc_final: 0.8474 (m) REVERT: G 62 LYS cc_start: 0.8222 (mmtp) cc_final: 0.7583 (mmmm) REVERT: G 66 ILE cc_start: 0.8572 (mt) cc_final: 0.8262 (mm) REVERT: G 78 MET cc_start: 0.8070 (tpp) cc_final: 0.7672 (tpp) REVERT: G 242 LYS cc_start: 0.7376 (mttt) cc_final: 0.7003 (mmmt) REVERT: G 277 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.5732 (tm-30) REVERT: G 335 GLU cc_start: 0.5177 (OUTLIER) cc_final: 0.4705 (mp0) REVERT: G 349 LYS cc_start: 0.8063 (mmtp) cc_final: 0.7764 (mmtt) REVERT: H 48 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7213 (mt-10) REVERT: H 60 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8438 (m) REVERT: H 66 ILE cc_start: 0.8605 (mt) cc_final: 0.8211 (mm) REVERT: H 98 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7089 (mm-30) REVERT: H 242 LYS cc_start: 0.7246 (mttt) cc_final: 0.6927 (mmtt) REVERT: H 274 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7275 (m-30) REVERT: H 277 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.5603 (tm-30) REVERT: H 349 LYS cc_start: 0.8050 (mmtp) cc_final: 0.7751 (mmtt) outliers start: 64 outliers final: 36 residues processed: 591 average time/residue: 2.7860 time to fit residues: 1882.9295 Evaluate side-chains 589 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 529 time to evaluate : 3.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -9 LEU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain B residue -9 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain D residue -9 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue -9 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 274 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue -9 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue -9 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 496 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 237 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 236 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN B 21 GLN B 343 GLN C 343 GLN D 241 GLN D 343 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN F 241 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 GLN G 454 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20704 Z= 0.289 Angle : 0.554 6.194 27952 Z= 0.293 Chirality : 0.042 0.147 3240 Planarity : 0.004 0.032 3592 Dihedral : 4.700 22.774 2896 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.34 % Favored : 96.35 % Rotamer: Outliers : 3.18 % Allowed : 16.62 % Favored : 80.20 % 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: 0.98 (0.17), residues: 2632 helix: 2.10 (0.15), residues: 1168 sheet: -0.66 (0.26), residues: 264 loop : -0.47 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 296 PHE 0.014 0.001 PHE C 110 TYR 0.013 0.002 TYR C 282 ARG 0.005 0.000 ARG G 253 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 536 time to evaluate : 3.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 THR cc_start: 0.8883 (t) cc_final: 0.8479 (m) REVERT: A 62 LYS cc_start: 0.8183 (mmtp) cc_final: 0.7517 (mmmt) REVERT: A 66 ILE cc_start: 0.8598 (mt) cc_final: 0.8278 (mm) REVERT: A 274 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7281 (m-30) REVERT: A 276 SER cc_start: 0.8607 (p) cc_final: 0.8370 (p) REVERT: A 277 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.5768 (tm-30) REVERT: A 349 LYS cc_start: 0.8035 (mmtp) cc_final: 0.7781 (mmtt) REVERT: B 21 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7511 (mt0) REVERT: B 60 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8519 (m) REVERT: B 62 LYS cc_start: 0.8261 (mmtp) cc_final: 0.7657 (mmmm) REVERT: B 66 ILE cc_start: 0.8651 (mt) cc_final: 0.8250 (mm) REVERT: B 75 GLU cc_start: 0.6674 (mt-10) cc_final: 0.6240 (mm-30) REVERT: B 94 ASN cc_start: 0.8052 (m110) cc_final: 0.7702 (t0) REVERT: B 277 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.5776 (tm-30) REVERT: B 349 LYS cc_start: 0.8051 (mmtp) cc_final: 0.7744 (mmtt) REVERT: C 28 ASP cc_start: 0.7137 (p0) cc_final: 0.6920 (p0) REVERT: C 60 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8500 (m) REVERT: C 62 LYS cc_start: 0.8218 (mmtp) cc_final: 0.7609 (mmmm) REVERT: C 66 ILE cc_start: 0.8553 (mt) cc_final: 0.8243 (mm) REVERT: C 233 TYR cc_start: 0.8172 (m-10) cc_final: 0.7920 (m-80) REVERT: C 242 LYS cc_start: 0.7454 (mttt) cc_final: 0.7117 (mmmt) REVERT: C 277 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.5826 (tm-30) REVERT: C 322 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.7425 (ttm170) REVERT: C 500 GLU cc_start: 0.6827 (tp30) cc_final: 0.6576 (tt0) REVERT: D 48 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7224 (mt-10) REVERT: D 60 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8445 (m) REVERT: D 62 LYS cc_start: 0.8263 (mttp) cc_final: 0.7608 (mmmt) REVERT: D 66 ILE cc_start: 0.8565 (mt) cc_final: 0.8226 (mm) REVERT: D 75 GLU cc_start: 0.6801 (mt-10) cc_final: 0.6278 (mt-10) REVERT: D 242 LYS cc_start: 0.7410 (mttt) cc_final: 0.7047 (mmmt) REVERT: D 274 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.7147 (m-30) REVERT: D 277 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.5812 (tm-30) REVERT: D 322 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7331 (ttm170) REVERT: D 349 LYS cc_start: 0.8070 (mmtp) cc_final: 0.7758 (mmtt) REVERT: D 500 GLU cc_start: 0.6066 (tt0) cc_final: 0.5714 (pt0) REVERT: E 60 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8510 (m) REVERT: E 62 LYS cc_start: 0.8251 (mmtm) cc_final: 0.7682 (mmmm) REVERT: E 66 ILE cc_start: 0.8555 (mt) cc_final: 0.8248 (mm) REVERT: E 78 MET cc_start: 0.8030 (tpp) cc_final: 0.7651 (tpp) REVERT: E 242 LYS cc_start: 0.7372 (mttt) cc_final: 0.7013 (mmmt) REVERT: E 274 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7306 (m-30) REVERT: E 277 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.5807 (tm-30) REVERT: E 322 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.7323 (ttm170) REVERT: E 349 LYS cc_start: 0.8047 (mmtp) cc_final: 0.7731 (mmtt) REVERT: E 500 GLU cc_start: 0.6079 (tt0) cc_final: 0.5761 (pt0) REVERT: F 21 GLN cc_start: 0.7809 (mt0) cc_final: 0.7559 (mt0) REVERT: F 60 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8454 (m) REVERT: F 62 LYS cc_start: 0.8221 (mttt) cc_final: 0.7994 (mtpt) REVERT: F 94 ASN cc_start: 0.7890 (m110) cc_final: 0.7498 (t0) REVERT: F 98 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7145 (mm-30) REVERT: F 242 LYS cc_start: 0.7307 (mttt) cc_final: 0.6930 (mmmt) REVERT: F 277 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.6116 (tm-30) REVERT: F 349 LYS cc_start: 0.8055 (mmtp) cc_final: 0.7758 (mmtt) REVERT: F 496 SER cc_start: 0.7403 (OUTLIER) cc_final: 0.7091 (m) REVERT: G 45 ILE cc_start: 0.7146 (OUTLIER) cc_final: 0.6834 (pt) REVERT: G 60 THR cc_start: 0.8872 (t) cc_final: 0.8466 (m) REVERT: G 62 LYS cc_start: 0.8199 (mmtp) cc_final: 0.7578 (mmmm) REVERT: G 66 ILE cc_start: 0.8647 (mt) cc_final: 0.8344 (mm) REVERT: G 78 MET cc_start: 0.8080 (tpp) cc_final: 0.7677 (tpp) REVERT: G 242 LYS cc_start: 0.7384 (mttt) cc_final: 0.7017 (mmmt) REVERT: G 277 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.5838 (tm-30) REVERT: G 335 GLU cc_start: 0.5249 (OUTLIER) cc_final: 0.4764 (mp0) REVERT: G 349 LYS cc_start: 0.8032 (mmtp) cc_final: 0.7739 (mmtt) REVERT: G 500 GLU cc_start: 0.6301 (tt0) cc_final: 0.6049 (tt0) REVERT: H 48 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7213 (mt-10) REVERT: H 60 THR cc_start: 0.8901 (OUTLIER) cc_final: 0.8461 (m) REVERT: H 66 ILE cc_start: 0.8655 (mt) cc_final: 0.8258 (mm) REVERT: H 98 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7173 (mm-30) REVERT: H 242 LYS cc_start: 0.7326 (mttt) cc_final: 0.7024 (mmtt) REVERT: H 274 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7267 (m-30) REVERT: H 277 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.5809 (tm-30) REVERT: H 349 LYS cc_start: 0.8054 (mmtp) cc_final: 0.7754 (mmtt) outliers start: 68 outliers final: 40 residues processed: 586 average time/residue: 2.8387 time to fit residues: 1904.4325 Evaluate side-chains 588 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 523 time to evaluate : 3.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -9 LEU Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain B residue -9 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain D residue -9 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue -9 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 274 ASP Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue -9 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue -9 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 496 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 chunk 263 optimal weight: 0.8980 chunk 242 optimal weight: 0.6980 chunk 209 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 128 optimal weight: 0.6980 chunk 166 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN B 343 GLN C 343 GLN D 241 GLN D 343 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 GLN G 454 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 20704 Z= 0.259 Angle : 0.704 59.192 27952 Z= 0.401 Chirality : 0.041 0.183 3240 Planarity : 0.004 0.032 3592 Dihedral : 4.691 22.802 2896 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.34 % Favored : 96.35 % Rotamer: Outliers : 3.18 % Allowed : 16.99 % Favored : 79.82 % 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: 0.99 (0.17), residues: 2632 helix: 2.11 (0.16), residues: 1168 sheet: -0.64 (0.26), residues: 264 loop : -0.47 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 296 PHE 0.012 0.001 PHE C 110 TYR 0.012 0.001 TYR B 353 ARG 0.004 0.000 ARG G 253 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 525 time to evaluate : 3.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 THR cc_start: 0.8881 (t) cc_final: 0.8476 (m) REVERT: A 62 LYS cc_start: 0.8182 (mmtp) cc_final: 0.7515 (mmmt) REVERT: A 66 ILE cc_start: 0.8591 (mt) cc_final: 0.8277 (mm) REVERT: A 274 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7283 (m-30) REVERT: A 276 SER cc_start: 0.8608 (p) cc_final: 0.8369 (p) REVERT: A 277 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.5764 (tm-30) REVERT: A 349 LYS cc_start: 0.8029 (mmtp) cc_final: 0.7774 (mmtt) REVERT: B 21 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7439 (mt0) REVERT: B 60 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8518 (m) REVERT: B 62 LYS cc_start: 0.8259 (mmtp) cc_final: 0.7655 (mmmm) REVERT: B 66 ILE cc_start: 0.8644 (mt) cc_final: 0.8247 (mm) REVERT: B 75 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6237 (mm-30) REVERT: B 94 ASN cc_start: 0.8050 (m110) cc_final: 0.7700 (t0) REVERT: B 277 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.5811 (tm-30) REVERT: B 349 LYS cc_start: 0.8044 (mmtp) cc_final: 0.7740 (mmtt) REVERT: C 28 ASP cc_start: 0.7135 (p0) cc_final: 0.6896 (p0) REVERT: C 60 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8497 (m) REVERT: C 62 LYS cc_start: 0.8218 (mmtp) cc_final: 0.7608 (mmmm) REVERT: C 66 ILE cc_start: 0.8547 (mt) cc_final: 0.8242 (mm) REVERT: C 233 TYR cc_start: 0.8145 (m-10) cc_final: 0.7889 (m-80) REVERT: C 242 LYS cc_start: 0.7449 (mttt) cc_final: 0.7114 (mmmt) REVERT: C 277 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.5821 (tm-30) REVERT: C 322 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.7420 (ttm170) REVERT: C 500 GLU cc_start: 0.6824 (tp30) cc_final: 0.6573 (tt0) REVERT: D 48 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7205 (mt-10) REVERT: D 60 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8443 (m) REVERT: D 62 LYS cc_start: 0.8262 (mttp) cc_final: 0.7571 (mmmt) REVERT: D 66 ILE cc_start: 0.8561 (mt) cc_final: 0.8223 (mm) REVERT: D 75 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6273 (mt-10) REVERT: D 242 LYS cc_start: 0.7408 (mttt) cc_final: 0.7046 (mmmt) REVERT: D 274 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7145 (m-30) REVERT: D 277 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.5809 (tm-30) REVERT: D 322 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.7326 (ttm170) REVERT: D 349 LYS cc_start: 0.8065 (mmtp) cc_final: 0.7752 (mmtt) REVERT: D 500 GLU cc_start: 0.6088 (tt0) cc_final: 0.5737 (pt0) REVERT: E 60 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8507 (m) REVERT: E 62 LYS cc_start: 0.8250 (mmtm) cc_final: 0.7680 (mmmm) REVERT: E 66 ILE cc_start: 0.8547 (mt) cc_final: 0.8244 (mm) REVERT: E 78 MET cc_start: 0.8028 (tpp) cc_final: 0.7653 (tpp) REVERT: E 242 LYS cc_start: 0.7370 (mttt) cc_final: 0.7012 (mmmt) REVERT: E 274 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.7300 (m-30) REVERT: E 277 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.5802 (tm-30) REVERT: E 322 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7320 (ttm170) REVERT: E 349 LYS cc_start: 0.8040 (mmtp) cc_final: 0.7722 (mmtt) REVERT: E 500 GLU cc_start: 0.6075 (tt0) cc_final: 0.5755 (pt0) REVERT: F 21 GLN cc_start: 0.7805 (mt0) cc_final: 0.7558 (mt0) REVERT: F 60 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8452 (m) REVERT: F 62 LYS cc_start: 0.8215 (mttt) cc_final: 0.7985 (mtpt) REVERT: F 94 ASN cc_start: 0.7889 (m110) cc_final: 0.7495 (t0) REVERT: F 98 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7146 (mm-30) REVERT: F 242 LYS cc_start: 0.7304 (mttt) cc_final: 0.6928 (mmmt) REVERT: F 277 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.6111 (tm-30) REVERT: F 349 LYS cc_start: 0.8049 (mmtp) cc_final: 0.7753 (mmtt) REVERT: F 454 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7435 (mt0) REVERT: F 496 SER cc_start: 0.7403 (OUTLIER) cc_final: 0.7087 (m) REVERT: G 45 ILE cc_start: 0.7146 (OUTLIER) cc_final: 0.6832 (pt) REVERT: G 60 THR cc_start: 0.8873 (t) cc_final: 0.8466 (m) REVERT: G 62 LYS cc_start: 0.8198 (mmtp) cc_final: 0.7576 (mmmm) REVERT: G 66 ILE cc_start: 0.8644 (mt) cc_final: 0.8341 (mm) REVERT: G 78 MET cc_start: 0.8079 (tpp) cc_final: 0.7681 (tpp) REVERT: G 242 LYS cc_start: 0.7382 (mttt) cc_final: 0.7016 (mmmt) REVERT: G 277 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.5834 (tm-30) REVERT: G 335 GLU cc_start: 0.5245 (OUTLIER) cc_final: 0.4758 (mp0) REVERT: G 349 LYS cc_start: 0.8027 (mmtp) cc_final: 0.7731 (mmtt) REVERT: G 500 GLU cc_start: 0.6296 (tt0) cc_final: 0.6046 (tt0) REVERT: H 48 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7210 (mt-10) REVERT: H 60 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8476 (m) REVERT: H 66 ILE cc_start: 0.8651 (mt) cc_final: 0.8256 (mm) REVERT: H 98 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7131 (mm-30) REVERT: H 242 LYS cc_start: 0.7324 (mttt) cc_final: 0.7022 (mmtt) REVERT: H 274 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7264 (m-30) REVERT: H 277 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.5806 (tm-30) REVERT: H 349 LYS cc_start: 0.8048 (mmtp) cc_final: 0.7748 (mmtt) outliers start: 68 outliers final: 40 residues processed: 573 average time/residue: 2.7691 time to fit residues: 1816.3467 Evaluate side-chains 592 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 526 time to evaluate : 2.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -9 LEU Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain B residue -9 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain D residue -9 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue -9 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 274 ASP Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue -9 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 454 GLN Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue -9 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 454 GLN Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 496 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 193 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 209 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 184 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 GLN C 343 GLN D 343 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 GLN ** H 92 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 = 0.3775 r_free = 0.3775 target = 0.156591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.126355 restraints weight = 65905.454| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.05 r_work: 0.3280 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.351 20704 Z= 0.383 Angle : 0.896 59.181 27952 Z= 0.565 Chirality : 0.041 0.191 3240 Planarity : 0.005 0.107 3592 Dihedral : 4.696 22.794 2896 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.34 % Favored : 96.35 % Rotamer: Outliers : 3.14 % Allowed : 17.04 % Favored : 79.82 % Cbeta Deviations : 0.04 % 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: 0.97 (0.17), residues: 2632 helix: 2.11 (0.16), residues: 1168 sheet: -0.64 (0.26), residues: 264 loop : -0.50 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 296 PHE 0.012 0.001 PHE C 110 TYR 0.012 0.001 TYR B 353 ARG 0.003 0.000 ARG G 253 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24123.84 seconds wall clock time: 423 minutes 21.34 seconds (25401.34 seconds total)