Starting phenix.real_space_refine on Sun Aug 24 00:22:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v46_42966/08_2025/8v46_42966.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v46_42966/08_2025/8v46_42966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v46_42966/08_2025/8v46_42966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v46_42966/08_2025/8v46_42966.map" model { file = "/net/cci-nas-00/data/ceres_data/8v46_42966/08_2025/8v46_42966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v46_42966/08_2025/8v46_42966.cif" } resolution = 3.09 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= 0.015 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 1 5.21 5 S 57 5.16 5 C 9956 2.51 5 N 2627 2.21 5 O 2985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15632 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3320 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 10, 'TRANS': 401} Chain breaks: 4 Chain: "B" Number of atoms: 3225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3225 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 10, 'TRANS': 389} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2422 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 6, 'TRANS': 298} Chain: "C" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3301 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 10, 'TRANS': 399} Chain breaks: 4 Chain: "F" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3301 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 10, 'TRANS': 399} Chain breaks: 4 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.48, per 1000 atoms: 0.29 Number of scatterers: 15632 At special positions: 0 Unit cell: (95.37, 163.625, 154.275, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 57 16.00 P 6 15.00 Mg 1 11.99 O 2985 8.00 N 2627 7.00 C 9956 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 702.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3702 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 15 sheets defined 55.0% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 38 through 51 Processing helix chain 'A' and resid 53 through 60 removed outlier: 3.679A pdb=" N ALA A 58 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 60 " --> pdb=" O PHE A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 114 Processing helix chain 'A' and resid 125 through 138 removed outlier: 3.522A pdb=" N ASN A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 161 removed outlier: 3.574A pdb=" N ALA A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 189 Processing helix chain 'A' and resid 199 through 238 removed outlier: 4.313A pdb=" N PHE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 264 removed outlier: 3.707A pdb=" N LYS A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 269 removed outlier: 3.565A pdb=" N ASN A 268 " --> pdb=" O SER A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 287 removed outlier: 3.550A pdb=" N VAL A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 319 removed outlier: 3.874A pdb=" N ALA A 300 " --> pdb=" O SER A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 331 Processing helix chain 'A' and resid 367 through 379 Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.694A pdb=" N GLU A 404 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU A 407 " --> pdb=" O GLN A 403 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LYS A 408 " --> pdb=" O GLU A 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 52 Processing helix chain 'B' and resid 53 through 60 removed outlier: 3.579A pdb=" N ALA B 58 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 60 " --> pdb=" O PHE B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 Processing helix chain 'B' and resid 127 through 139 Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 199 through 237 removed outlier: 4.013A pdb=" N SER B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 264 Processing helix chain 'B' and resid 273 through 288 removed outlier: 4.055A pdb=" N VAL B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 319 removed outlier: 3.759A pdb=" N SER B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 319 " --> pdb=" O GLN B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 331 Processing helix chain 'B' and resid 362 through 366 removed outlier: 3.527A pdb=" N VAL B 365 " --> pdb=" O PRO B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 380 removed outlier: 3.656A pdb=" N ALA B 380 " --> pdb=" O MET B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 412 removed outlier: 4.070A pdb=" N ASP B 405 " --> pdb=" O ASP B 401 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU B 407 " --> pdb=" O GLN B 403 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LYS B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'D' and resid 7 through 18 Processing helix chain 'D' and resid 27 through 42 removed outlier: 3.759A pdb=" N PHE D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 55 No H-bonds generated for 'chain 'D' and resid 53 through 55' Processing helix chain 'D' and resid 59 through 64 removed outlier: 4.399A pdb=" N LYS D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 77 Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 127 through 138 Processing helix chain 'D' and resid 143 through 172 removed outlier: 3.590A pdb=" N GLU D 153 " --> pdb=" O GLU D 149 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER D 156 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N SER D 157 " --> pdb=" O GLU D 153 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE D 159 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ALA D 160 " --> pdb=" O SER D 156 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL D 161 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE D 172 " --> pdb=" O ALA D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 182 removed outlier: 3.988A pdb=" N ALA D 180 " --> pdb=" O GLY D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 187 Processing helix chain 'D' and resid 205 through 225 Proline residue: D 221 - end of helix Processing helix chain 'D' and resid 227 through 232 Processing helix chain 'D' and resid 236 through 257 removed outlier: 3.571A pdb=" N ILE D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU D 242 " --> pdb=" O HIS D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 275 through 291 Processing helix chain 'D' and resid 300 through 307 Processing helix chain 'C' and resid 38 through 51 Processing helix chain 'C' and resid 53 through 60 removed outlier: 3.585A pdb=" N ARG C 56 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA C 58 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU C 60 " --> pdb=" O PHE C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 114 Processing helix chain 'C' and resid 125 through 138 Processing helix chain 'C' and resid 151 through 161 Processing helix chain 'C' and resid 177 through 189 Processing helix chain 'C' and resid 199 through 234 removed outlier: 3.768A pdb=" N PHE C 234 " --> pdb=" O PHE C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 264 Processing helix chain 'C' and resid 265 through 269 removed outlier: 3.639A pdb=" N ASN C 268 " --> pdb=" O SER C 265 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY C 269 " --> pdb=" O ILE C 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 265 through 269' Processing helix chain 'C' and resid 273 through 287 removed outlier: 3.803A pdb=" N VAL C 277 " --> pdb=" O GLU C 273 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG C 287 " --> pdb=" O SER C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 319 removed outlier: 3.518A pdb=" N ALA C 300 " --> pdb=" O SER C 296 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU C 316 " --> pdb=" O GLN C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 331 Processing helix chain 'C' and resid 362 through 366 removed outlier: 3.661A pdb=" N VAL C 365 " --> pdb=" O PRO C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 380 Processing helix chain 'C' and resid 399 through 413 removed outlier: 3.845A pdb=" N GLU C 404 " --> pdb=" O ILE C 400 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP C 405 " --> pdb=" O ASP C 401 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU C 407 " --> pdb=" O GLN C 403 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LYS C 408 " --> pdb=" O GLU C 404 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing helix chain 'F' and resid 13 through 16 Processing helix chain 'F' and resid 38 through 51 Processing helix chain 'F' and resid 53 through 60 removed outlier: 3.578A pdb=" N ALA F 58 " --> pdb=" O ILE F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 114 Processing helix chain 'F' and resid 125 through 138 Processing helix chain 'F' and resid 151 through 161 Processing helix chain 'F' and resid 177 through 188 Processing helix chain 'F' and resid 199 through 234 removed outlier: 4.492A pdb=" N PHE F 230 " --> pdb=" O PHE F 226 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL F 231 " --> pdb=" O SER F 227 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 264 removed outlier: 3.945A pdb=" N LYS F 253 " --> pdb=" O GLY F 249 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU F 254 " --> pdb=" O GLU F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 288 removed outlier: 3.881A pdb=" N VAL F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN F 288 " --> pdb=" O LEU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 319 Processing helix chain 'F' and resid 319 through 331 removed outlier: 3.509A pdb=" N SER F 331 " --> pdb=" O SER F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 366 removed outlier: 3.651A pdb=" N VAL F 365 " --> pdb=" O PRO F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 380 Processing helix chain 'F' and resid 399 through 413 removed outlier: 3.675A pdb=" N GLU F 404 " --> pdb=" O ILE F 400 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP F 405 " --> pdb=" O ASP F 401 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU F 407 " --> pdb=" O GLN F 403 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS F 408 " --> pdb=" O GLU F 404 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN F 413 " --> pdb=" O ARG F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 434 No H-bonds generated for 'chain 'F' and resid 432 through 434' Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 101 removed outlier: 6.744A pdb=" N GLU A 64 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU A 11 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS A 66 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE A 9 " --> pdb=" O LYS A 66 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR A 68 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N TYR A 18 " --> pdb=" O LYS A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 148 removed outlier: 7.472A pdb=" N ALA A 387 " --> pdb=" O GLN A 418 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N ILE A 420 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL A 389 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N CYS A 422 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ILE A 391 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE A 437 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL A 30 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ILE A 439 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N HIS A 32 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 337 through 341 Processing sheet with id=AA4, first strand: chain 'B' and resid 97 through 101 removed outlier: 6.881A pdb=" N GLU B 64 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU B 11 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LYS B 66 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE B 9 " --> pdb=" O LYS B 66 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR B 68 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N TYR B 18 " --> pdb=" O LYS B 13 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 144 through 148 removed outlier: 7.150A pdb=" N ALA B 387 " --> pdb=" O GLN B 418 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N ILE B 420 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL B 389 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N CYS B 422 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE B 391 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE B 437 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL B 30 " --> pdb=" O ILE B 437 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 337 through 341 Processing sheet with id=AA7, first strand: chain 'D' and resid 48 through 51 removed outlier: 6.198A pdb=" N LEU D 23 " --> pdb=" O ASP D 50 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG D 22 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LEU D 86 " --> pdb=" O ARG D 22 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU D 24 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 94 through 96 Processing sheet with id=AA9, first strand: chain 'C' and resid 97 through 101 removed outlier: 3.669A pdb=" N GLU C 64 " --> pdb=" O SER C 12 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS C 8 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N TYR C 18 " --> pdb=" O LYS C 13 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 144 through 148 removed outlier: 7.054A pdb=" N ALA C 387 " --> pdb=" O GLN C 418 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ILE C 420 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL C 389 " --> pdb=" O ILE C 420 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N CYS C 422 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE C 391 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ILE C 437 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL C 30 " --> pdb=" O ILE C 437 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 337 through 341 Processing sheet with id=AB3, first strand: chain 'F' and resid 21 through 23 removed outlier: 3.719A pdb=" N GLU F 64 " --> pdb=" O SER F 12 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 18 through 19 Processing sheet with id=AB5, first strand: chain 'F' and resid 146 through 148 removed outlier: 7.567A pdb=" N ILE F 437 " --> pdb=" O LEU F 28 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL F 30 " --> pdb=" O ILE F 437 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 337 through 341 875 hydrogen bonds defined for protein. 2505 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: 2.91 Time building geometry restraints manager: 1.69 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: 5018 1.34 - 1.46: 2968 1.46 - 1.58: 7819 1.58 - 1.69: 6 1.69 - 1.81: 103 Bond restraints: 15914 Sorted by residual: bond pdb=" C LEU D 220 " pdb=" N PRO D 221 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.28e-02 6.10e+03 3.01e+00 bond pdb=" C LYS B 354 " pdb=" N PHE B 355 " ideal model delta sigma weight residual 1.327 1.297 0.030 1.71e-02 3.42e+03 3.00e+00 bond pdb=" C LEU D 177 " pdb=" N PRO D 178 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.19e-02 7.06e+03 2.54e+00 bond pdb=" CA LEU D 220 " pdb=" C LEU D 220 " ideal model delta sigma weight residual 1.520 1.535 -0.015 1.23e-02 6.61e+03 1.39e+00 bond pdb=" CA LEU D 177 " pdb=" C LEU D 177 " ideal model delta sigma weight residual 1.520 1.534 -0.014 1.23e-02 6.61e+03 1.31e+00 ... (remaining 15909 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 21187 2.07 - 4.14: 221 4.14 - 6.21: 16 6.21 - 8.28: 8 8.28 - 10.36: 3 Bond angle restraints: 21435 Sorted by residual: angle pdb=" C ASP C 83 " pdb=" N GLU C 84 " pdb=" CA GLU C 84 " ideal model delta sigma weight residual 121.54 130.80 -9.26 1.91e+00 2.74e-01 2.35e+01 angle pdb=" C4' ATP A 501 " pdb=" C5' ATP A 501 " pdb=" O5' ATP A 501 " ideal model delta sigma weight residual 108.83 119.19 -10.36 2.33e+00 1.85e-01 1.98e+01 angle pdb=" N VAL A 365 " pdb=" CA VAL A 365 " pdb=" C VAL A 365 " ideal model delta sigma weight residual 112.29 108.30 3.99 9.40e-01 1.13e+00 1.80e+01 angle pdb=" C ASP F 83 " pdb=" N GLU F 84 " pdb=" CA GLU F 84 " ideal model delta sigma weight residual 125.02 130.62 -5.60 1.76e+00 3.23e-01 1.01e+01 angle pdb=" C HIS C 15 " pdb=" N ASN C 16 " pdb=" CA ASN C 16 " ideal model delta sigma weight residual 122.08 126.45 -4.37 1.47e+00 4.63e-01 8.84e+00 ... (remaining 21430 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 9106 17.38 - 34.75: 446 34.75 - 52.13: 92 52.13 - 69.50: 28 69.50 - 86.88: 8 Dihedral angle restraints: 9680 sinusoidal: 3977 harmonic: 5703 Sorted by residual: dihedral pdb=" CA LEU A 192 " pdb=" CB LEU A 192 " pdb=" CG LEU A 192 " pdb=" CD1 LEU A 192 " ideal model delta sinusoidal sigma weight residual 60.00 119.27 -59.27 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB ARG B 56 " pdb=" CG ARG B 56 " pdb=" CD ARG B 56 " pdb=" NE ARG B 56 " ideal model delta sinusoidal sigma weight residual 60.00 118.75 -58.75 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N LEU A 308 " pdb=" CA LEU A 308 " pdb=" CB LEU A 308 " pdb=" CG LEU A 308 " ideal model delta sinusoidal sigma weight residual -60.00 -117.90 57.90 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 9677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1512 0.036 - 0.072: 600 0.072 - 0.107: 170 0.107 - 0.143: 77 0.143 - 0.179: 11 Chirality restraints: 2370 Sorted by residual: chirality pdb=" CA ILE D 204 " pdb=" N ILE D 204 " pdb=" C ILE D 204 " pdb=" CB ILE D 204 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.02e-01 chirality pdb=" CB ILE D 204 " pdb=" CA ILE D 204 " pdb=" CG1 ILE D 204 " pdb=" CG2 ILE D 204 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" CA LEU D 220 " pdb=" N LEU D 220 " pdb=" C LEU D 220 " pdb=" CB LEU D 220 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 2367 not shown) Planarity restraints: 2727 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 123 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.46e+00 pdb=" C ASN D 123 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN D 123 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR D 124 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 132 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.44e+00 pdb=" C ILE D 132 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE D 132 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP D 133 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 196 " 0.011 2.00e-02 2.50e+03 2.33e-02 5.44e+00 pdb=" C LEU D 196 " -0.040 2.00e-02 2.50e+03 pdb=" O LEU D 196 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE D 197 " 0.014 2.00e-02 2.50e+03 ... (remaining 2724 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 151 2.64 - 3.21: 13372 3.21 - 3.77: 23687 3.77 - 4.34: 33433 4.34 - 4.90: 55027 Nonbonded interactions: 125670 Sorted by model distance: nonbonded pdb="MG MG B 501 " pdb=" O2B ATP B 502 " model vdw 2.079 2.170 nonbonded pdb="MG MG B 501 " pdb=" O1G ATP B 502 " model vdw 2.187 2.170 nonbonded pdb=" O ALA F 380 " pdb=" OG SER F 415 " model vdw 2.329 3.040 nonbonded pdb=" O ASN B 177 " pdb=" OG SER B 181 " model vdw 2.337 3.040 nonbonded pdb=" O ALA A 380 " pdb=" OG SER A 415 " model vdw 2.337 3.040 ... (remaining 125665 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 112 or resid 126 through 162 or resid 175 throug \ h 236 or resid 249 through 310 or (resid 311 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name NE or name NH1 or name NH2)) or \ resid 312 through 342 or resid 348 through 444)) selection = (chain 'B' and (resid 3 through 236 or resid 249 through 288 or resid 295 throug \ h 444)) selection = (chain 'C' and (resid 3 through 112 or resid 126 through 162 or resid 175 throug \ h 236 or resid 249 through 310 or (resid 311 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name NE or name NH1 or name NH2)) or \ resid 312 through 342 or resid 348 through 444)) selection = (chain 'F' and (resid 3 through 112 or resid 126 through 162 or resid 175 throug \ h 236 or resid 249 through 310 or (resid 311 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name NE or name NH1 or name NH2)) or \ resid 312 through 342 or resid 348 through 444)) } 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: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 16.480 Find NCS groups from input model: 0.350 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15914 Z= 0.177 Angle : 0.589 10.355 21435 Z= 0.339 Chirality : 0.045 0.179 2370 Planarity : 0.004 0.051 2727 Dihedral : 11.450 86.880 5978 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.58 % Allowed : 4.04 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.18), residues: 1893 helix: 0.06 (0.15), residues: 989 sheet: 0.35 (0.30), residues: 323 loop : -0.76 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 222 TYR 0.021 0.002 TYR A 197 PHE 0.018 0.002 PHE D 216 TRP 0.008 0.001 TRP D 287 HIS 0.004 0.001 HIS B 424 Details of bonding type rmsd covalent geometry : bond 0.00378 (15914) covalent geometry : angle 0.58909 (21435) hydrogen bonds : bond 0.12268 ( 875) hydrogen bonds : angle 5.94399 ( 2505) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8357 (mtmm) REVERT: A 129 MET cc_start: 0.9140 (mtp) cc_final: 0.8917 (mmt) REVERT: A 276 LYS cc_start: 0.9267 (tttt) cc_final: 0.9027 (tttm) REVERT: A 364 ARG cc_start: 0.9004 (ptt-90) cc_final: 0.8792 (ptp90) REVERT: A 442 GLU cc_start: 0.8406 (tt0) cc_final: 0.8169 (tt0) REVERT: B 195 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8668 (mp) REVERT: B 201 MET cc_start: 0.8354 (mmt) cc_final: 0.7735 (mtm) REVERT: B 209 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8011 (mm-30) REVERT: D 17 MET cc_start: 0.9323 (mtp) cc_final: 0.9109 (mtm) REVERT: D 99 GLN cc_start: 0.8275 (tt0) cc_final: 0.8026 (tp40) REVERT: D 212 PHE cc_start: 0.9706 (t80) cc_final: 0.9367 (t80) REVERT: C 106 MET cc_start: 0.8476 (mtt) cc_final: 0.7914 (tmm) REVERT: C 126 MET cc_start: 0.9249 (mtm) cc_final: 0.8782 (tmm) REVERT: C 342 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.8094 (p90) REVERT: F 436 MET cc_start: 0.7153 (mtp) cc_final: 0.6444 (mmm) outliers start: 44 outliers final: 11 residues processed: 234 average time/residue: 0.1710 time to fit residues: 56.3183 Evaluate side-chains 123 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain F residue 231 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 98 optimal weight: 0.0670 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 30.0000 overall best weight: 2.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN D 99 GLN C 32 HIS C 324 ASN F 32 HIS F 262 GLN F 312 GLN F 315 GLN F 424 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.136192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.074703 restraints weight = 37897.143| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.66 r_work: 0.3108 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15914 Z= 0.232 Angle : 0.545 13.724 21435 Z= 0.286 Chirality : 0.043 0.188 2370 Planarity : 0.004 0.030 2727 Dihedral : 7.724 81.437 2213 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.93 % Allowed : 8.49 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.19), residues: 1893 helix: 1.53 (0.16), residues: 987 sheet: 0.31 (0.30), residues: 328 loop : -0.50 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 17 TYR 0.016 0.001 TYR A 197 PHE 0.016 0.001 PHE C 100 TRP 0.014 0.001 TRP C 158 HIS 0.005 0.001 HIS B 424 Details of bonding type rmsd covalent geometry : bond 0.00547 (15914) covalent geometry : angle 0.54549 (21435) hydrogen bonds : bond 0.03584 ( 875) hydrogen bonds : angle 4.29454 ( 2505) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 MET cc_start: 0.9193 (mtp) cc_final: 0.8967 (mmt) REVERT: A 206 ARG cc_start: 0.8515 (mmm-85) cc_final: 0.8156 (tpt90) REVERT: B 201 MET cc_start: 0.8742 (mmt) cc_final: 0.8474 (mtm) REVERT: B 209 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8354 (mm-30) REVERT: B 230 PHE cc_start: 0.8638 (t80) cc_final: 0.8078 (t80) REVERT: D 35 TYR cc_start: 0.9107 (OUTLIER) cc_final: 0.8464 (m-10) REVERT: D 136 GLN cc_start: 0.9054 (tm-30) cc_final: 0.8721 (pp30) REVERT: D 212 PHE cc_start: 0.9700 (t80) cc_final: 0.9372 (t80) REVERT: C 106 MET cc_start: 0.8431 (mtt) cc_final: 0.7944 (tmm) REVERT: C 126 MET cc_start: 0.9275 (mtm) cc_final: 0.8873 (tmm) REVERT: C 342 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7743 (p90) REVERT: F 436 MET cc_start: 0.7094 (mtp) cc_final: 0.6410 (mmm) outliers start: 33 outliers final: 17 residues processed: 143 average time/residue: 0.1606 time to fit residues: 32.8138 Evaluate side-chains 117 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain D residue 35 TYR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain F residue 231 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 85 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 116 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 187 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.135170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.072937 restraints weight = 37653.566| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.83 r_work: 0.2999 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15914 Z= 0.123 Angle : 0.465 12.739 21435 Z= 0.242 Chirality : 0.041 0.163 2370 Planarity : 0.003 0.027 2727 Dihedral : 7.009 85.025 2199 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.87 % Allowed : 8.61 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.20), residues: 1893 helix: 2.04 (0.16), residues: 989 sheet: 0.46 (0.31), residues: 323 loop : -0.35 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 309 TYR 0.014 0.001 TYR A 197 PHE 0.023 0.001 PHE A 230 TRP 0.012 0.001 TRP C 158 HIS 0.003 0.001 HIS B 424 Details of bonding type rmsd covalent geometry : bond 0.00280 (15914) covalent geometry : angle 0.46500 (21435) hydrogen bonds : bond 0.03070 ( 875) hydrogen bonds : angle 3.96685 ( 2505) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7879 (mtm-85) REVERT: A 129 MET cc_start: 0.9280 (mtp) cc_final: 0.8994 (mmt) REVERT: A 206 ARG cc_start: 0.8474 (mmm-85) cc_final: 0.8099 (tpt90) REVERT: B 106 MET cc_start: 0.8467 (mtt) cc_final: 0.8253 (mtt) REVERT: B 201 MET cc_start: 0.8572 (mmt) cc_final: 0.8277 (mtm) REVERT: B 209 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8332 (mm-30) REVERT: B 230 PHE cc_start: 0.8696 (t80) cc_final: 0.8207 (t80) REVERT: D 35 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.8513 (m-10) REVERT: D 136 GLN cc_start: 0.9019 (tm-30) cc_final: 0.8683 (pp30) REVERT: D 212 PHE cc_start: 0.9717 (t80) cc_final: 0.9390 (t80) REVERT: C 106 MET cc_start: 0.8405 (mtt) cc_final: 0.7958 (tmm) REVERT: C 126 MET cc_start: 0.9348 (mtm) cc_final: 0.8922 (pmm) REVERT: C 129 MET cc_start: 0.8908 (mmm) cc_final: 0.8706 (mmm) REVERT: C 158 TRP cc_start: 0.8227 (t60) cc_final: 0.7927 (t60) REVERT: C 342 PHE cc_start: 0.8010 (OUTLIER) cc_final: 0.7685 (p90) REVERT: C 406 LEU cc_start: 0.9349 (tt) cc_final: 0.8867 (tt) REVERT: F 209 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7956 (tm-30) REVERT: F 406 LEU cc_start: 0.9030 (mt) cc_final: 0.8800 (mt) REVERT: F 436 MET cc_start: 0.7152 (mtp) cc_final: 0.6496 (mmm) outliers start: 32 outliers final: 19 residues processed: 132 average time/residue: 0.1629 time to fit residues: 30.6534 Evaluate side-chains 121 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain D residue 35 TYR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain F residue 231 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 158 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 45 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 123 optimal weight: 20.0000 chunk 160 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.132800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.070251 restraints weight = 37541.274| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.74 r_work: 0.2951 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 15914 Z= 0.311 Angle : 0.578 9.983 21435 Z= 0.304 Chirality : 0.044 0.200 2370 Planarity : 0.004 0.040 2727 Dihedral : 7.854 84.574 2197 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.64 % Allowed : 8.49 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.20), residues: 1893 helix: 1.93 (0.16), residues: 993 sheet: 0.12 (0.30), residues: 327 loop : -0.37 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 364 TYR 0.019 0.002 TYR A 197 PHE 0.031 0.002 PHE A 230 TRP 0.011 0.001 TRP D 287 HIS 0.006 0.001 HIS B 424 Details of bonding type rmsd covalent geometry : bond 0.00734 (15914) covalent geometry : angle 0.57795 (21435) hydrogen bonds : bond 0.03752 ( 875) hydrogen bonds : angle 4.22857 ( 2505) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 100 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8068 (mtt180) REVERT: A 129 MET cc_start: 0.9271 (mtp) cc_final: 0.9009 (mmt) REVERT: A 206 ARG cc_start: 0.8566 (mmm-85) cc_final: 0.8121 (tpt90) REVERT: B 201 MET cc_start: 0.8789 (mmt) cc_final: 0.8486 (mtm) REVERT: B 209 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8351 (mm-30) REVERT: B 230 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8502 (t80) REVERT: D 35 TYR cc_start: 0.9143 (OUTLIER) cc_final: 0.8462 (m-10) REVERT: D 212 PHE cc_start: 0.9716 (t80) cc_final: 0.9444 (t80) REVERT: C 106 MET cc_start: 0.8348 (mtt) cc_final: 0.7860 (tmm) REVERT: C 126 MET cc_start: 0.9298 (mtm) cc_final: 0.8875 (pmm) REVERT: C 158 TRP cc_start: 0.8215 (t60) cc_final: 0.7913 (t60) REVERT: C 342 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7625 (p90) REVERT: C 436 MET cc_start: 0.8814 (mtt) cc_final: 0.8592 (mtt) REVERT: F 436 MET cc_start: 0.7145 (mtp) cc_final: 0.6508 (mmm) outliers start: 45 outliers final: 26 residues processed: 136 average time/residue: 0.1538 time to fit residues: 30.4085 Evaluate side-chains 125 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 35 TYR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain F residue 231 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 110 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 139 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 167 optimal weight: 20.0000 chunk 76 optimal weight: 0.6980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.135147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.073190 restraints weight = 37974.234| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.67 r_work: 0.3033 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15914 Z= 0.196 Angle : 0.506 11.679 21435 Z= 0.262 Chirality : 0.042 0.179 2370 Planarity : 0.003 0.045 2727 Dihedral : 7.397 83.353 2197 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.11 % Allowed : 9.37 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.20), residues: 1893 helix: 2.16 (0.17), residues: 989 sheet: 0.08 (0.29), residues: 333 loop : -0.28 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 364 TYR 0.017 0.001 TYR A 197 PHE 0.030 0.001 PHE A 230 TRP 0.008 0.001 TRP C 158 HIS 0.005 0.001 HIS B 424 Details of bonding type rmsd covalent geometry : bond 0.00465 (15914) covalent geometry : angle 0.50561 (21435) hydrogen bonds : bond 0.03285 ( 875) hydrogen bonds : angle 4.02685 ( 2505) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8040 (mtt180) REVERT: A 129 MET cc_start: 0.9193 (mtp) cc_final: 0.8952 (mmt) REVERT: A 206 ARG cc_start: 0.8551 (mmm-85) cc_final: 0.8130 (tpt90) REVERT: A 364 ARG cc_start: 0.9200 (ptt-90) cc_final: 0.8894 (ptm-80) REVERT: B 201 MET cc_start: 0.8748 (mmt) cc_final: 0.8441 (mtm) REVERT: B 230 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8551 (t80) REVERT: D 35 TYR cc_start: 0.9050 (OUTLIER) cc_final: 0.8453 (m-10) REVERT: D 212 PHE cc_start: 0.9713 (t80) cc_final: 0.9442 (t80) REVERT: C 106 MET cc_start: 0.8318 (mtt) cc_final: 0.7841 (tmm) REVERT: C 126 MET cc_start: 0.9255 (mtm) cc_final: 0.8838 (pmm) REVERT: C 188 PHE cc_start: 0.9122 (OUTLIER) cc_final: 0.8862 (t80) REVERT: C 342 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7673 (p90) REVERT: C 436 MET cc_start: 0.8831 (mtt) cc_final: 0.8545 (mtt) REVERT: F 376 MET cc_start: 0.9544 (mtt) cc_final: 0.9271 (mmm) REVERT: F 436 MET cc_start: 0.7068 (mtp) cc_final: 0.6387 (mmm) outliers start: 36 outliers final: 25 residues processed: 124 average time/residue: 0.1520 time to fit residues: 27.4912 Evaluate side-chains 122 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 35 TYR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain F residue 231 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 112 optimal weight: 20.0000 chunk 185 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 46 optimal weight: 0.5980 chunk 165 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 179 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.133687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.073706 restraints weight = 37120.601| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.49 r_work: 0.2910 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15914 Z= 0.175 Angle : 0.499 13.281 21435 Z= 0.256 Chirality : 0.041 0.175 2370 Planarity : 0.003 0.030 2727 Dihedral : 7.153 83.352 2197 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.17 % Allowed : 9.90 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.20), residues: 1893 helix: 2.27 (0.17), residues: 990 sheet: 0.05 (0.30), residues: 333 loop : -0.19 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 364 TYR 0.016 0.001 TYR A 197 PHE 0.012 0.001 PHE A 230 TRP 0.012 0.001 TRP C 158 HIS 0.004 0.001 HIS B 424 Details of bonding type rmsd covalent geometry : bond 0.00413 (15914) covalent geometry : angle 0.49938 (21435) hydrogen bonds : bond 0.03185 ( 875) hydrogen bonds : angle 3.93361 ( 2505) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 97 time to evaluate : 0.687 Fit side-chains TARDY: cannot create tardy model for: "ARG B 311 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.8012 (mtm-85) REVERT: A 129 MET cc_start: 0.9223 (mtp) cc_final: 0.8956 (mmt) REVERT: A 206 ARG cc_start: 0.8388 (mmm-85) cc_final: 0.7955 (tpt90) REVERT: B 201 MET cc_start: 0.8505 (mmt) cc_final: 0.8220 (mtm) REVERT: B 230 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8585 (t80) REVERT: D 35 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.8388 (m-10) REVERT: C 106 MET cc_start: 0.8286 (mtt) cc_final: 0.7874 (tmm) REVERT: C 126 MET cc_start: 0.9272 (mtm) cc_final: 0.8857 (pmm) REVERT: C 188 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8948 (t80) REVERT: C 342 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7641 (p90) REVERT: F 376 MET cc_start: 0.9532 (mtt) cc_final: 0.9226 (mmm) REVERT: F 436 MET cc_start: 0.7076 (mtp) cc_final: 0.6411 (mmm) outliers start: 37 outliers final: 28 residues processed: 126 average time/residue: 0.1614 time to fit residues: 29.3831 Evaluate side-chains 126 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 35 TYR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain F residue 231 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 77 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 40 optimal weight: 0.4980 chunk 176 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 168 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 159 optimal weight: 20.0000 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.133572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.073663 restraints weight = 37276.439| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 3.53 r_work: 0.2932 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15914 Z= 0.173 Angle : 0.503 13.400 21435 Z= 0.256 Chirality : 0.042 0.315 2370 Planarity : 0.003 0.051 2727 Dihedral : 7.023 81.999 2197 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.23 % Allowed : 10.08 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.20), residues: 1893 helix: 2.31 (0.17), residues: 990 sheet: 0.03 (0.30), residues: 333 loop : -0.14 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 364 TYR 0.016 0.001 TYR A 197 PHE 0.039 0.001 PHE A 230 TRP 0.011 0.001 TRP C 158 HIS 0.004 0.001 HIS B 424 Details of bonding type rmsd covalent geometry : bond 0.00409 (15914) covalent geometry : angle 0.50310 (21435) hydrogen bonds : bond 0.03162 ( 875) hydrogen bonds : angle 3.90911 ( 2505) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 0.648 Fit side-chains TARDY: cannot create tardy model for: "ARG B 311 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8003 (mtm-85) REVERT: A 129 MET cc_start: 0.9212 (mtp) cc_final: 0.8948 (mmt) REVERT: A 206 ARG cc_start: 0.8375 (mmm-85) cc_final: 0.7945 (tpt90) REVERT: A 224 ARG cc_start: 0.7561 (ttm-80) cc_final: 0.7085 (tpp80) REVERT: B 201 MET cc_start: 0.8500 (mmt) cc_final: 0.8217 (mtm) REVERT: B 230 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8582 (t80) REVERT: D 35 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.8377 (m-10) REVERT: C 106 MET cc_start: 0.8285 (mtt) cc_final: 0.7930 (tmm) REVERT: C 126 MET cc_start: 0.9288 (mtm) cc_final: 0.8877 (pmm) REVERT: C 342 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7632 (p90) REVERT: F 326 MET cc_start: 0.9142 (mmm) cc_final: 0.8939 (mmm) REVERT: F 338 MET cc_start: 0.8856 (ptp) cc_final: 0.7919 (ptp) REVERT: F 376 MET cc_start: 0.9524 (mtt) cc_final: 0.9250 (mmm) REVERT: F 436 MET cc_start: 0.7109 (mtp) cc_final: 0.6521 (mmm) outliers start: 38 outliers final: 29 residues processed: 125 average time/residue: 0.1410 time to fit residues: 26.2731 Evaluate side-chains 128 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 35 TYR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain F residue 231 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 174 optimal weight: 8.9990 chunk 86 optimal weight: 0.0040 chunk 45 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 78 optimal weight: 0.0770 chunk 143 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 chunk 70 optimal weight: 0.6980 chunk 148 optimal weight: 0.5980 overall best weight: 0.4750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.141115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.080046 restraints weight = 37703.812| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.80 r_work: 0.3117 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15914 Z= 0.090 Angle : 0.465 12.948 21435 Z= 0.234 Chirality : 0.040 0.281 2370 Planarity : 0.003 0.052 2727 Dihedral : 6.464 89.707 2197 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.64 % Allowed : 10.60 % 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 aren not related in a simple way. whole: 1.96 (0.20), residues: 1893 helix: 2.50 (0.17), residues: 988 sheet: 0.15 (0.30), residues: 333 loop : -0.07 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 364 TYR 0.013 0.001 TYR A 197 PHE 0.032 0.001 PHE A 230 TRP 0.012 0.001 TRP C 158 HIS 0.002 0.000 HIS B 424 Details of bonding type rmsd covalent geometry : bond 0.00195 (15914) covalent geometry : angle 0.46543 (21435) hydrogen bonds : bond 0.02777 ( 875) hydrogen bonds : angle 3.67422 ( 2505) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.764 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 311 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 129 MET cc_start: 0.9192 (mtp) cc_final: 0.8963 (mmt) REVERT: A 206 ARG cc_start: 0.8545 (mmm-85) cc_final: 0.8147 (tpt90) REVERT: A 224 ARG cc_start: 0.7787 (ttm-80) cc_final: 0.7290 (ttm-80) REVERT: A 374 LEU cc_start: 0.9201 (tp) cc_final: 0.8966 (tp) REVERT: B 201 MET cc_start: 0.8593 (mmt) cc_final: 0.8298 (mtm) REVERT: B 234 PHE cc_start: 0.7420 (OUTLIER) cc_final: 0.7003 (t80) REVERT: D 291 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8006 (mm) REVERT: C 106 MET cc_start: 0.8394 (mtt) cc_final: 0.7940 (tmm) REVERT: C 126 MET cc_start: 0.9238 (mtm) cc_final: 0.8792 (pmm) REVERT: C 158 TRP cc_start: 0.8126 (t60) cc_final: 0.7687 (t-100) REVERT: C 342 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7686 (p90) REVERT: F 376 MET cc_start: 0.9521 (mtt) cc_final: 0.9203 (mmm) REVERT: F 436 MET cc_start: 0.7100 (mtp) cc_final: 0.6472 (mmm) outliers start: 28 outliers final: 14 residues processed: 123 average time/residue: 0.1469 time to fit residues: 26.7067 Evaluate side-chains 113 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 342 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 48 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 151 optimal weight: 30.0000 chunk 176 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.131220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.068644 restraints weight = 37592.027| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.69 r_work: 0.2891 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.107 15914 Z= 0.463 Angle : 0.708 13.455 21435 Z= 0.365 Chirality : 0.050 0.467 2370 Planarity : 0.004 0.071 2727 Dihedral : 8.160 80.127 2194 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.76 % Allowed : 10.90 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.20), residues: 1893 helix: 1.87 (0.16), residues: 996 sheet: -0.14 (0.29), residues: 337 loop : -0.34 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 364 TYR 0.020 0.002 TYR C 304 PHE 0.029 0.002 PHE A 230 TRP 0.011 0.002 TRP D 287 HIS 0.008 0.002 HIS B 424 Details of bonding type rmsd covalent geometry : bond 0.01097 (15914) covalent geometry : angle 0.70808 (21435) hydrogen bonds : bond 0.04139 ( 875) hydrogen bonds : angle 4.40092 ( 2505) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.682 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 311 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 MET cc_start: 0.9271 (mtp) cc_final: 0.8999 (mmt) REVERT: A 206 ARG cc_start: 0.8592 (mmm-85) cc_final: 0.8160 (tpt90) REVERT: A 222 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7888 (mm-30) REVERT: B 201 MET cc_start: 0.8832 (mmt) cc_final: 0.8496 (mtm) REVERT: D 35 TYR cc_start: 0.9180 (OUTLIER) cc_final: 0.8657 (m-10) REVERT: C 106 MET cc_start: 0.8281 (mtt) cc_final: 0.7875 (tmm) REVERT: C 126 MET cc_start: 0.9304 (mtm) cc_final: 0.8830 (tmm) REVERT: C 342 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7288 (p90) REVERT: F 436 MET cc_start: 0.7147 (mtp) cc_final: 0.6681 (mmm) outliers start: 30 outliers final: 22 residues processed: 120 average time/residue: 0.1433 time to fit residues: 25.8827 Evaluate side-chains 114 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 35 TYR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 342 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 144 optimal weight: 0.9990 chunk 98 optimal weight: 0.0870 chunk 137 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 173 optimal weight: 10.0000 chunk 44 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.140394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.078846 restraints weight = 37403.072| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.78 r_work: 0.3092 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15914 Z= 0.110 Angle : 0.504 14.846 21435 Z= 0.255 Chirality : 0.042 0.389 2370 Planarity : 0.003 0.059 2727 Dihedral : 7.070 81.981 2194 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.41 % Allowed : 11.13 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.20), residues: 1893 helix: 2.33 (0.17), residues: 987 sheet: -0.09 (0.29), residues: 335 loop : -0.06 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 364 TYR 0.015 0.001 TYR A 197 PHE 0.013 0.001 PHE A 230 TRP 0.014 0.001 TRP C 158 HIS 0.003 0.001 HIS F 44 Details of bonding type rmsd covalent geometry : bond 0.00247 (15914) covalent geometry : angle 0.50446 (21435) hydrogen bonds : bond 0.03023 ( 875) hydrogen bonds : angle 3.86398 ( 2505) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.650 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 311 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 MET cc_start: 0.9230 (mtp) cc_final: 0.8982 (mmt) REVERT: A 206 ARG cc_start: 0.8599 (mmm-85) cc_final: 0.8127 (tpt90) REVERT: A 224 ARG cc_start: 0.7797 (ttm-80) cc_final: 0.7328 (tpp80) REVERT: B 201 MET cc_start: 0.8616 (mmt) cc_final: 0.8298 (mtm) REVERT: B 234 PHE cc_start: 0.7346 (OUTLIER) cc_final: 0.7043 (t80) REVERT: D 35 TYR cc_start: 0.9001 (OUTLIER) cc_final: 0.8486 (m-10) REVERT: C 106 MET cc_start: 0.8325 (mtt) cc_final: 0.7892 (tmm) REVERT: C 126 MET cc_start: 0.9257 (mtm) cc_final: 0.8777 (tmm) REVERT: C 158 TRP cc_start: 0.8133 (t60) cc_final: 0.7700 (t-100) REVERT: C 342 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7580 (p90) REVERT: F 376 MET cc_start: 0.9494 (mtt) cc_final: 0.9217 (mmm) REVERT: F 436 MET cc_start: 0.7044 (mtp) cc_final: 0.6473 (mmm) outliers start: 24 outliers final: 17 residues processed: 114 average time/residue: 0.1168 time to fit residues: 20.2783 Evaluate side-chains 112 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain D residue 35 TYR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain F residue 97 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 72 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 187 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 182 optimal weight: 6.9990 chunk 152 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 154 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.133123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.071104 restraints weight = 37502.322| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.73 r_work: 0.2969 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15914 Z= 0.223 Angle : 0.554 14.368 21435 Z= 0.280 Chirality : 0.043 0.392 2370 Planarity : 0.003 0.063 2727 Dihedral : 6.643 85.487 2194 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.29 % Allowed : 11.13 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.20), residues: 1893 helix: 2.24 (0.17), residues: 990 sheet: -0.13 (0.29), residues: 339 loop : -0.06 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 364 TYR 0.017 0.001 TYR A 197 PHE 0.012 0.001 PHE B 230 TRP 0.012 0.001 TRP C 158 HIS 0.005 0.001 HIS B 424 Details of bonding type rmsd covalent geometry : bond 0.00529 (15914) covalent geometry : angle 0.55411 (21435) hydrogen bonds : bond 0.03341 ( 875) hydrogen bonds : angle 4.00735 ( 2505) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7222.59 seconds wall clock time: 123 minutes 51.59 seconds (7431.59 seconds total)