Starting phenix.real_space_refine on Sat Sep 12 09:42:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8a11_15065/09_2026/8a11_15065.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a11_15065/09_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_15065/09_2026/8a11_15065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a11_15065/09_2026/8a11_15065.map" model { file = "/net/cci-nas-00/data/ceres_data/8a11_15065/09_2026/8a11_15065.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a11_15065/09_2026/8a11_15065.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8a11_15065/09_2026/8a11_15065.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8a11_15065/09_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-2.2.1-6174/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: {'RNAv2': 6} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 4} Time building chain proxies: 3.43, 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: 1.24 Conformation dependent library (CDL) restraints added in 668.0 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: 0.52 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: 2.40 Time building geometry restraints manager: 1.67 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: 20008 2.14 - 4.29: 178 4.29 - 6.43: 57 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: 8622 22.60 - 45.20: 303 45.20 - 67.80: 18 67.80 - 90.39: 15 90.39 - 112.99: 1 Dihedral angle restraints: 8959 sinusoidal: 3582 harmonic: 5377 Sorted by residual: dihedral pdb=" C4' C E 29 " pdb=" C3' C E 29 " pdb=" C2' C E 29 " pdb=" C1' C E 29 " ideal model delta sinusoidal sigma weight residual 36.35 -35.12 71.46 1 3.10e+00 1.04e-01 6.81e+02 dihedral pdb=" O4' C E 29 " pdb=" C4' C E 29 " pdb=" C3' C E 29 " pdb=" C2' C E 29 " ideal model delta sinusoidal sigma weight residual -35.15 23.85 -58.99 1 4.00e+00 6.25e-02 2.91e+02 dihedral pdb=" O4' C E 29 " pdb=" C2' C E 29 " pdb=" C1' C E 29 " pdb=" C3' C E 29 " ideal model delta sinusoidal sigma weight residual -94.41 -35.19 -59.22 3 3.80e+00 6.93e-02 1.48e+02 ... (remaining 8956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1948 0.054 - 0.108: 266 0.108 - 0.162: 25 0.162 - 0.216: 0 0.216 - 0.270: 8 Chirality restraints: 2247 Sorted by residual: chirality pdb=" C2' C E 29 " pdb=" C3' C E 29 " pdb=" O2' C E 29 " pdb=" C1' C E 29 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" P A E 31 " pdb=" OP1 A E 31 " pdb=" OP2 A E 31 " pdb=" O5' A E 31 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" P A E 34 " pdb=" OP1 A E 34 " pdb=" OP2 A E 34 " pdb=" O5' A E 34 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (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: 5.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.420 Find NCS groups from input model: 0.310 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.670 ------------------------------------------------------------------------------- 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 : 0.605 10.717 20257 Z= 0.313 Chirality : 0.039 0.270 2247 Planarity : 0.010 0.280 2621 Dihedral : 11.145 112.994 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 0.60458 / 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 : 0.824 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: 0.1204 time to fit residues: 28.8374 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 : 0.587 ------------------------------------------------------------------------------- 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 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3874 r_free = 0.3874 target = 0.084038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.065358 restraints weight = 62893.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.067230 restraints weight = 35064.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.068498 restraints weight = 24313.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.069334 restraints weight = 19514.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.069838 restraints weight = 16949.790| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1496 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= 0.111 Angle : 0.501 8.192 20257 Z= 0.243 Chirality : 0.038 0.213 2247 Planarity : 0.003 0.041 2621 Dihedral : 6.932 129.384 2139 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.91 % Allowed : 7.25 % Favored : 91.84 % 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: -0.79 (0.19), residues: 1855 helix: 0.87 (0.18), residues: 895 sheet: -1.04 (0.36), residues: 196 loop : -2.13 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 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 0.006 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (14943) covalent geometry : angle 0.50067 / 0.24 (20257) hydrogen bonds : bond 0.03012 / 1.98 ( 694) hydrogen bonds : angle 3.82115 / 2.70 ( 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 116 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 226 MET cc_start: 0.7981 (tmm) cc_final: 0.7665 (tmm) REVERT: A 287 ASN cc_start: 0.8145 (t0) cc_final: 0.7844 (t0) outliers start: 14 outliers final: 12 residues processed: 111 average time/residue: 0.1148 time to fit residues: 19.9338 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 : 0.537 ------------------------------------------------------------------------------- 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: 3.9990 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 168 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 HIS ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** 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 = 0.3846 r_free = 0.3846 target = 0.082712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.063620 restraints weight = 63937.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.065471 restraints weight = 35781.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.066727 restraints weight = 25087.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.067533 restraints weight = 20066.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.067888 restraints weight = 17497.353| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1904 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= 0.104 Angle : 0.481 7.147 20257 Z= 0.236 Chirality : 0.038 0.190 2247 Planarity : 0.003 0.046 2621 Dihedral : 7.063 136.848 2139 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.98 % Allowed : 8.94 % Favored : 90.08 % 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: -0.21 (0.20), residues: 1855 helix: 1.37 (0.18), residues: 893 sheet: -0.82 (0.37), residues: 194 loop : -1.83 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 213 TYR 0.009 0.001 TYR C 183 PHE 0.012 0.001 PHE D 268 TRP 0.002 0.001 TRP A 111 HIS 0.016 0.001 HIS C 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (14943) covalent geometry : angle 0.48109 / 0.24 (20257) hydrogen bonds : bond 0.02848 / 1.87 ( 694) hydrogen bonds : angle 3.65526 / 2.59 ( 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 109 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 287 ASN cc_start: 0.8221 (t0) cc_final: 0.7936 (t0) REVERT: C 142 ASP cc_start: 0.8260 (t0) cc_final: 0.8056 (t0) outliers start: 15 outliers final: 11 residues processed: 104 average time/residue: 0.0998 time to fit residues: 16.9476 Evaluate side-chains 98 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 132 VAL 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: 3.9990 chunk 166 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 chunk 104 optimal weight: 0.0980 chunk 134 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 chunk 175 optimal weight: 0.8980 chunk 78 optimal weight: 9.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 HIS C 148 HIS D 70 ASN ** 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 = 0.3747 r_free = 0.3747 target = 0.078608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.059214 restraints weight = 64563.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.061010 restraints weight = 36622.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.062226 restraints weight = 25981.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.062852 restraints weight = 21213.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.063284 restraints weight = 18940.072| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 14943 Z= 0.248 Angle : 0.635 8.193 20257 Z= 0.319 Chirality : 0.042 0.177 2247 Planarity : 0.005 0.102 2621 Dihedral : 7.589 132.209 2139 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.57 % Allowed : 11.03 % 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: -0.15 (0.20), residues: 1855 helix: 1.38 (0.18), residues: 892 sheet: -0.89 (0.37), residues: 196 loop : -1.72 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 213 TYR 0.018 0.002 TYR A 183 PHE 0.019 0.002 PHE D 268 TRP 0.007 0.002 TRP B 111 HIS 0.006 0.001 HIS B 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.25 (14943) covalent geometry : angle 0.63450 / 0.32 (20257) hydrogen bonds : bond 0.03940 / 2.58 ( 694) hydrogen bonds : angle 4.12288 / 2.90 ( 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 101 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8235 (pp) REVERT: C 231 HIS cc_start: 0.8187 (OUTLIER) cc_final: 0.7631 (t-90) REVERT: D 229 MET cc_start: 0.8129 (ppp) cc_final: 0.7816 (ppp) outliers start: 24 outliers final: 17 residues processed: 93 average time/residue: 0.0986 time to fit residues: 15.2173 Evaluate side-chains 93 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 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 135 HIS 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 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: 0.0980 chunk 36 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 180 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 231 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 = 0.3801 r_free = 0.3801 target = 0.080919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.061595 restraints weight = 62392.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.063415 restraints weight = 35276.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.064695 restraints weight = 24802.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.065475 restraints weight = 20051.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.065849 restraints weight = 17590.767| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14943 Z= 0.098 Angle : 0.492 7.975 20257 Z= 0.243 Chirality : 0.038 0.171 2247 Planarity : 0.003 0.048 2621 Dihedral : 7.306 131.485 2139 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.72 % Allowed : 12.08 % Favored : 87.21 % 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: 0.29 (0.20), residues: 1855 helix: 1.75 (0.18), residues: 892 sheet: -0.72 (0.37), residues: 193 loop : -1.49 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 213 TYR 0.008 0.001 TYR A 172 PHE 0.011 0.001 PHE D 268 TRP 0.004 0.001 TRP A 111 HIS 0.003 0.000 HIS D 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (14943) covalent geometry : angle 0.49160 / 0.24 (20257) hydrogen bonds : bond 0.02851 / 1.86 ( 694) hydrogen bonds : angle 3.71177 / 2.62 ( 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: 11 poor density : 87 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 287 ASN cc_start: 0.8348 (t0) cc_final: 0.8088 (t0) REVERT: A 358 LEU cc_start: 0.8435 (pp) cc_final: 0.8199 (pp) REVERT: D 229 MET cc_start: 0.8169 (ppp) cc_final: 0.7918 (ppp) outliers start: 11 outliers final: 10 residues processed: 95 average time/residue: 0.1023 time to fit residues: 16.0893 Evaluate side-chains 91 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 300 LEU 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 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 0.4980 chunk 183 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 114 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 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 = 0.3792 r_free = 0.3792 target = 0.080610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.061134 restraints weight = 63167.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.062997 restraints weight = 35972.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.064190 restraints weight = 25435.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.064988 restraints weight = 20692.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.065377 restraints weight = 18197.093| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14943 Z= 0.111 Angle : 0.498 8.662 20257 Z= 0.247 Chirality : 0.038 0.165 2247 Planarity : 0.003 0.048 2621 Dihedral : 7.246 130.687 2139 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.04 % Allowed : 11.95 % Favored : 87.01 % 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: 0.45 (0.20), residues: 1855 helix: 1.88 (0.18), residues: 892 sheet: -0.67 (0.38), residues: 193 loop : -1.39 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 213 TYR 0.008 0.001 TYR A 183 PHE 0.012 0.001 PHE D 268 TRP 0.002 0.001 TRP C 111 HIS 0.009 0.001 HIS C 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (14943) covalent geometry : angle 0.49797 / 0.25 (20257) hydrogen bonds : bond 0.02923 / 1.91 ( 694) hydrogen bonds : angle 3.68230 / 2.60 ( 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: 16 poor density : 84 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 139 MET cc_start: 0.6901 (mtt) cc_final: 0.6517 (mtm) REVERT: A 287 ASN cc_start: 0.8322 (t0) cc_final: 0.8082 (t0) REVERT: A 358 LEU cc_start: 0.8411 (pp) cc_final: 0.8168 (pp) REVERT: D 229 MET cc_start: 0.8199 (ppp) cc_final: 0.7957 (ppp) outliers start: 16 outliers final: 14 residues processed: 95 average time/residue: 0.0976 time to fit residues: 15.2574 Evaluate side-chains 94 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 231 HIS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 300 LEU 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 300 LEU 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: 3.9990 chunk 22 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 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 = 0.3785 r_free = 0.3785 target = 0.080256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.060779 restraints weight = 62999.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.062600 restraints weight = 36050.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.063839 restraints weight = 25602.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.064583 restraints weight = 20707.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.064976 restraints weight = 18287.501| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3073 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= 0.124 Angle : 0.507 8.980 20257 Z= 0.252 Chirality : 0.038 0.161 2247 Planarity : 0.003 0.049 2621 Dihedral : 7.241 130.544 2139 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.50 % Allowed : 11.55 % 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: 0.56 (0.20), residues: 1855 helix: 1.96 (0.18), residues: 886 sheet: -0.67 (0.38), residues: 193 loop : -1.27 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 213 TYR 0.008 0.001 TYR D 172 PHE 0.013 0.001 PHE D 268 TRP 0.010 0.001 TRP B 15 HIS 0.007 0.001 HIS C 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (14943) covalent geometry : angle 0.50689 / 0.25 (20257) hydrogen bonds : bond 0.02998 / 1.96 ( 694) hydrogen bonds : angle 3.70946 / 2.62 ( 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 107 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 287 ASN cc_start: 0.8335 (t0) cc_final: 0.8099 (t0) REVERT: A 358 LEU cc_start: 0.8467 (pp) cc_final: 0.8217 (pp) REVERT: B 251 VAL cc_start: 0.8893 (t) cc_final: 0.8547 (p) REVERT: D 229 MET cc_start: 0.8145 (ppp) cc_final: 0.7937 (ppp) outliers start: 23 outliers final: 18 residues processed: 102 average time/residue: 0.0969 time to fit residues: 16.3947 Evaluate side-chains 100 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 262 CYS 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 300 LEU 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 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.080008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.060485 restraints weight = 63432.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.062323 restraints weight = 36160.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.063554 restraints weight = 25635.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.064309 restraints weight = 20822.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.064787 restraints weight = 18342.485| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3202 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= 0.136 Angle : 0.522 9.584 20257 Z= 0.260 Chirality : 0.039 0.158 2247 Planarity : 0.003 0.049 2621 Dihedral : 7.276 130.172 2139 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.50 % Allowed : 11.88 % Favored : 86.62 % 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: 0.64 (0.20), residues: 1855 helix: 1.98 (0.18), residues: 886 sheet: -0.49 (0.36), residues: 204 loop : -1.22 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 213 TYR 0.008 0.001 TYR A 183 PHE 0.014 0.001 PHE D 268 TRP 0.007 0.001 TRP B 15 HIS 0.008 0.001 HIS C 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (14943) covalent geometry : angle 0.52154 / 0.26 (20257) hydrogen bonds : bond 0.03103 / 2.03 ( 694) hydrogen bonds : angle 3.74278 / 2.64 ( 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 103 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 287 ASN cc_start: 0.8348 (t0) cc_final: 0.8120 (t0) REVERT: A 358 LEU cc_start: 0.8455 (pp) cc_final: 0.8235 (pp) outliers start: 23 outliers final: 21 residues processed: 98 average time/residue: 0.1019 time to fit residues: 16.6035 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 : 0.601 ------------------------------------------------------------------------------- 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 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 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 300 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 153 optimal weight: 0.5980 chunk 154 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 HIS A 231 HIS A 306 ASN C 231 HIS ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.080877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.061431 restraints weight = 63035.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.063296 restraints weight = 36037.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.064535 restraints weight = 25494.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.065328 restraints weight = 20642.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.065579 restraints weight = 18105.808| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14943 Z= 0.099 Angle : 0.507 12.363 20257 Z= 0.250 Chirality : 0.038 0.158 2247 Planarity : 0.003 0.049 2621 Dihedral : 7.228 130.137 2139 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.31 % Allowed : 12.21 % 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: 0.74 (0.20), residues: 1855 helix: 2.04 (0.18), residues: 886 sheet: -0.44 (0.36), residues: 204 loop : -1.13 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 213 TYR 0.007 0.001 TYR A 172 PHE 0.011 0.001 PHE D 268 TRP 0.006 0.001 TRP B 15 HIS 0.009 0.001 HIS C 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (14943) covalent geometry : angle 0.50728 / 0.25 (20257) hydrogen bonds : bond 0.02823 / 1.84 ( 694) hydrogen bonds : angle 3.65256 / 2.57 ( 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: 20 poor density : 87 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 287 ASN cc_start: 0.8378 (t0) cc_final: 0.8152 (t0) REVERT: A 358 LEU cc_start: 0.8436 (pp) cc_final: 0.8210 (pp) REVERT: B 251 VAL cc_start: 0.8808 (t) cc_final: 0.8447 (p) REVERT: C 345 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7679 (mt) outliers start: 20 outliers final: 18 residues processed: 102 average time/residue: 0.1066 time to fit residues: 17.7111 Evaluate side-chains 103 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 132 VAL 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 164 SER Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 345 LEU 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 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 152 optimal weight: 6.9990 chunk 93 optimal weight: 0.0030 chunk 43 optimal weight: 0.7980 chunk 47 optimal weight: 0.0670 chunk 81 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 overall best weight: 0.4928 ------------------------------------------------------------------------------- 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 = 0.3807 r_free = 0.3807 target = 0.081392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.062003 restraints weight = 63079.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.063871 restraints weight = 36016.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.065139 restraints weight = 25476.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.065832 restraints weight = 20618.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.066341 restraints weight = 18259.483| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14943 Z= 0.091 Angle : 0.507 10.446 20257 Z= 0.251 Chirality : 0.038 0.158 2247 Planarity : 0.003 0.048 2621 Dihedral : 7.170 130.049 2139 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.17 % Allowed : 12.47 % Favored : 86.36 % 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: 0.87 (0.20), residues: 1855 helix: 2.13 (0.18), residues: 886 sheet: -0.46 (0.36), residues: 207 loop : -1.03 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 213 TYR 0.008 0.001 TYR A 183 PHE 0.010 0.001 PHE D 268 TRP 0.004 0.001 TRP B 15 HIS 0.010 0.001 HIS C 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (14943) covalent geometry : angle 0.50661 / 0.25 (20257) hydrogen bonds : bond 0.02663 / 1.73 ( 694) hydrogen bonds : angle 3.55892 / 2.51 ( 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 107 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 287 ASN cc_start: 0.8364 (t0) cc_final: 0.8158 (t0) REVERT: A 358 LEU cc_start: 0.8411 (pp) cc_final: 0.8180 (pp) REVERT: C 226 MET cc_start: 0.8042 (ttp) cc_final: 0.7753 (ttt) REVERT: C 345 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7680 (mt) outliers start: 18 outliers final: 17 residues processed: 103 average time/residue: 0.1049 time to fit residues: 17.5682 Evaluate side-chains 102 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 132 VAL 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 164 SER Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 345 LEU 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 253 THR Chi-restraints excluded: chain D residue 300 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: 0.7980 chunk 74 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 139 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 5 optimal weight: 0.0030 chunk 110 optimal weight: 0.0770 chunk 34 optimal weight: 1.9990 overall best weight: 0.4948 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.081574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.062199 restraints weight = 62555.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.064066 restraints weight = 35803.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.065317 restraints weight = 25289.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.066067 restraints weight = 20515.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.066451 restraints weight = 18046.552| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14943 Z= 0.091 Angle : 0.492 10.100 20257 Z= 0.244 Chirality : 0.038 0.158 2247 Planarity : 0.003 0.047 2621 Dihedral : 7.138 129.955 2139 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.04 % Allowed : 12.60 % Favored : 86.36 % 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: 0.92 (0.20), residues: 1855 helix: 2.17 (0.18), residues: 885 sheet: -0.53 (0.36), residues: 210 loop : -0.97 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 393 TYR 0.008 0.001 TYR A 172 PHE 0.010 0.001 PHE D 268 TRP 0.005 0.001 TRP B 15 HIS 0.013 0.001 HIS C 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (14943) covalent geometry : angle 0.49228 / 0.24 (20257) hydrogen bonds : bond 0.02597 / 1.68 ( 694) hydrogen bonds : angle 3.51767 / 2.49 ( 2001) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2543.31 seconds wall clock time: 44 minutes 55.96 seconds (2695.96 seconds total)