Starting phenix.real_space_refine on Wed Mar 4 15:47:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u9g_26397/03_2026/7u9g_26397.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u9g_26397/03_2026/7u9g_26397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u9g_26397/03_2026/7u9g_26397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u9g_26397/03_2026/7u9g_26397.map" model { file = "/net/cci-nas-00/data/ceres_data/7u9g_26397/03_2026/7u9g_26397.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u9g_26397/03_2026/7u9g_26397.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 9198 2.51 5 N 2457 2.21 5 O 2802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14553 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3041 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 25, 'TRANS': 363} Chain breaks: 2 Chain: "B" Number of atoms: 3041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3041 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 25, 'TRANS': 363} Chain breaks: 2 Chain: "C" Number of atoms: 3041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3041 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 25, 'TRANS': 363} Chain breaks: 2 Chain: "D" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 816 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "E" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 816 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "F" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 816 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "G" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 952 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "H" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 952 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "I" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 952 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.09, per 1000 atoms: 0.21 Number of scatterers: 14553 At special positions: 0 Unit cell: (122.1, 115.5, 129.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 2802 8.00 N 2457 7.00 C 9198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 283 " distance=2.03 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 207 " distance=2.02 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 228 " distance=2.03 Simple disulfide: pdb=" SG CYS A 223 " - pdb=" SG CYS A 252 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 351 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 283 " distance=2.03 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 207 " distance=2.02 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 228 " distance=2.03 Simple disulfide: pdb=" SG CYS B 223 " - pdb=" SG CYS B 252 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 351 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 283 " distance=2.03 Simple disulfide: pdb=" SG CYS C 35 " - pdb=" SG CYS C 207 " distance=2.02 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 169 " distance=2.03 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 228 " distance=2.03 Simple disulfide: pdb=" SG CYS C 223 " - pdb=" SG CYS C 252 " distance=2.03 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 351 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " distance=2.04 Simple disulfide: pdb=" SG CYS G 239 " - pdb=" SG CYS G 312 " distance=2.04 Simple disulfide: pdb=" SG CYS H 239 " - pdb=" SG CYS H 312 " distance=2.04 Simple disulfide: pdb=" SG CYS I 239 " - pdb=" SG CYS I 312 " distance=2.04 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 319 " " NAG A 502 " - " ASN A 158 " " NAG A 503 " - " ASN A 247 " " NAG B 501 " - " ASN B 319 " " NAG B 502 " - " ASN B 158 " " NAG B 503 " - " ASN B 247 " " NAG C 501 " - " ASN C 319 " " NAG C 502 " - " ASN C 247 " " NAG C 503 " - " ASN C 158 " Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 654.0 milliseconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3402 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 42 sheets defined 17.1% alpha, 40.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 90 through 104 Processing helix chain 'A' and resid 105 through 114 removed outlier: 3.671A pdb=" N GLU A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 158 removed outlier: 4.150A pdb=" N ASN A 158 " --> pdb=" O PRO A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 269 Processing helix chain 'A' and resid 276 through 294 Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 334 through 339 removed outlier: 4.262A pdb=" N ILE A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 380 removed outlier: 3.784A pdb=" N SER A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.033A pdb=" N LEU A 388 " --> pdb=" O HIS A 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 90 through 104 Processing helix chain 'B' and resid 105 through 114 removed outlier: 3.671A pdb=" N GLU B 109 " --> pdb=" O ASP B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 158 removed outlier: 4.151A pdb=" N ASN B 158 " --> pdb=" O PRO B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 269 Processing helix chain 'B' and resid 276 through 294 Processing helix chain 'B' and resid 298 through 302 Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 334 through 339 removed outlier: 4.263A pdb=" N ILE B 338 " --> pdb=" O THR B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 380 removed outlier: 3.785A pdb=" N SER B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 4.034A pdb=" N LEU B 388 " --> pdb=" O HIS B 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 90 through 104 Processing helix chain 'C' and resid 105 through 114 removed outlier: 3.671A pdb=" N GLU C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 158 removed outlier: 4.150A pdb=" N ASN C 158 " --> pdb=" O PRO C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 269 Processing helix chain 'C' and resid 276 through 294 Processing helix chain 'C' and resid 298 through 302 Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 334 through 339 removed outlier: 4.262A pdb=" N ILE C 338 " --> pdb=" O THR C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 380 removed outlier: 3.785A pdb=" N SER C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.034A pdb=" N LEU C 388 " --> pdb=" O HIS C 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.917A pdb=" N GLU D 84 " --> pdb=" O SER D 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.916A pdb=" N GLU E 84 " --> pdb=" O SER E 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.916A pdb=" N GLU F 84 " --> pdb=" O SER F 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 281 Processing helix chain 'G' and resid 290 through 292 No H-bonds generated for 'chain 'G' and resid 290 through 292' Processing helix chain 'G' and resid 303 through 307 Processing helix chain 'H' and resid 278 through 281 Processing helix chain 'H' and resid 290 through 292 No H-bonds generated for 'chain 'H' and resid 290 through 292' Processing helix chain 'H' and resid 303 through 307 Processing helix chain 'I' and resid 278 through 281 Processing helix chain 'I' and resid 290 through 292 No H-bonds generated for 'chain 'I' and resid 290 through 292' Processing helix chain 'I' and resid 303 through 307 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 11 removed outlier: 4.132A pdb=" N TYR A 5 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N HIS A 328 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU A 11 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP A 326 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 5 through 11 removed outlier: 4.132A pdb=" N TYR A 5 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N HIS A 328 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU A 11 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP A 326 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 218 removed outlier: 5.068A pdb=" N THR A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS A 202 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A 37 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N MET A 44 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU A 46 " --> pdb=" O TRP A 240 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N TRP A 240 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 87 removed outlier: 3.530A pdb=" N GLY A 63 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 126 through 134 Processing sheet with id=AA6, first strand: chain 'A' and resid 295 through 297 Processing sheet with id=AA7, first strand: chain 'A' and resid 346 through 347 Processing sheet with id=AA8, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AA9, first strand: chain 'B' and resid 5 through 11 removed outlier: 4.132A pdb=" N TYR B 5 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N HIS B 328 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU B 11 " --> pdb=" O ASP B 326 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP B 326 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 5 through 11 removed outlier: 4.132A pdb=" N TYR B 5 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N HIS B 328 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU B 11 " --> pdb=" O ASP B 326 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP B 326 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 216 through 218 removed outlier: 5.067A pdb=" N THR B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS B 202 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN B 37 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N MET B 44 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU B 46 " --> pdb=" O TRP B 240 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N TRP B 240 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 82 through 87 removed outlier: 3.530A pdb=" N GLY B 63 " --> pdb=" O PHE B 87 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 126 through 134 Processing sheet with id=AB5, first strand: chain 'B' and resid 295 through 297 Processing sheet with id=AB6, first strand: chain 'B' and resid 346 through 347 Processing sheet with id=AB7, first strand: chain 'B' and resid 364 through 365 Processing sheet with id=AB8, first strand: chain 'C' and resid 5 through 11 removed outlier: 4.132A pdb=" N TYR C 5 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N HIS C 328 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU C 11 " --> pdb=" O ASP C 326 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP C 326 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 5 through 11 removed outlier: 4.132A pdb=" N TYR C 5 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N HIS C 328 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU C 11 " --> pdb=" O ASP C 326 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP C 326 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 216 through 218 removed outlier: 5.067A pdb=" N THR C 206 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS C 202 " --> pdb=" O THR C 206 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN C 37 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N MET C 44 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU C 46 " --> pdb=" O TRP C 240 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N TRP C 240 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 82 through 87 removed outlier: 3.530A pdb=" N GLY C 63 " --> pdb=" O PHE C 87 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 126 through 134 Processing sheet with id=AC4, first strand: chain 'C' and resid 295 through 297 Processing sheet with id=AC5, first strand: chain 'C' and resid 346 through 347 Processing sheet with id=AC6, first strand: chain 'C' and resid 364 through 365 Processing sheet with id=AC7, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AC8, first strand: chain 'D' and resid 9 through 12 Processing sheet with id=AC9, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.720A pdb=" N GLY D 98 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AD2, first strand: chain 'E' and resid 9 through 12 Processing sheet with id=AD3, first strand: chain 'E' and resid 9 through 12 removed outlier: 3.720A pdb=" N GLY E 98 " --> pdb=" O ASP E 93 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AD5, first strand: chain 'F' and resid 9 through 12 Processing sheet with id=AD6, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.721A pdb=" N GLY F 98 " --> pdb=" O ASP F 93 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 220 through 224 Processing sheet with id=AD8, first strand: chain 'G' and resid 228 through 229 removed outlier: 3.824A pdb=" N GLY G 266 " --> pdb=" O TRP G 253 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG G 255 " --> pdb=" O TRP G 264 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N TRP G 264 " --> pdb=" O ARG G 255 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 228 through 229 removed outlier: 4.457A pdb=" N VAL G 329 " --> pdb=" O ARG G 314 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N SER G 316 " --> pdb=" O MET G 327 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N MET G 327 " --> pdb=" O SER G 316 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 220 through 224 Processing sheet with id=AE2, first strand: chain 'H' and resid 228 through 229 removed outlier: 3.824A pdb=" N GLY H 266 " --> pdb=" O TRP H 253 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG H 255 " --> pdb=" O TRP H 264 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N TRP H 264 " --> pdb=" O ARG H 255 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 228 through 229 removed outlier: 4.456A pdb=" N VAL H 329 " --> pdb=" O ARG H 314 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N SER H 316 " --> pdb=" O MET H 327 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N MET H 327 " --> pdb=" O SER H 316 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 220 through 224 Processing sheet with id=AE5, first strand: chain 'I' and resid 228 through 229 removed outlier: 3.824A pdb=" N GLY I 266 " --> pdb=" O TRP I 253 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARG I 255 " --> pdb=" O TRP I 264 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N TRP I 264 " --> pdb=" O ARG I 255 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 228 through 229 removed outlier: 4.457A pdb=" N VAL I 329 " --> pdb=" O ARG I 314 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N SER I 316 " --> pdb=" O MET I 327 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N MET I 327 " --> pdb=" O SER I 316 " (cutoff:3.500A) 579 hydrogen bonds defined for protein. 1467 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: 2.64 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4638 1.34 - 1.46: 3521 1.46 - 1.58: 6619 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 14916 Sorted by residual: bond pdb=" C1 NAG C 501 " pdb=" O5 NAG C 501 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.96e+00 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.92e+00 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.82e+00 bond pdb=" C1 NAG A 503 " pdb=" O5 NAG A 503 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.70e+00 bond pdb=" C1 NAG B 503 " pdb=" O5 NAG B 503 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.65e+00 ... (remaining 14911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 18869 1.43 - 2.86: 1186 2.86 - 4.29: 163 4.29 - 5.71: 29 5.71 - 7.14: 12 Bond angle restraints: 20259 Sorted by residual: angle pdb=" N HIS C 113 " pdb=" CA HIS C 113 " pdb=" C HIS C 113 " ideal model delta sigma weight residual 111.28 115.33 -4.05 1.09e+00 8.42e-01 1.38e+01 angle pdb=" N HIS B 113 " pdb=" CA HIS B 113 " pdb=" C HIS B 113 " ideal model delta sigma weight residual 111.28 115.27 -3.99 1.09e+00 8.42e-01 1.34e+01 angle pdb=" N HIS A 113 " pdb=" CA HIS A 113 " pdb=" C HIS A 113 " ideal model delta sigma weight residual 111.28 115.25 -3.97 1.09e+00 8.42e-01 1.32e+01 angle pdb=" N GLU A 267 " pdb=" CA GLU A 267 " pdb=" C GLU A 267 " ideal model delta sigma weight residual 111.14 114.57 -3.43 1.08e+00 8.57e-01 1.01e+01 angle pdb=" N GLU B 267 " pdb=" CA GLU B 267 " pdb=" C GLU B 267 " ideal model delta sigma weight residual 111.14 114.48 -3.34 1.08e+00 8.57e-01 9.57e+00 ... (remaining 20254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 8398 17.30 - 34.60: 512 34.60 - 51.90: 99 51.90 - 69.20: 21 69.20 - 86.51: 3 Dihedral angle restraints: 9033 sinusoidal: 3696 harmonic: 5337 Sorted by residual: dihedral pdb=" CB CYS A 24 " pdb=" SG CYS A 24 " pdb=" SG CYS A 283 " pdb=" CB CYS A 283 " ideal model delta sinusoidal sigma weight residual 93.00 146.41 -53.41 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CB CYS B 24 " pdb=" SG CYS B 24 " pdb=" SG CYS B 283 " pdb=" CB CYS B 283 " ideal model delta sinusoidal sigma weight residual 93.00 146.40 -53.40 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CB CYS C 24 " pdb=" SG CYS C 24 " pdb=" SG CYS C 283 " pdb=" CB CYS C 283 " ideal model delta sinusoidal sigma weight residual 93.00 146.39 -53.39 1 1.00e+01 1.00e-02 3.88e+01 ... (remaining 9030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1500 0.040 - 0.080: 477 0.080 - 0.120: 226 0.120 - 0.160: 41 0.160 - 0.200: 9 Chirality restraints: 2253 Sorted by residual: chirality pdb=" C1 NAG A 502 " pdb=" ND2 ASN A 158 " pdb=" C2 NAG A 502 " pdb=" O5 NAG A 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" C1 NAG B 502 " pdb=" ND2 ASN B 158 " pdb=" C2 NAG B 502 " pdb=" O5 NAG B 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.93e-01 chirality pdb=" C1 NAG C 503 " pdb=" ND2 ASN C 158 " pdb=" C2 NAG C 503 " pdb=" O5 NAG C 503 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.73e-01 ... (remaining 2250 not shown) Planarity restraints: 2577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 308 " -0.041 5.00e-02 4.00e+02 6.16e-02 6.06e+00 pdb=" N PRO B 309 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 309 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 309 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 308 " 0.041 5.00e-02 4.00e+02 6.15e-02 6.05e+00 pdb=" N PRO C 309 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO C 309 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 309 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 308 " 0.041 5.00e-02 4.00e+02 6.13e-02 6.02e+00 pdb=" N PRO A 309 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 309 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 309 " 0.034 5.00e-02 4.00e+02 ... (remaining 2574 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4190 2.81 - 3.34: 12376 3.34 - 3.86: 22701 3.86 - 4.38: 26055 4.38 - 4.90: 45596 Nonbonded interactions: 110918 Sorted by model distance: nonbonded pdb=" O PRO G 231 " pdb=" OG SER G 232 " model vdw 2.293 3.040 nonbonded pdb=" O PRO H 231 " pdb=" OG SER H 232 " model vdw 2.294 3.040 nonbonded pdb=" O PRO I 231 " pdb=" OG SER I 232 " model vdw 2.294 3.040 nonbonded pdb=" OG SER C 15 " pdb=" OE2 GLU C 324 " model vdw 2.389 3.040 nonbonded pdb=" OG SER B 15 " pdb=" OE2 GLU B 324 " model vdw 2.389 3.040 ... (remaining 110913 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.130 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 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 : 0.007 0.052 14952 Z= 0.305 Angle : 0.780 7.143 20340 Z= 0.450 Chirality : 0.049 0.200 2253 Planarity : 0.005 0.062 2568 Dihedral : 11.019 86.505 5550 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.19), residues: 1830 helix: 0.19 (0.36), residues: 225 sheet: 0.84 (0.21), residues: 534 loop : -0.07 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 300 TYR 0.016 0.002 TYR G 322 PHE 0.022 0.002 PHE I 295 TRP 0.017 0.002 TRP G 253 HIS 0.008 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00674 (14916) covalent geometry : angle 0.77050 (20259) SS BOND : bond 0.00384 ( 27) SS BOND : angle 1.09973 ( 54) hydrogen bonds : bond 0.25512 ( 537) hydrogen bonds : angle 9.32012 ( 1467) link_NAG-ASN : bond 0.00649 ( 9) link_NAG-ASN : angle 3.18225 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7954 (mt) cc_final: 0.7746 (mm) REVERT: A 244 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8050 (tm-30) REVERT: A 323 MET cc_start: 0.8939 (mmt) cc_final: 0.8277 (mmt) REVERT: B 244 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8321 (tm-30) REVERT: B 323 MET cc_start: 0.8873 (mmt) cc_final: 0.8412 (mmt) REVERT: C 244 GLN cc_start: 0.9005 (mm-40) cc_final: 0.8205 (tm-30) REVERT: D 12 ASP cc_start: 0.7142 (t0) cc_final: 0.6903 (t70) REVERT: D 79 LEU cc_start: 0.8590 (tp) cc_final: 0.8212 (tt) REVERT: D 82 GLU cc_start: 0.8696 (pm20) cc_final: 0.8311 (pm20) REVERT: D 86 ASP cc_start: 0.8727 (m-30) cc_final: 0.7932 (p0) REVERT: E 12 ASP cc_start: 0.7251 (t0) cc_final: 0.7017 (t70) REVERT: F 79 LEU cc_start: 0.8400 (tp) cc_final: 0.8144 (tt) REVERT: F 86 ASP cc_start: 0.8596 (m-30) cc_final: 0.7851 (p0) REVERT: G 233 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8537 (mm-30) REVERT: H 233 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8461 (mm-30) REVERT: H 244 ASP cc_start: 0.8341 (t70) cc_final: 0.8008 (t70) REVERT: H 246 MET cc_start: 0.8534 (mtp) cc_final: 0.8123 (mtp) REVERT: H 328 ASP cc_start: 0.8465 (m-30) cc_final: 0.8162 (m-30) REVERT: I 233 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8473 (mm-30) REVERT: I 244 ASP cc_start: 0.8438 (t70) cc_final: 0.8201 (t70) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.1347 time to fit residues: 50.3493 Evaluate side-chains 164 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN E 6 GLN F 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.077266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.051344 restraints weight = 43596.442| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 4.72 r_work: 0.2560 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14952 Z= 0.162 Angle : 0.587 7.540 20340 Z= 0.310 Chirality : 0.043 0.211 2253 Planarity : 0.005 0.052 2568 Dihedral : 4.341 21.235 2205 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.11 % Allowed : 7.54 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.19), residues: 1830 helix: 0.40 (0.36), residues: 210 sheet: 0.90 (0.20), residues: 570 loop : -0.13 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 17 TYR 0.014 0.001 TYR I 322 PHE 0.020 0.002 PHE G 295 TRP 0.010 0.001 TRP F 36 HIS 0.003 0.001 HIS G 220 Details of bonding type rmsd covalent geometry : bond 0.00378 (14916) covalent geometry : angle 0.57805 (20259) SS BOND : bond 0.00413 ( 27) SS BOND : angle 0.94743 ( 54) hydrogen bonds : bond 0.04586 ( 537) hydrogen bonds : angle 6.39674 ( 1467) link_NAG-ASN : bond 0.00411 ( 9) link_NAG-ASN : angle 2.67576 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 PHE cc_start: 0.9191 (p90) cc_final: 0.8975 (m-80) REVERT: A 323 MET cc_start: 0.8883 (mmt) cc_final: 0.8406 (mmt) REVERT: B 244 GLN cc_start: 0.9269 (mm-40) cc_final: 0.8205 (tm-30) REVERT: B 323 MET cc_start: 0.8868 (mmt) cc_final: 0.8615 (mmt) REVERT: B 399 LEU cc_start: 0.9567 (mt) cc_final: 0.9355 (tt) REVERT: C 323 MET cc_start: 0.8723 (mmt) cc_final: 0.8097 (mmm) REVERT: C 399 LEU cc_start: 0.9392 (mt) cc_final: 0.9153 (tp) REVERT: D 12 ASP cc_start: 0.7135 (t0) cc_final: 0.6864 (t70) REVERT: D 76 ILE cc_start: 0.8410 (mp) cc_final: 0.8081 (mt) REVERT: D 82 GLU cc_start: 0.8866 (pm20) cc_final: 0.8582 (pm20) REVERT: E 12 ASP cc_start: 0.7279 (t0) cc_final: 0.6991 (t70) REVERT: E 54 LYS cc_start: 0.9163 (mttp) cc_final: 0.8863 (mmmm) REVERT: E 76 ILE cc_start: 0.8337 (mp) cc_final: 0.8124 (mt) REVERT: F 17 ARG cc_start: 0.8933 (mtp-110) cc_final: 0.8556 (ttm-80) REVERT: F 76 ILE cc_start: 0.8380 (mp) cc_final: 0.7816 (mt) REVERT: F 82 GLU cc_start: 0.8768 (pm20) cc_final: 0.8533 (mp0) REVERT: G 289 ASP cc_start: 0.7913 (t0) cc_final: 0.7649 (t0) REVERT: G 292 LYS cc_start: 0.9601 (mtmt) cc_final: 0.9369 (mttp) REVERT: H 233 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8398 (mm-30) REVERT: H 244 ASP cc_start: 0.8446 (t70) cc_final: 0.8063 (t70) REVERT: H 289 ASP cc_start: 0.7884 (t0) cc_final: 0.7651 (t0) REVERT: H 328 ASP cc_start: 0.8808 (m-30) cc_final: 0.8541 (m-30) REVERT: I 218 GLN cc_start: 0.8568 (tp40) cc_final: 0.8236 (tp40) REVERT: I 233 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8085 (mm-30) REVERT: I 244 ASP cc_start: 0.8471 (t70) cc_final: 0.8154 (t70) REVERT: I 281 LYS cc_start: 0.9135 (ttmm) cc_final: 0.8739 (ttmm) REVERT: I 289 ASP cc_start: 0.8040 (t0) cc_final: 0.7830 (t0) outliers start: 18 outliers final: 12 residues processed: 183 average time/residue: 0.1249 time to fit residues: 33.5357 Evaluate side-chains 164 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 108 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 83 optimal weight: 20.0000 chunk 173 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 161 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 120 optimal weight: 8.9990 chunk 134 optimal weight: 9.9990 chunk 170 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 HIS C 261 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.076200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.050493 restraints weight = 43716.211| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 4.63 r_work: 0.2570 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 14952 Z= 0.106 Angle : 0.508 7.979 20340 Z= 0.264 Chirality : 0.041 0.180 2253 Planarity : 0.004 0.047 2568 Dihedral : 3.955 20.107 2205 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.18 % Allowed : 8.72 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.19), residues: 1830 helix: 0.66 (0.37), residues: 210 sheet: 0.81 (0.20), residues: 579 loop : -0.06 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 264 TYR 0.024 0.001 TYR E 50 PHE 0.013 0.001 PHE I 295 TRP 0.007 0.001 TRP F 36 HIS 0.003 0.000 HIS C 261 Details of bonding type rmsd covalent geometry : bond 0.00249 (14916) covalent geometry : angle 0.49873 (20259) SS BOND : bond 0.00174 ( 27) SS BOND : angle 1.00992 ( 54) hydrogen bonds : bond 0.03681 ( 537) hydrogen bonds : angle 5.67814 ( 1467) link_NAG-ASN : bond 0.00475 ( 9) link_NAG-ASN : angle 2.41874 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLN cc_start: 0.9090 (mm-40) cc_final: 0.7961 (tm-30) REVERT: A 263 PHE cc_start: 0.9238 (p90) cc_final: 0.9036 (m-80) REVERT: A 323 MET cc_start: 0.8814 (mmt) cc_final: 0.8367 (mmt) REVERT: A 396 MET cc_start: 0.9176 (tpp) cc_final: 0.8605 (ttp) REVERT: B 244 GLN cc_start: 0.9302 (mm-40) cc_final: 0.8248 (tm-30) REVERT: B 323 MET cc_start: 0.8791 (mmt) cc_final: 0.8578 (mmt) REVERT: B 396 MET cc_start: 0.9179 (tpp) cc_final: 0.8668 (ttp) REVERT: B 399 LEU cc_start: 0.9535 (mt) cc_final: 0.9314 (tt) REVERT: C 244 GLN cc_start: 0.9152 (mm110) cc_final: 0.7837 (tm-30) REVERT: C 261 HIS cc_start: 0.7493 (OUTLIER) cc_final: 0.7018 (m-70) REVERT: C 323 MET cc_start: 0.8736 (mmt) cc_final: 0.8131 (mmm) REVERT: C 399 LEU cc_start: 0.9373 (mt) cc_final: 0.9101 (tp) REVERT: D 12 ASP cc_start: 0.6919 (t0) cc_final: 0.6630 (t70) REVERT: D 61 ASP cc_start: 0.9275 (m-30) cc_final: 0.8581 (t0) REVERT: D 79 LEU cc_start: 0.8158 (tp) cc_final: 0.7849 (tp) REVERT: D 82 GLU cc_start: 0.8849 (pm20) cc_final: 0.8643 (pm20) REVERT: E 50 TYR cc_start: 0.7965 (p90) cc_final: 0.7634 (p90) REVERT: E 54 LYS cc_start: 0.9064 (mttp) cc_final: 0.8704 (mmmm) REVERT: E 61 ASP cc_start: 0.9294 (m-30) cc_final: 0.8621 (t0) REVERT: E 79 LEU cc_start: 0.8171 (tt) cc_final: 0.7754 (tt) REVERT: F 76 ILE cc_start: 0.8311 (mp) cc_final: 0.8097 (mt) REVERT: F 82 GLU cc_start: 0.8945 (pm20) cc_final: 0.8671 (mp0) REVERT: F 84 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7769 (tp30) REVERT: G 222 GLN cc_start: 0.8048 (tp-100) cc_final: 0.7682 (tp-100) REVERT: G 318 ASP cc_start: 0.9133 (OUTLIER) cc_final: 0.8832 (m-30) REVERT: H 233 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8195 (mm-30) REVERT: H 244 ASP cc_start: 0.8491 (t70) cc_final: 0.8060 (t70) REVERT: H 328 ASP cc_start: 0.8668 (m-30) cc_final: 0.8376 (m-30) REVERT: I 233 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8060 (mm-30) REVERT: I 244 ASP cc_start: 0.8436 (t70) cc_final: 0.8106 (t70) REVERT: I 281 LYS cc_start: 0.9084 (ttmm) cc_final: 0.8679 (ttmm) REVERT: I 289 ASP cc_start: 0.8011 (t0) cc_final: 0.7778 (t0) REVERT: I 318 ASP cc_start: 0.9127 (OUTLIER) cc_final: 0.8864 (m-30) outliers start: 19 outliers final: 9 residues processed: 177 average time/residue: 0.1247 time to fit residues: 32.5140 Evaluate side-chains 162 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 261 HIS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain G residue 318 ASP Chi-restraints excluded: chain I residue 318 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 77 optimal weight: 2.9990 chunk 130 optimal weight: 0.0050 chunk 106 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 39 optimal weight: 0.1980 chunk 164 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 147 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 93 optimal weight: 0.0020 overall best weight: 0.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.077394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.051191 restraints weight = 43541.364| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 4.74 r_work: 0.2580 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 14952 Z= 0.092 Angle : 0.502 6.042 20340 Z= 0.258 Chirality : 0.041 0.177 2253 Planarity : 0.004 0.044 2568 Dihedral : 3.811 17.968 2205 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.42 % Allowed : 8.66 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.19), residues: 1830 helix: 0.70 (0.37), residues: 210 sheet: 0.80 (0.20), residues: 609 loop : 0.07 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 80 TYR 0.016 0.001 TYR E 50 PHE 0.017 0.001 PHE C 263 TRP 0.007 0.001 TRP G 251 HIS 0.017 0.000 HIS C 261 Details of bonding type rmsd covalent geometry : bond 0.00217 (14916) covalent geometry : angle 0.49384 (20259) SS BOND : bond 0.00134 ( 27) SS BOND : angle 0.89889 ( 54) hydrogen bonds : bond 0.03264 ( 537) hydrogen bonds : angle 5.41680 ( 1467) link_NAG-ASN : bond 0.00469 ( 9) link_NAG-ASN : angle 2.26268 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLN cc_start: 0.9120 (mm-40) cc_final: 0.7996 (tm-30) REVERT: A 263 PHE cc_start: 0.9211 (p90) cc_final: 0.8876 (p90) REVERT: A 323 MET cc_start: 0.8814 (mmt) cc_final: 0.8364 (mmt) REVERT: A 396 MET cc_start: 0.9136 (tpp) cc_final: 0.8596 (ttp) REVERT: B 244 GLN cc_start: 0.9333 (mm-40) cc_final: 0.8275 (tm-30) REVERT: B 323 MET cc_start: 0.8795 (mmt) cc_final: 0.8582 (mmt) REVERT: B 396 MET cc_start: 0.9175 (tpp) cc_final: 0.8696 (ttp) REVERT: C 244 GLN cc_start: 0.9157 (mm110) cc_final: 0.7899 (tm-30) REVERT: C 323 MET cc_start: 0.8758 (mmt) cc_final: 0.8139 (mmm) REVERT: C 399 LEU cc_start: 0.9376 (mt) cc_final: 0.9099 (tp) REVERT: D 12 ASP cc_start: 0.7096 (t0) cc_final: 0.6310 (t0) REVERT: D 79 LEU cc_start: 0.8180 (tp) cc_final: 0.7500 (tp) REVERT: D 80 ARG cc_start: 0.7556 (mmm-85) cc_final: 0.6623 (ttm110) REVERT: D 82 GLU cc_start: 0.8852 (pm20) cc_final: 0.8622 (pm20) REVERT: E 17 ARG cc_start: 0.8662 (mmm-85) cc_final: 0.8321 (ttm-80) REVERT: E 54 LYS cc_start: 0.9104 (mttp) cc_final: 0.8728 (mmmm) REVERT: E 61 ASP cc_start: 0.9262 (m-30) cc_final: 0.8615 (t0) REVERT: E 79 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7604 (tt) REVERT: E 84 GLU cc_start: 0.8392 (pm20) cc_final: 0.8180 (pm20) REVERT: F 12 ASP cc_start: 0.7254 (t70) cc_final: 0.6575 (t70) REVERT: F 17 ARG cc_start: 0.8851 (mmm-85) cc_final: 0.8421 (ttm-80) REVERT: F 80 ARG cc_start: 0.7758 (ttm110) cc_final: 0.7533 (ttm110) REVERT: F 82 GLU cc_start: 0.8998 (pm20) cc_final: 0.8702 (mp0) REVERT: F 84 GLU cc_start: 0.8446 (tt0) cc_final: 0.8017 (mm-30) REVERT: G 222 GLN cc_start: 0.8091 (tp-100) cc_final: 0.7704 (tp-100) REVERT: G 318 ASP cc_start: 0.9139 (OUTLIER) cc_final: 0.8811 (m-30) REVERT: H 233 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8067 (mm-30) REVERT: H 244 ASP cc_start: 0.8390 (t70) cc_final: 0.7948 (t70) REVERT: H 292 LYS cc_start: 0.9612 (mtmm) cc_final: 0.9367 (mtmm) REVERT: H 328 ASP cc_start: 0.8637 (m-30) cc_final: 0.8351 (m-30) REVERT: I 233 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7957 (mm-30) REVERT: I 244 ASP cc_start: 0.8358 (t70) cc_final: 0.8038 (t70) REVERT: I 281 LYS cc_start: 0.9060 (ttmm) cc_final: 0.8673 (ttmm) REVERT: I 289 ASP cc_start: 0.7983 (t0) cc_final: 0.7708 (t0) REVERT: I 318 ASP cc_start: 0.9115 (OUTLIER) cc_final: 0.8861 (m-30) outliers start: 23 outliers final: 11 residues processed: 186 average time/residue: 0.1293 time to fit residues: 35.1933 Evaluate side-chains 164 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain G residue 318 ASP Chi-restraints excluded: chain I residue 318 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 24 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 130 optimal weight: 0.0770 chunk 143 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.073479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.047242 restraints weight = 44671.253| |-----------------------------------------------------------------------------| r_work (start): 0.2617 rms_B_bonded: 4.68 r_work: 0.2465 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14952 Z= 0.252 Angle : 0.612 5.870 20340 Z= 0.320 Chirality : 0.043 0.155 2253 Planarity : 0.005 0.046 2568 Dihedral : 4.384 21.573 2205 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.42 % Allowed : 9.65 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.19), residues: 1830 helix: 0.52 (0.37), residues: 207 sheet: 0.77 (0.20), residues: 603 loop : -0.25 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 17 TYR 0.019 0.002 TYR A 168 PHE 0.023 0.002 PHE G 295 TRP 0.017 0.002 TRP E 36 HIS 0.004 0.001 HIS C 20 Details of bonding type rmsd covalent geometry : bond 0.00592 (14916) covalent geometry : angle 0.60678 (20259) SS BOND : bond 0.00317 ( 27) SS BOND : angle 1.11387 ( 54) hydrogen bonds : bond 0.04281 ( 537) hydrogen bonds : angle 5.53742 ( 1467) link_NAG-ASN : bond 0.00218 ( 9) link_NAG-ASN : angle 1.95808 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 PHE cc_start: 0.9230 (p90) cc_final: 0.8903 (p90) REVERT: A 323 MET cc_start: 0.8860 (mmt) cc_final: 0.8379 (mmt) REVERT: B 244 GLN cc_start: 0.9453 (mm-40) cc_final: 0.8391 (tm-30) REVERT: C 244 GLN cc_start: 0.9240 (mm110) cc_final: 0.7988 (tm-30) REVERT: C 323 MET cc_start: 0.8756 (mmt) cc_final: 0.8406 (mmt) REVERT: D 12 ASP cc_start: 0.7408 (t0) cc_final: 0.7141 (t70) REVERT: D 61 ASP cc_start: 0.9249 (m-30) cc_final: 0.8601 (t0) REVERT: D 82 GLU cc_start: 0.8837 (pm20) cc_final: 0.8538 (pm20) REVERT: E 17 ARG cc_start: 0.8864 (mmm-85) cc_final: 0.8474 (ttm-80) REVERT: E 61 ASP cc_start: 0.9254 (m-30) cc_final: 0.8635 (t0) REVERT: E 79 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8277 (tt) REVERT: E 84 GLU cc_start: 0.8518 (pm20) cc_final: 0.8231 (pm20) REVERT: F 12 ASP cc_start: 0.8007 (t70) cc_final: 0.7306 (t70) REVERT: F 16 GLN cc_start: 0.8888 (mp10) cc_final: 0.8438 (pm20) REVERT: F 61 ASP cc_start: 0.9278 (m-30) cc_final: 0.8635 (t0) REVERT: F 82 GLU cc_start: 0.8998 (pm20) cc_final: 0.8702 (mp0) REVERT: F 84 GLU cc_start: 0.8436 (tt0) cc_final: 0.7884 (tp30) REVERT: G 318 ASP cc_start: 0.9283 (OUTLIER) cc_final: 0.9018 (m-30) REVERT: H 233 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8428 (mm-30) REVERT: H 244 ASP cc_start: 0.8828 (t70) cc_final: 0.8441 (t70) REVERT: I 218 GLN cc_start: 0.8474 (tp40) cc_final: 0.8138 (tp40) REVERT: I 233 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8169 (mm-30) REVERT: I 244 ASP cc_start: 0.8584 (t70) cc_final: 0.8233 (t70) REVERT: I 281 LYS cc_start: 0.9221 (ttmm) cc_final: 0.8835 (ttmm) REVERT: I 289 ASP cc_start: 0.8267 (t0) cc_final: 0.7886 (t0) outliers start: 23 outliers final: 19 residues processed: 166 average time/residue: 0.1288 time to fit residues: 31.4651 Evaluate side-chains 167 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 318 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.074607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.048414 restraints weight = 43820.592| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 4.67 r_work: 0.2514 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14952 Z= 0.119 Angle : 0.516 6.960 20340 Z= 0.265 Chirality : 0.041 0.169 2253 Planarity : 0.004 0.045 2568 Dihedral : 3.976 17.222 2205 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.61 % Allowed : 10.02 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.19), residues: 1830 helix: 0.58 (0.37), residues: 210 sheet: 0.85 (0.20), residues: 603 loop : -0.19 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 80 TYR 0.020 0.001 TYR C 168 PHE 0.013 0.001 PHE C 263 TRP 0.008 0.001 TRP I 330 HIS 0.005 0.000 HIS C 261 Details of bonding type rmsd covalent geometry : bond 0.00280 (14916) covalent geometry : angle 0.50972 (20259) SS BOND : bond 0.00228 ( 27) SS BOND : angle 0.79937 ( 54) hydrogen bonds : bond 0.03352 ( 537) hydrogen bonds : angle 5.34580 ( 1467) link_NAG-ASN : bond 0.00351 ( 9) link_NAG-ASN : angle 2.12065 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 GLN cc_start: 0.9171 (mm-40) cc_final: 0.8100 (tm-30) REVERT: A 263 PHE cc_start: 0.9209 (p90) cc_final: 0.8870 (p90) REVERT: A 323 MET cc_start: 0.8840 (mmt) cc_final: 0.8348 (mmt) REVERT: A 396 MET cc_start: 0.9183 (tpp) cc_final: 0.8632 (ttp) REVERT: B 244 GLN cc_start: 0.9468 (mm-40) cc_final: 0.8502 (tm-30) REVERT: B 385 MET cc_start: 0.7743 (tpt) cc_final: 0.7438 (tpt) REVERT: B 396 MET cc_start: 0.9200 (tpp) cc_final: 0.8686 (ttp) REVERT: C 244 GLN cc_start: 0.9213 (mm110) cc_final: 0.7980 (tm-30) REVERT: C 323 MET cc_start: 0.8734 (mmt) cc_final: 0.8378 (mmt) REVERT: D 12 ASP cc_start: 0.7219 (t0) cc_final: 0.6475 (t0) REVERT: D 61 ASP cc_start: 0.9183 (m-30) cc_final: 0.8549 (t0) REVERT: D 79 LEU cc_start: 0.8552 (tp) cc_final: 0.8168 (tp) REVERT: D 80 ARG cc_start: 0.7662 (mmm-85) cc_final: 0.7056 (mmm-85) REVERT: D 82 GLU cc_start: 0.8871 (pm20) cc_final: 0.8666 (pm20) REVERT: D 84 GLU cc_start: 0.8292 (tt0) cc_final: 0.7775 (tp30) REVERT: E 17 ARG cc_start: 0.8858 (mmm-85) cc_final: 0.8417 (ttm-80) REVERT: E 61 ASP cc_start: 0.9213 (m-30) cc_final: 0.8604 (t0) REVERT: E 79 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7933 (tt) REVERT: E 84 GLU cc_start: 0.8565 (pm20) cc_final: 0.8202 (pm20) REVERT: F 12 ASP cc_start: 0.7862 (t70) cc_final: 0.7443 (t70) REVERT: F 17 ARG cc_start: 0.8776 (ttm-80) cc_final: 0.8106 (ttm-80) REVERT: F 61 ASP cc_start: 0.9272 (m-30) cc_final: 0.8615 (t0) REVERT: F 82 GLU cc_start: 0.9036 (pm20) cc_final: 0.8706 (mp0) REVERT: F 84 GLU cc_start: 0.8474 (tt0) cc_final: 0.7899 (mm-30) REVERT: F 96 LEU cc_start: 0.9503 (tp) cc_final: 0.9290 (tt) REVERT: G 289 ASP cc_start: 0.8012 (t0) cc_final: 0.7717 (t0) REVERT: G 318 ASP cc_start: 0.9236 (OUTLIER) cc_final: 0.8954 (m-30) REVERT: H 233 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8300 (mm-30) REVERT: H 244 ASP cc_start: 0.8671 (t70) cc_final: 0.8188 (t70) REVERT: H 292 LYS cc_start: 0.9652 (mtmm) cc_final: 0.9364 (mtmm) REVERT: I 218 GLN cc_start: 0.8498 (tp40) cc_final: 0.8181 (tp40) REVERT: I 233 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8046 (mm-30) REVERT: I 244 ASP cc_start: 0.8534 (t70) cc_final: 0.8188 (t70) REVERT: I 246 MET cc_start: 0.9111 (mtp) cc_final: 0.8847 (tpp) REVERT: I 281 LYS cc_start: 0.9198 (ttmm) cc_final: 0.8810 (ttmm) REVERT: I 289 ASP cc_start: 0.8096 (t0) cc_final: 0.7796 (t0) outliers start: 26 outliers final: 17 residues processed: 176 average time/residue: 0.1268 time to fit residues: 32.9073 Evaluate side-chains 165 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 318 ASP Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain I residue 239 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 11 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 165 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 48 optimal weight: 20.0000 chunk 153 optimal weight: 5.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.071552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.044625 restraints weight = 45512.913| |-----------------------------------------------------------------------------| r_work (start): 0.2579 rms_B_bonded: 4.73 r_work: 0.2429 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 14952 Z= 0.310 Angle : 0.649 8.170 20340 Z= 0.336 Chirality : 0.044 0.153 2253 Planarity : 0.005 0.062 2568 Dihedral : 4.578 21.448 2205 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.98 % Allowed : 10.14 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.19), residues: 1830 helix: -0.08 (0.36), residues: 225 sheet: 0.71 (0.21), residues: 579 loop : -0.38 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 80 TYR 0.021 0.002 TYR A 168 PHE 0.021 0.002 PHE G 295 TRP 0.016 0.001 TRP E 36 HIS 0.006 0.001 HIS C 20 Details of bonding type rmsd covalent geometry : bond 0.00729 (14916) covalent geometry : angle 0.64394 (20259) SS BOND : bond 0.00358 ( 27) SS BOND : angle 1.04324 ( 54) hydrogen bonds : bond 0.04458 ( 537) hydrogen bonds : angle 5.54776 ( 1467) link_NAG-ASN : bond 0.00125 ( 9) link_NAG-ASN : angle 1.92864 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 244 GLN cc_start: 0.9222 (mm-40) cc_final: 0.8139 (tm-30) REVERT: A 263 PHE cc_start: 0.9273 (p90) cc_final: 0.8904 (p90) REVERT: A 323 MET cc_start: 0.8879 (mmt) cc_final: 0.8360 (mmt) REVERT: B 244 GLN cc_start: 0.9490 (mm-40) cc_final: 0.8456 (tm-30) REVERT: B 385 MET cc_start: 0.7841 (tpt) cc_final: 0.7563 (tpt) REVERT: C 244 GLN cc_start: 0.9257 (mm110) cc_final: 0.7986 (tm-30) REVERT: C 323 MET cc_start: 0.8798 (mmt) cc_final: 0.8433 (mmt) REVERT: D 12 ASP cc_start: 0.7480 (t0) cc_final: 0.7068 (t70) REVERT: D 16 GLN cc_start: 0.8590 (mp-120) cc_final: 0.8181 (mp10) REVERT: D 17 ARG cc_start: 0.8727 (mmm-85) cc_final: 0.8432 (tpp80) REVERT: D 61 ASP cc_start: 0.9219 (m-30) cc_final: 0.8623 (t0) REVERT: D 79 LEU cc_start: 0.8897 (tp) cc_final: 0.8634 (tp) REVERT: D 82 GLU cc_start: 0.8795 (pm20) cc_final: 0.8570 (pm20) REVERT: D 84 GLU cc_start: 0.8128 (tt0) cc_final: 0.7549 (tp30) REVERT: E 12 ASP cc_start: 0.7414 (t70) cc_final: 0.6990 (t70) REVERT: E 17 ARG cc_start: 0.8851 (mmm-85) cc_final: 0.8299 (ttm-80) REVERT: E 61 ASP cc_start: 0.9246 (m-30) cc_final: 0.8678 (t0) REVERT: E 79 LEU cc_start: 0.8688 (tt) cc_final: 0.8355 (tt) REVERT: E 84 GLU cc_start: 0.8554 (pm20) cc_final: 0.8182 (pm20) REVERT: F 12 ASP cc_start: 0.8024 (t70) cc_final: 0.7471 (t70) REVERT: F 16 GLN cc_start: 0.9096 (mp10) cc_final: 0.8831 (pm20) REVERT: F 17 ARG cc_start: 0.8686 (ttm-80) cc_final: 0.8137 (ttm-80) REVERT: F 61 ASP cc_start: 0.9294 (m-30) cc_final: 0.8668 (t0) REVERT: F 82 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8815 (mp0) REVERT: F 84 GLU cc_start: 0.8458 (tt0) cc_final: 0.7870 (tp30) REVERT: G 233 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8270 (mm-30) REVERT: G 289 ASP cc_start: 0.8319 (t0) cc_final: 0.7940 (t0) REVERT: H 233 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8293 (mm-30) REVERT: H 244 ASP cc_start: 0.8955 (t70) cc_final: 0.8612 (t70) REVERT: H 292 LYS cc_start: 0.9639 (mtmm) cc_final: 0.9361 (mtmm) REVERT: I 218 GLN cc_start: 0.8576 (tp40) cc_final: 0.8216 (tp40) REVERT: I 233 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8209 (mm-30) REVERT: I 244 ASP cc_start: 0.8747 (t70) cc_final: 0.8409 (t70) REVERT: I 281 LYS cc_start: 0.9352 (ttmm) cc_final: 0.8920 (ttmm) REVERT: I 289 ASP cc_start: 0.8249 (t0) cc_final: 0.7819 (t0) outliers start: 32 outliers final: 26 residues processed: 176 average time/residue: 0.1225 time to fit residues: 32.0357 Evaluate side-chains 170 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 283 CYS Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 82 GLU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 239 CYS Chi-restraints excluded: chain I residue 239 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 85 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 125 optimal weight: 0.1980 chunk 101 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.074417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.048336 restraints weight = 44229.294| |-----------------------------------------------------------------------------| r_work (start): 0.2649 rms_B_bonded: 4.65 r_work: 0.2498 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14952 Z= 0.115 Angle : 0.531 8.071 20340 Z= 0.270 Chirality : 0.041 0.163 2253 Planarity : 0.004 0.055 2568 Dihedral : 4.044 16.142 2205 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.48 % Allowed : 10.82 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.20), residues: 1830 helix: 0.02 (0.36), residues: 228 sheet: 0.84 (0.21), residues: 579 loop : -0.27 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 80 TYR 0.021 0.001 TYR C 168 PHE 0.021 0.001 PHE C 263 TRP 0.009 0.001 TRP G 251 HIS 0.004 0.000 HIS C 261 Details of bonding type rmsd covalent geometry : bond 0.00272 (14916) covalent geometry : angle 0.52545 (20259) SS BOND : bond 0.00211 ( 27) SS BOND : angle 0.72816 ( 54) hydrogen bonds : bond 0.03349 ( 537) hydrogen bonds : angle 5.31069 ( 1467) link_NAG-ASN : bond 0.00297 ( 9) link_NAG-ASN : angle 2.12483 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 GLN cc_start: 0.9192 (mm-40) cc_final: 0.8134 (tm-30) REVERT: A 263 PHE cc_start: 0.9231 (p90) cc_final: 0.8885 (p90) REVERT: A 323 MET cc_start: 0.8886 (mmt) cc_final: 0.8373 (mmt) REVERT: A 385 MET cc_start: 0.7872 (tpt) cc_final: 0.7391 (tpt) REVERT: A 396 MET cc_start: 0.9221 (tpp) cc_final: 0.8691 (ttp) REVERT: B 244 GLN cc_start: 0.9480 (mm-40) cc_final: 0.8450 (tm-30) REVERT: B 396 MET cc_start: 0.9281 (tpp) cc_final: 0.8748 (ttp) REVERT: C 244 GLN cc_start: 0.9236 (mm110) cc_final: 0.8043 (tm-30) REVERT: C 323 MET cc_start: 0.8798 (mmt) cc_final: 0.8426 (mmt) REVERT: D 12 ASP cc_start: 0.7195 (t0) cc_final: 0.6530 (t0) REVERT: D 17 ARG cc_start: 0.8762 (mmm-85) cc_final: 0.8448 (tpp80) REVERT: D 61 ASP cc_start: 0.9196 (m-30) cc_final: 0.8596 (t0) REVERT: D 79 LEU cc_start: 0.8796 (tp) cc_final: 0.8527 (tp) REVERT: D 80 ARG cc_start: 0.7803 (mmm-85) cc_final: 0.7507 (mmm-85) REVERT: D 84 GLU cc_start: 0.8212 (tt0) cc_final: 0.7725 (tp30) REVERT: E 12 ASP cc_start: 0.7179 (t70) cc_final: 0.6895 (t70) REVERT: E 16 GLN cc_start: 0.8660 (mp10) cc_final: 0.8337 (pm20) REVERT: E 17 ARG cc_start: 0.8737 (mmm-85) cc_final: 0.8136 (ttm-80) REVERT: E 61 ASP cc_start: 0.9211 (m-30) cc_final: 0.8655 (t0) REVERT: E 79 LEU cc_start: 0.8507 (tt) cc_final: 0.8299 (tt) REVERT: E 84 GLU cc_start: 0.8556 (pm20) cc_final: 0.8157 (pm20) REVERT: F 12 ASP cc_start: 0.8008 (t70) cc_final: 0.7738 (t70) REVERT: F 17 ARG cc_start: 0.8656 (ttm-80) cc_final: 0.8262 (ttm-80) REVERT: F 61 ASP cc_start: 0.9266 (m-30) cc_final: 0.8649 (t0) REVERT: F 80 ARG cc_start: 0.7703 (ttm110) cc_final: 0.7424 (mtp-110) REVERT: F 82 GLU cc_start: 0.9106 (pm20) cc_final: 0.8826 (mp0) REVERT: F 84 GLU cc_start: 0.8425 (tt0) cc_final: 0.7830 (mm-30) REVERT: F 96 LEU cc_start: 0.9531 (tp) cc_final: 0.9323 (tt) REVERT: G 233 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8257 (mm-30) REVERT: G 289 ASP cc_start: 0.8189 (t0) cc_final: 0.7856 (t0) REVERT: H 233 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8497 (mm-30) REVERT: H 244 ASP cc_start: 0.8787 (t70) cc_final: 0.8335 (t70) REVERT: H 292 LYS cc_start: 0.9659 (mtmm) cc_final: 0.9386 (mtmm) REVERT: I 218 GLN cc_start: 0.8569 (tp40) cc_final: 0.8214 (tp40) REVERT: I 233 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8224 (mm-30) REVERT: I 244 ASP cc_start: 0.8622 (t70) cc_final: 0.8220 (t70) REVERT: I 281 LYS cc_start: 0.9300 (ttmm) cc_final: 0.8907 (ttmm) REVERT: I 289 ASP cc_start: 0.8055 (t0) cc_final: 0.7761 (t0) outliers start: 24 outliers final: 22 residues processed: 172 average time/residue: 0.1264 time to fit residues: 32.1272 Evaluate side-chains 169 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 283 CYS Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain I residue 239 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 169 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 154 optimal weight: 5.9990 chunk 71 optimal weight: 0.1980 chunk 31 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.074367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.048136 restraints weight = 43904.687| |-----------------------------------------------------------------------------| r_work (start): 0.2630 rms_B_bonded: 4.66 r_work: 0.2477 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14952 Z= 0.178 Angle : 0.557 7.300 20340 Z= 0.284 Chirality : 0.042 0.154 2253 Planarity : 0.004 0.051 2568 Dihedral : 4.087 16.715 2205 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.73 % Allowed : 10.88 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.20), residues: 1830 helix: 0.04 (0.36), residues: 225 sheet: 0.86 (0.21), residues: 579 loop : -0.30 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 80 TYR 0.021 0.001 TYR C 168 PHE 0.015 0.001 PHE I 295 TRP 0.008 0.001 TRP I 251 HIS 0.003 0.001 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.00420 (14916) covalent geometry : angle 0.55177 (20259) SS BOND : bond 0.00268 ( 27) SS BOND : angle 0.78555 ( 54) hydrogen bonds : bond 0.03671 ( 537) hydrogen bonds : angle 5.31488 ( 1467) link_NAG-ASN : bond 0.00214 ( 9) link_NAG-ASN : angle 1.97982 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 244 GLN cc_start: 0.9210 (mm-40) cc_final: 0.8164 (tm-30) REVERT: A 263 PHE cc_start: 0.9256 (p90) cc_final: 0.8909 (p90) REVERT: A 323 MET cc_start: 0.8878 (mmt) cc_final: 0.8381 (mmt) REVERT: A 385 MET cc_start: 0.7960 (tpt) cc_final: 0.7435 (tpt) REVERT: B 244 GLN cc_start: 0.9478 (mm-40) cc_final: 0.8472 (tm-30) REVERT: C 244 GLN cc_start: 0.9249 (mm110) cc_final: 0.8056 (tm-30) REVERT: C 323 MET cc_start: 0.8793 (mmt) cc_final: 0.8419 (mmt) REVERT: D 12 ASP cc_start: 0.7226 (t0) cc_final: 0.6857 (t70) REVERT: D 16 GLN cc_start: 0.8577 (mp-120) cc_final: 0.8307 (mp10) REVERT: D 61 ASP cc_start: 0.9185 (m-30) cc_final: 0.8633 (t0) REVERT: D 79 LEU cc_start: 0.8831 (tp) cc_final: 0.8523 (tp) REVERT: D 80 ARG cc_start: 0.7875 (mmm-85) cc_final: 0.7660 (mmm-85) REVERT: D 84 GLU cc_start: 0.8207 (tt0) cc_final: 0.7662 (mm-30) REVERT: E 17 ARG cc_start: 0.8783 (mmm-85) cc_final: 0.8330 (ttm-80) REVERT: E 61 ASP cc_start: 0.9220 (m-30) cc_final: 0.8676 (t0) REVERT: E 79 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8365 (tt) REVERT: E 84 GLU cc_start: 0.8581 (pm20) cc_final: 0.8156 (pm20) REVERT: F 12 ASP cc_start: 0.7928 (t70) cc_final: 0.7387 (t70) REVERT: F 16 GLN cc_start: 0.8877 (pm20) cc_final: 0.8547 (pm20) REVERT: F 17 ARG cc_start: 0.8619 (ttm-80) cc_final: 0.8168 (ttm-80) REVERT: F 61 ASP cc_start: 0.9260 (m-30) cc_final: 0.8666 (t0) REVERT: F 80 ARG cc_start: 0.7810 (ttm110) cc_final: 0.7608 (mtp-110) REVERT: F 82 GLU cc_start: 0.9136 (pm20) cc_final: 0.8833 (mp0) REVERT: F 84 GLU cc_start: 0.8421 (tt0) cc_final: 0.7820 (mm-30) REVERT: F 96 LEU cc_start: 0.9549 (tp) cc_final: 0.9334 (tt) REVERT: G 233 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8244 (mm-30) REVERT: G 289 ASP cc_start: 0.8226 (t0) cc_final: 0.7892 (t0) REVERT: H 233 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8297 (mm-30) REVERT: H 244 ASP cc_start: 0.8864 (t70) cc_final: 0.8496 (t70) REVERT: H 292 LYS cc_start: 0.9656 (mtmm) cc_final: 0.9367 (mtmm) REVERT: I 218 GLN cc_start: 0.8575 (tp40) cc_final: 0.8358 (tp40) REVERT: I 233 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8210 (mm-30) REVERT: I 289 ASP cc_start: 0.8355 (t0) cc_final: 0.7858 (t0) outliers start: 28 outliers final: 25 residues processed: 172 average time/residue: 0.1241 time to fit residues: 31.8029 Evaluate side-chains 172 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 283 CYS Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 239 CYS Chi-restraints excluded: chain I residue 239 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 19 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 48 optimal weight: 20.0000 chunk 178 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.073882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.047020 restraints weight = 44705.197| |-----------------------------------------------------------------------------| r_work (start): 0.2642 rms_B_bonded: 4.79 r_work: 0.2490 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14952 Z= 0.137 Angle : 0.540 9.602 20340 Z= 0.273 Chirality : 0.041 0.159 2253 Planarity : 0.004 0.049 2568 Dihedral : 3.944 15.232 2205 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.48 % Allowed : 11.13 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.20), residues: 1830 helix: 0.09 (0.37), residues: 225 sheet: 0.93 (0.21), residues: 579 loop : -0.25 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 80 TYR 0.021 0.001 TYR A 168 PHE 0.022 0.001 PHE C 263 TRP 0.009 0.001 TRP G 251 HIS 0.003 0.000 HIS C 20 Details of bonding type rmsd covalent geometry : bond 0.00325 (14916) covalent geometry : angle 0.53516 (20259) SS BOND : bond 0.00239 ( 27) SS BOND : angle 0.72645 ( 54) hydrogen bonds : bond 0.03386 ( 537) hydrogen bonds : angle 5.24631 ( 1467) link_NAG-ASN : bond 0.00266 ( 9) link_NAG-ASN : angle 1.99980 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: A 244 GLN cc_start: 0.9250 (mm-40) cc_final: 0.8231 (tm-30) REVERT: A 263 PHE cc_start: 0.9258 (p90) cc_final: 0.8919 (p90) REVERT: A 323 MET cc_start: 0.8868 (mmt) cc_final: 0.8370 (mmt) REVERT: A 385 MET cc_start: 0.7878 (tpt) cc_final: 0.7403 (tpt) REVERT: B 244 GLN cc_start: 0.9488 (mm-40) cc_final: 0.8477 (tm-30) REVERT: C 244 GLN cc_start: 0.9255 (mm110) cc_final: 0.8091 (tm-30) REVERT: C 323 MET cc_start: 0.8797 (mmt) cc_final: 0.8431 (mmt) REVERT: D 12 ASP cc_start: 0.7121 (t0) cc_final: 0.6351 (t0) REVERT: D 16 GLN cc_start: 0.8589 (mp-120) cc_final: 0.8276 (mp10) REVERT: D 17 ARG cc_start: 0.8661 (mmm-85) cc_final: 0.8361 (tpp80) REVERT: D 61 ASP cc_start: 0.9179 (m-30) cc_final: 0.8626 (t0) REVERT: D 79 LEU cc_start: 0.8816 (tp) cc_final: 0.8391 (tp) REVERT: D 80 ARG cc_start: 0.7852 (mmm-85) cc_final: 0.7643 (mmm-85) REVERT: D 84 GLU cc_start: 0.8208 (tt0) cc_final: 0.7691 (mm-30) REVERT: E 16 GLN cc_start: 0.8834 (mp10) cc_final: 0.8550 (pm20) REVERT: E 17 ARG cc_start: 0.8700 (mmm-85) cc_final: 0.8197 (ttm-80) REVERT: E 61 ASP cc_start: 0.9214 (m-30) cc_final: 0.8662 (t0) REVERT: E 79 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8270 (tt) REVERT: E 84 GLU cc_start: 0.8576 (pm20) cc_final: 0.8134 (pm20) REVERT: F 12 ASP cc_start: 0.7904 (t70) cc_final: 0.7358 (t70) REVERT: F 16 GLN cc_start: 0.8836 (pm20) cc_final: 0.8520 (pm20) REVERT: F 17 ARG cc_start: 0.8564 (ttm-80) cc_final: 0.8135 (ttm-80) REVERT: F 61 ASP cc_start: 0.9245 (m-30) cc_final: 0.8651 (t0) REVERT: F 80 ARG cc_start: 0.7814 (ttm110) cc_final: 0.7518 (mtp-110) REVERT: F 82 GLU cc_start: 0.9110 (pm20) cc_final: 0.8812 (mp0) REVERT: F 84 GLU cc_start: 0.8438 (tt0) cc_final: 0.7809 (mm-30) REVERT: F 96 LEU cc_start: 0.9535 (tp) cc_final: 0.9331 (tt) REVERT: G 233 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8228 (mm-30) REVERT: H 233 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8272 (mm-30) REVERT: H 244 ASP cc_start: 0.8810 (t70) cc_final: 0.8391 (t70) REVERT: H 292 LYS cc_start: 0.9661 (mtmm) cc_final: 0.9375 (mtmm) REVERT: I 218 GLN cc_start: 0.8549 (tp40) cc_final: 0.8340 (tp40) REVERT: I 233 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8193 (mm-30) REVERT: I 244 ASP cc_start: 0.8482 (t70) cc_final: 0.8192 (t70) REVERT: I 246 MET cc_start: 0.9125 (mtp) cc_final: 0.8883 (tpp) REVERT: I 289 ASP cc_start: 0.8157 (t0) cc_final: 0.7756 (t0) outliers start: 24 outliers final: 23 residues processed: 169 average time/residue: 0.1254 time to fit residues: 31.4386 Evaluate side-chains 171 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 283 CYS Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 239 CYS Chi-restraints excluded: chain I residue 239 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 54 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 134 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.075491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.049256 restraints weight = 43846.315| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 4.71 r_work: 0.2543 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 14952 Z= 0.088 Angle : 0.512 9.605 20340 Z= 0.254 Chirality : 0.041 0.160 2253 Planarity : 0.004 0.047 2568 Dihedral : 3.601 13.870 2205 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.42 % Allowed : 11.19 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.20), residues: 1830 helix: 0.20 (0.36), residues: 228 sheet: 0.99 (0.20), residues: 612 loop : -0.11 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 80 TYR 0.021 0.001 TYR C 168 PHE 0.014 0.001 PHE C 263 TRP 0.011 0.001 TRP I 251 HIS 0.004 0.000 HIS B 384 Details of bonding type rmsd covalent geometry : bond 0.00209 (14916) covalent geometry : angle 0.50661 (20259) SS BOND : bond 0.00197 ( 27) SS BOND : angle 0.63875 ( 54) hydrogen bonds : bond 0.02899 ( 537) hydrogen bonds : angle 5.03181 ( 1467) link_NAG-ASN : bond 0.00350 ( 9) link_NAG-ASN : angle 1.96190 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3289.54 seconds wall clock time: 57 minutes 11.65 seconds (3431.65 seconds total)