Starting phenix.real_space_refine on Fri Jul 3 14:47:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7u9g_26397/07_2026/7u9g_26397.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u9g_26397/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7u9g_26397/07_2026/7u9g_26397.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7u9g_26397/07_2026/7u9g_26397.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u9g_26397/07_2026/7u9g_26397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u9g_26397/07_2026/7u9g_26397.map" model { file = "/net/cci-nas-00/data/ceres_data/7u9g_26397/07_2026/7u9g_26397.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u9g_26397/07_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-6108/lib/python3.11/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 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 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 chiralities: 3 Time building chain proxies: 2.95, per 1000 atoms: 0.20 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: 1.09 Conformation dependent library (CDL) restraints added in 635.0 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: 0.55 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: 2.55 Time building geometry restraints manager: 1.48 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: 8227 17.30 - 34.60: 494 34.60 - 51.90: 99 51.90 - 69.20: 21 69.20 - 86.51: 3 Dihedral angle restraints: 8844 sinusoidal: 3507 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 8841 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 13.010 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 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 : 11.090 86.505 5361 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/Z covalent geometry : bond 0.00674 / 0.31 (14916) covalent geometry : angle 0.77050 / 0.45 (20259) SS BOND : bond 0.00384 / 0.25 ( 27) SS BOND : angle 1.09973 / 0.72 ( 54) hydrogen bonds : bond 0.25512 / 17.65 ( 537) hydrogen bonds : angle 9.32012 / 6.48 ( 1467) link_NAG-ASN : bond 0.00649 / 0.28 ( 9) link_NAG-ASN : angle 3.18225 / 2.05 ( 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 : 0.358 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: 0.1197 time to fit residues: 45.0417 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 : 0.547 ------------------------------------------------------------------------------- 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... 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 = 0.3331 r_free = 0.3331 target = 0.076369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.050052 restraints weight = 43757.502| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 4.75 r_work: 0.2552 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14952 Z= 0.165 Angle : 0.583 7.496 20340 Z= 0.306 Chirality : 0.043 0.203 2253 Planarity : 0.005 0.051 2568 Dihedral : 4.294 14.092 2016 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.93 % Allowed : 7.79 % Favored : 91.28 % 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: 0.38 (0.36), residues: 210 sheet: 0.88 (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 270 PHE 0.021 0.002 PHE G 295 TRP 0.010 0.001 TRP F 36 HIS 0.004 0.001 HIS C 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (14916) covalent geometry : angle 0.57499 / 0.30 (20259) SS BOND : bond 0.00165 / 0.08 ( 27) SS BOND : angle 0.91126 / 0.58 ( 54) hydrogen bonds : bond 0.04456 / 3.07 ( 537) hydrogen bonds : angle 6.36391 / 4.43 ( 1467) link_NAG-ASN : bond 0.00559 / 0.23 ( 9) link_NAG-ASN : angle 2.50973 / 1.84 ( 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 182 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 0.536 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 323 MET cc_start: 0.8850 (mmt) cc_final: 0.8420 (mmt) REVERT: B 244 GLN cc_start: 0.9268 (mm-40) cc_final: 0.8201 (tm-30) REVERT: B 399 LEU cc_start: 0.9566 (mt) cc_final: 0.9360 (tt) REVERT: C 323 MET cc_start: 0.8744 (mmt) cc_final: 0.8146 (mmm) REVERT: C 399 LEU cc_start: 0.9392 (mt) cc_final: 0.9172 (tp) REVERT: D 12 ASP cc_start: 0.7063 (t0) cc_final: 0.6793 (t70) REVERT: D 76 ILE cc_start: 0.8411 (mp) cc_final: 0.8200 (mp) REVERT: D 82 GLU cc_start: 0.8868 (pm20) cc_final: 0.8588 (pm20) REVERT: E 12 ASP cc_start: 0.7261 (t0) cc_final: 0.6945 (t70) REVERT: E 54 LYS cc_start: 0.9154 (mttp) cc_final: 0.8863 (mmmm) REVERT: E 76 ILE cc_start: 0.8323 (mp) cc_final: 0.8114 (mt) REVERT: F 17 ARG cc_start: 0.8964 (mtp-110) cc_final: 0.8594 (ttm-80) REVERT: F 76 ILE cc_start: 0.8360 (mp) cc_final: 0.7795 (mt) REVERT: F 82 GLU cc_start: 0.8783 (pm20) cc_final: 0.8379 (pm20) REVERT: G 244 ASP cc_start: 0.8461 (t0) cc_final: 0.8136 (t0) REVERT: G 292 LYS cc_start: 0.9599 (mtmt) cc_final: 0.9383 (mtmm) REVERT: H 233 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8281 (mm-30) REVERT: H 244 ASP cc_start: 0.8443 (t70) cc_final: 0.8054 (t70) REVERT: H 318 ASP cc_start: 0.9159 (OUTLIER) cc_final: 0.8951 (m-30) REVERT: H 328 ASP cc_start: 0.8801 (m-30) cc_final: 0.8532 (m-30) REVERT: I 218 GLN cc_start: 0.8547 (tp40) cc_final: 0.8181 (tp40) REVERT: I 233 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8072 (mm-30) REVERT: I 244 ASP cc_start: 0.8456 (t70) cc_final: 0.8134 (t70) REVERT: I 281 LYS cc_start: 0.9130 (ttmm) cc_final: 0.8929 (ttmm) REVERT: I 289 ASP cc_start: 0.8036 (t0) cc_final: 0.7819 (t0) outliers start: 15 outliers final: 11 residues processed: 178 average time/residue: 0.1252 time to fit residues: 32.7893 Evaluate side-chains 163 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 108 THR Chi-restraints excluded: chain H residue 318 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 83 optimal weight: 9.9990 chunk 173 optimal weight: 2.9990 chunk 101 optimal weight: 20.0000 chunk 161 optimal weight: 0.0040 chunk 90 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 overall best weight: 2.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 HIS B 261 HIS C 261 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.076094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.049525 restraints weight = 43574.187| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 4.76 r_work: 0.2518 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14952 Z= 0.153 Angle : 0.543 8.339 20340 Z= 0.283 Chirality : 0.042 0.177 2253 Planarity : 0.004 0.048 2568 Dihedral : 4.122 16.700 2016 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.67 % Allowed : 8.29 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.31 (0.19), residues: 1830 helix: 0.64 (0.37), residues: 207 sheet: 0.78 (0.20), residues: 573 loop : -0.15 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 264 TYR 0.023 0.001 TYR E 50 PHE 0.015 0.001 PHE I 295 TRP 0.010 0.001 TRP E 36 HIS 0.002 0.000 HIS C 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (14916) covalent geometry : angle 0.53323 / 0.28 (20259) SS BOND : bond 0.00197 / 0.13 ( 27) SS BOND : angle 1.14140 / 0.87 ( 54) hydrogen bonds : bond 0.04058 / 2.78 ( 537) hydrogen bonds : angle 5.81123 / 4.01 ( 1467) link_NAG-ASN : bond 0.00407 / 0.17 ( 9) link_NAG-ASN : angle 2.41230 / 1.83 ( 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 182 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLN cc_start: 0.9111 (mm-40) cc_final: 0.7964 (tm-30) REVERT: A 323 MET cc_start: 0.8855 (mmt) cc_final: 0.8403 (mmt) REVERT: B 244 GLN cc_start: 0.9307 (mm-40) cc_final: 0.8242 (tm-30) REVERT: B 399 LEU cc_start: 0.9561 (mt) cc_final: 0.9346 (tt) REVERT: C 102 MET cc_start: 0.9029 (mmm) cc_final: 0.8816 (mmm) REVERT: C 244 GLN cc_start: 0.9195 (mm110) cc_final: 0.7940 (tm-30) REVERT: C 323 MET cc_start: 0.8739 (mmt) cc_final: 0.8138 (mmm) REVERT: C 399 LEU cc_start: 0.9385 (mt) cc_final: 0.9145 (tp) REVERT: D 12 ASP cc_start: 0.7041 (t0) cc_final: 0.6751 (t70) REVERT: D 61 ASP cc_start: 0.9291 (m-30) cc_final: 0.8627 (t0) REVERT: E 12 ASP cc_start: 0.7235 (t0) cc_final: 0.6976 (t70) REVERT: E 50 TYR cc_start: 0.8028 (p90) cc_final: 0.7769 (p90) REVERT: E 54 LYS cc_start: 0.9148 (mttp) cc_final: 0.8774 (mmmm) REVERT: E 61 ASP cc_start: 0.9258 (m-30) cc_final: 0.8613 (t0) REVERT: F 76 ILE cc_start: 0.8309 (mp) cc_final: 0.8097 (mt) REVERT: F 82 GLU cc_start: 0.8831 (pm20) cc_final: 0.8568 (pm20) REVERT: G 318 ASP cc_start: 0.9154 (OUTLIER) cc_final: 0.8876 (m-30) REVERT: H 233 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8236 (mm-30) REVERT: H 244 ASP cc_start: 0.8586 (t70) cc_final: 0.8179 (t70) REVERT: H 292 LYS cc_start: 0.9609 (mtmm) cc_final: 0.9382 (mtmm) REVERT: H 318 ASP cc_start: 0.9187 (OUTLIER) cc_final: 0.8895 (m-30) REVERT: I 233 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8104 (mm-30) REVERT: I 244 ASP cc_start: 0.8542 (t70) cc_final: 0.8194 (t70) REVERT: I 281 LYS cc_start: 0.9146 (ttmm) cc_final: 0.8748 (ttmm) REVERT: I 289 ASP cc_start: 0.8145 (t0) cc_final: 0.7944 (t0) REVERT: I 318 ASP cc_start: 0.9211 (OUTLIER) cc_final: 0.8983 (m-30) outliers start: 27 outliers final: 16 residues processed: 181 average time/residue: 0.1115 time to fit residues: 30.1369 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 : 0.607 ------------------------------------------------------------------------------- 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 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 F residue 13 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 318 ASP Chi-restraints excluded: chain H 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: 0.9980 chunk 130 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 173 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.077439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.051299 restraints weight = 43248.252| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 4.70 r_work: 0.2543 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2869 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= 0.114 Angle : 0.515 6.036 20340 Z= 0.266 Chirality : 0.041 0.172 2253 Planarity : 0.004 0.045 2568 Dihedral : 3.957 16.949 2016 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.73 % Allowed : 8.78 % Favored : 89.49 % 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: 0.40 (0.19), residues: 1830 helix: 0.67 (0.37), residues: 210 sheet: 0.75 (0.20), residues: 603 loop : -0.04 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 17 TYR 0.017 0.001 TYR E 50 PHE 0.015 0.001 PHE I 295 TRP 0.007 0.001 TRP G 251 HIS 0.002 0.000 HIS C 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 (14916) covalent geometry : angle 0.50671 / 0.26 (20259) SS BOND : bond 0.00191 / 0.14 ( 27) SS BOND : angle 0.95948 / 0.74 ( 54) hydrogen bonds : bond 0.03473 / 2.36 ( 537) hydrogen bonds : angle 5.52522 / 3.81 ( 1467) link_NAG-ASN : bond 0.00422 / 0.18 ( 9) link_NAG-ASN : angle 2.29703 / 1.74 ( 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 182 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLN cc_start: 0.9139 (mm-40) cc_final: 0.8007 (tm-30) REVERT: A 323 MET cc_start: 0.8842 (mmt) cc_final: 0.8392 (mmt) REVERT: A 396 MET cc_start: 0.9162 (tpp) cc_final: 0.8599 (ttp) REVERT: B 244 GLN cc_start: 0.9370 (mm-40) cc_final: 0.8316 (tm-30) REVERT: B 396 MET cc_start: 0.9196 (tpp) cc_final: 0.8702 (ttp) REVERT: B 399 LEU cc_start: 0.9551 (mt) cc_final: 0.9275 (tt) REVERT: C 244 GLN cc_start: 0.9195 (mm110) cc_final: 0.7939 (tm-30) REVERT: C 323 MET cc_start: 0.8764 (mmt) cc_final: 0.8470 (mmt) REVERT: C 399 LEU cc_start: 0.9372 (mt) cc_final: 0.9128 (tp) REVERT: D 12 ASP cc_start: 0.6911 (t0) cc_final: 0.6629 (t70) REVERT: D 61 ASP cc_start: 0.9219 (m-30) cc_final: 0.8574 (t0) REVERT: D 80 ARG cc_start: 0.7644 (mmm-85) cc_final: 0.7384 (mmm-85) REVERT: D 82 GLU cc_start: 0.8726 (pm20) cc_final: 0.8307 (pm20) REVERT: E 17 ARG cc_start: 0.8605 (mmm-85) cc_final: 0.8314 (ttt90) REVERT: E 54 LYS cc_start: 0.9141 (mttp) cc_final: 0.8743 (mmmm) REVERT: E 61 ASP cc_start: 0.9249 (m-30) cc_final: 0.8614 (t0) REVERT: E 79 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7820 (tt) REVERT: E 84 GLU cc_start: 0.8465 (pm20) cc_final: 0.8251 (pm20) REVERT: F 82 GLU cc_start: 0.8859 (pm20) cc_final: 0.8454 (mp0) REVERT: G 222 GLN cc_start: 0.8155 (tp-100) cc_final: 0.7825 (tp-100) REVERT: G 318 ASP cc_start: 0.9174 (OUTLIER) cc_final: 0.8893 (m-30) REVERT: H 233 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8216 (mm-30) REVERT: H 244 ASP cc_start: 0.8564 (t70) cc_final: 0.8081 (t70) REVERT: H 292 LYS cc_start: 0.9632 (mtmm) cc_final: 0.9383 (mtmm) REVERT: H 318 ASP cc_start: 0.9205 (OUTLIER) cc_final: 0.8936 (m-30) REVERT: I 233 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8083 (mm-30) REVERT: I 244 ASP cc_start: 0.8468 (t70) cc_final: 0.8135 (t70) REVERT: I 281 LYS cc_start: 0.9112 (ttmm) cc_final: 0.8721 (ttmm) REVERT: I 289 ASP cc_start: 0.8089 (t0) cc_final: 0.7825 (t0) outliers start: 28 outliers final: 15 residues processed: 180 average time/residue: 0.1163 time to fit residues: 31.1330 Evaluate side-chains 164 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 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 D residue 13 THR 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 4 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 318 ASP Chi-restraints excluded: chain H residue 239 CYS Chi-restraints excluded: chain H 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: 7.9990 chunk 3 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 139 optimal weight: 0.0270 chunk 130 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.076404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.050332 restraints weight = 44058.161| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 4.70 r_work: 0.2539 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14952 Z= 0.119 Angle : 0.506 5.682 20340 Z= 0.260 Chirality : 0.041 0.165 2253 Planarity : 0.004 0.045 2568 Dihedral : 3.895 15.519 2016 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.36 % Allowed : 9.65 % Favored : 88.99 % 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: 0.46 (0.19), residues: 1830 helix: 0.77 (0.37), residues: 207 sheet: 0.82 (0.20), residues: 609 loop : -0.04 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 17 TYR 0.016 0.001 TYR D 50 PHE 0.018 0.001 PHE C 263 TRP 0.008 0.001 TRP H 251 HIS 0.003 0.000 HIS C 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (14916) covalent geometry : angle 0.49918 / 0.26 (20259) SS BOND : bond 0.00208 / 0.15 ( 27) SS BOND : angle 0.83549 / 0.63 ( 54) hydrogen bonds : bond 0.03358 / 2.28 ( 537) hydrogen bonds : angle 5.33140 / 3.68 ( 1467) link_NAG-ASN : bond 0.00380 / 0.16 ( 9) link_NAG-ASN : angle 2.12631 / 1.61 ( 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 175 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLN cc_start: 0.9153 (mm-40) cc_final: 0.8040 (tm-30) REVERT: A 323 MET cc_start: 0.8841 (mmt) cc_final: 0.8376 (mmt) REVERT: A 396 MET cc_start: 0.9179 (tpp) cc_final: 0.8610 (ttp) REVERT: B 244 GLN cc_start: 0.9433 (mm-40) cc_final: 0.8450 (tm-30) REVERT: B 396 MET cc_start: 0.9194 (tpp) cc_final: 0.8696 (ttp) REVERT: C 244 GLN cc_start: 0.9216 (mm110) cc_final: 0.7980 (tm-30) REVERT: C 323 MET cc_start: 0.8779 (mmt) cc_final: 0.8462 (mmt) REVERT: C 399 LEU cc_start: 0.9357 (mt) cc_final: 0.9086 (tp) REVERT: D 12 ASP cc_start: 0.6820 (t0) cc_final: 0.6084 (t0) REVERT: D 17 ARG cc_start: 0.8570 (mmm-85) cc_final: 0.8316 (tpp80) REVERT: D 61 ASP cc_start: 0.9232 (m-30) cc_final: 0.8608 (t0) REVERT: D 79 LEU cc_start: 0.8430 (tp) cc_final: 0.7965 (tp) REVERT: D 80 ARG cc_start: 0.7656 (mmm-85) cc_final: 0.7419 (mmm-85) REVERT: D 84 GLU cc_start: 0.8307 (tt0) cc_final: 0.7706 (tp30) REVERT: E 17 ARG cc_start: 0.8719 (mmm-85) cc_final: 0.8411 (ttt90) REVERT: E 54 LYS cc_start: 0.9156 (mttp) cc_final: 0.8782 (mmmm) REVERT: E 61 ASP cc_start: 0.9212 (m-30) cc_final: 0.8588 (t0) REVERT: E 79 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7906 (tt) REVERT: E 84 GLU cc_start: 0.8573 (pm20) cc_final: 0.8312 (pm20) REVERT: F 17 ARG cc_start: 0.9012 (mmm-85) cc_final: 0.8794 (tpp80) REVERT: F 80 ARG cc_start: 0.7907 (ttm-80) cc_final: 0.7682 (ttm110) REVERT: F 82 GLU cc_start: 0.9055 (pm20) cc_final: 0.8706 (mp0) REVERT: F 84 GLU cc_start: 0.8269 (tt0) cc_final: 0.7754 (tp30) REVERT: G 246 MET cc_start: 0.9053 (mtp) cc_final: 0.8811 (tpp) REVERT: G 318 ASP cc_start: 0.9186 (OUTLIER) cc_final: 0.8891 (m-30) REVERT: H 233 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8193 (mm-30) REVERT: H 244 ASP cc_start: 0.8564 (t70) cc_final: 0.8072 (t70) REVERT: H 318 ASP cc_start: 0.9203 (OUTLIER) cc_final: 0.8914 (m-30) REVERT: I 233 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8025 (mm-30) REVERT: I 244 ASP cc_start: 0.8514 (t70) cc_final: 0.8179 (t70) REVERT: I 246 MET cc_start: 0.9097 (mtp) cc_final: 0.8584 (ttm) REVERT: I 281 LYS cc_start: 0.9143 (ttmm) cc_final: 0.8762 (ttmm) REVERT: I 289 ASP cc_start: 0.8123 (t0) cc_final: 0.7740 (t0) outliers start: 22 outliers final: 18 residues processed: 174 average time/residue: 0.1191 time to fit residues: 30.7386 Evaluate side-chains 168 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 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 D residue 13 THR 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 18 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 318 ASP Chi-restraints excluded: chain H residue 239 CYS Chi-restraints excluded: chain H 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: 0.8980 chunk 29 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 109 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.075915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.049946 restraints weight = 43749.362| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 4.66 r_work: 0.2529 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3219 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= 0.129 Angle : 0.505 6.817 20340 Z= 0.259 Chirality : 0.041 0.163 2253 Planarity : 0.004 0.046 2568 Dihedral : 3.856 14.802 2016 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.10 % Allowed : 9.15 % Favored : 88.74 % 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: 0.44 (0.19), residues: 1830 helix: 0.77 (0.38), residues: 207 sheet: 0.82 (0.20), residues: 612 loop : -0.07 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 17 TYR 0.020 0.001 TYR C 168 PHE 0.014 0.001 PHE G 295 TRP 0.008 0.001 TRP G 251 HIS 0.003 0.000 HIS C 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (14916) covalent geometry : angle 0.49902 / 0.26 (20259) SS BOND : bond 0.00222 / 0.16 ( 27) SS BOND : angle 0.79130 / 0.59 ( 54) hydrogen bonds : bond 0.03335 / 2.26 ( 537) hydrogen bonds : angle 5.25577 / 3.63 ( 1467) link_NAG-ASN : bond 0.00334 / 0.14 ( 9) link_NAG-ASN : angle 2.01111 / 1.51 ( 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 184 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8014 (tm-30) REVERT: A 323 MET cc_start: 0.8854 (mmt) cc_final: 0.8387 (mmt) REVERT: B 244 GLN cc_start: 0.9461 (mm-40) cc_final: 0.8493 (tm-30) REVERT: B 396 MET cc_start: 0.9193 (tpp) cc_final: 0.8684 (ttp) REVERT: C 244 GLN cc_start: 0.9225 (mm110) cc_final: 0.7979 (tm-30) REVERT: C 323 MET cc_start: 0.8797 (mmt) cc_final: 0.8459 (mmt) REVERT: D 12 ASP cc_start: 0.6842 (t0) cc_final: 0.6216 (t0) REVERT: D 17 ARG cc_start: 0.8648 (mmm-85) cc_final: 0.8407 (tpp80) REVERT: D 80 ARG cc_start: 0.7984 (mmm-85) cc_final: 0.7719 (mmm-85) REVERT: E 17 ARG cc_start: 0.8758 (mmm-85) cc_final: 0.8359 (tpp80) REVERT: E 61 ASP cc_start: 0.9211 (m-30) cc_final: 0.8621 (t0) REVERT: E 79 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7956 (tt) REVERT: E 84 GLU cc_start: 0.8577 (pm20) cc_final: 0.8227 (pm20) REVERT: F 17 ARG cc_start: 0.9075 (mmm-85) cc_final: 0.8847 (tpp80) REVERT: F 80 ARG cc_start: 0.7868 (ttm-80) cc_final: 0.7589 (ttm110) REVERT: F 82 GLU cc_start: 0.9066 (pm20) cc_final: 0.8736 (mp0) REVERT: F 84 GLU cc_start: 0.8396 (tt0) cc_final: 0.7929 (tp30) REVERT: F 96 LEU cc_start: 0.9509 (tp) cc_final: 0.9288 (tt) REVERT: G 289 ASP cc_start: 0.8004 (t0) cc_final: 0.7785 (t0) REVERT: G 318 ASP cc_start: 0.9208 (OUTLIER) cc_final: 0.8885 (m-30) REVERT: H 233 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8205 (mm-30) REVERT: H 244 ASP cc_start: 0.8605 (t70) cc_final: 0.8111 (t70) REVERT: H 292 LYS cc_start: 0.9642 (mtmm) cc_final: 0.9363 (mtmm) REVERT: H 318 ASP cc_start: 0.9244 (OUTLIER) cc_final: 0.8987 (m-30) REVERT: I 233 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8070 (mm-30) REVERT: I 244 ASP cc_start: 0.8511 (t70) cc_final: 0.8134 (t70) REVERT: I 281 LYS cc_start: 0.9138 (ttmm) cc_final: 0.8775 (ttmm) REVERT: I 289 ASP cc_start: 0.8142 (t0) cc_final: 0.7797 (t0) outliers start: 34 outliers final: 24 residues processed: 183 average time/residue: 0.1168 time to fit residues: 31.9240 Evaluate side-chains 173 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 54 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 245 THR 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 D residue 13 THR 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 18 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 34 VAL 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 H residue 239 CYS Chi-restraints excluded: chain H residue 318 ASP 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: 2.9990 chunk 36 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 165 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 153 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.074921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.048620 restraints weight = 43940.240| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 4.66 r_work: 0.2517 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3326 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= 0.124 Angle : 0.508 7.544 20340 Z= 0.259 Chirality : 0.041 0.159 2253 Planarity : 0.004 0.045 2568 Dihedral : 3.823 14.388 2016 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.16 % Allowed : 9.89 % Favored : 87.94 % 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: 0.42 (0.19), residues: 1830 helix: 0.31 (0.36), residues: 225 sheet: 0.86 (0.20), residues: 612 loop : -0.01 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 17 TYR 0.020 0.001 TYR C 168 PHE 0.013 0.001 PHE I 295 TRP 0.008 0.001 TRP H 251 HIS 0.002 0.000 HIS C 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 (14916) covalent geometry : angle 0.50255 / 0.26 (20259) SS BOND : bond 0.00212 / 0.15 ( 27) SS BOND : angle 0.73607 / 0.55 ( 54) hydrogen bonds : bond 0.03273 / 2.22 ( 537) hydrogen bonds : angle 5.21618 / 3.61 ( 1467) link_NAG-ASN : bond 0.00315 / 0.14 ( 9) link_NAG-ASN : angle 1.95675 / 1.47 ( 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 182 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLN cc_start: 0.9217 (mm-40) cc_final: 0.8116 (tm-30) REVERT: A 323 MET cc_start: 0.8877 (mmt) cc_final: 0.8402 (mmt) REVERT: A 385 MET cc_start: 0.7719 (tpt) cc_final: 0.7172 (tpt) REVERT: B 244 GLN cc_start: 0.9469 (mm-40) cc_final: 0.8509 (tm-30) REVERT: C 244 GLN cc_start: 0.9225 (mm110) cc_final: 0.7994 (tm-30) REVERT: C 323 MET cc_start: 0.8798 (mmt) cc_final: 0.8456 (mmt) REVERT: D 12 ASP cc_start: 0.6842 (t0) cc_final: 0.6365 (t70) REVERT: D 17 ARG cc_start: 0.8672 (mmm-85) cc_final: 0.8416 (tpp80) REVERT: D 61 ASP cc_start: 0.9266 (m-30) cc_final: 0.8622 (t0) REVERT: D 80 ARG cc_start: 0.7957 (mmm-85) cc_final: 0.7733 (mmm-85) REVERT: D 84 GLU cc_start: 0.8215 (tt0) cc_final: 0.7703 (tp30) REVERT: E 17 ARG cc_start: 0.8761 (mmm-85) cc_final: 0.8387 (tpp80) REVERT: E 61 ASP cc_start: 0.9173 (m-30) cc_final: 0.8607 (t0) REVERT: E 79 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7936 (tt) REVERT: E 84 GLU cc_start: 0.8616 (pm20) cc_final: 0.8179 (pm20) REVERT: F 17 ARG cc_start: 0.9022 (mmm-85) cc_final: 0.8739 (tpp80) REVERT: F 80 ARG cc_start: 0.7855 (ttm-80) cc_final: 0.7575 (ttm110) REVERT: F 82 GLU cc_start: 0.9097 (pm20) cc_final: 0.8707 (mp0) REVERT: F 84 GLU cc_start: 0.8427 (tt0) cc_final: 0.7918 (tp30) REVERT: F 96 LEU cc_start: 0.9522 (tp) cc_final: 0.9296 (tt) REVERT: G 246 MET cc_start: 0.9095 (mtp) cc_final: 0.7861 (mmm) REVERT: G 318 ASP cc_start: 0.9197 (OUTLIER) cc_final: 0.8871 (m-30) REVERT: H 233 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8237 (mm-30) REVERT: H 244 ASP cc_start: 0.8624 (t70) cc_final: 0.8130 (t70) REVERT: H 292 LYS cc_start: 0.9642 (mtmm) cc_final: 0.9381 (mtmm) REVERT: H 318 ASP cc_start: 0.9204 (OUTLIER) cc_final: 0.8993 (m-30) REVERT: I 233 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8041 (mm-30) REVERT: I 244 ASP cc_start: 0.8448 (t70) cc_final: 0.8104 (t70) REVERT: I 246 MET cc_start: 0.9066 (mtp) cc_final: 0.8772 (tpp) REVERT: I 281 LYS cc_start: 0.9150 (ttmm) cc_final: 0.8780 (ttmm) REVERT: I 289 ASP cc_start: 0.8061 (t0) cc_final: 0.7669 (t0) REVERT: I 292 LYS cc_start: 0.9538 (mtmm) cc_final: 0.9029 (mtmm) outliers start: 35 outliers final: 28 residues processed: 179 average time/residue: 0.1192 time to fit residues: 32.0982 Evaluate side-chains 176 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 245 THR 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 393 ILE Chi-restraints excluded: chain D residue 13 THR 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 18 VAL 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 Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 239 CYS Chi-restraints excluded: chain H residue 318 ASP 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: 0.5980 chunk 110 optimal weight: 0.4980 chunk 87 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.074139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.047555 restraints weight = 44233.800| |-----------------------------------------------------------------------------| r_work (start): 0.2641 rms_B_bonded: 4.70 r_work: 0.2489 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14952 Z= 0.164 Angle : 0.538 7.281 20340 Z= 0.275 Chirality : 0.041 0.156 2253 Planarity : 0.004 0.045 2568 Dihedral : 3.960 15.293 2016 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.23 % Allowed : 10.02 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.19), residues: 1830 helix: 0.20 (0.36), residues: 225 sheet: 0.88 (0.20), residues: 612 loop : -0.10 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 17 TYR 0.022 0.001 TYR A 168 PHE 0.015 0.001 PHE G 295 TRP 0.010 0.001 TRP E 36 HIS 0.004 0.000 HIS C 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (14916) covalent geometry : angle 0.53272 / 0.27 (20259) SS BOND : bond 0.00251 / 0.18 ( 27) SS BOND : angle 0.80779 / 0.59 ( 54) hydrogen bonds : bond 0.03549 / 2.41 ( 537) hydrogen bonds : angle 5.24244 / 3.64 ( 1467) link_NAG-ASN : bond 0.00244 / 0.11 ( 9) link_NAG-ASN : angle 1.88307 / 1.38 ( 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 182 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLN cc_start: 0.9280 (mm-40) cc_final: 0.8137 (tm-30) REVERT: A 323 MET cc_start: 0.8862 (mmt) cc_final: 0.8382 (mmt) REVERT: A 385 MET cc_start: 0.7712 (tpt) cc_final: 0.7125 (tpt) REVERT: B 244 GLN cc_start: 0.9479 (mm-40) cc_final: 0.8426 (tm-30) REVERT: C 244 GLN cc_start: 0.9254 (mm110) cc_final: 0.8040 (tm-30) REVERT: C 323 MET cc_start: 0.8752 (mmt) cc_final: 0.8386 (mmt) REVERT: D 12 ASP cc_start: 0.6932 (t0) cc_final: 0.6450 (t70) REVERT: D 17 ARG cc_start: 0.8683 (mmm-85) cc_final: 0.8374 (tpp80) REVERT: D 61 ASP cc_start: 0.9275 (m-30) cc_final: 0.8619 (t0) REVERT: D 80 ARG cc_start: 0.7922 (mmm-85) cc_final: 0.7657 (mmm-85) REVERT: D 84 GLU cc_start: 0.8200 (tt0) cc_final: 0.7663 (tp30) REVERT: E 17 ARG cc_start: 0.8763 (mmm-85) cc_final: 0.8385 (tpp80) REVERT: E 61 ASP cc_start: 0.9168 (m-30) cc_final: 0.8639 (t0) REVERT: E 79 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8177 (tt) REVERT: E 84 GLU cc_start: 0.8641 (pm20) cc_final: 0.8199 (pm20) REVERT: F 16 GLN cc_start: 0.8978 (mp10) cc_final: 0.8546 (pm20) REVERT: F 82 GLU cc_start: 0.9096 (pm20) cc_final: 0.8692 (mp0) REVERT: F 84 GLU cc_start: 0.8432 (tt0) cc_final: 0.7877 (tp30) REVERT: F 96 LEU cc_start: 0.9516 (tp) cc_final: 0.9305 (tt) REVERT: G 289 ASP cc_start: 0.8186 (t0) cc_final: 0.7864 (t0) REVERT: G 318 ASP cc_start: 0.9259 (OUTLIER) cc_final: 0.8947 (m-30) REVERT: H 233 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8168 (mm-30) REVERT: H 244 ASP cc_start: 0.8750 (t70) cc_final: 0.8348 (t70) REVERT: I 233 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8084 (mm-30) REVERT: I 244 ASP cc_start: 0.8567 (t70) cc_final: 0.8098 (t70) REVERT: I 246 MET cc_start: 0.9180 (mtp) cc_final: 0.8765 (tpp) REVERT: I 281 LYS cc_start: 0.9175 (ttmm) cc_final: 0.8798 (ttmm) REVERT: I 289 ASP cc_start: 0.8064 (t0) cc_final: 0.7715 (t0) outliers start: 36 outliers final: 30 residues processed: 178 average time/residue: 0.1167 time to fit residues: 31.1652 Evaluate side-chains 175 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 389 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain D residue 13 THR 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 18 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 169 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.074820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.048252 restraints weight = 43951.001| |-----------------------------------------------------------------------------| r_work (start): 0.2646 rms_B_bonded: 4.67 r_work: 0.2493 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14952 Z= 0.155 Angle : 0.532 8.848 20340 Z= 0.271 Chirality : 0.041 0.157 2253 Planarity : 0.004 0.045 2568 Dihedral : 3.939 15.403 2016 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.04 % Allowed : 10.08 % 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: 0.31 (0.20), residues: 1830 helix: 0.14 (0.36), residues: 225 sheet: 0.97 (0.21), residues: 579 loop : -0.17 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 17 TYR 0.021 0.001 TYR C 168 PHE 0.015 0.001 PHE A 263 TRP 0.007 0.001 TRP H 251 HIS 0.002 0.000 HIS C 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (14916) covalent geometry : angle 0.52680 / 0.27 (20259) SS BOND : bond 0.00242 / 0.17 ( 27) SS BOND : angle 0.76404 / 0.55 ( 54) hydrogen bonds : bond 0.03465 / 2.34 ( 537) hydrogen bonds : angle 5.23582 / 3.62 ( 1467) link_NAG-ASN : bond 0.00257 / 0.11 ( 9) link_NAG-ASN : angle 1.92590 / 1.40 ( 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 178 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLN cc_start: 0.9300 (mm-40) cc_final: 0.8292 (pp30) REVERT: A 323 MET cc_start: 0.8851 (mmt) cc_final: 0.8353 (mmt) REVERT: A 385 MET cc_start: 0.7689 (tpt) cc_final: 0.7117 (tpt) REVERT: B 244 GLN cc_start: 0.9481 (mm-40) cc_final: 0.8442 (tm-30) REVERT: C 244 GLN cc_start: 0.9257 (mm110) cc_final: 0.8063 (tm-30) REVERT: C 323 MET cc_start: 0.8762 (mmt) cc_final: 0.8396 (mmt) REVERT: C 385 MET cc_start: 0.8019 (tpt) cc_final: 0.7716 (tpt) REVERT: D 12 ASP cc_start: 0.6919 (t0) cc_final: 0.6433 (t70) REVERT: D 17 ARG cc_start: 0.8679 (mmm-85) cc_final: 0.8377 (tpp80) REVERT: D 61 ASP cc_start: 0.9211 (m-30) cc_final: 0.8551 (t0) REVERT: D 80 ARG cc_start: 0.7908 (mmm-85) cc_final: 0.7645 (mmm-85) REVERT: D 84 GLU cc_start: 0.8221 (tt0) cc_final: 0.7628 (mm-30) REVERT: E 17 ARG cc_start: 0.8732 (mmm-85) cc_final: 0.8358 (tpp80) REVERT: E 61 ASP cc_start: 0.9165 (m-30) cc_final: 0.8653 (t0) REVERT: E 79 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8208 (tt) REVERT: E 84 GLU cc_start: 0.8645 (pm20) cc_final: 0.8200 (pm20) REVERT: F 16 GLN cc_start: 0.8981 (mp10) cc_final: 0.8764 (pm20) REVERT: F 17 ARG cc_start: 0.8931 (ttm110) cc_final: 0.8670 (ttm-80) REVERT: F 80 ARG cc_start: 0.7757 (ttm-80) cc_final: 0.7541 (ttm110) REVERT: F 84 GLU cc_start: 0.8457 (tt0) cc_final: 0.7890 (tp30) REVERT: F 96 LEU cc_start: 0.9518 (tp) cc_final: 0.9303 (tt) REVERT: G 289 ASP cc_start: 0.8142 (t0) cc_final: 0.7806 (t0) REVERT: G 318 ASP cc_start: 0.9265 (OUTLIER) cc_final: 0.8985 (m-30) REVERT: H 233 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8191 (mm-30) REVERT: H 244 ASP cc_start: 0.8735 (t70) cc_final: 0.8338 (t70) REVERT: I 233 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8140 (mm-30) REVERT: I 244 ASP cc_start: 0.8559 (t70) cc_final: 0.8127 (t70) REVERT: I 246 MET cc_start: 0.9141 (mtp) cc_final: 0.8732 (tpp) REVERT: I 281 LYS cc_start: 0.9184 (ttmm) cc_final: 0.8797 (ttmm) REVERT: I 289 ASP cc_start: 0.8000 (t0) cc_final: 0.7658 (t0) outliers start: 33 outliers final: 30 residues processed: 175 average time/residue: 0.1133 time to fit residues: 29.6130 Evaluate side-chains 176 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 389 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain D residue 13 THR 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 18 VAL 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 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: 6.9990 chunk 116 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 178 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 73 optimal weight: 0.0980 chunk 102 optimal weight: 2.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.074564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.048318 restraints weight = 43987.554| |-----------------------------------------------------------------------------| r_work (start): 0.2637 rms_B_bonded: 4.64 r_work: 0.2483 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14952 Z= 0.165 Angle : 0.543 8.549 20340 Z= 0.277 Chirality : 0.041 0.153 2253 Planarity : 0.004 0.045 2568 Dihedral : 3.983 16.196 2016 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.86 % Allowed : 10.39 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.20), residues: 1830 helix: 0.19 (0.37), residues: 225 sheet: 0.97 (0.21), residues: 579 loop : -0.21 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 80 TYR 0.021 0.001 TYR C 168 PHE 0.017 0.002 PHE A 263 TRP 0.008 0.001 TRP D 36 HIS 0.002 0.000 HIS B 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (14916) covalent geometry : angle 0.53796 / 0.28 (20259) SS BOND : bond 0.00257 / 0.18 ( 27) SS BOND : angle 0.78868 / 0.57 ( 54) hydrogen bonds : bond 0.03563 / 2.42 ( 537) hydrogen bonds : angle 5.24906 / 3.63 ( 1467) link_NAG-ASN : bond 0.00229 / 0.10 ( 9) link_NAG-ASN : angle 1.89928 / 1.37 ( 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 175 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLN cc_start: 0.9301 (mm-40) cc_final: 0.8309 (pp30) REVERT: A 323 MET cc_start: 0.8896 (mmt) cc_final: 0.8392 (mmt) REVERT: A 385 MET cc_start: 0.7706 (tpt) cc_final: 0.7120 (tpt) REVERT: B 244 GLN cc_start: 0.9486 (mm-40) cc_final: 0.8457 (tm-30) REVERT: B 385 MET cc_start: 0.8280 (tpt) cc_final: 0.8031 (tpt) REVERT: C 244 GLN cc_start: 0.9275 (mm110) cc_final: 0.8081 (tm-30) REVERT: C 323 MET cc_start: 0.8794 (mmt) cc_final: 0.8411 (mmt) REVERT: C 385 MET cc_start: 0.8162 (tpt) cc_final: 0.7807 (tpt) REVERT: D 12 ASP cc_start: 0.6901 (t0) cc_final: 0.6419 (t70) REVERT: D 17 ARG cc_start: 0.8674 (mmm-85) cc_final: 0.8375 (tpp80) REVERT: D 61 ASP cc_start: 0.9223 (m-30) cc_final: 0.8593 (t0) REVERT: D 80 ARG cc_start: 0.7823 (mmm-85) cc_final: 0.7555 (mmm-85) REVERT: D 84 GLU cc_start: 0.8238 (tt0) cc_final: 0.7675 (mm-30) REVERT: E 17 ARG cc_start: 0.8727 (mmm-85) cc_final: 0.8458 (ttt90) REVERT: E 61 ASP cc_start: 0.9133 (m-30) cc_final: 0.8626 (t0) REVERT: E 79 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8361 (tt) REVERT: E 84 GLU cc_start: 0.8682 (pm20) cc_final: 0.8235 (pm20) REVERT: F 12 ASP cc_start: 0.8393 (t70) cc_final: 0.7994 (t0) REVERT: F 16 GLN cc_start: 0.9002 (mp10) cc_final: 0.8739 (pm20) REVERT: F 17 ARG cc_start: 0.8796 (ttm110) cc_final: 0.8314 (ttm-80) REVERT: F 84 GLU cc_start: 0.8482 (tt0) cc_final: 0.7894 (mm-30) REVERT: F 96 LEU cc_start: 0.9538 (tp) cc_final: 0.9331 (tt) REVERT: G 289 ASP cc_start: 0.8160 (t0) cc_final: 0.7802 (t0) REVERT: G 318 ASP cc_start: 0.9271 (OUTLIER) cc_final: 0.8986 (m-30) REVERT: H 233 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8207 (mm-30) REVERT: H 244 ASP cc_start: 0.8790 (t70) cc_final: 0.8395 (t70) REVERT: I 218 GLN cc_start: 0.8506 (tp40) cc_final: 0.8203 (tp40) REVERT: I 233 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8165 (mm-30) REVERT: I 244 ASP cc_start: 0.8581 (t70) cc_final: 0.8130 (t70) REVERT: I 281 LYS cc_start: 0.9275 (ttmm) cc_final: 0.8884 (ttmm) REVERT: I 289 ASP cc_start: 0.8078 (t0) cc_final: 0.7762 (t0) outliers start: 30 outliers final: 28 residues processed: 172 average time/residue: 0.0935 time to fit residues: 24.2289 Evaluate side-chains 173 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 389 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain D residue 13 THR 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 18 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 107 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 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: 0.0470 chunk 73 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 chunk 163 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 overall best weight: 1.3880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.074812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.048827 restraints weight = 44016.350| |-----------------------------------------------------------------------------| r_work (start): 0.2666 rms_B_bonded: 4.63 r_work: 0.2516 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3687 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= 0.111 Angle : 0.516 8.636 20340 Z= 0.260 Chirality : 0.041 0.156 2253 Planarity : 0.004 0.064 2568 Dihedral : 3.800 14.920 2016 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.79 % Allowed : 10.51 % 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: 0.38 (0.20), residues: 1830 helix: 0.19 (0.37), residues: 228 sheet: 0.98 (0.20), residues: 612 loop : -0.14 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 80 TYR 0.020 0.001 TYR C 168 PHE 0.018 0.001 PHE A 263 TRP 0.009 0.001 TRP I 251 HIS 0.001 0.000 HIS A 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (14916) covalent geometry : angle 0.51084 / 0.26 (20259) SS BOND : bond 0.00207 / 0.14 ( 27) SS BOND : angle 0.69716 / 0.51 ( 54) hydrogen bonds : bond 0.03180 / 2.15 ( 537) hydrogen bonds : angle 5.15745 / 3.56 ( 1467) link_NAG-ASN : bond 0.00296 / 0.13 ( 9) link_NAG-ASN : angle 1.93083 / 1.40 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3048.52 seconds wall clock time: 53 minutes 12.46 seconds (3192.46 seconds total)