Starting phenix.real_space_refine on Mon Jun 16 22:04:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gyo_34374/06_2025/8gyo_34374.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gyo_34374/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8gyo_34374/06_2025/8gyo_34374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gyo_34374/06_2025/8gyo_34374.map" model { file = "/net/cci-nas-00/data/ceres_data/8gyo_34374/06_2025/8gyo_34374.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gyo_34374/06_2025/8gyo_34374.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.93, per 1000 atoms: 0.93 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: 5.65 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 1.80 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: 5.79 Time building geometry restraints manager: 6.59 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 376 or resid 501)) selection = (chain 'B' and (resid 29 through 376 or resid 501)) selection = (chain 'C' and (resid 29 through 376 or resid 501)) selection = (chain 'D' and (resid 29 through 376 or resid 501)) selection = (chain 'E' and (resid 29 through 376 or resid 501)) selection = (chain 'F' and (resid 29 through 376 or resid 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 51.990 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.080 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.540 ------------------------------------------------------------------------------- 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 : 8.41 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (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 TRP 0.009 0.001 TRP A 104 HIS 0.001 0.000 HIS D 106 PHE 0.012 0.001 PHE D 244 TYR 0.018 0.001 TYR F 234 ARG 0.006 0.000 ARG G 254 Details of bonding type rmsd link_NAG-ASN : bond 0.07152 ( 7) link_NAG-ASN : angle 12.28578 ( 21) hydrogen bonds : bond 0.17884 ( 1139) hydrogen bonds : angle 5.54678 ( 3345) SS BOND : bond 0.00141 ( 14) SS BOND : angle 0.65118 ( 28) covalent geometry : bond 0.00410 (19698) covalent geometry : angle 0.64827 (26740) *********************** 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 : 2.242 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: 0.3227 time to fit residues: 140.2837 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 : 2.282 ------------------------------------------------------------------------------- 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 195 optimal weight: 9.9990 chunk 175 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 181 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 210 optimal weight: 6.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN B 198 GLN D 89 GLN D 262 GLN D 353 ASN ** E 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4364 r_free = 0.4364 target = 0.210333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.177222 restraints weight = 23251.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.175188 restraints weight = 41195.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.175280 restraints weight = 38285.947| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19719 Z= 0.162 Angle : 1.149 35.649 26789 Z= 0.453 Chirality : 0.090 1.841 3227 Planarity : 0.005 0.055 3169 Dihedral : 19.756 179.151 3446 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.76 % Allowed : 18.05 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.18), residues: 2301 helix: 1.68 (0.13), residues: 1562 sheet: -4.03 (0.51), residues: 84 loop : -1.41 (0.26), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 127 HIS 0.002 0.000 HIS A 134 PHE 0.017 0.001 PHE C 141 TYR 0.026 0.002 TYR G 230 ARG 0.007 0.001 ARG A 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00842 ( 7) link_NAG-ASN : angle 7.02649 ( 21) hydrogen bonds : bond 0.04477 ( 1139) hydrogen bonds : angle 3.82828 ( 3345) SS BOND : bond 0.00381 ( 14) SS BOND : angle 1.19400 ( 28) covalent geometry : bond 0.00380 (19698) covalent geometry : angle 1.13275 (26740) *********************** 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 357 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 256 time to evaluate : 2.634 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 114 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6479 (mm) REVERT: A 211 ILE cc_start: 0.8466 (tt) cc_final: 0.8217 (tt) REVERT: A 242 ASP cc_start: 0.8450 (p0) cc_final: 0.8232 (p0) REVERT: A 331 TYR cc_start: 0.7762 (m-80) cc_final: 0.7358 (m-80) REVERT: B 229 ILE cc_start: 0.8758 (tp) cc_final: 0.8246 (tp) REVERT: B 253 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6580 (mt) REVERT: C 101 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6732 (tt) REVERT: C 253 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7252 (mp) REVERT: C 348 LEU cc_start: 0.7811 (pp) cc_final: 0.7245 (mm) REVERT: D 253 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6789 (mp) REVERT: F 60 ILE cc_start: 0.2906 (OUTLIER) cc_final: 0.2312 (mm) REVERT: G 128 ARG cc_start: 0.7099 (mtp180) cc_final: 0.6780 (ttp-170) REVERT: G 253 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7580 (mt) outliers start: 101 outliers final: 58 residues processed: 329 average time/residue: 0.3009 time to fit residues: 159.1989 Evaluate side-chains 290 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 225 time to evaluate : 2.164 ------------------------------------------------------------------------------- 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 220 THR 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 B residue 285 VAL Chi-restraints excluded: chain C residue 39 THR 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 89 GLN 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 D residue 285 VAL 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 202 THR 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 F residue 285 VAL Chi-restraints excluded: chain G residue 38 VAL 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 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 195 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 chunk 231 optimal weight: 6.9990 chunk 147 optimal weight: 0.9980 chunk 208 optimal weight: 0.7980 chunk 175 optimal weight: 4.9990 chunk 77 optimal weight: 0.0870 chunk 67 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 D 151 ASN ** E 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.211773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.162320 restraints weight = 23401.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.161566 restraints weight = 26930.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.163760 restraints weight = 21145.159| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19719 Z= 0.130 Angle : 1.054 35.946 26789 Z= 0.412 Chirality : 0.086 1.783 3227 Planarity : 0.004 0.053 3169 Dihedral : 18.535 176.508 3446 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.01 % Allowed : 20.31 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.19), residues: 2301 helix: 1.93 (0.13), residues: 1534 sheet: -3.74 (0.52), residues: 84 loop : -1.17 (0.26), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 127 HIS 0.002 0.000 HIS G 134 PHE 0.011 0.001 PHE G 244 TYR 0.016 0.001 TYR G 193 ARG 0.005 0.001 ARG F 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00987 ( 7) link_NAG-ASN : angle 6.55225 ( 21) hydrogen bonds : bond 0.03920 ( 1139) hydrogen bonds : angle 3.57064 ( 3345) SS BOND : bond 0.00232 ( 14) SS BOND : angle 1.11283 ( 28) covalent geometry : bond 0.00287 (19698) covalent geometry : angle 1.03784 (26740) *********************** 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 344 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 259 time to evaluate : 2.203 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: A 331 TYR cc_start: 0.7864 (m-80) cc_final: 0.7350 (m-80) REVERT: A 339 ILE cc_start: 0.8710 (tp) cc_final: 0.8456 (tp) REVERT: B 229 ILE cc_start: 0.8766 (tp) cc_final: 0.8257 (tp) REVERT: B 375 MET cc_start: -0.0658 (mmm) cc_final: -0.0911 (mmm) REVERT: C 9 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6602 (mm-30) REVERT: C 101 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6581 (tt) REVERT: C 219 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8632 (tt) REVERT: C 253 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6242 (mt) REVERT: C 348 LEU cc_start: 0.8290 (pp) cc_final: 0.7838 (mm) REVERT: D 127 TRP cc_start: 0.7954 (t-100) cc_final: 0.7600 (t-100) REVERT: D 253 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6162 (mp) REVERT: D 309 TYR cc_start: 0.7010 (OUTLIER) cc_final: 0.6558 (t80) REVERT: D 335 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7673 (mm) REVERT: D 375 MET cc_start: 0.0599 (mtt) cc_final: 0.0109 (mtt) REVERT: E 234 TYR cc_start: 0.8433 (t80) cc_final: 0.8089 (t80) REVERT: E 295 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7412 (mt) REVERT: F 47 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8394 (mt) REVERT: F 60 ILE cc_start: 0.2646 (OUTLIER) cc_final: 0.2184 (mm) REVERT: F 341 GLU cc_start: 0.8122 (tp30) cc_final: 0.7783 (mm-30) REVERT: G 45 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7605 (tp) REVERT: G 128 ARG cc_start: 0.7178 (mtp180) cc_final: 0.6858 (ttp-170) outliers start: 85 outliers final: 46 residues processed: 317 average time/residue: 0.2735 time to fit residues: 138.9764 Evaluate side-chains 294 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 238 time to evaluate : 2.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 210 ILE 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 B residue 40 CYS 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 342 VAL 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 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 D residue 62 THR Chi-restraints excluded: chain D residue 68 SER 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 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 43 VAL Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 62 THR 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 265 CYS 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 347 CYS Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 210 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 265 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 118 optimal weight: 1.9990 chunk 228 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 190 optimal weight: 0.7980 chunk 201 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 chunk 11 optimal weight: 0.0970 chunk 87 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.4366 r_free = 0.4366 target = 0.209555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.159720 restraints weight = 23565.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.158989 restraints weight = 31812.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.161357 restraints weight = 23307.502| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.2405 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= 0.138 Angle : 1.049 35.549 26789 Z= 0.410 Chirality : 0.085 1.751 3227 Planarity : 0.004 0.055 3169 Dihedral : 18.316 176.828 3444 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.85 % Allowed : 20.12 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.19), residues: 2301 helix: 1.91 (0.13), residues: 1554 sheet: -3.62 (0.53), residues: 84 loop : -1.30 (0.26), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 127 HIS 0.002 0.000 HIS G 134 PHE 0.014 0.001 PHE G 244 TYR 0.013 0.001 TYR F 234 ARG 0.005 0.001 ARG F 254 Details of bonding type rmsd link_NAG-ASN : bond 0.00978 ( 7) link_NAG-ASN : angle 6.05926 ( 21) hydrogen bonds : bond 0.03733 ( 1139) hydrogen bonds : angle 3.52289 ( 3345) SS BOND : bond 0.00344 ( 14) SS BOND : angle 1.20734 ( 28) covalent geometry : bond 0.00322 (19698) covalent geometry : angle 1.03589 (26740) *********************** 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 362 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 259 time to evaluate : 2.284 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 114 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6564 (mm) REVERT: A 331 TYR cc_start: 0.7791 (m-80) cc_final: 0.7352 (m-80) REVERT: A 339 ILE cc_start: 0.8747 (tp) cc_final: 0.8510 (tp) REVERT: B 229 ILE cc_start: 0.8758 (tp) cc_final: 0.8273 (tp) REVERT: B 375 MET cc_start: -0.0797 (mmm) cc_final: -0.1015 (mmm) REVERT: C 9 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6933 (mm-30) REVERT: C 10 TYR cc_start: 0.6891 (m-10) cc_final: 0.6626 (m-80) REVERT: C 219 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8574 (tt) REVERT: C 253 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6248 (mt) REVERT: C 254 ARG cc_start: 0.7404 (mtt180) cc_final: 0.7199 (mtt180) REVERT: C 336 GLU cc_start: 0.8397 (tp30) cc_final: 0.7412 (mt-10) REVERT: D 253 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6398 (mp) REVERT: D 309 TYR cc_start: 0.7062 (OUTLIER) cc_final: 0.6633 (t80) REVERT: D 335 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7529 (mm) REVERT: D 345 TYR cc_start: 0.6292 (t80) cc_final: 0.5875 (t80) REVERT: E 201 LYS cc_start: 0.7283 (mttp) cc_final: 0.6957 (mttp) REVERT: E 234 TYR cc_start: 0.8453 (t80) cc_final: 0.8158 (t80) REVERT: E 253 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6675 (mt) REVERT: E 295 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7397 (mt) REVERT: F 47 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8444 (mt) REVERT: F 60 ILE cc_start: 0.2806 (OUTLIER) cc_final: 0.2187 (mm) REVERT: F 341 GLU cc_start: 0.8142 (tp30) cc_final: 0.7815 (mm-30) REVERT: G 37 MET cc_start: 0.6900 (tmm) cc_final: 0.6445 (tmm) REVERT: G 340 SER cc_start: 0.8621 (p) cc_final: 0.8281 (m) outliers start: 103 outliers final: 65 residues processed: 332 average time/residue: 0.2742 time to fit residues: 147.7640 Evaluate side-chains 305 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 230 time to evaluate : 2.056 ------------------------------------------------------------------------------- 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 210 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 285 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 62 THR 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 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 68 SER Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 248 ILE 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 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 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 43 VAL 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 240 LEU Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 253 LEU 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 E residue 333 LEU 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 240 LEU Chi-restraints excluded: chain F residue 265 CYS Chi-restraints excluded: chain F residue 278 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 163 optimal weight: 0.0770 chunk 187 optimal weight: 1.9990 chunk 197 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 178 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 chunk 193 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 overall best weight: 2.1544 ------------------------------------------------------------------------------- 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 G 56 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.204250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.157342 restraints weight = 23986.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.156022 restraints weight = 28930.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.157557 restraints weight = 26642.380| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19719 Z= 0.190 Angle : 1.086 36.983 26789 Z= 0.435 Chirality : 0.084 1.738 3227 Planarity : 0.005 0.057 3169 Dihedral : 18.177 177.459 3444 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 6.50 % Allowed : 20.08 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.18), residues: 2301 helix: 1.68 (0.13), residues: 1554 sheet: -4.27 (0.58), residues: 58 loop : -1.36 (0.25), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 85 HIS 0.004 0.001 HIS A 134 PHE 0.020 0.001 PHE F 244 TYR 0.016 0.002 TYR B 230 ARG 0.006 0.001 ARG A 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00976 ( 7) link_NAG-ASN : angle 5.71429 ( 21) hydrogen bonds : bond 0.04131 ( 1139) hydrogen bonds : angle 3.65428 ( 3345) SS BOND : bond 0.00511 ( 14) SS BOND : angle 1.35646 ( 28) covalent geometry : bond 0.00461 (19698) covalent geometry : angle 1.07441 (26740) *********************** 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 373 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 235 time to evaluate : 2.178 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: 0.9005 (OUTLIER) cc_final: 0.8675 (tt) REVERT: A 331 TYR cc_start: 0.7948 (m-80) cc_final: 0.7604 (m-80) REVERT: A 339 ILE cc_start: 0.8858 (tp) cc_final: 0.8604 (tp) REVERT: B 56 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.6887 (tp40) REVERT: B 229 ILE cc_start: 0.8705 (tp) cc_final: 0.8286 (tp) REVERT: B 244 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.8324 (m-80) REVERT: C 10 TYR cc_start: 0.6777 (m-10) cc_final: 0.6412 (m-80) REVERT: C 143 MET cc_start: 0.5528 (ppp) cc_final: 0.5109 (ppp) REVERT: C 253 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.6419 (mt) REVERT: C 336 GLU cc_start: 0.8404 (tp30) cc_final: 0.7525 (mt-10) REVERT: D 253 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.6723 (mp) REVERT: D 335 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7509 (mm) REVERT: E 201 LYS cc_start: 0.7432 (mttp) cc_final: 0.7176 (mttp) REVERT: F 47 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8521 (mt) REVERT: F 60 ILE cc_start: 0.2658 (OUTLIER) cc_final: 0.1832 (mm) REVERT: F 165 MET cc_start: 0.1693 (ttt) cc_final: -0.0695 (mmm) REVERT: F 253 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.6822 (mt) REVERT: G 37 MET cc_start: 0.6910 (tmm) cc_final: 0.6441 (tmm) REVERT: G 45 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8046 (tp) REVERT: G 128 ARG cc_start: 0.7299 (mtp180) cc_final: 0.6961 (ttp-170) REVERT: G 340 SER cc_start: 0.8771 (p) cc_final: 0.8486 (m) outliers start: 138 outliers final: 82 residues processed: 346 average time/residue: 0.2571 time to fit residues: 144.5535 Evaluate side-chains 314 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 222 time to evaluate : 2.246 ------------------------------------------------------------------------------- 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 120 LEU Chi-restraints excluded: chain A residue 202 THR 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 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 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 B residue 56 GLN 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 222 ILE Chi-restraints excluded: chain B residue 244 PHE 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 40 CYS 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 209 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 248 ILE 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 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 210 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 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 218 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 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 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 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 45 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 32 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 146 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 chunk 209 optimal weight: 0.9980 chunk 203 optimal weight: 0.0010 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 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 = 0.4332 r_free = 0.4332 target = 0.206428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.158350 restraints weight = 23832.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.157921 restraints weight = 27692.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.159797 restraints weight = 23396.827| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.3088 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= 0.137 Angle : 1.051 36.127 26789 Z= 0.411 Chirality : 0.084 1.748 3227 Planarity : 0.004 0.057 3169 Dihedral : 17.964 177.578 3444 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.76 % Allowed : 21.72 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.18), residues: 2301 helix: 1.79 (0.13), residues: 1557 sheet: -3.11 (0.65), residues: 69 loop : -1.32 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 127 HIS 0.002 0.000 HIS A 134 PHE 0.015 0.001 PHE G 244 TYR 0.023 0.001 TYR F 199 ARG 0.007 0.000 ARG G 254 Details of bonding type rmsd link_NAG-ASN : bond 0.00919 ( 7) link_NAG-ASN : angle 6.35818 ( 21) hydrogen bonds : bond 0.03705 ( 1139) hydrogen bonds : angle 3.51962 ( 3345) SS BOND : bond 0.00410 ( 14) SS BOND : angle 1.04476 ( 28) covalent geometry : bond 0.00324 (19698) covalent geometry : angle 1.03597 (26740) *********************** 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 342 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 241 time to evaluate : 2.284 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 120 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8748 (tt) REVERT: A 331 TYR cc_start: 0.8088 (m-80) cc_final: 0.7644 (m-80) REVERT: A 339 ILE cc_start: 0.8802 (tp) cc_final: 0.8582 (tp) REVERT: B 229 ILE cc_start: 0.8675 (tp) cc_final: 0.8252 (tp) REVERT: C 10 TYR cc_start: 0.6539 (m-10) cc_final: 0.6232 (m-80) REVERT: C 143 MET cc_start: 0.5434 (ppp) cc_final: 0.5097 (ppp) REVERT: C 253 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6037 (mt) REVERT: C 336 GLU cc_start: 0.8398 (tp30) cc_final: 0.7477 (mt-10) REVERT: D 253 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.6676 (mp) REVERT: D 335 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7351 (mm) REVERT: E 201 LYS cc_start: 0.7423 (mttp) cc_final: 0.7153 (mttp) REVERT: E 234 TYR cc_start: 0.8485 (t80) cc_final: 0.8174 (t80) REVERT: E 253 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.6843 (mt) REVERT: F 60 ILE cc_start: 0.2632 (OUTLIER) cc_final: 0.2046 (mm) REVERT: F 165 MET cc_start: 0.2021 (ttt) cc_final: -0.0591 (mmm) REVERT: F 253 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.6891 (mt) REVERT: F 281 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8565 (tp) REVERT: G 37 MET cc_start: 0.7111 (tmm) cc_final: 0.6642 (tmm) REVERT: G 45 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8034 (tp) REVERT: G 128 ARG cc_start: 0.7234 (mtp180) cc_final: 0.6897 (ttp-170) REVERT: G 198 GLN cc_start: 0.6518 (mp10) cc_final: 0.6088 (tp40) REVERT: G 202 THR cc_start: 0.6471 (p) cc_final: 0.6201 (p) REVERT: G 340 SER cc_start: 0.8756 (p) cc_final: 0.8513 (m) outliers start: 101 outliers final: 72 residues processed: 320 average time/residue: 0.2667 time to fit residues: 139.6862 Evaluate side-chains 305 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 224 time to evaluate : 2.213 ------------------------------------------------------------------------------- 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 120 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 248 ILE 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 310 GLU Chi-restraints excluded: chain B residue 38 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 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 C residue 19 GLU Chi-restraints excluded: chain C residue 37 MET 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 68 SER Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 248 ILE 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 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 278 VAL Chi-restraints excluded: chain D residue 285 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 45 LEU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 200 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 253 LEU 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 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 114 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 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 45 LEU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 174 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 205 optimal weight: 0.7980 chunk 224 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 221 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.202444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.155266 restraints weight = 23898.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.152676 restraints weight = 33099.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.154764 restraints weight = 26507.090| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19719 Z= 0.185 Angle : 1.088 37.020 26789 Z= 0.436 Chirality : 0.084 1.745 3227 Planarity : 0.005 0.057 3169 Dihedral : 18.047 178.879 3444 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 6.08 % Allowed : 21.25 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.18), residues: 2301 helix: 1.63 (0.13), residues: 1533 sheet: -4.21 (0.49), residues: 78 loop : -1.35 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 127 HIS 0.004 0.001 HIS A 134 PHE 0.020 0.001 PHE G 244 TYR 0.020 0.002 TYR B 193 ARG 0.009 0.001 ARG D 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00914 ( 7) link_NAG-ASN : angle 5.46547 ( 21) hydrogen bonds : bond 0.04065 ( 1139) hydrogen bonds : angle 3.70505 ( 3345) SS BOND : bond 0.00551 ( 14) SS BOND : angle 1.36175 ( 28) covalent geometry : bond 0.00452 (19698) covalent geometry : angle 1.07728 (26740) *********************** 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 371 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 242 time to evaluate : 2.003 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 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 331 TYR cc_start: 0.8104 (m-80) cc_final: 0.7669 (m-80) REVERT: B 165 MET cc_start: 0.4284 (mmt) cc_final: 0.3064 (mpp) REVERT: B 229 ILE cc_start: 0.8658 (tp) cc_final: 0.8240 (tp) REVERT: C 10 TYR cc_start: 0.6394 (m-10) cc_final: 0.6086 (m-80) REVERT: C 253 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6839 (mp) REVERT: C 336 GLU cc_start: 0.8474 (tp30) cc_final: 0.7588 (tt0) REVERT: C 372 MET cc_start: -0.1310 (tpp) cc_final: -0.1984 (ttt) REVERT: D 201 LYS cc_start: 0.6683 (mttt) cc_final: 0.6440 (mtmm) REVERT: D 253 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.6879 (mp) REVERT: E 244 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7530 (t80) REVERT: E 253 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6716 (mt) REVERT: F 60 ILE cc_start: 0.2661 (OUTLIER) cc_final: 0.2083 (mm) REVERT: F 165 MET cc_start: 0.1686 (ttt) cc_final: -0.0808 (mmm) REVERT: F 198 GLN cc_start: 0.6148 (mm-40) cc_final: 0.5630 (tm-30) REVERT: F 253 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.6942 (mt) REVERT: F 267 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8858 (mp) REVERT: F 349 LYS cc_start: 0.8456 (tptt) cc_final: 0.8133 (tppt) REVERT: F 353 ASN cc_start: 0.6484 (m110) cc_final: 0.6070 (t0) REVERT: G 128 ARG cc_start: 0.7353 (mtp180) cc_final: 0.7015 (ttp-170) REVERT: G 198 GLN cc_start: 0.6718 (mp10) cc_final: 0.6208 (tp-100) outliers start: 129 outliers final: 93 residues processed: 342 average time/residue: 0.2810 time to fit residues: 154.8364 Evaluate side-chains 328 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 228 time to evaluate : 2.078 ------------------------------------------------------------------------------- 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 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 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 39 THR 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 195 ILE Chi-restraints excluded: chain B residue 208 ASN 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 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 39 THR Chi-restraints excluded: chain C residue 47 LEU 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 202 THR 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 248 ILE 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 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 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 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 200 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 253 LEU 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 52 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 114 LEU 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 267 LEU 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 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 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 252 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 183 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 89 optimal weight: 0.3980 chunk 15 optimal weight: 0.3980 chunk 65 optimal weight: 0.2980 chunk 144 optimal weight: 6.9990 chunk 184 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN ** C 5 GLN ** 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 = 0.4347 r_free = 0.4347 target = 0.207946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.160218 restraints weight = 23691.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.158565 restraints weight = 30184.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.161395 restraints weight = 24178.777| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.3634 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= 0.118 Angle : 1.032 35.711 26789 Z= 0.401 Chirality : 0.084 1.767 3227 Planarity : 0.004 0.056 3169 Dihedral : 17.877 178.266 3444 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.72 % Allowed : 23.52 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.18), residues: 2301 helix: 1.91 (0.13), residues: 1529 sheet: -2.99 (0.66), residues: 69 loop : -1.38 (0.25), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 127 HIS 0.001 0.000 HIS G 134 PHE 0.011 0.001 PHE A 244 TYR 0.013 0.001 TYR G 213 ARG 0.007 0.000 ARG G 254 Details of bonding type rmsd link_NAG-ASN : bond 0.01002 ( 7) link_NAG-ASN : angle 5.31459 ( 21) hydrogen bonds : bond 0.03407 ( 1139) hydrogen bonds : angle 3.46879 ( 3345) SS BOND : bond 0.00222 ( 14) SS BOND : angle 0.95665 ( 28) covalent geometry : bond 0.00264 (19698) covalent geometry : angle 1.02153 (26740) *********************** 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 322 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 243 time to evaluate : 2.154 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 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 225 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7773 (mt) REVERT: A 234 TYR cc_start: 0.9213 (t80) cc_final: 0.8677 (t80) REVERT: A 326 ASN cc_start: 0.7794 (m-40) cc_final: 0.7356 (m-40) REVERT: A 331 TYR cc_start: 0.7995 (m-80) cc_final: 0.7536 (m-80) REVERT: B 165 MET cc_start: 0.4243 (mmt) cc_final: 0.3801 (mpp) REVERT: B 229 ILE cc_start: 0.8593 (tp) cc_final: 0.8128 (tp) REVERT: C 10 TYR cc_start: 0.6426 (m-10) cc_final: 0.6163 (m-80) REVERT: C 253 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6172 (mp) REVERT: C 336 GLU cc_start: 0.8395 (tp30) cc_final: 0.7571 (tt0) REVERT: C 372 MET cc_start: -0.1847 (tpp) cc_final: -0.2549 (ttt) REVERT: D 201 LYS cc_start: 0.6662 (mttt) cc_final: 0.6178 (mtmm) REVERT: E 234 TYR cc_start: 0.8459 (t80) cc_final: 0.8118 (t80) REVERT: E 244 PHE cc_start: 0.7637 (OUTLIER) cc_final: 0.7396 (t80) REVERT: E 253 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6783 (mt) REVERT: E 295 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7387 (mt) REVERT: F 165 MET cc_start: 0.1914 (ttt) cc_final: -0.0795 (mmm) REVERT: F 198 GLN cc_start: 0.5900 (mm-40) cc_final: 0.5469 (tm-30) REVERT: F 253 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6787 (mt) REVERT: F 281 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8530 (tp) REVERT: G 45 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7851 (tp) REVERT: G 128 ARG cc_start: 0.7255 (mtp180) cc_final: 0.7020 (ttp-170) REVERT: G 198 GLN cc_start: 0.6656 (mp10) cc_final: 0.6231 (tp40) REVERT: G 202 THR cc_start: 0.6311 (p) cc_final: 0.6085 (p) outliers start: 79 outliers final: 52 residues processed: 309 average time/residue: 0.2784 time to fit residues: 138.7293 Evaluate side-chains 280 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 220 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE 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 291 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 354 ILE 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 208 ASN 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 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 209 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 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 265 CYS Chi-restraints excluded: chain D residue 293 TYR Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain E residue 62 THR 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 253 LEU 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 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 281 LEU Chi-restraints excluded: chain F residue 347 CYS Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 210 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 265 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 219 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 206 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 208 optimal weight: 0.9980 chunk 217 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN B 359 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.207149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.159909 restraints weight = 23671.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.158536 restraints weight = 29858.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.161237 restraints weight = 24385.602| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3778 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= 0.125 Angle : 1.036 35.884 26789 Z= 0.404 Chirality : 0.084 1.768 3227 Planarity : 0.004 0.057 3169 Dihedral : 17.848 178.606 3444 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.49 % Allowed : 24.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.18), residues: 2301 helix: 1.98 (0.13), residues: 1526 sheet: -4.02 (0.50), residues: 78 loop : -1.33 (0.25), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 127 HIS 0.001 0.000 HIS A 134 PHE 0.012 0.001 PHE G 244 TYR 0.016 0.001 TYR C 234 ARG 0.006 0.000 ARG G 254 Details of bonding type rmsd link_NAG-ASN : bond 0.00959 ( 7) link_NAG-ASN : angle 5.14507 ( 21) hydrogen bonds : bond 0.03390 ( 1139) hydrogen bonds : angle 3.46206 ( 3345) SS BOND : bond 0.00276 ( 14) SS BOND : angle 0.91712 ( 28) covalent geometry : bond 0.00292 (19698) covalent geometry : angle 1.02626 (26740) *********************** 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 304 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 230 time to evaluate : 2.310 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 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 225 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7832 (mt) REVERT: A 234 TYR cc_start: 0.9225 (t80) cc_final: 0.8700 (t80) REVERT: A 326 ASN cc_start: 0.7840 (m-40) cc_final: 0.7406 (m-40) REVERT: A 331 TYR cc_start: 0.8002 (m-80) cc_final: 0.7559 (m-80) REVERT: B 165 MET cc_start: 0.4379 (mmt) cc_final: 0.3407 (mpp) REVERT: B 229 ILE cc_start: 0.8586 (tp) cc_final: 0.8099 (tp) REVERT: B 364 MET cc_start: 0.5820 (mpp) cc_final: 0.5441 (mpp) REVERT: C 9 GLU cc_start: 0.6975 (mm-30) cc_final: 0.6721 (mm-30) REVERT: C 10 TYR cc_start: 0.6403 (m-10) cc_final: 0.6083 (m-80) REVERT: C 336 GLU cc_start: 0.8404 (tp30) cc_final: 0.7583 (tt0) REVERT: C 372 MET cc_start: -0.1573 (tpp) cc_final: -0.2875 (ttt) REVERT: D 201 LYS cc_start: 0.6722 (mttt) cc_final: 0.6255 (mtmm) REVERT: D 345 TYR cc_start: 0.6491 (t80) cc_final: 0.5504 (t80) REVERT: E 234 TYR cc_start: 0.8483 (t80) cc_final: 0.8129 (t80) REVERT: E 244 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.7516 (t80) REVERT: E 253 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6668 (mt) REVERT: E 295 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7472 (mt) REVERT: E 329 SER cc_start: 0.7918 (m) cc_final: 0.7346 (t) REVERT: F 165 MET cc_start: 0.2153 (ttt) cc_final: -0.0525 (mmm) REVERT: F 198 GLN cc_start: 0.5954 (mm-40) cc_final: 0.5494 (tm-30) REVERT: F 253 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6847 (mt) REVERT: F 281 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8522 (tp) REVERT: G 45 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7769 (tp) REVERT: G 128 ARG cc_start: 0.7284 (ttp-170) cc_final: 0.7075 (ttt180) REVERT: G 198 GLN cc_start: 0.6679 (mp10) cc_final: 0.6352 (tp40) REVERT: G 202 THR cc_start: 0.6656 (p) cc_final: 0.6453 (p) REVERT: G 211 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8019 (tp) outliers start: 74 outliers final: 59 residues processed: 287 average time/residue: 0.2677 time to fit residues: 124.4665 Evaluate side-chains 290 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 223 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE 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 291 VAL Chi-restraints excluded: chain A residue 354 ILE 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 208 ASN 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 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 60 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 265 CYS 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 240 LEU Chi-restraints excluded: chain D residue 265 CYS Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 200 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 244 PHE Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 299 PHE 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 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 305 VAL Chi-restraints excluded: chain F residue 347 CYS Chi-restraints excluded: chain G residue 45 LEU 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 265 CYS Chi-restraints excluded: chain G residue 278 VAL 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 130 optimal weight: 7.9990 chunk 52 optimal weight: 0.0060 chunk 65 optimal weight: 7.9990 chunk 93 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 167 optimal weight: 0.0020 chunk 114 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 188 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 overall best weight: 0.4606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN B 359 GLN C 100 ASN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.209886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.162541 restraints weight = 23566.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.162097 restraints weight = 27788.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.163993 restraints weight = 23476.538| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.3962 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= 0.114 Angle : 1.022 35.338 26789 Z= 0.396 Chirality : 0.085 1.778 3227 Planarity : 0.004 0.057 3169 Dihedral : 17.765 178.613 3444 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.87 % Allowed : 25.35 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.18), residues: 2301 helix: 1.97 (0.13), residues: 1564 sheet: -3.12 (0.57), residues: 84 loop : -1.47 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 127 HIS 0.001 0.000 HIS D 134 PHE 0.010 0.001 PHE A 244 TYR 0.015 0.001 TYR C 234 ARG 0.007 0.000 ARG G 254 Details of bonding type rmsd link_NAG-ASN : bond 0.00983 ( 7) link_NAG-ASN : angle 5.01775 ( 21) hydrogen bonds : bond 0.03145 ( 1139) hydrogen bonds : angle 3.40964 ( 3345) SS BOND : bond 0.00227 ( 14) SS BOND : angle 0.88848 ( 28) covalent geometry : bond 0.00253 (19698) covalent geometry : angle 1.01263 (26740) ********************** 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 297 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 236 time to evaluate : 2.105 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 revert: symmetry clash 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 10 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.7010 (m-10) REVERT: A 39 THR cc_start: 0.8894 (t) cc_final: 0.8585 (m) REVERT: A 225 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7888 (mt) REVERT: A 234 TYR cc_start: 0.9152 (t80) cc_final: 0.8859 (t80) REVERT: A 326 ASN cc_start: 0.7937 (m-40) cc_final: 0.7485 (m-40) REVERT: A 331 TYR cc_start: 0.7925 (m-80) cc_final: 0.7492 (m-80) REVERT: A 364 MET cc_start: 0.3772 (mmm) cc_final: 0.3555 (mmm) REVERT: B 165 MET cc_start: 0.4283 (mmt) cc_final: 0.3313 (mpp) REVERT: B 229 ILE cc_start: 0.8573 (tp) cc_final: 0.8087 (tp) REVERT: C 10 TYR cc_start: 0.6390 (m-10) cc_final: 0.6089 (m-80) REVERT: C 336 GLU cc_start: 0.8368 (tp30) cc_final: 0.7569 (tt0) REVERT: C 372 MET cc_start: -0.1795 (tpp) cc_final: -0.3524 (ttt) REVERT: C 375 MET cc_start: 0.2767 (mpp) cc_final: 0.2437 (mmt) REVERT: E 234 TYR cc_start: 0.8448 (t80) cc_final: 0.8093 (t80) REVERT: E 253 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6786 (mt) REVERT: E 295 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7464 (mt) REVERT: E 329 SER cc_start: 0.7939 (m) cc_final: 0.7339 (t) REVERT: E 343 LYS cc_start: 0.6712 (mmmt) cc_final: 0.5916 (tppt) REVERT: E 375 MET cc_start: -0.0361 (mtt) cc_final: -0.0774 (mtt) REVERT: F 165 MET cc_start: 0.2005 (ttt) cc_final: -0.0601 (mmm) REVERT: F 198 GLN cc_start: 0.5907 (mm-40) cc_final: 0.5447 (tm-30) REVERT: F 253 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6675 (mt) REVERT: F 281 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8545 (tp) REVERT: G 198 GLN cc_start: 0.6654 (mp10) cc_final: 0.6261 (tp-100) outliers start: 61 outliers final: 48 residues processed: 281 average time/residue: 0.3089 time to fit residues: 140.1904 Evaluate side-chains 280 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 226 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR 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 291 VAL Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain C residue 47 LEU 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 240 LEU Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 265 CYS Chi-restraints excluded: chain D residue 16 LEU 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 265 CYS Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 62 THR 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 281 LEU Chi-restraints excluded: chain F residue 347 CYS 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 250 SER Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 278 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 90 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 171 optimal weight: 0.0010 chunk 141 optimal weight: 8.9990 chunk 184 optimal weight: 3.9990 chunk 220 optimal weight: 0.0970 chunk 83 optimal weight: 7.9990 chunk 204 optimal weight: 0.0970 chunk 192 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 153 optimal weight: 0.9980 overall best weight: 0.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN B 359 GLN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.210229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.163380 restraints weight = 23682.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.162648 restraints weight = 27977.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.164543 restraints weight = 24325.116| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.3989 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= 0.119 Angle : 1.135 58.022 26789 Z= 0.485 Chirality : 0.085 1.778 3227 Planarity : 0.004 0.057 3169 Dihedral : 17.781 178.601 3444 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.64 % Allowed : 25.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.18), residues: 2301 helix: 1.99 (0.13), residues: 1564 sheet: -3.13 (0.56), residues: 84 loop : -1.45 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 127 HIS 0.001 0.000 HIS E 134 PHE 0.011 0.001 PHE F 15 TYR 0.018 0.001 TYR E 331 ARG 0.006 0.000 ARG G 254 Details of bonding type rmsd link_NAG-ASN : bond 0.00853 ( 7) link_NAG-ASN : angle 7.47758 ( 21) hydrogen bonds : bond 0.03163 ( 1139) hydrogen bonds : angle 3.39557 ( 3345) SS BOND : bond 0.00212 ( 14) SS BOND : angle 0.86264 ( 28) covalent geometry : bond 0.00261 (19698) covalent geometry : angle 1.11593 (26740) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5895.09 seconds wall clock time: 105 minutes 57.91 seconds (6357.91 seconds total)