Starting phenix.real_space_refine on Sun Aug 24 10:35:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gyo_34374/08_2025/8gyo_34374.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gyo_34374/08_2025/8gyo_34374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gyo_34374/08_2025/8gyo_34374.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gyo_34374/08_2025/8gyo_34374.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gyo_34374/08_2025/8gyo_34374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gyo_34374/08_2025/8gyo_34374.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.004 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 P 3 5.49 5 S 105 5.16 5 C 12776 2.51 5 N 2922 2.21 5 O 3447 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19253 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2742 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 14, 'TRANS': 327} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2590 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 13, 'TRANS': 309} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 2742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2742 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 14, 'TRANS': 327} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 2742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2742 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 14, 'TRANS': 327} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2590 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 13, 'TRANS': 309} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 2742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2742 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 14, 'TRANS': 327} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2590 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 13, 'TRANS': 309} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 153 Unusual residues: {'AJP': 1, 'NAG': 1, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 68 Unusual residues: {'NAG': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 99 Unusual residues: {'AJP': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 68 Unusual residues: {'NAG': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 99 Unusual residues: {'AJP': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.29, per 1000 atoms: 0.27 Number of scatterers: 19253 At special positions: 0 Unit cell: (112.373, 113.464, 130.92, 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 105 16.00 P 3 15.00 O 3447 8.00 N 2922 7.00 C 12776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 255 " " NAG B 501 " - " ASN B 255 " " NAG C 501 " - " ASN C 255 " " NAG D 501 " - " ASN D 255 " " NAG E 501 " - " ASN E 255 " " NAG F 501 " - " ASN F 255 " " NAG G 501 " - " ASN G 255 " Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 861.2 milliseconds Enol-peptide restraints added in 1.2 microseconds 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4534 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 14 sheets defined 72.6% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 2 through 19 removed outlier: 3.643A pdb=" N LEU A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 17 " --> pdb=" O SER A 13 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS A 18 " --> pdb=" O ASP A 14 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 19 " --> pdb=" O PHE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 60 removed outlier: 4.074A pdb=" N MET A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL A 43 " --> pdb=" O THR A 39 " (cutoff:3.500A) Proline residue: A 46 - end of helix removed outlier: 3.621A pdb=" N ILE A 58 " --> pdb=" O PHE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 Processing helix chain 'A' and resid 104 through 129 Proline residue: A 110 - end of helix Proline residue: A 123 - end of helix removed outlier: 3.506A pdb=" N PHE A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 165 Processing helix chain 'A' and resid 194 through 205 removed outlier: 3.855A pdb=" N ASN A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 238 removed outlier: 3.889A pdb=" N ARG A 217 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 269 through 296 Proline residue: A 289 - end of helix removed outlier: 3.849A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 removed outlier: 3.784A pdb=" N GLN A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.887A pdb=" N TYR A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 removed outlier: 3.554A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 343 through 358 removed outlier: 3.817A pdb=" N CYS A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 354 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 369 Processing helix chain 'B' and resid 32 through 60 removed outlier: 4.065A pdb=" N MET B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 43 " --> pdb=" O THR B 39 " (cutoff:3.500A) Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 73 through 87 Processing helix chain 'B' and resid 103 through 131 removed outlier: 4.043A pdb=" N LYS B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Proline residue: B 110 - end of helix removed outlier: 4.589A pdb=" N LEU B 114 " --> pdb=" O PRO B 110 " (cutoff:3.500A) Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 165 Processing helix chain 'B' and resid 194 through 204 Processing helix chain 'B' and resid 208 through 238 removed outlier: 3.655A pdb=" N ARG B 217 " --> pdb=" O TYR B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.708A pdb=" N ASN B 255 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 296 removed outlier: 3.542A pdb=" N PHE B 273 " --> pdb=" O ALA B 269 " (cutoff:3.500A) Proline residue: B 289 - end of helix removed outlier: 3.953A pdb=" N PHE B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 301 removed outlier: 3.674A pdb=" N ARG B 300 " --> pdb=" O PHE B 296 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN B 301 " --> pdb=" O VAL B 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 296 through 301' Processing helix chain 'B' and resid 305 through 310 removed outlier: 4.020A pdb=" N TYR B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 339 removed outlier: 3.661A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 357 removed outlier: 4.415A pdb=" N LYS B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS B 347 " --> pdb=" O LYS B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 368 Processing helix chain 'C' and resid 3 through 19 removed outlier: 3.672A pdb=" N GLU C 9 " --> pdb=" O GLN C 5 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR C 10 " --> pdb=" O LEU C 6 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C 17 " --> pdb=" O SER C 13 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS C 18 " --> pdb=" O ASP C 14 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU C 19 " --> pdb=" O PHE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 60 removed outlier: 3.936A pdb=" N MET C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 73 through 87 Processing helix chain 'C' and resid 103 through 129 removed outlier: 4.044A pdb=" N LYS C 107 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Proline residue: C 110 - end of helix removed outlier: 3.798A pdb=" N LEU C 114 " --> pdb=" O PRO C 110 " (cutoff:3.500A) Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 165 Processing helix chain 'C' and resid 194 through 206 removed outlier: 3.895A pdb=" N ASN C 205 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER C 206 " --> pdb=" O THR C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 238 removed outlier: 3.631A pdb=" N ARG C 217 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 removed outlier: 4.014A pdb=" N ASN C 255 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 296 removed outlier: 3.608A pdb=" N PHE C 273 " --> pdb=" O ALA C 269 " (cutoff:3.500A) Proline residue: C 289 - end of helix removed outlier: 4.050A pdb=" N PHE C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 301 removed outlier: 3.770A pdb=" N GLN C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.766A pdb=" N TYR C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 339 removed outlier: 3.510A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 342 No H-bonds generated for 'chain 'C' and resid 340 through 342' Processing helix chain 'C' and resid 343 through 357 removed outlier: 4.359A pdb=" N CYS C 347 " --> pdb=" O LYS C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'D' and resid 3 through 19 removed outlier: 3.557A pdb=" N LEU D 17 " --> pdb=" O SER D 13 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS D 18 " --> pdb=" O ASP D 14 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU D 19 " --> pdb=" O PHE D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 60 removed outlier: 3.795A pdb=" N MET D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL D 43 " --> pdb=" O THR D 39 " (cutoff:3.500A) Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 73 through 87 Processing helix chain 'D' and resid 103 through 131 removed outlier: 4.076A pdb=" N LYS D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) Proline residue: D 110 - end of helix removed outlier: 4.261A pdb=" N LEU D 114 " --> pdb=" O PRO D 110 " (cutoff:3.500A) Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 132 through 165 Processing helix chain 'D' and resid 194 through 205 removed outlier: 4.037A pdb=" N ASN D 205 " --> pdb=" O LYS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 238 removed outlier: 3.522A pdb=" N ARG D 217 " --> pdb=" O TYR D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.679A pdb=" N ASN D 255 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 296 Proline residue: D 289 - end of helix removed outlier: 3.885A pdb=" N PHE D 296 " --> pdb=" O VAL D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 301 Processing helix chain 'D' and resid 305 through 310 removed outlier: 4.122A pdb=" N TYR D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 339 removed outlier: 3.595A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 357 removed outlier: 4.307A pdb=" N LYS D 346 " --> pdb=" O VAL D 342 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS D 347 " --> pdb=" O LYS D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 369 Processing helix chain 'E' and resid 32 through 60 removed outlier: 4.031A pdb=" N MET E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL E 43 " --> pdb=" O THR E 39 " (cutoff:3.500A) Proline residue: E 46 - end of helix removed outlier: 3.706A pdb=" N GLU E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE E 58 " --> pdb=" O PHE E 54 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 87 Processing helix chain 'E' and resid 103 through 129 removed outlier: 4.023A pdb=" N LYS E 107 " --> pdb=" O LEU E 103 " (cutoff:3.500A) Proline residue: E 110 - end of helix removed outlier: 4.447A pdb=" N LEU E 114 " --> pdb=" O PRO E 110 " (cutoff:3.500A) Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 165 removed outlier: 3.552A pdb=" N ILE E 154 " --> pdb=" O TYR E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 204 Processing helix chain 'E' and resid 208 through 238 removed outlier: 3.676A pdb=" N ARG E 217 " --> pdb=" O TYR E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 256 removed outlier: 3.772A pdb=" N ASN E 255 " --> pdb=" O ILE E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 296 removed outlier: 3.626A pdb=" N PHE E 273 " --> pdb=" O ALA E 269 " (cutoff:3.500A) Proline residue: E 289 - end of helix removed outlier: 3.942A pdb=" N PHE E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 301 removed outlier: 3.615A pdb=" N ARG E 300 " --> pdb=" O PHE E 296 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN E 301 " --> pdb=" O VAL E 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 296 through 301' Processing helix chain 'E' and resid 305 through 310 removed outlier: 4.038A pdb=" N TYR E 309 " --> pdb=" O VAL E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 339 removed outlier: 3.539A pdb=" N LEU E 330 " --> pdb=" O ASN E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 357 removed outlier: 4.338A pdb=" N LYS E 346 " --> pdb=" O VAL E 342 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N CYS E 347 " --> pdb=" O LYS E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 368 Processing helix chain 'F' and resid 3 through 19 removed outlier: 3.675A pdb=" N GLU F 9 " --> pdb=" O GLN F 5 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU F 17 " --> pdb=" O SER F 13 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS F 18 " --> pdb=" O ASP F 14 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU F 19 " --> pdb=" O PHE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 60 removed outlier: 3.890A pdb=" N MET F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL F 43 " --> pdb=" O THR F 39 " (cutoff:3.500A) Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 73 through 87 Processing helix chain 'F' and resid 103 through 129 removed outlier: 4.020A pdb=" N LYS F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Proline residue: F 110 - end of helix removed outlier: 3.995A pdb=" N LEU F 114 " --> pdb=" O PRO F 110 " (cutoff:3.500A) Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 165 removed outlier: 3.570A pdb=" N ILE F 135 " --> pdb=" O ALA F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 204 Processing helix chain 'F' and resid 208 through 238 removed outlier: 3.594A pdb=" N ARG F 217 " --> pdb=" O TYR F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 256 removed outlier: 3.553A pdb=" N ASN F 255 " --> pdb=" O ILE F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 296 Proline residue: F 289 - end of helix removed outlier: 4.000A pdb=" N PHE F 296 " --> pdb=" O VAL F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 301 removed outlier: 3.532A pdb=" N ARG F 300 " --> pdb=" O PHE F 296 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN F 301 " --> pdb=" O VAL F 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 296 through 301' Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.966A pdb=" N TYR F 309 " --> pdb=" O VAL F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 339 removed outlier: 3.593A pdb=" N LEU F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU F 337 " --> pdb=" O LEU F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 358 removed outlier: 4.226A pdb=" N LYS F 346 " --> pdb=" O VAL F 342 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS F 347 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU F 352 " --> pdb=" O LEU F 348 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY F 358 " --> pdb=" O ILE F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 368 Processing helix chain 'G' and resid 32 through 60 removed outlier: 3.827A pdb=" N MET G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Proline residue: G 46 - end of helix removed outlier: 3.666A pdb=" N SER G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 87 Processing helix chain 'G' and resid 104 through 131 Proline residue: G 110 - end of helix removed outlier: 4.463A pdb=" N LEU G 114 " --> pdb=" O PRO G 110 " (cutoff:3.500A) Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 165 removed outlier: 3.555A pdb=" N ILE G 154 " --> pdb=" O TYR G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 204 removed outlier: 3.848A pdb=" N GLN G 198 " --> pdb=" O PRO G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 238 removed outlier: 4.051A pdb=" N ARG G 217 " --> pdb=" O TYR G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 256 removed outlier: 4.329A pdb=" N ASN G 255 " --> pdb=" O ILE G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 296 removed outlier: 3.532A pdb=" N PHE G 273 " --> pdb=" O ALA G 269 " (cutoff:3.500A) Proline residue: G 289 - end of helix removed outlier: 3.920A pdb=" N PHE G 296 " --> pdb=" O VAL G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 301 removed outlier: 3.727A pdb=" N ARG G 300 " --> pdb=" O PHE G 296 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN G 301 " --> pdb=" O VAL G 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 296 through 301' Processing helix chain 'G' and resid 305 through 310 removed outlier: 4.028A pdb=" N TYR G 309 " --> pdb=" O VAL G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 339 removed outlier: 3.612A pdb=" N GLU G 337 " --> pdb=" O LEU G 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 357 removed outlier: 4.373A pdb=" N LYS G 346 " --> pdb=" O VAL G 342 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS G 347 " --> pdb=" O LYS G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 370 removed outlier: 3.502A pdb=" N ASN G 369 " --> pdb=" O LEU G 365 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 Processing sheet with id=AA2, first strand: chain 'A' and resid 246 through 247 Processing sheet with id=AA3, first strand: chain 'B' and resid 64 through 65 Processing sheet with id=AA4, first strand: chain 'B' and resid 246 through 247 Processing sheet with id=AA5, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AA6, first strand: chain 'C' and resid 246 through 247 Processing sheet with id=AA7, first strand: chain 'D' and resid 64 through 65 Processing sheet with id=AA8, first strand: chain 'D' and resid 246 through 247 Processing sheet with id=AA9, first strand: chain 'E' and resid 64 through 65 Processing sheet with id=AB1, first strand: chain 'E' and resid 246 through 247 Processing sheet with id=AB2, first strand: chain 'F' and resid 64 through 65 Processing sheet with id=AB3, first strand: chain 'F' and resid 246 through 247 Processing sheet with id=AB4, first strand: chain 'G' and resid 64 through 65 Processing sheet with id=AB5, first strand: chain 'G' and resid 246 through 247 1139 hydrogen bonds defined for protein. 3345 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: 3.00 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3019 1.32 - 1.45: 5107 1.45 - 1.57: 11418 1.57 - 1.69: 7 1.69 - 1.81: 147 Bond restraints: 19698 Sorted by residual: bond pdb=" CB TYR B 193 " pdb=" CG TYR B 193 " ideal model delta sigma weight residual 1.512 1.445 0.067 2.20e-02 2.07e+03 9.30e+00 bond pdb=" CG LEU B 146 " pdb=" CD1 LEU B 146 " ideal model delta sigma weight residual 1.521 1.422 0.099 3.30e-02 9.18e+02 8.99e+00 bond pdb=" C LYS B 192 " pdb=" N TYR B 193 " ideal model delta sigma weight residual 1.327 1.372 -0.044 1.54e-02 4.22e+03 8.17e+00 bond pdb=" C ASN E 100 " pdb=" N LEU E 101 " ideal model delta sigma weight residual 1.331 1.388 -0.057 2.07e-02 2.33e+03 7.49e+00 bond pdb=" C1 PC1 A 503 " pdb=" O11 PC1 A 503 " ideal model delta sigma weight residual 1.411 1.462 -0.051 2.00e-02 2.50e+03 6.59e+00 ... (remaining 19693 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 26245 2.21 - 4.41: 439 4.41 - 6.62: 50 6.62 - 8.83: 5 8.83 - 11.03: 1 Bond angle restraints: 26740 Sorted by residual: angle pdb=" C LYS B 192 " pdb=" N TYR B 193 " pdb=" CA TYR B 193 " ideal model delta sigma weight residual 120.83 131.86 -11.03 1.43e+00 4.89e-01 5.95e+01 angle pdb=" CA PRO A 102 " pdb=" N PRO A 102 " pdb=" CD PRO A 102 " ideal model delta sigma weight residual 112.00 104.37 7.63 1.40e+00 5.10e-01 2.97e+01 angle pdb=" CA TYR B 193 " pdb=" C TYR B 193 " pdb=" N PRO B 194 " ideal model delta sigma weight residual 118.83 121.39 -2.56 8.70e-01 1.32e+00 8.68e+00 angle pdb=" CA TYR B 193 " pdb=" C TYR B 193 " pdb=" O TYR B 193 " ideal model delta sigma weight residual 119.71 117.30 2.41 8.40e-01 1.42e+00 8.22e+00 angle pdb=" CA LEU E 101 " pdb=" C LEU E 101 " pdb=" N PRO E 102 " ideal model delta sigma weight residual 118.44 122.92 -4.48 1.59e+00 3.96e-01 7.94e+00 ... (remaining 26735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 11736 35.84 - 71.69: 464 71.69 - 107.53: 89 107.53 - 143.38: 205 143.38 - 179.22: 18 Dihedral angle restraints: 12512 sinusoidal: 5543 harmonic: 6969 Sorted by residual: dihedral pdb=" CA PHE C 244 " pdb=" C PHE C 244 " pdb=" N VAL C 245 " pdb=" CA VAL C 245 " ideal model delta harmonic sigma weight residual 180.00 153.69 26.31 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA PHE E 244 " pdb=" C PHE E 244 " pdb=" N VAL E 245 " pdb=" CA VAL E 245 " ideal model delta harmonic sigma weight residual 180.00 154.08 25.92 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA PHE D 244 " pdb=" C PHE D 244 " pdb=" N VAL D 245 " pdb=" CA VAL D 245 " ideal model delta harmonic sigma weight residual 180.00 154.39 25.61 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 12509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.200: 3158 1.200 - 2.401: 0 2.401 - 3.601: 0 3.601 - 4.801: 12 4.801 - 6.002: 57 Chirality restraints: 3227 Sorted by residual: chirality pdb=" C12 AJP A 502 " pdb=" C07 AJP A 502 " pdb=" C11 AJP A 502 " pdb=" C13 AJP A 502 " both_signs ideal model delta sigma weight residual False 3.01 -2.99 6.00 2.00e-01 2.50e+01 9.01e+02 chirality pdb=" C12 AJP F 502 " pdb=" C07 AJP F 502 " pdb=" C11 AJP F 502 " pdb=" C13 AJP F 502 " both_signs ideal model delta sigma weight residual False 3.01 -2.99 6.00 2.00e-01 2.50e+01 9.00e+02 chirality pdb=" C12 AJP D 502 " pdb=" C07 AJP D 502 " pdb=" C11 AJP D 502 " pdb=" C13 AJP D 502 " both_signs ideal model delta sigma weight residual False 3.01 -2.99 6.00 2.00e-01 2.50e+01 8.99e+02 ... (remaining 3224 not shown) Planarity restraints: 3176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 255 " 0.101 2.00e-02 2.50e+03 3.33e-01 1.39e+03 pdb=" CG ASN G 255 " -0.137 2.00e-02 2.50e+03 pdb=" OD1 ASN G 255 " 0.232 2.00e-02 2.50e+03 pdb=" ND2 ASN G 255 " -0.574 2.00e-02 2.50e+03 pdb=" C1 NAG G 501 " 0.378 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 255 " 0.072 2.00e-02 2.50e+03 1.92e-01 4.59e+02 pdb=" CG ASN E 255 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN E 255 " 0.116 2.00e-02 2.50e+03 pdb=" ND2 ASN E 255 " -0.343 2.00e-02 2.50e+03 pdb=" C1 NAG E 501 " 0.210 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 255 " 0.023 2.00e-02 2.50e+03 1.66e-01 3.44e+02 pdb=" CG ASN C 255 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN C 255 " -0.151 2.00e-02 2.50e+03 pdb=" ND2 ASN C 255 " 0.277 2.00e-02 2.50e+03 pdb=" C1 NAG C 501 " -0.189 2.00e-02 2.50e+03 ... (remaining 3173 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 92 2.49 - 3.09: 14206 3.09 - 3.69: 28637 3.69 - 4.30: 39902 4.30 - 4.90: 65306 Nonbonded interactions: 148143 Sorted by model distance: nonbonded pdb=" OE1 GLU A 57 " pdb=" OG SER G 59 " model vdw 1.882 3.040 nonbonded pdb=" OD2 ASP F 138 " pdb=" OH TYR F 331 " model vdw 1.963 3.040 nonbonded pdb=" OD2 ASP C 138 " pdb=" OH TYR C 331 " model vdw 1.974 3.040 nonbonded pdb=" OD2 ASP E 138 " pdb=" OH TYR E 331 " model vdw 1.976 3.040 nonbonded pdb=" OG SER E 59 " pdb=" OE1 GLU F 57 " model vdw 1.987 3.040 ... (remaining 148138 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 29 through 501) selection = (chain 'B' and resid 29 through 501) selection = (chain 'C' and resid 29 through 501) selection = (chain 'D' and resid 29 through 501) selection = (chain 'E' and resid 29 through 501) selection = (chain 'F' and resid 29 through 501) selection = chain 'G' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.010 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 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 : 0.004 0.099 19719 Z= 0.204 Angle : 0.734 33.313 26789 Z= 0.333 Chirality : 0.742 6.002 3227 Planarity : 0.004 0.078 3169 Dihedral : 28.228 179.224 7936 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.33 % Allowed : 20.69 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.19), residues: 2301 helix: 1.73 (0.14), residues: 1492 sheet: -3.99 (0.57), residues: 69 loop : -1.19 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 254 TYR 0.018 0.001 TYR F 234 PHE 0.012 0.001 PHE D 244 TRP 0.009 0.001 TRP A 104 HIS 0.001 0.000 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00410 (19698) covalent geometry : angle 0.64827 (26740) SS BOND : bond 0.00141 ( 14) SS BOND : angle 0.65118 ( 28) hydrogen bonds : bond 0.17884 ( 1139) hydrogen bonds : angle 5.54678 ( 3345) link_NAG-ASN : bond 0.07152 ( 7) link_NAG-ASN : angle 12.28578 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 268 time to evaluate : 0.621 Fit side-chains TARDY: cannot create tardy model for: "LEU B 30 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 30 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU F 30 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8222 (mmm) cc_final: 0.7750 (mmm) REVERT: A 211 ILE cc_start: 0.8325 (tt) cc_final: 0.7977 (tt) REVERT: C 36 LYS cc_start: 0.7612 (tppt) cc_final: 0.7237 (ptpp) REVERT: C 326 ASN cc_start: 0.7693 (m-40) cc_final: 0.7148 (p0) REVERT: E 201 LYS cc_start: 0.7239 (mttt) cc_final: 0.6741 (mttp) REVERT: F 5 GLN cc_start: 0.8085 (mt0) cc_final: 0.7640 (mt0) REVERT: F 331 TYR cc_start: 0.7798 (m-80) cc_final: 0.7571 (m-80) REVERT: G 37 MET cc_start: 0.6540 (tmm) cc_final: 0.6000 (tmm) REVERT: G 74 TRP cc_start: 0.8513 (t60) cc_final: 0.8276 (t-100) REVERT: G 128 ARG cc_start: 0.7138 (mtp180) cc_final: 0.6718 (ttp-170) outliers start: 7 outliers final: 2 residues processed: 274 average time/residue: 0.1383 time to fit residues: 59.7618 Evaluate side-chains 237 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 235 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain F residue 52 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.0060 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 6.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN B 198 GLN D 89 GLN D 262 GLN D 353 ASN F 89 GLN G 134 HIS G 262 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.211158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.175939 restraints weight = 23338.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.171135 restraints weight = 31844.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.166204 restraints weight = 27547.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.166474 restraints weight = 26480.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.166778 restraints weight = 21436.601| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19719 Z= 0.160 Angle : 1.145 36.251 26789 Z= 0.450 Chirality : 0.088 1.789 3227 Planarity : 0.005 0.054 3169 Dihedral : 19.847 179.870 3446 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.34 % Allowed : 17.91 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.18), residues: 2301 helix: 1.76 (0.13), residues: 1552 sheet: -4.02 (0.51), residues: 84 loop : -1.42 (0.26), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 217 TYR 0.024 0.002 TYR G 230 PHE 0.016 0.001 PHE C 141 TRP 0.017 0.001 TRP D 127 HIS 0.002 0.000 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00365 (19698) covalent geometry : angle 1.12715 (26740) SS BOND : bond 0.00362 ( 14) SS BOND : angle 1.21201 ( 28) hydrogen bonds : bond 0.04606 ( 1139) hydrogen bonds : angle 3.83346 ( 3345) link_NAG-ASN : bond 0.00819 ( 7) link_NAG-ASN : angle 7.30799 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 256 time to evaluate : 0.826 Fit side-chains TARDY: cannot create tardy model for: "LEU A 30 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 30 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU F 30 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.7747 (tp-100) cc_final: 0.7528 (tp-100) REVERT: A 114 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6588 (mm) REVERT: A 211 ILE cc_start: 0.8517 (tt) cc_final: 0.8250 (tt) REVERT: A 331 TYR cc_start: 0.7941 (m-80) cc_final: 0.7442 (m-80) REVERT: B 229 ILE cc_start: 0.8798 (tp) cc_final: 0.8308 (tp) REVERT: B 253 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6501 (mt) REVERT: C 101 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.6812 (tt) REVERT: C 253 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.6469 (mt) REVERT: C 336 GLU cc_start: 0.8089 (tp30) cc_final: 0.7802 (mt-10) REVERT: C 348 LEU cc_start: 0.8351 (pp) cc_final: 0.7748 (mm) REVERT: D 199 TYR cc_start: 0.6008 (t80) cc_final: 0.5725 (t80) REVERT: D 253 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6803 (mp) REVERT: E 201 LYS cc_start: 0.7346 (mttt) cc_final: 0.7063 (mttp) REVERT: F 60 ILE cc_start: 0.2947 (OUTLIER) cc_final: 0.2344 (mm) REVERT: G 128 ARG cc_start: 0.7287 (mtp180) cc_final: 0.6902 (ttp-170) REVERT: G 253 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7477 (mt) outliers start: 92 outliers final: 50 residues processed: 320 average time/residue: 0.1317 time to fit residues: 67.6634 Evaluate side-chains 285 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 228 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 265 CYS Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 265 CYS Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 265 CYS Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 265 CYS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 285 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 133 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 181 optimal weight: 7.9990 chunk 164 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 202 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN B 89 GLN D 89 GLN ** E 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.210572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.160595 restraints weight = 23572.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.160235 restraints weight = 26670.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.162036 restraints weight = 22184.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.161104 restraints weight = 16396.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.161806 restraints weight = 14833.989| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19719 Z= 0.139 Angle : 1.062 36.204 26789 Z= 0.416 Chirality : 0.086 1.786 3227 Planarity : 0.004 0.054 3169 Dihedral : 18.513 176.061 3446 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.04 % Allowed : 19.04 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.19), residues: 2301 helix: 1.88 (0.13), residues: 1534 sheet: -3.74 (0.52), residues: 84 loop : -1.16 (0.26), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 217 TYR 0.018 0.002 TYR G 193 PHE 0.013 0.001 PHE G 244 TRP 0.018 0.001 TRP D 127 HIS 0.002 0.000 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00318 (19698) covalent geometry : angle 1.04646 (26740) SS BOND : bond 0.00260 ( 14) SS BOND : angle 1.15944 ( 28) hydrogen bonds : bond 0.03991 ( 1139) hydrogen bonds : angle 3.59687 ( 3345) link_NAG-ASN : bond 0.00967 ( 7) link_NAG-ASN : angle 6.45055 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 253 time to evaluate : 0.730 Fit side-chains TARDY: cannot create tardy model for: "LEU A 30 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU B 30 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 30 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU F 30 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6630 (mm) REVERT: A 331 TYR cc_start: 0.7863 (m-80) cc_final: 0.7383 (m-80) REVERT: B 229 ILE cc_start: 0.8747 (tp) cc_final: 0.8270 (tp) REVERT: B 375 MET cc_start: -0.0672 (mmm) cc_final: -0.0923 (mmm) REVERT: C 9 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6737 (mm-30) REVERT: C 101 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6937 (tt) REVERT: C 219 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8613 (tt) REVERT: C 253 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.6315 (mt) REVERT: C 336 GLU cc_start: 0.8207 (tp30) cc_final: 0.7846 (mt-10) REVERT: D 127 TRP cc_start: 0.7932 (t-100) cc_final: 0.7689 (t-100) REVERT: D 253 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6238 (mp) REVERT: D 309 TYR cc_start: 0.7066 (OUTLIER) cc_final: 0.6610 (t80) REVERT: D 335 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7693 (mm) REVERT: D 375 MET cc_start: 0.0229 (mtt) cc_final: -0.0140 (mtt) REVERT: E 234 TYR cc_start: 0.8472 (t80) cc_final: 0.8133 (t80) REVERT: E 295 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7431 (mt) REVERT: F 47 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8437 (mt) REVERT: F 60 ILE cc_start: 0.2646 (OUTLIER) cc_final: 0.2022 (mm) REVERT: F 140 LYS cc_start: 0.7774 (mtmt) cc_final: 0.7443 (ptmm) REVERT: F 341 GLU cc_start: 0.8160 (tp30) cc_final: 0.7815 (mm-30) REVERT: G 45 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7685 (tp) REVERT: G 128 ARG cc_start: 0.7220 (mtp180) cc_final: 0.6877 (ttp-170) REVERT: G 222 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8864 (tt) REVERT: G 340 SER cc_start: 0.8386 (p) cc_final: 0.7953 (m) outliers start: 107 outliers final: 60 residues processed: 329 average time/residue: 0.1286 time to fit residues: 68.7138 Evaluate side-chains 297 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 225 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 265 CYS Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 265 CYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 265 CYS Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 265 CYS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 347 CYS Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 244 PHE Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 285 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 161 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 117 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN B 89 GLN C 5 GLN D 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.202999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.155924 restraints weight = 23896.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.153625 restraints weight = 30891.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.155841 restraints weight = 27644.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.155999 restraints weight = 17474.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.156653 restraints weight = 16706.194| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 19719 Z= 0.217 Angle : 1.122 36.761 26789 Z= 0.453 Chirality : 0.085 1.720 3227 Planarity : 0.005 0.057 3169 Dihedral : 18.493 178.078 3444 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 6.55 % Allowed : 19.89 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.18), residues: 2301 helix: 1.57 (0.13), residues: 1530 sheet: -4.53 (0.46), residues: 78 loop : -1.39 (0.26), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 217 TYR 0.016 0.002 TYR A 10 PHE 0.021 0.002 PHE G 244 TRP 0.018 0.002 TRP F 127 HIS 0.005 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00532 (19698) covalent geometry : angle 1.10909 (26740) SS BOND : bond 0.00904 ( 14) SS BOND : angle 1.60551 ( 28) hydrogen bonds : bond 0.04446 ( 1139) hydrogen bonds : angle 3.82269 ( 3345) link_NAG-ASN : bond 0.00935 ( 7) link_NAG-ASN : angle 5.89854 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 245 time to evaluate : 0.682 Fit side-chains TARDY: cannot create tardy model for: "LEU A 30 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU B 30 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 30 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU F 30 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8706 (tt) REVERT: A 211 ILE cc_start: 0.8527 (tt) cc_final: 0.8299 (tt) REVERT: A 331 TYR cc_start: 0.7958 (m-80) cc_final: 0.7611 (m-80) REVERT: B 52 LEU cc_start: 0.8015 (pp) cc_final: 0.7734 (pp) REVERT: B 196 VAL cc_start: 0.5598 (OUTLIER) cc_final: 0.5125 (p) REVERT: B 375 MET cc_start: -0.0873 (mmm) cc_final: -0.1095 (mmm) REVERT: C 9 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7041 (mm-30) REVERT: C 10 TYR cc_start: 0.6825 (m-10) cc_final: 0.6437 (m-80) REVERT: C 101 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7029 (tt) REVERT: C 219 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8580 (tt) REVERT: C 253 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7075 (mp) REVERT: C 336 GLU cc_start: 0.8496 (tp30) cc_final: 0.7928 (mt-10) REVERT: D 253 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.6635 (mp) REVERT: D 309 TYR cc_start: 0.7066 (OUTLIER) cc_final: 0.6619 (t80) REVERT: D 335 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7550 (mm) REVERT: D 345 TYR cc_start: 0.6264 (t80) cc_final: 0.5876 (t80) REVERT: D 375 MET cc_start: 0.0059 (mtt) cc_final: -0.0194 (mtt) REVERT: F 37 MET cc_start: 0.8638 (tpp) cc_final: 0.8275 (tpp) REVERT: F 47 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8563 (mt) REVERT: F 60 ILE cc_start: 0.2881 (OUTLIER) cc_final: 0.2038 (mm) REVERT: F 165 MET cc_start: 0.1779 (ttt) cc_final: -0.0894 (mmm) REVERT: F 198 GLN cc_start: 0.6076 (tm-30) cc_final: 0.5845 (mm-40) REVERT: F 253 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7131 (mt) REVERT: G 37 MET cc_start: 0.6874 (tmm) cc_final: 0.6440 (tmm) REVERT: G 128 ARG cc_start: 0.7327 (mtp180) cc_final: 0.6963 (ttp-170) REVERT: G 340 SER cc_start: 0.8762 (p) cc_final: 0.8471 (m) outliers start: 139 outliers final: 83 residues processed: 356 average time/residue: 0.1256 time to fit residues: 72.1491 Evaluate side-chains 317 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 223 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 265 CYS Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 265 CYS Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 265 CYS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 347 CYS Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 244 PHE Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 73 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 220 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN D 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.205482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.158109 restraints weight = 23791.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.156592 restraints weight = 30600.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.159283 restraints weight = 25710.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.158647 restraints weight = 17964.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.159472 restraints weight = 16475.327| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19719 Z= 0.142 Angle : 1.051 36.343 26789 Z= 0.414 Chirality : 0.084 1.746 3227 Planarity : 0.005 0.057 3169 Dihedral : 18.140 177.338 3444 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 5.28 % Allowed : 22.10 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.18), residues: 2301 helix: 1.72 (0.13), residues: 1533 sheet: -3.18 (0.69), residues: 64 loop : -1.37 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 254 TYR 0.025 0.001 TYR F 199 PHE 0.016 0.001 PHE D 244 TRP 0.015 0.001 TRP F 127 HIS 0.002 0.000 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00341 (19698) covalent geometry : angle 1.03959 (26740) SS BOND : bond 0.00366 ( 14) SS BOND : angle 1.17578 ( 28) hydrogen bonds : bond 0.03832 ( 1139) hydrogen bonds : angle 3.59813 ( 3345) link_NAG-ASN : bond 0.01006 ( 7) link_NAG-ASN : angle 5.64913 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 254 time to evaluate : 0.728 Fit side-chains TARDY: cannot create tardy model for: "LEU A 30 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU B 30 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 30 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU F 30 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ILE cc_start: 0.8508 (tt) cc_final: 0.8282 (tt) REVERT: A 331 TYR cc_start: 0.7898 (m-80) cc_final: 0.7558 (m-80) REVERT: B 52 LEU cc_start: 0.7887 (pp) cc_final: 0.7646 (pp) REVERT: B 229 ILE cc_start: 0.8658 (tp) cc_final: 0.8222 (tp) REVERT: C 9 GLU cc_start: 0.7335 (mm-30) cc_final: 0.7003 (mm-30) REVERT: C 10 TYR cc_start: 0.6688 (m-10) cc_final: 0.6324 (m-80) REVERT: C 101 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6799 (tt) REVERT: C 211 ILE cc_start: 0.6824 (OUTLIER) cc_final: 0.6621 (tp) REVERT: C 253 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.6466 (mt) REVERT: C 336 GLU cc_start: 0.8485 (tp30) cc_final: 0.7944 (mt-10) REVERT: D 309 TYR cc_start: 0.7032 (OUTLIER) cc_final: 0.6456 (t80) REVERT: D 335 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7499 (mm) REVERT: D 375 MET cc_start: -0.0061 (mtt) cc_final: -0.0277 (mtt) REVERT: F 60 ILE cc_start: 0.2567 (OUTLIER) cc_final: 0.1984 (mm) REVERT: F 165 MET cc_start: 0.1736 (ttt) cc_final: -0.0688 (mmm) REVERT: F 253 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.6958 (mt) REVERT: G 128 ARG cc_start: 0.7267 (mtp180) cc_final: 0.6937 (ttp-170) REVERT: G 198 GLN cc_start: 0.6446 (mp10) cc_final: 0.5814 (tp40) REVERT: G 202 THR cc_start: 0.6578 (p) cc_final: 0.6283 (p) REVERT: G 340 SER cc_start: 0.8781 (p) cc_final: 0.8518 (m) outliers start: 112 outliers final: 74 residues processed: 341 average time/residue: 0.1075 time to fit residues: 60.3696 Evaluate side-chains 314 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 233 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 265 CYS Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 265 CYS Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 265 CYS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 347 CYS Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 244 PHE Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 291 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 32 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 204 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 202 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 52 optimal weight: 0.0980 chunk 138 optimal weight: 0.0970 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.208468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.159569 restraints weight = 23534.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.158201 restraints weight = 30219.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.159954 restraints weight = 24414.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.160255 restraints weight = 16611.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.160378 restraints weight = 15456.653| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19719 Z= 0.117 Angle : 1.024 35.624 26789 Z= 0.397 Chirality : 0.084 1.755 3227 Planarity : 0.004 0.055 3169 Dihedral : 17.895 177.503 3444 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.96 % Allowed : 23.14 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.18), residues: 2301 helix: 1.86 (0.13), residues: 1553 sheet: -3.43 (0.55), residues: 84 loop : -1.34 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 254 TYR 0.020 0.001 TYR F 199 PHE 0.013 0.001 PHE D 15 TRP 0.012 0.001 TRP F 127 HIS 0.001 0.000 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00257 (19698) covalent geometry : angle 1.01285 (26740) SS BOND : bond 0.00253 ( 14) SS BOND : angle 0.98608 ( 28) hydrogen bonds : bond 0.03461 ( 1139) hydrogen bonds : angle 3.47001 ( 3345) link_NAG-ASN : bond 0.01030 ( 7) link_NAG-ASN : angle 5.46768 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 250 time to evaluate : 0.986 Fit side-chains TARDY: cannot create tardy model for: "LEU A 30 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU B 30 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 30 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 30 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU F 30 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ILE cc_start: 0.8454 (tt) cc_final: 0.8210 (tt) REVERT: A 225 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7844 (mt) REVERT: A 234 TYR cc_start: 0.9180 (t80) cc_final: 0.8782 (t80) REVERT: A 331 TYR cc_start: 0.8104 (m-80) cc_final: 0.7637 (m-80) REVERT: B 229 ILE cc_start: 0.8654 (tp) cc_final: 0.8187 (tp) REVERT: C 9 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6822 (mm-30) REVERT: C 10 TYR cc_start: 0.6711 (m-10) cc_final: 0.6302 (m-80) REVERT: C 253 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6183 (mt) REVERT: C 336 GLU cc_start: 0.8498 (tp30) cc_final: 0.7944 (mt-10) REVERT: D 253 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6454 (mp) REVERT: D 335 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7534 (mm) REVERT: D 345 TYR cc_start: 0.6101 (t80) cc_final: 0.5476 (t80) REVERT: E 234 TYR cc_start: 0.8479 (t80) cc_final: 0.8148 (t80) REVERT: E 244 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.7406 (t80) REVERT: E 295 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7360 (mt) REVERT: F 37 MET cc_start: 0.8466 (tpp) cc_final: 0.8261 (tpp) REVERT: F 60 ILE cc_start: 0.2280 (OUTLIER) cc_final: 0.1635 (mm) REVERT: F 281 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8529 (tp) REVERT: G 37 MET cc_start: 0.6921 (tmm) cc_final: 0.6434 (tmm) REVERT: G 128 ARG cc_start: 0.7260 (mtp180) cc_final: 0.7023 (ttp-170) REVERT: G 198 GLN cc_start: 0.6539 (mp10) cc_final: 0.6018 (tp-100) REVERT: G 340 SER cc_start: 0.8749 (p) cc_final: 0.8496 (m) outliers start: 84 outliers final: 53 residues processed: 315 average time/residue: 0.1168 time to fit residues: 59.9591 Evaluate side-chains 289 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 228 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 265 CYS Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 265 CYS Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain E residue 334 PHE Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 265 CYS Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 347 CYS Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 244 PHE Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 265 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 44 optimal weight: 0.6980 chunk 148 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 94 optimal weight: 0.0870 chunk 38 optimal weight: 2.9990 chunk 192 optimal weight: 0.4980 chunk 69 optimal weight: 0.8980 chunk 222 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.208565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.160971 restraints weight = 23654.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.159405 restraints weight = 31597.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.161636 restraints weight = 27377.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.162256 restraints weight = 17954.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.162634 restraints weight = 16743.318| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19719 Z= 0.122 Angle : 1.028 35.741 26789 Z= 0.400 Chirality : 0.084 1.760 3227 Planarity : 0.004 0.056 3169 Dihedral : 17.866 178.042 3444 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.24 % Allowed : 23.42 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.18), residues: 2301 helix: 1.89 (0.13), residues: 1553 sheet: -3.33 (0.56), residues: 84 loop : -1.38 (0.26), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 254 TYR 0.014 0.001 TYR A 293 PHE 0.011 0.001 PHE G 244 TRP 0.013 0.001 TRP F 127 HIS 0.001 0.000 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00280 (19698) covalent geometry : angle 1.01766 (26740) SS BOND : bond 0.00249 ( 14) SS BOND : angle 0.97288 ( 28) hydrogen bonds : bond 0.03412 ( 1139) hydrogen bonds : angle 3.47871 ( 3345) link_NAG-ASN : bond 0.01004 ( 7) link_NAG-ASN : angle 5.30639 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 242 time to evaluate : 0.528 Fit side-chains TARDY: cannot create tardy model for: "LEU A 30 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU B 30 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 30 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 30 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU F 30 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ILE cc_start: 0.8473 (tt) cc_final: 0.8253 (tt) REVERT: A 225 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7816 (mt) REVERT: A 326 ASN cc_start: 0.7892 (m-40) cc_final: 0.7478 (m-40) REVERT: A 331 TYR cc_start: 0.8024 (m-80) cc_final: 0.7542 (m-80) REVERT: A 364 MET cc_start: 0.3344 (mmm) cc_final: 0.2934 (mmm) REVERT: B 165 MET cc_start: 0.3840 (mmt) cc_final: 0.3343 (mpp) REVERT: B 229 ILE cc_start: 0.8627 (tp) cc_final: 0.8111 (tp) REVERT: C 5 GLN cc_start: 0.7625 (pm20) cc_final: 0.7291 (pm20) REVERT: C 10 TYR cc_start: 0.6709 (m-10) cc_final: 0.6337 (m-80) REVERT: C 253 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6134 (mt) REVERT: C 336 GLU cc_start: 0.8497 (tp30) cc_final: 0.7942 (mt-10) REVERT: C 372 MET cc_start: -0.0875 (tpp) cc_final: -0.2043 (ttt) REVERT: D 201 LYS cc_start: 0.6828 (mttt) cc_final: 0.6550 (mtmm) REVERT: D 253 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6591 (mp) REVERT: D 335 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7527 (mm) REVERT: E 234 TYR cc_start: 0.8497 (t80) cc_final: 0.8162 (t80) REVERT: E 295 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7376 (mt) REVERT: E 343 LYS cc_start: 0.6773 (mmmt) cc_final: 0.6086 (tppt) REVERT: F 37 MET cc_start: 0.8465 (tpp) cc_final: 0.8207 (tpp) REVERT: F 253 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7010 (mt) REVERT: F 281 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8564 (tp) REVERT: G 37 MET cc_start: 0.7015 (tmm) cc_final: 0.6534 (tmm) REVERT: G 128 ARG cc_start: 0.7446 (ttp-170) cc_final: 0.7063 (ttp-170) REVERT: G 198 GLN cc_start: 0.6526 (mp10) cc_final: 0.6136 (tp-100) REVERT: G 202 THR cc_start: 0.6360 (p) cc_final: 0.6101 (p) REVERT: G 340 SER cc_start: 0.8753 (p) cc_final: 0.8503 (m) outliers start: 90 outliers final: 64 residues processed: 311 average time/residue: 0.1134 time to fit residues: 57.6324 Evaluate side-chains 299 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 228 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 265 CYS Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 265 CYS Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain E residue 334 PHE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 265 CYS Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 347 CYS Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 244 PHE Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 265 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 82 optimal weight: 0.9980 chunk 202 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 214 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 GLN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.206898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.159118 restraints weight = 23753.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.157503 restraints weight = 32173.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.159585 restraints weight = 28775.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.159733 restraints weight = 18694.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.160416 restraints weight = 16633.845| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19719 Z= 0.136 Angle : 1.045 36.028 26789 Z= 0.408 Chirality : 0.085 1.763 3227 Planarity : 0.004 0.057 3169 Dihedral : 17.896 178.319 3444 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.57 % Allowed : 23.23 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.18), residues: 2301 helix: 2.00 (0.13), residues: 1525 sheet: -3.27 (0.57), residues: 84 loop : -1.36 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 254 TYR 0.014 0.001 TYR D 345 PHE 0.014 0.001 PHE G 244 TRP 0.013 0.001 TRP F 127 HIS 0.002 0.000 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00324 (19698) covalent geometry : angle 1.03062 (26740) SS BOND : bond 0.00313 ( 14) SS BOND : angle 1.03845 ( 28) hydrogen bonds : bond 0.03427 ( 1139) hydrogen bonds : angle 3.49310 ( 3345) link_NAG-ASN : bond 0.01086 ( 7) link_NAG-ASN : angle 6.19501 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 237 time to evaluate : 0.538 Fit side-chains TARDY: cannot create tardy model for: "LEU A 30 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU B 30 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 30 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 30 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU F 30 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ILE cc_start: 0.8504 (tt) cc_final: 0.8284 (tt) REVERT: A 326 ASN cc_start: 0.7911 (m-40) cc_final: 0.7503 (m-40) REVERT: A 331 TYR cc_start: 0.8078 (m-80) cc_final: 0.7585 (m-80) REVERT: A 364 MET cc_start: 0.3439 (mmm) cc_final: 0.3109 (mmm) REVERT: B 165 MET cc_start: 0.4188 (mmt) cc_final: 0.3695 (mpp) REVERT: B 229 ILE cc_start: 0.8620 (tp) cc_final: 0.8133 (tp) REVERT: C 10 TYR cc_start: 0.6591 (m-10) cc_final: 0.6230 (m-80) REVERT: C 253 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.7065 (mp) REVERT: C 372 MET cc_start: -0.1377 (tpp) cc_final: -0.3053 (ttm) REVERT: D 253 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.6666 (mp) REVERT: E 234 TYR cc_start: 0.8536 (t80) cc_final: 0.8174 (t80) REVERT: E 295 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7370 (mt) REVERT: E 343 LYS cc_start: 0.6730 (mmmt) cc_final: 0.6143 (tppt) REVERT: F 37 MET cc_start: 0.8443 (tpp) cc_final: 0.8205 (tpp) REVERT: F 253 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.6871 (mt) REVERT: F 267 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8807 (mp) REVERT: F 281 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8555 (tp) REVERT: G 128 ARG cc_start: 0.7399 (ttp-170) cc_final: 0.7110 (ttp-170) REVERT: G 198 GLN cc_start: 0.6736 (mp10) cc_final: 0.6304 (tp40) REVERT: G 228 CYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7742 (t) outliers start: 97 outliers final: 79 residues processed: 310 average time/residue: 0.1081 time to fit residues: 54.5428 Evaluate side-chains 313 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 227 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 265 CYS Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 265 CYS Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain E residue 334 PHE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 127 TRP Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 265 CYS Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 347 CYS Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 228 CYS Chi-restraints excluded: chain G residue 244 PHE Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 278 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 148 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 210 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 GLN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.207091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.160069 restraints weight = 23686.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.158623 restraints weight = 29256.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.160910 restraints weight = 26620.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.160659 restraints weight = 19108.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.161418 restraints weight = 17874.078| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 19719 Z= 0.138 Angle : 1.065 35.956 26789 Z= 0.418 Chirality : 0.086 1.765 3227 Planarity : 0.004 0.057 3169 Dihedral : 17.952 178.571 3444 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.71 % Allowed : 23.28 % Favored : 72.01 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.18), residues: 2301 helix: 2.04 (0.13), residues: 1518 sheet: -3.26 (0.56), residues: 84 loop : -1.34 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 254 TYR 0.015 0.001 TYR E 345 PHE 0.013 0.001 PHE G 244 TRP 0.013 0.001 TRP F 127 HIS 0.002 0.000 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00323 (19698) covalent geometry : angle 1.04032 (26740) SS BOND : bond 0.00276 ( 14) SS BOND : angle 1.02606 ( 28) hydrogen bonds : bond 0.03398 ( 1139) hydrogen bonds : angle 3.48104 ( 3345) link_NAG-ASN : bond 0.01968 ( 7) link_NAG-ASN : angle 8.20694 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 236 time to evaluate : 0.758 Fit side-chains TARDY: cannot create tardy model for: "LEU A 30 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU B 30 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 30 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 30 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU F 30 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ILE cc_start: 0.8503 (tt) cc_final: 0.8291 (tt) REVERT: A 326 ASN cc_start: 0.7862 (m-40) cc_final: 0.7434 (m-40) REVERT: A 331 TYR cc_start: 0.8020 (m-80) cc_final: 0.7563 (m-80) REVERT: A 364 MET cc_start: 0.3627 (mmm) cc_final: 0.3321 (mmm) REVERT: B 165 MET cc_start: 0.4261 (mmt) cc_final: 0.3824 (mpp) REVERT: B 229 ILE cc_start: 0.8624 (tp) cc_final: 0.8134 (tp) REVERT: C 9 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6643 (mm-30) REVERT: C 10 TYR cc_start: 0.6607 (m-10) cc_final: 0.6245 (m-80) REVERT: C 253 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6285 (mt) REVERT: C 372 MET cc_start: -0.1452 (tpp) cc_final: -0.3098 (ttm) REVERT: D 201 LYS cc_start: 0.6848 (mttt) cc_final: 0.6482 (mtmm) REVERT: D 253 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.6665 (mp) REVERT: E 234 TYR cc_start: 0.8532 (t80) cc_final: 0.8177 (t80) REVERT: E 295 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7361 (mt) REVERT: E 343 LYS cc_start: 0.6677 (mmmt) cc_final: 0.6123 (tppt) REVERT: F 37 MET cc_start: 0.8403 (tpp) cc_final: 0.8143 (tpp) REVERT: F 253 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7029 (mt) REVERT: F 267 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8806 (mp) REVERT: F 281 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8585 (tp) REVERT: G 128 ARG cc_start: 0.7377 (ttp-170) cc_final: 0.7108 (ttp-170) REVERT: G 198 GLN cc_start: 0.6713 (mp10) cc_final: 0.6347 (tp40) outliers start: 100 outliers final: 88 residues processed: 307 average time/residue: 0.1023 time to fit residues: 51.7462 Evaluate side-chains 325 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 231 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 265 CYS Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 265 CYS Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain E residue 334 PHE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 127 TRP Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 265 CYS Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 347 CYS Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 244 PHE Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 285 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 164 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 chunk 4 optimal weight: 0.2980 chunk 207 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.205986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.158429 restraints weight = 23723.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.156990 restraints weight = 30461.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.159164 restraints weight = 25569.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.158944 restraints weight = 17328.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.160128 restraints weight = 15795.175| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19719 Z= 0.140 Angle : 1.048 36.126 26789 Z= 0.412 Chirality : 0.084 1.767 3227 Planarity : 0.004 0.057 3169 Dihedral : 17.990 178.913 3444 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.76 % Allowed : 23.37 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.18), residues: 2301 helix: 1.99 (0.13), residues: 1536 sheet: -3.26 (0.56), residues: 84 loop : -1.51 (0.25), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 254 TYR 0.014 0.001 TYR D 345 PHE 0.014 0.001 PHE G 244 TRP 0.013 0.001 TRP F 127 HIS 0.002 0.000 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00333 (19698) covalent geometry : angle 1.03673 (26740) SS BOND : bond 0.00307 ( 14) SS BOND : angle 1.04061 ( 28) hydrogen bonds : bond 0.03463 ( 1139) hydrogen bonds : angle 3.49371 ( 3345) link_NAG-ASN : bond 0.00910 ( 7) link_NAG-ASN : angle 5.51679 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 234 time to evaluate : 0.542 Fit side-chains TARDY: cannot create tardy model for: "LEU A 30 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU B 30 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 30 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 30 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU F 30 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 ASN cc_start: 0.7912 (m-40) cc_final: 0.7490 (m-40) REVERT: A 331 TYR cc_start: 0.8049 (m-80) cc_final: 0.7609 (m-80) REVERT: A 364 MET cc_start: 0.3897 (mmm) cc_final: 0.3594 (mmm) REVERT: B 165 MET cc_start: 0.4412 (mmt) cc_final: 0.3527 (mpp) REVERT: B 229 ILE cc_start: 0.8623 (tp) cc_final: 0.8133 (tp) REVERT: C 9 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6621 (mm-30) REVERT: C 10 TYR cc_start: 0.6615 (m-10) cc_final: 0.6215 (m-80) REVERT: C 19 GLU cc_start: 0.4221 (OUTLIER) cc_final: 0.3985 (tt0) REVERT: C 253 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6290 (mt) REVERT: C 372 MET cc_start: -0.1325 (tpp) cc_final: -0.3088 (ttm) REVERT: D 201 LYS cc_start: 0.6783 (mttt) cc_final: 0.6185 (mtmm) REVERT: D 253 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6589 (mp) REVERT: E 234 TYR cc_start: 0.8534 (t80) cc_final: 0.8174 (t80) REVERT: E 295 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7427 (mt) REVERT: E 329 SER cc_start: 0.7693 (m) cc_final: 0.7079 (t) REVERT: E 343 LYS cc_start: 0.6701 (mmmt) cc_final: 0.6215 (tppt) REVERT: E 375 MET cc_start: -0.0178 (mtt) cc_final: -0.0585 (mtt) REVERT: F 165 MET cc_start: 0.1918 (ttt) cc_final: -0.0733 (mmm) REVERT: F 253 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6938 (mt) REVERT: F 267 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8829 (mp) REVERT: F 281 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8549 (tp) REVERT: G 128 ARG cc_start: 0.7340 (ttp-170) cc_final: 0.7099 (ttt180) REVERT: G 138 ASP cc_start: 0.8102 (m-30) cc_final: 0.7681 (m-30) REVERT: G 198 GLN cc_start: 0.6921 (mp10) cc_final: 0.6351 (tp-100) REVERT: G 228 CYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7728 (t) outliers start: 101 outliers final: 86 residues processed: 309 average time/residue: 0.1035 time to fit residues: 52.8313 Evaluate side-chains 321 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 227 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 265 CYS Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 265 CYS Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain E residue 334 PHE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 265 CYS Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 347 CYS Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 228 CYS Chi-restraints excluded: chain G residue 244 PHE Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 291 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 2 optimal weight: 0.6980 chunk 221 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 71 optimal weight: 20.0000 chunk 174 optimal weight: 9.9990 chunk 86 optimal weight: 0.0670 chunk 162 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 72 optimal weight: 0.7980 chunk 52 optimal weight: 0.4980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 GLN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.209552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.162951 restraints weight = 23501.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.161434 restraints weight = 31279.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.163943 restraints weight = 25375.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.163707 restraints weight = 17057.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.164396 restraints weight = 16176.886| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19719 Z= 0.115 Angle : 1.027 35.354 26789 Z= 0.399 Chirality : 0.084 1.778 3227 Planarity : 0.004 0.057 3169 Dihedral : 17.877 178.859 3444 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.06 % Allowed : 25.26 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.18), residues: 2301 helix: 2.06 (0.13), residues: 1564 sheet: -3.20 (0.57), residues: 84 loop : -1.49 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 254 TYR 0.013 0.001 TYR D 345 PHE 0.011 0.001 PHE A 244 TRP 0.018 0.001 TRP F 127 HIS 0.001 0.000 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00255 (19698) covalent geometry : angle 1.01713 (26740) SS BOND : bond 0.00200 ( 14) SS BOND : angle 0.93416 ( 28) hydrogen bonds : bond 0.03141 ( 1139) hydrogen bonds : angle 3.39611 ( 3345) link_NAG-ASN : bond 0.00874 ( 7) link_NAG-ASN : angle 5.14821 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2539.26 seconds wall clock time: 45 minutes 20.71 seconds (2720.71 seconds total)