Starting phenix.real_space_refine on Fri Jul 3 16:36:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8a11_15065/07_2026/8a11_15065.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a11_15065/07_2026/8a11_15065.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a11_15065/07_2026/8a11_15065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a11_15065/07_2026/8a11_15065.map" model { file = "/net/cci-nas-00/data/ceres_data/8a11_15065/07_2026/8a11_15065.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a11_15065/07_2026/8a11_15065.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8a11_15065/07_2026/8a11_15065.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8a11_15065/07_2026/8a11_15065.cif" } resolution = 3.52 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= 0.050 sd= 0.669 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 72 5.16 5 C 9209 2.51 5 N 2557 2.21 5 O 2782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14630 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3605 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 445} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'LLP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3639 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 448} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'LLP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3639 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 448} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'LLP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 3621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3621 Classifications: {'peptide': 468} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 446} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'LLP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 4} Time building chain proxies: 3.37, per 1000 atoms: 0.23 Number of scatterers: 14630 At special positions: 0 Unit cell: (123.571, 135.128, 96.901, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 10 15.00 O 2782 8.00 N 2557 7.00 C 9209 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: 1.16 Conformation dependent library (CDL) restraints added in 704.8 milliseconds 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 15 sheets defined 54.8% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 16 through 23 removed outlier: 3.778A pdb=" N LYS A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 30 Processing helix chain 'A' and resid 31 through 46 Processing helix chain 'A' and resid 58 through 66 removed outlier: 3.501A pdb=" N LEU A 62 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 86 through 104 removed outlier: 3.597A pdb=" N GLU A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 132 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 161 through 167 removed outlier: 3.528A pdb=" N ILE A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 194 removed outlier: 3.622A pdb=" N LEU A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A 187 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A 192 " --> pdb=" O GLU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 221 removed outlier: 3.880A pdb=" N LEU A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 287 through 297 removed outlier: 3.576A pdb=" N LEU A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 319 Processing helix chain 'A' and resid 321 through 346 removed outlier: 4.249A pdb=" N LYS A 325 " --> pdb=" O THR A 321 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 369 through 380 Processing helix chain 'A' and resid 405 through 412 Processing helix chain 'A' and resid 414 through 440 removed outlier: 3.612A pdb=" N PHE A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 453 removed outlier: 4.089A pdb=" N ALA A 453 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 473 removed outlier: 4.431A pdb=" N ALA A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ALA A 460 " --> pdb=" O LYS A 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 23 removed outlier: 3.702A pdb=" N MET B 21 " --> pdb=" O SER B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 31 through 47 Processing helix chain 'B' and resid 58 through 66 removed outlier: 3.724A pdb=" N LEU B 62 " --> pdb=" O SER B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 71 removed outlier: 3.970A pdb=" N ASN B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN B 71 " --> pdb=" O CYS B 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 67 through 71' Processing helix chain 'B' and resid 86 through 104 removed outlier: 4.012A pdb=" N TYR B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 132 Processing helix chain 'B' and resid 148 through 152 removed outlier: 3.830A pdb=" N HIS B 151 " --> pdb=" O HIS B 148 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY B 152 " --> pdb=" O LEU B 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 148 through 152' Processing helix chain 'B' and resid 161 through 167 Processing helix chain 'B' and resid 182 through 194 removed outlier: 3.691A pdb=" N GLU B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 222 removed outlier: 3.641A pdb=" N LEU B 214 " --> pdb=" O GLU B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'B' and resid 243 through 247 removed outlier: 4.004A pdb=" N GLU B 246 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS B 247 " --> pdb=" O PRO B 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 243 through 247' Processing helix chain 'B' and resid 287 through 297 Processing helix chain 'B' and resid 305 through 320 Processing helix chain 'B' and resid 321 through 345 removed outlier: 4.287A pdb=" N LYS B 325 " --> pdb=" O THR B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 363 through 367 removed outlier: 3.527A pdb=" N GLY B 367 " --> pdb=" O ARG B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 380 removed outlier: 3.678A pdb=" N VAL B 376 " --> pdb=" O ARG B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.396A pdb=" N LEU B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B 410 " --> pdb=" O PRO B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 440 Processing helix chain 'B' and resid 444 through 451 Processing helix chain 'B' and resid 454 through 474 removed outlier: 4.215A pdb=" N ALA B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ALA B 460 " --> pdb=" O LYS B 456 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 23 Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 30 through 46 removed outlier: 3.687A pdb=" N TYR C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 66 Processing helix chain 'C' and resid 67 through 71 removed outlier: 4.180A pdb=" N ASN C 70 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 104 removed outlier: 3.980A pdb=" N TYR C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 132 Processing helix chain 'C' and resid 148 through 152 removed outlier: 3.588A pdb=" N GLY C 152 " --> pdb=" O LEU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 167 Processing helix chain 'C' and resid 183 through 194 removed outlier: 3.601A pdb=" N GLU C 187 " --> pdb=" O TYR C 183 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 221 removed outlier: 3.566A pdb=" N ASN C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 239 Processing helix chain 'C' and resid 288 through 297 Processing helix chain 'C' and resid 305 through 320 removed outlier: 3.875A pdb=" N ILE C 309 " --> pdb=" O HIS C 305 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA C 310 " --> pdb=" O ASN C 306 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY C 311 " --> pdb=" O HIS C 307 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 346 removed outlier: 3.762A pdb=" N LYS C 325 " --> pdb=" O THR C 321 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 380 removed outlier: 3.837A pdb=" N ALA C 373 " --> pdb=" O ASP C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 412 removed outlier: 3.560A pdb=" N ARG C 411 " --> pdb=" O ALA C 407 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY C 412 " --> pdb=" O LEU C 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 407 through 412' Processing helix chain 'C' and resid 414 through 440 Processing helix chain 'C' and resid 444 through 452 removed outlier: 3.589A pdb=" N PHE C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 473 Processing helix chain 'D' and resid 17 through 23 Processing helix chain 'D' and resid 25 through 30 Processing helix chain 'D' and resid 30 through 46 removed outlier: 3.724A pdb=" N TYR D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 66 removed outlier: 3.599A pdb=" N LEU D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 72 Processing helix chain 'D' and resid 86 through 104 removed outlier: 3.834A pdb=" N TYR D 104 " --> pdb=" O ALA D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 109 No H-bonds generated for 'chain 'D' and resid 107 through 109' Processing helix chain 'D' and resid 119 through 132 Processing helix chain 'D' and resid 148 through 152 Processing helix chain 'D' and resid 161 through 167 Processing helix chain 'D' and resid 183 through 194 removed outlier: 3.996A pdb=" N ARG D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU D 192 " --> pdb=" O GLU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 222 Processing helix chain 'D' and resid 232 through 239 removed outlier: 3.566A pdb=" N GLY D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 247 removed outlier: 3.735A pdb=" N GLU D 246 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS D 247 " --> pdb=" O PRO D 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 243 through 247' Processing helix chain 'D' and resid 287 through 297 removed outlier: 4.084A pdb=" N LEU D 291 " --> pdb=" O ASN D 287 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL D 296 " --> pdb=" O ILE D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 318 Processing helix chain 'D' and resid 321 through 344 removed outlier: 3.913A pdb=" N LYS D 325 " --> pdb=" O THR D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 380 removed outlier: 3.698A pdb=" N ALA D 373 " --> pdb=" O ASP D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 412 removed outlier: 3.635A pdb=" N THR D 409 " --> pdb=" O THR D 405 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY D 412 " --> pdb=" O LEU D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 440 Processing helix chain 'D' and resid 444 through 452 Processing helix chain 'D' and resid 454 through 473 Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 114 removed outlier: 6.316A pdb=" N LEU A 225 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N THR A 252 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA A 227 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N THR A 254 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE A 198 " --> pdb=" O MET A 226 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ASP A 228 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ALA A 200 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ARG A 137 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N ILE A 199 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N MET A 139 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 276 removed outlier: 3.738A pdb=" N SER A 275 " --> pdb=" O ILE A 284 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 349 removed outlier: 4.427A pdb=" N LYS A 348 " --> pdb=" O ASP A 362 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN A 385 " --> pdb=" O ARG A 402 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 48 through 49 removed outlier: 7.366A pdb=" N LEU B 48 " --> pdb=" O ALA B 383 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 168 through 169 removed outlier: 7.483A pdb=" N ARG B 137 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N ILE B 199 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N MET B 139 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N GLY B 201 " --> pdb=" O MET B 139 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE B 198 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ASP B 228 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA B 200 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 174 through 175 removed outlier: 3.608A pdb=" N TYR B 180 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 276 removed outlier: 7.068A pdb=" N ILE B 284 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 359 through 361 Processing sheet with id=AA9, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.011A pdb=" N ILE C 198 " --> pdb=" O MET C 226 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ASP C 228 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 137 through 138 Processing sheet with id=AB2, first strand: chain 'C' and resid 273 through 276 removed outlier: 6.996A pdb=" N ILE C 284 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 348 through 349 removed outlier: 4.102A pdb=" N LYS C 348 " --> pdb=" O ASP C 362 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL C 361 " --> pdb=" O LEU C 401 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 111 through 114 removed outlier: 6.477A pdb=" N LEU D 225 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N THR D 252 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA D 227 " --> pdb=" O THR D 252 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR D 254 " --> pdb=" O ALA D 227 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 273 through 276 removed outlier: 6.795A pdb=" N ILE D 284 " --> pdb=" O LYS D 274 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 358 through 362 removed outlier: 3.956A pdb=" N ASN D 385 " --> pdb=" O ARG D 402 " (cutoff:3.500A) 694 hydrogen bonds defined for protein. 2001 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: 2.50 Time building geometry restraints manager: 1.56 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: 4751 1.34 - 1.46: 1966 1.46 - 1.57: 8107 1.57 - 1.69: 15 1.69 - 1.81: 104 Bond restraints: 14943 Sorted by residual: bond pdb=" OP4 LLP A 257 " pdb=" P LLP A 257 " ideal model delta sigma weight residual 1.726 1.544 0.182 2.00e-02 2.50e+03 8.25e+01 bond pdb=" OP4 LLP C 257 " pdb=" P LLP C 257 " ideal model delta sigma weight residual 1.726 1.545 0.181 2.00e-02 2.50e+03 8.20e+01 bond pdb=" OP4 LLP D 257 " pdb=" P LLP D 257 " ideal model delta sigma weight residual 1.726 1.545 0.181 2.00e-02 2.50e+03 8.20e+01 bond pdb=" OP4 LLP B 257 " pdb=" P LLP B 257 " ideal model delta sigma weight residual 1.726 1.545 0.181 2.00e-02 2.50e+03 8.17e+01 bond pdb=" NZ LLP A 257 " pdb=" C4' LLP A 257 " ideal model delta sigma weight residual 1.273 1.433 -0.160 2.00e-02 2.50e+03 6.40e+01 ... (remaining 14938 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 20024 2.14 - 4.29: 163 4.29 - 6.43: 56 6.43 - 8.57: 2 8.57 - 10.72: 12 Bond angle restraints: 20257 Sorted by residual: angle pdb=" NZ LLP B 257 " pdb=" C4' LLP B 257 " pdb=" C4 LLP B 257 " ideal model delta sigma weight residual 120.09 109.37 10.72 3.00e+00 1.11e-01 1.28e+01 angle pdb=" NZ LLP D 257 " pdb=" C4' LLP D 257 " pdb=" C4 LLP D 257 " ideal model delta sigma weight residual 120.09 109.43 10.66 3.00e+00 1.11e-01 1.26e+01 angle pdb=" NZ LLP C 257 " pdb=" C4' LLP C 257 " pdb=" C4 LLP C 257 " ideal model delta sigma weight residual 120.09 109.43 10.66 3.00e+00 1.11e-01 1.26e+01 angle pdb=" CE LLP C 257 " pdb=" NZ LLP C 257 " pdb=" C4' LLP C 257 " ideal model delta sigma weight residual 119.26 109.23 10.03 3.00e+00 1.11e-01 1.12e+01 angle pdb=" NZ LLP A 257 " pdb=" C4' LLP A 257 " pdb=" C4 LLP A 257 " ideal model delta sigma weight residual 120.09 110.17 9.92 3.00e+00 1.11e-01 1.09e+01 ... (remaining 20252 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.60: 8631 22.60 - 45.20: 298 45.20 - 67.80: 14 67.80 - 90.39: 14 90.39 - 112.99: 2 Dihedral angle restraints: 8959 sinusoidal: 3582 harmonic: 5377 Sorted by residual: dihedral pdb=" CD LLP A 257 " pdb=" CE LLP A 257 " pdb=" NZ LLP A 257 " pdb=" C4' LLP A 257 " ideal model delta sinusoidal sigma weight residual 249.72 136.73 112.99 1 3.00e+01 1.11e-03 1.48e+01 dihedral pdb=" CB GLU C 133 " pdb=" CG GLU C 133 " pdb=" CD GLU C 133 " pdb=" OE1 GLU C 133 " ideal model delta sinusoidal sigma weight residual 0.00 89.19 -89.19 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU C 63 " pdb=" CG GLU C 63 " pdb=" CD GLU C 63 " pdb=" OE1 GLU C 63 " ideal model delta sinusoidal sigma weight residual 0.00 86.71 -86.71 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 8956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1604 0.032 - 0.064: 437 0.064 - 0.096: 142 0.096 - 0.128: 60 0.128 - 0.160: 4 Chirality restraints: 2247 Sorted by residual: chirality pdb=" CA ILE D 199 " pdb=" N ILE D 199 " pdb=" C ILE D 199 " pdb=" CB ILE D 199 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CA PRO D 134 " pdb=" N PRO D 134 " pdb=" C PRO D 134 " pdb=" CB PRO D 134 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA PRO C 134 " pdb=" N PRO C 134 " pdb=" C PRO C 134 " pdb=" CB PRO C 134 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 2244 not shown) Planarity restraints: 2621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP D 257 " 0.162 2.00e-02 2.50e+03 2.80e-01 7.83e+02 pdb=" NZ LLP D 257 " -0.380 2.00e-02 2.50e+03 pdb=" C4 LLP D 257 " -0.134 2.00e-02 2.50e+03 pdb=" C4' LLP D 257 " 0.353 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP A 257 " -0.159 2.00e-02 2.50e+03 2.77e-01 7.67e+02 pdb=" NZ LLP A 257 " 0.374 2.00e-02 2.50e+03 pdb=" C4 LLP A 257 " 0.135 2.00e-02 2.50e+03 pdb=" C4' LLP A 257 " -0.351 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP C 257 " -0.152 2.00e-02 2.50e+03 2.47e-01 6.12e+02 pdb=" NZ LLP C 257 " 0.329 2.00e-02 2.50e+03 pdb=" C4 LLP C 257 " 0.133 2.00e-02 2.50e+03 pdb=" C4' LLP C 257 " -0.310 2.00e-02 2.50e+03 ... (remaining 2618 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1834 2.75 - 3.29: 14271 3.29 - 3.83: 24043 3.83 - 4.36: 27429 4.36 - 4.90: 47827 Nonbonded interactions: 115404 Sorted by model distance: nonbonded pdb=" OG1 THR C 155 " pdb=" O LYS C 158 " model vdw 2.214 3.040 nonbonded pdb=" OG SER B 354 " pdb=" OD1 ASN B 356 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR C 327 " pdb=" O PRO C 406 " model vdw 2.261 3.040 nonbonded pdb=" OD2 ASP B 438 " pdb=" OH TYR B 457 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR C 77 " pdb=" O ASN C 293 " model vdw 2.266 3.040 ... (remaining 115399 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' selection = (chain 'B' and resid 16 through 482) selection = (chain 'C' and resid 16 through 482) selection = (chain 'D' and (resid 16 through 278 or (resid 279 and (name N or name CA or nam \ e C or name O or name CB )) or resid 280 through 482)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.490 Find NCS groups from input model: 0.290 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 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 : 0.006 0.182 14943 Z= 0.290 Angle : 0.597 10.717 20257 Z= 0.311 Chirality : 0.036 0.160 2247 Planarity : 0.010 0.280 2621 Dihedral : 11.003 112.994 5529 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.91 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.17), residues: 1855 helix: -0.37 (0.16), residues: 884 sheet: -1.45 (0.35), residues: 192 loop : -2.76 (0.18), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 213 TYR 0.005 0.000 TYR D 457 PHE 0.010 0.001 PHE A 418 TRP 0.001 0.000 TRP B 111 HIS 0.002 0.000 HIS D 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.29 (14943) covalent geometry : angle 0.59744 / 0.31 (20257) hydrogen bonds : bond 0.15815 / 10.74 ( 694) hydrogen bonds : angle 5.31832 / 3.73 ( 2001) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.7599 (ptm) cc_final: 0.7075 (ttp) REVERT: A 191 ARG cc_start: 0.8520 (mtm-85) cc_final: 0.8016 (ttp80) REVERT: A 287 ASN cc_start: 0.7847 (t0) cc_final: 0.7569 (t0) REVERT: C 142 ASP cc_start: 0.8375 (t0) cc_final: 0.8149 (t0) REVERT: C 229 MET cc_start: 0.7628 (ptm) cc_final: 0.7419 (ptm) REVERT: D 447 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8236 (tm-30) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1032 time to fit residues: 24.4502 Evaluate side-chains 94 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN A 185 GLN B 44 GLN B 109 GLN ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 HIS C 307 HIS C 385 ASN D 44 GLN D 70 ASN D 221 ASN D 328 GLN ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.084121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.065467 restraints weight = 62930.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.067351 restraints weight = 35039.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.068643 restraints weight = 24388.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.069416 restraints weight = 19463.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.069912 restraints weight = 17037.754| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14943 Z= 0.104 Angle : 0.479 6.166 20257 Z= 0.238 Chirality : 0.037 0.129 2247 Planarity : 0.003 0.041 2621 Dihedral : 6.266 94.573 2139 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.91 % Allowed : 7.18 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.19), residues: 1855 helix: 0.87 (0.18), residues: 895 sheet: -1.03 (0.36), residues: 196 loop : -2.14 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 213 TYR 0.010 0.001 TYR D 77 PHE 0.012 0.001 PHE D 268 TRP 0.004 0.001 TRP C 15 HIS 0.007 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (14943) covalent geometry : angle 0.47934 / 0.24 (20257) hydrogen bonds : bond 0.03039 / 2.00 ( 694) hydrogen bonds : angle 3.83887 / 2.72 ( 2001) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 226 MET cc_start: 0.7950 (tmm) cc_final: 0.7635 (tmm) REVERT: A 287 ASN cc_start: 0.8128 (t0) cc_final: 0.7839 (t0) outliers start: 14 outliers final: 12 residues processed: 112 average time/residue: 0.1061 time to fit residues: 18.5505 Evaluate side-chains 95 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 73 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 165 optimal weight: 3.9990 chunk 168 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 16 optimal weight: 0.0570 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 HIS ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 ASN ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.083250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.064211 restraints weight = 63959.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.066081 restraints weight = 35545.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.067344 restraints weight = 24871.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.068137 restraints weight = 19947.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.068539 restraints weight = 17442.754| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14943 Z= 0.095 Angle : 0.460 7.265 20257 Z= 0.228 Chirality : 0.037 0.130 2247 Planarity : 0.003 0.046 2621 Dihedral : 6.298 93.793 2139 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.91 % Allowed : 8.94 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.20), residues: 1855 helix: 1.38 (0.18), residues: 894 sheet: -0.82 (0.37), residues: 194 loop : -1.81 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 213 TYR 0.010 0.001 TYR C 183 PHE 0.011 0.001 PHE D 268 TRP 0.002 0.000 TRP A 111 HIS 0.020 0.001 HIS C 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 (14943) covalent geometry : angle 0.46039 / 0.23 (20257) hydrogen bonds : bond 0.02746 / 1.80 ( 694) hydrogen bonds : angle 3.63716 / 2.58 ( 2001) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: A 287 ASN cc_start: 0.8194 (t0) cc_final: 0.7903 (t0) REVERT: C 142 ASP cc_start: 0.8249 (t0) cc_final: 0.8036 (t0) outliers start: 14 outliers final: 10 residues processed: 108 average time/residue: 0.0997 time to fit residues: 17.2630 Evaluate side-chains 98 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 23 optimal weight: 4.9990 chunk 166 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 104 optimal weight: 0.1980 chunk 134 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 175 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 HIS D 70 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.077948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.058534 restraints weight = 65275.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.060311 restraints weight = 37133.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.061517 restraints weight = 26405.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.062300 restraints weight = 21525.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.062621 restraints weight = 18947.588| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 14943 Z= 0.295 Angle : 0.681 8.151 20257 Z= 0.348 Chirality : 0.043 0.171 2247 Planarity : 0.005 0.069 2621 Dihedral : 7.127 93.316 2139 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.83 % Allowed : 10.77 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.19), residues: 1855 helix: 1.30 (0.17), residues: 883 sheet: -0.93 (0.36), residues: 198 loop : -1.73 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 81 TYR 0.017 0.002 TYR D 269 PHE 0.021 0.002 PHE B 193 TRP 0.009 0.002 TRP B 111 HIS 0.008 0.002 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00672 / 0.29 (14943) covalent geometry : angle 0.68111 / 0.35 (20257) hydrogen bonds : bond 0.04313 / 2.84 ( 694) hydrogen bonds : angle 4.31259 / 3.03 ( 2001) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 358 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8272 (pp) REVERT: D 229 MET cc_start: 0.8084 (ppp) cc_final: 0.7807 (ppp) outliers start: 28 outliers final: 19 residues processed: 97 average time/residue: 0.0896 time to fit residues: 14.3631 Evaluate side-chains 94 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 180 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 118 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 HIS ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.080346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.060966 restraints weight = 63311.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.062822 restraints weight = 35850.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.064084 restraints weight = 25318.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.064869 restraints weight = 20460.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.065209 restraints weight = 17931.615| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14943 Z= 0.110 Angle : 0.506 8.730 20257 Z= 0.253 Chirality : 0.038 0.134 2247 Planarity : 0.003 0.050 2621 Dihedral : 6.732 91.591 2139 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.04 % Allowed : 12.01 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.20), residues: 1855 helix: 1.68 (0.18), residues: 892 sheet: -0.63 (0.36), residues: 205 loop : -1.53 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 213 TYR 0.008 0.001 TYR A 172 PHE 0.013 0.001 PHE D 268 TRP 0.004 0.001 TRP A 111 HIS 0.003 0.001 HIS D 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (14943) covalent geometry : angle 0.50588 / 0.25 (20257) hydrogen bonds : bond 0.03033 / 1.98 ( 694) hydrogen bonds : angle 3.81496 / 2.69 ( 2001) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 358 LEU cc_start: 0.8465 (pp) cc_final: 0.8236 (pp) REVERT: D 229 MET cc_start: 0.8148 (ppp) cc_final: 0.7746 (ppp) outliers start: 16 outliers final: 12 residues processed: 93 average time/residue: 0.0915 time to fit residues: 13.8703 Evaluate side-chains 87 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 135 HIS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 117 optimal weight: 0.0870 chunk 108 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 HIS A 306 ASN ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.079572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.060316 restraints weight = 62915.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.062139 restraints weight = 35495.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.063379 restraints weight = 25049.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.064092 restraints weight = 20282.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.064568 restraints weight = 17882.230| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14943 Z= 0.147 Angle : 0.526 8.710 20257 Z= 0.265 Chirality : 0.038 0.134 2247 Planarity : 0.004 0.049 2621 Dihedral : 6.760 90.157 2139 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.37 % Allowed : 12.14 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.20), residues: 1855 helix: 1.77 (0.18), residues: 892 sheet: -0.56 (0.36), residues: 205 loop : -1.47 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 213 TYR 0.010 0.001 TYR A 183 PHE 0.015 0.001 PHE D 268 TRP 0.003 0.001 TRP B 15 HIS 0.003 0.001 HIS B 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (14943) covalent geometry : angle 0.52582 / 0.27 (20257) hydrogen bonds : bond 0.03270 / 2.14 ( 694) hydrogen bonds : angle 3.86327 / 2.72 ( 2001) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: A 358 LEU cc_start: 0.8492 (pp) cc_final: 0.8277 (pp) REVERT: C 231 HIS cc_start: 0.8102 (OUTLIER) cc_final: 0.7485 (t-90) REVERT: D 229 MET cc_start: 0.8117 (ppp) cc_final: 0.7806 (ppp) outliers start: 21 outliers final: 15 residues processed: 94 average time/residue: 0.0943 time to fit residues: 14.4319 Evaluate side-chains 90 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 135 HIS Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 121 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 179 optimal weight: 0.0270 chunk 127 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 162 optimal weight: 0.8980 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 HIS A 231 HIS C 231 HIS ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.079787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.060327 restraints weight = 63481.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.062152 restraints weight = 36386.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.063346 restraints weight = 25801.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.064166 restraints weight = 21063.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.064523 restraints weight = 18479.457| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14943 Z= 0.136 Angle : 0.519 9.184 20257 Z= 0.262 Chirality : 0.038 0.138 2247 Planarity : 0.003 0.049 2621 Dihedral : 6.724 88.308 2139 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.76 % Allowed : 11.95 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.20), residues: 1855 helix: 1.86 (0.18), residues: 891 sheet: -0.48 (0.36), residues: 204 loop : -1.37 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 213 TYR 0.009 0.001 TYR D 172 PHE 0.014 0.001 PHE D 268 TRP 0.005 0.001 TRP B 15 HIS 0.004 0.001 HIS A 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (14943) covalent geometry : angle 0.51912 / 0.26 (20257) hydrogen bonds : bond 0.03149 / 2.06 ( 694) hydrogen bonds : angle 3.81840 / 2.68 ( 2001) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 358 LEU cc_start: 0.8474 (pp) cc_final: 0.8264 (pp) REVERT: B 251 VAL cc_start: 0.8880 (t) cc_final: 0.8529 (p) REVERT: D 229 MET cc_start: 0.8102 (ppp) cc_final: 0.7842 (ppp) outliers start: 27 outliers final: 24 residues processed: 100 average time/residue: 0.0878 time to fit residues: 14.4865 Evaluate side-chains 101 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 135 HIS Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 155 optimal weight: 0.0370 chunk 126 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 109 optimal weight: 0.0570 chunk 91 optimal weight: 9.9990 overall best weight: 1.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 HIS A 231 HIS C 231 HIS ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.079836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.060581 restraints weight = 63096.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.062434 restraints weight = 35622.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.063643 restraints weight = 25037.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.064466 restraints weight = 20242.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.064960 restraints weight = 17732.591| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14943 Z= 0.128 Angle : 0.524 9.551 20257 Z= 0.262 Chirality : 0.038 0.314 2247 Planarity : 0.003 0.050 2621 Dihedral : 6.704 87.463 2139 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.83 % Allowed : 12.27 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.20), residues: 1855 helix: 1.90 (0.18), residues: 891 sheet: -0.51 (0.36), residues: 204 loop : -1.30 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 213 TYR 0.011 0.001 TYR A 269 PHE 0.013 0.001 PHE D 268 TRP 0.003 0.001 TRP B 15 HIS 0.003 0.001 HIS D 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (14943) covalent geometry : angle 0.52422 / 0.26 (20257) hydrogen bonds : bond 0.03103 / 2.03 ( 694) hydrogen bonds : angle 3.81488 / 2.68 ( 2001) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: A 287 ASN cc_start: 0.8407 (t0) cc_final: 0.8171 (t0) REVERT: A 358 LEU cc_start: 0.8465 (pp) cc_final: 0.8257 (pp) REVERT: B 251 VAL cc_start: 0.8872 (t) cc_final: 0.8519 (p) REVERT: D 229 MET cc_start: 0.8101 (ppp) cc_final: 0.7806 (ppp) outliers start: 28 outliers final: 27 residues processed: 99 average time/residue: 0.0894 time to fit residues: 14.5915 Evaluate side-chains 104 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 135 HIS Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 chunk 153 optimal weight: 10.0000 chunk 154 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 HIS C 231 HIS ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.079990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.060773 restraints weight = 62743.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.062604 restraints weight = 35544.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.063828 restraints weight = 25079.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.064625 restraints weight = 20346.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.064975 restraints weight = 17813.993| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14943 Z= 0.120 Angle : 0.516 9.793 20257 Z= 0.257 Chirality : 0.038 0.273 2247 Planarity : 0.003 0.050 2621 Dihedral : 6.679 86.499 2139 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.76 % Allowed : 12.47 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.20), residues: 1855 helix: 1.95 (0.18), residues: 891 sheet: -0.50 (0.36), residues: 204 loop : -1.23 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 213 TYR 0.009 0.001 TYR D 172 PHE 0.013 0.001 PHE D 268 TRP 0.003 0.001 TRP B 15 HIS 0.007 0.001 HIS A 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (14943) covalent geometry : angle 0.51607 / 0.26 (20257) hydrogen bonds : bond 0.03026 / 1.97 ( 694) hydrogen bonds : angle 3.77902 / 2.66 ( 2001) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 287 ASN cc_start: 0.8401 (t0) cc_final: 0.8162 (t0) REVERT: A 358 LEU cc_start: 0.8452 (pp) cc_final: 0.8233 (pp) REVERT: B 251 VAL cc_start: 0.8871 (t) cc_final: 0.8517 (p) REVERT: D 229 MET cc_start: 0.8117 (ppp) cc_final: 0.7820 (ppp) outliers start: 27 outliers final: 27 residues processed: 99 average time/residue: 0.0969 time to fit residues: 15.7991 Evaluate side-chains 106 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 135 HIS Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 152 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 43 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 HIS A 231 HIS C 231 HIS ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.079248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.059980 restraints weight = 63038.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.061805 restraints weight = 35798.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.063026 restraints weight = 25302.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.063781 restraints weight = 20550.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.064035 restraints weight = 18079.839| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14943 Z= 0.163 Angle : 0.550 10.075 20257 Z= 0.276 Chirality : 0.039 0.249 2247 Planarity : 0.004 0.050 2621 Dihedral : 6.761 85.694 2139 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.83 % Allowed : 12.34 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.20), residues: 1855 helix: 1.91 (0.18), residues: 890 sheet: -0.58 (0.36), residues: 206 loop : -1.23 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 213 TYR 0.010 0.001 TYR D 172 PHE 0.014 0.001 PHE D 268 TRP 0.004 0.001 TRP B 111 HIS 0.005 0.001 HIS C 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (14943) covalent geometry : angle 0.55048 / 0.28 (20257) hydrogen bonds : bond 0.03312 / 2.17 ( 694) hydrogen bonds : angle 3.88203 / 2.72 ( 2001) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: A 358 LEU cc_start: 0.8482 (pp) cc_final: 0.8274 (pp) REVERT: B 251 VAL cc_start: 0.8892 (t) cc_final: 0.8527 (p) REVERT: D 229 MET cc_start: 0.8033 (ppp) cc_final: 0.7825 (ppp) outliers start: 28 outliers final: 26 residues processed: 98 average time/residue: 0.0992 time to fit residues: 16.0929 Evaluate side-chains 102 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 135 HIS Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 94 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 8 optimal weight: 0.2980 chunk 44 optimal weight: 9.9990 chunk 139 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 HIS A 231 HIS C 231 HIS ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.080062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.060593 restraints weight = 63404.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.062438 restraints weight = 36361.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.063655 restraints weight = 26027.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.064405 restraints weight = 21171.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.064893 restraints weight = 18651.522| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14943 Z= 0.116 Angle : 0.521 10.246 20257 Z= 0.259 Chirality : 0.038 0.235 2247 Planarity : 0.003 0.050 2621 Dihedral : 6.690 84.891 2139 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.70 % Allowed : 12.53 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.20), residues: 1855 helix: 1.98 (0.18), residues: 891 sheet: -0.62 (0.36), residues: 209 loop : -1.15 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 213 TYR 0.009 0.001 TYR D 172 PHE 0.012 0.001 PHE D 268 TRP 0.003 0.001 TRP A 111 HIS 0.004 0.001 HIS A 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (14943) covalent geometry : angle 0.52063 / 0.26 (20257) hydrogen bonds : bond 0.03027 / 1.97 ( 694) hydrogen bonds : angle 3.77196 / 2.65 ( 2001) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2370.59 seconds wall clock time: 41 minutes 54.31 seconds (2514.31 seconds total)