Starting phenix.real_space_refine on Wed Mar 4 17:09:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a11_15065/03_2026/8a11_15065.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a11_15065/03_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_15065/03_2026/8a11_15065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a11_15065/03_2026/8a11_15065.map" model { file = "/net/cci-nas-00/data/ceres_data/8a11_15065/03_2026/8a11_15065.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a11_15065/03_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14630 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3605 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 445} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'LLP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3639 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 448} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'LLP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3639 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 448} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'LLP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 3621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3621 Classifications: {'peptide': 468} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 446} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'LLP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 4} Time building chain proxies: 3.84, per 1000 atoms: 0.26 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: 1.37 Conformation dependent library (CDL) restraints added in 764.4 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: 0.51 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: 2.45 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4751 1.34 - 1.46: 1966 1.46 - 1.57: 8107 1.57 - 1.69: 15 1.69 - 1.81: 104 Bond restraints: 14943 Sorted by residual: bond pdb=" OP4 LLP A 257 " pdb=" P LLP A 257 " ideal model delta sigma weight residual 1.726 1.544 0.182 2.00e-02 2.50e+03 8.25e+01 bond pdb=" OP4 LLP C 257 " pdb=" P LLP C 257 " ideal model delta sigma weight residual 1.726 1.545 0.181 2.00e-02 2.50e+03 8.20e+01 bond pdb=" OP4 LLP D 257 " pdb=" P LLP D 257 " ideal model delta sigma weight residual 1.726 1.545 0.181 2.00e-02 2.50e+03 8.20e+01 bond pdb=" OP4 LLP B 257 " pdb=" P LLP B 257 " ideal model delta sigma weight residual 1.726 1.545 0.181 2.00e-02 2.50e+03 8.17e+01 bond pdb=" NZ LLP A 257 " pdb=" C4' LLP A 257 " ideal model delta sigma weight residual 1.273 1.433 -0.160 2.00e-02 2.50e+03 6.40e+01 ... (remaining 14938 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 20024 2.14 - 4.29: 163 4.29 - 6.43: 56 6.43 - 8.57: 2 8.57 - 10.72: 12 Bond angle restraints: 20257 Sorted by residual: angle pdb=" NZ LLP B 257 " pdb=" C4' LLP B 257 " pdb=" C4 LLP B 257 " ideal model delta sigma weight residual 120.09 109.37 10.72 3.00e+00 1.11e-01 1.28e+01 angle pdb=" NZ LLP D 257 " pdb=" C4' LLP D 257 " pdb=" C4 LLP D 257 " ideal model delta sigma weight residual 120.09 109.43 10.66 3.00e+00 1.11e-01 1.26e+01 angle pdb=" NZ LLP C 257 " pdb=" C4' LLP C 257 " pdb=" C4 LLP C 257 " ideal model delta sigma weight residual 120.09 109.43 10.66 3.00e+00 1.11e-01 1.26e+01 angle pdb=" CE LLP C 257 " pdb=" NZ LLP C 257 " pdb=" C4' LLP C 257 " ideal model delta sigma weight residual 119.26 109.23 10.03 3.00e+00 1.11e-01 1.12e+01 angle pdb=" NZ LLP A 257 " pdb=" C4' LLP A 257 " pdb=" C4 LLP A 257 " ideal model delta sigma weight residual 120.09 110.17 9.92 3.00e+00 1.11e-01 1.09e+01 ... (remaining 20252 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.60: 8634 22.60 - 45.20: 304 45.20 - 67.80: 15 67.80 - 90.39: 16 90.39 - 112.99: 2 Dihedral angle restraints: 8971 sinusoidal: 3594 harmonic: 5377 Sorted by residual: dihedral pdb=" CD LLP A 257 " pdb=" CE LLP A 257 " pdb=" NZ LLP A 257 " pdb=" C4' LLP A 257 " ideal model delta sinusoidal sigma weight residual 249.72 136.73 112.99 1 3.00e+01 1.11e-03 1.48e+01 dihedral pdb=" CB GLU C 133 " pdb=" CG GLU C 133 " pdb=" CD GLU C 133 " pdb=" OE1 GLU C 133 " ideal model delta sinusoidal sigma weight residual 0.00 89.19 -89.19 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU C 63 " pdb=" CG GLU C 63 " pdb=" CD GLU C 63 " pdb=" OE1 GLU C 63 " ideal model delta sinusoidal sigma weight residual 0.00 86.71 -86.71 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 8968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1604 0.032 - 0.064: 437 0.064 - 0.096: 142 0.096 - 0.128: 60 0.128 - 0.160: 4 Chirality restraints: 2247 Sorted by residual: chirality pdb=" CA ILE D 199 " pdb=" N ILE D 199 " pdb=" C ILE D 199 " pdb=" CB ILE D 199 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CA PRO D 134 " pdb=" N PRO D 134 " pdb=" C PRO D 134 " pdb=" CB PRO D 134 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA PRO C 134 " pdb=" N PRO C 134 " pdb=" C PRO C 134 " pdb=" CB PRO C 134 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 2244 not shown) Planarity restraints: 2621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP D 257 " 0.162 2.00e-02 2.50e+03 2.80e-01 7.83e+02 pdb=" NZ LLP D 257 " -0.380 2.00e-02 2.50e+03 pdb=" C4 LLP D 257 " -0.134 2.00e-02 2.50e+03 pdb=" C4' LLP D 257 " 0.353 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP A 257 " -0.159 2.00e-02 2.50e+03 2.77e-01 7.67e+02 pdb=" NZ LLP A 257 " 0.374 2.00e-02 2.50e+03 pdb=" C4 LLP A 257 " 0.135 2.00e-02 2.50e+03 pdb=" C4' LLP A 257 " -0.351 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP C 257 " -0.152 2.00e-02 2.50e+03 2.47e-01 6.12e+02 pdb=" NZ LLP C 257 " 0.329 2.00e-02 2.50e+03 pdb=" C4 LLP C 257 " 0.133 2.00e-02 2.50e+03 pdb=" C4' LLP C 257 " -0.310 2.00e-02 2.50e+03 ... (remaining 2618 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1834 2.75 - 3.29: 14271 3.29 - 3.83: 24043 3.83 - 4.36: 27429 4.36 - 4.90: 47827 Nonbonded interactions: 115404 Sorted by model distance: nonbonded pdb=" OG1 THR C 155 " pdb=" O LYS C 158 " model vdw 2.214 3.040 nonbonded pdb=" OG SER B 354 " pdb=" OD1 ASN B 356 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR C 327 " pdb=" O PRO C 406 " model vdw 2.261 3.040 nonbonded pdb=" OD2 ASP B 438 " pdb=" OH TYR B 457 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR C 77 " pdb=" O ASN C 293 " model vdw 2.266 3.040 ... (remaining 115399 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 16 through 482) selection = (chain 'C' and resid 16 through 482) selection = (chain 'D' and (resid 16 through 278 or (resid 279 and (name N or name CA or nam \ e C or name O or name CB )) or resid 280 through 482)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.150 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.770 Find NCS groups from input model: 0.330 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: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.182 14943 Z= 0.290 Angle : 0.597 10.717 20257 Z= 0.311 Chirality : 0.036 0.160 2247 Planarity : 0.010 0.280 2621 Dihedral : 11.178 112.994 5541 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 covalent geometry : bond 0.00572 (14943) covalent geometry : angle 0.59744 (20257) hydrogen bonds : bond 0.15815 ( 694) hydrogen bonds : angle 5.31832 ( 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 : 0.580 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: 0.8017 (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: 0.1084 time to fit residues: 25.6370 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 : 0.553 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN B 44 GLN B 109 GLN ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 HIS C 307 HIS C 385 ASN D 44 GLN D 70 ASN D 221 ASN D 328 GLN D 385 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.083900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.064927 restraints weight = 63296.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.066809 restraints weight = 35523.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.068033 restraints weight = 24868.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.068863 restraints weight = 20031.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.069178 restraints weight = 17502.454| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1518 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= 0.104 Angle : 0.478 6.282 20257 Z= 0.238 Chirality : 0.037 0.130 2247 Planarity : 0.003 0.045 2621 Dihedral : 6.936 95.160 2151 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.98 % Allowed : 7.31 % Favored : 91.71 % 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: -0.78 (0.19), residues: 1855 helix: 0.88 (0.18), residues: 895 sheet: -1.05 (0.36), residues: 196 loop : -2.11 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 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 D 111 HIS 0.005 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00228 (14943) covalent geometry : angle 0.47762 (20257) hydrogen bonds : bond 0.02989 ( 694) hydrogen bonds : angle 3.81117 ( 2001) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 154 MET cc_start: 0.8199 (ptm) cc_final: 0.7718 (ttp) REVERT: A 287 ASN cc_start: 0.8140 (t0) cc_final: 0.7841 (t0) outliers start: 15 outliers final: 12 residues processed: 112 average time/residue: 0.1127 time to fit residues: 19.2698 Evaluate side-chains 97 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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: 5.9990 chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 165 optimal weight: 0.9990 chunk 168 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 65 optimal weight: 0.2980 chunk 16 optimal weight: 0.0970 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 256 HIS ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.083220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.064208 restraints weight = 63827.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.066112 restraints weight = 35453.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.067380 restraints weight = 24683.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.068162 restraints weight = 19727.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.068487 restraints weight = 17248.083| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14943 Z= 0.091 Angle : 0.460 7.197 20257 Z= 0.228 Chirality : 0.037 0.131 2247 Planarity : 0.003 0.046 2621 Dihedral : 6.915 94.509 2151 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % 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: -0.17 (0.20), residues: 1855 helix: 1.37 (0.18), residues: 893 sheet: -0.67 (0.36), residues: 205 loop : -1.82 (0.21), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 213 TYR 0.010 0.001 TYR C 183 PHE 0.011 0.001 PHE D 268 TRP 0.002 0.000 TRP C 15 HIS 0.015 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00205 (14943) covalent geometry : angle 0.46007 (20257) hydrogen bonds : bond 0.02743 ( 694) hydrogen bonds : angle 3.62479 ( 2001) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: A 154 MET cc_start: 0.8209 (ptm) cc_final: 0.7715 (ttp) REVERT: A 287 ASN cc_start: 0.8215 (t0) cc_final: 0.7926 (t0) REVERT: C 142 ASP cc_start: 0.8196 (t0) cc_final: 0.7989 (t0) outliers start: 15 outliers final: 9 residues processed: 108 average time/residue: 0.1000 time to fit residues: 17.4388 Evaluate side-chains 95 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 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: 1.9990 chunk 166 optimal weight: 0.0270 chunk 106 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 chunk 154 optimal weight: 0.9990 chunk 104 optimal weight: 0.0980 chunk 134 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 175 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.082688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.063513 restraints weight = 63660.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.065396 restraints weight = 35434.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.066653 restraints weight = 24808.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.067396 restraints weight = 19945.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.067760 restraints weight = 17518.129| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14943 Z= 0.089 Angle : 0.457 9.717 20257 Z= 0.226 Chirality : 0.037 0.132 2247 Planarity : 0.003 0.047 2621 Dihedral : 6.926 93.773 2151 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.98 % Allowed : 9.79 % Favored : 89.23 % 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: 1.63 (0.18), residues: 898 sheet: -0.69 (0.37), residues: 195 loop : -1.60 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 213 TYR 0.007 0.001 TYR A 172 PHE 0.010 0.001 PHE D 268 TRP 0.002 0.000 TRP A 111 HIS 0.002 0.000 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00200 (14943) covalent geometry : angle 0.45698 (20257) hydrogen bonds : bond 0.02589 ( 694) hydrogen bonds : angle 3.51125 ( 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 112 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8274 (ptm) cc_final: 0.7800 (ttp) REVERT: A 287 ASN cc_start: 0.8258 (t0) cc_final: 0.7966 (t0) REVERT: C 142 ASP cc_start: 0.8077 (t0) cc_final: 0.7869 (t0) outliers start: 15 outliers final: 13 residues processed: 106 average time/residue: 0.1068 time to fit residues: 18.1624 Evaluate side-chains 104 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 21 MET Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 29 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 158 optimal weight: 0.0970 chunk 120 optimal weight: 0.4980 chunk 118 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.082211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.063016 restraints weight = 63762.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.064888 restraints weight = 35713.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.066127 restraints weight = 25080.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.066898 restraints weight = 20290.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.067390 restraints weight = 17797.034| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2382 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= 0.093 Angle : 0.471 10.417 20257 Z= 0.233 Chirality : 0.037 0.131 2247 Planarity : 0.003 0.047 2621 Dihedral : 6.965 92.877 2151 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.11 % Allowed : 10.25 % Favored : 88.64 % 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: 0.46 (0.20), residues: 1855 helix: 1.88 (0.18), residues: 897 sheet: -0.55 (0.38), residues: 195 loop : -1.43 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 213 TYR 0.008 0.001 TYR A 172 PHE 0.010 0.001 PHE D 268 TRP 0.002 0.000 TRP C 111 HIS 0.002 0.001 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00210 (14943) covalent geometry : angle 0.47096 (20257) hydrogen bonds : bond 0.02576 ( 694) hydrogen bonds : angle 3.46764 ( 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 112 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8287 (ptm) cc_final: 0.7868 (ttp) REVERT: A 287 ASN cc_start: 0.8291 (t0) cc_final: 0.8021 (t0) REVERT: C 142 ASP cc_start: 0.8092 (t0) cc_final: 0.7891 (t0) outliers start: 17 outliers final: 15 residues processed: 106 average time/residue: 0.1095 time to fit residues: 18.2106 Evaluate side-chains 102 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 21 MET 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 143 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 114 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 305 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.079270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.060082 restraints weight = 63116.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.061889 restraints weight = 35645.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.063122 restraints weight = 25100.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.063857 restraints weight = 20297.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.064315 restraints weight = 17867.499| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14943 Z= 0.182 Angle : 0.569 10.096 20257 Z= 0.287 Chirality : 0.040 0.146 2247 Planarity : 0.004 0.047 2621 Dihedral : 7.371 92.149 2151 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.70 % Allowed : 10.77 % Favored : 87.53 % 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: 0.41 (0.20), residues: 1855 helix: 1.81 (0.18), residues: 892 sheet: -0.60 (0.38), residues: 192 loop : -1.37 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 213 TYR 0.012 0.001 TYR D 269 PHE 0.017 0.002 PHE D 268 TRP 0.006 0.001 TRP B 111 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00417 (14943) covalent geometry : angle 0.56944 (20257) hydrogen bonds : bond 0.03562 ( 694) hydrogen bonds : angle 3.86832 ( 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 108 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 226 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8120 (ttm) REVERT: A 287 ASN cc_start: 0.8370 (t0) cc_final: 0.8089 (t0) REVERT: A 358 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8233 (pp) REVERT: C 142 ASP cc_start: 0.8224 (t0) cc_final: 0.8018 (t0) REVERT: C 231 HIS cc_start: 0.8103 (OUTLIER) cc_final: 0.7453 (t-90) outliers start: 26 outliers final: 19 residues processed: 97 average time/residue: 0.1007 time to fit residues: 16.0827 Evaluate side-chains 97 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 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 132 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 199 ILE 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 132 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 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 121 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 179 optimal weight: 0.0870 chunk 127 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 162 optimal weight: 1.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.080851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.061426 restraints weight = 63163.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.063272 restraints weight = 35878.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.064503 restraints weight = 25248.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.065323 restraints weight = 20507.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.065678 restraints weight = 17929.741| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14943 Z= 0.099 Angle : 0.495 9.089 20257 Z= 0.246 Chirality : 0.037 0.135 2247 Planarity : 0.003 0.047 2621 Dihedral : 7.222 91.076 2151 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.17 % Allowed : 11.95 % Favored : 86.88 % 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: 0.65 (0.20), residues: 1855 helix: 2.00 (0.18), residues: 892 sheet: -0.52 (0.38), residues: 195 loop : -1.23 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 213 TYR 0.008 0.001 TYR A 172 PHE 0.011 0.001 PHE D 268 TRP 0.007 0.001 TRP B 15 HIS 0.003 0.001 HIS C 194 Details of bonding type rmsd covalent geometry : bond 0.00223 (14943) covalent geometry : angle 0.49512 (20257) hydrogen bonds : bond 0.02803 ( 694) hydrogen bonds : angle 3.65505 ( 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 102 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 287 ASN cc_start: 0.8356 (t0) cc_final: 0.8104 (t0) REVERT: A 358 LEU cc_start: 0.8464 (pp) cc_final: 0.8232 (pp) REVERT: C 142 ASP cc_start: 0.8017 (t0) cc_final: 0.7796 (t0) REVERT: C 231 HIS cc_start: 0.8007 (OUTLIER) cc_final: 0.7556 (t-90) outliers start: 18 outliers final: 17 residues processed: 94 average time/residue: 0.1014 time to fit residues: 15.7863 Evaluate side-chains 98 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 253 THR 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 143 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 106 optimal weight: 0.0980 chunk 30 optimal weight: 0.6980 chunk 155 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.081156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.061696 restraints weight = 63680.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.063564 restraints weight = 36056.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.064842 restraints weight = 25392.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.065622 restraints weight = 20539.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.066075 restraints weight = 18025.883| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14943 Z= 0.096 Angle : 0.485 9.635 20257 Z= 0.240 Chirality : 0.037 0.136 2247 Planarity : 0.003 0.046 2621 Dihedral : 7.146 89.933 2151 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.17 % Allowed : 11.95 % Favored : 86.88 % 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: 0.86 (0.20), residues: 1855 helix: 2.15 (0.18), residues: 886 sheet: -0.41 (0.38), residues: 194 loop : -1.09 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 213 TYR 0.008 0.001 TYR A 172 PHE 0.011 0.001 PHE D 268 TRP 0.010 0.001 TRP B 15 HIS 0.002 0.001 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00216 (14943) covalent geometry : angle 0.48513 (20257) hydrogen bonds : bond 0.02654 ( 694) hydrogen bonds : angle 3.55353 ( 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: 18 poor density : 85 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 287 ASN cc_start: 0.8314 (t0) cc_final: 0.8088 (t0) REVERT: A 358 LEU cc_start: 0.8432 (pp) cc_final: 0.8160 (pp) REVERT: C 142 ASP cc_start: 0.7978 (t0) cc_final: 0.7769 (t0) REVERT: C 231 HIS cc_start: 0.7929 (OUTLIER) cc_final: 0.7513 (t-90) REVERT: D 170 MET cc_start: 0.8495 (tpt) cc_final: 0.8155 (tpt) outliers start: 18 outliers final: 14 residues processed: 95 average time/residue: 0.1065 time to fit residues: 16.1317 Evaluate side-chains 94 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 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 143 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 150 optimal weight: 0.0970 chunk 104 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 154 optimal weight: 0.2980 chunk 85 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.080645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.061409 restraints weight = 62837.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.063254 restraints weight = 35516.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.064469 restraints weight = 24969.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.065271 restraints weight = 20250.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.065584 restraints weight = 17739.181| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14943 Z= 0.117 Angle : 0.500 9.064 20257 Z= 0.250 Chirality : 0.037 0.138 2247 Planarity : 0.003 0.046 2621 Dihedral : 7.181 89.138 2151 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.31 % Allowed : 11.95 % Favored : 86.75 % 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: 0.88 (0.20), residues: 1855 helix: 2.16 (0.18), residues: 886 sheet: -0.37 (0.38), residues: 192 loop : -1.07 (0.22), residues: 777 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 0.013 0.001 PHE D 268 TRP 0.012 0.001 TRP B 15 HIS 0.008 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00268 (14943) covalent geometry : angle 0.50036 (20257) hydrogen bonds : bond 0.02828 ( 694) hydrogen bonds : angle 3.60149 ( 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 101 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 287 ASN cc_start: 0.8357 (t0) cc_final: 0.8129 (t0) REVERT: A 358 LEU cc_start: 0.8417 (pp) cc_final: 0.8185 (pp) REVERT: C 142 ASP cc_start: 0.7995 (t0) cc_final: 0.7783 (t0) REVERT: C 231 HIS cc_start: 0.7951 (OUTLIER) cc_final: 0.7527 (t-90) REVERT: D 170 MET cc_start: 0.8492 (tpt) cc_final: 0.8154 (tpt) outliers start: 20 outliers final: 18 residues processed: 95 average time/residue: 0.0994 time to fit residues: 15.3826 Evaluate side-chains 98 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 143 LEU 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 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 152 optimal weight: 0.3980 chunk 93 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.080986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.061778 restraints weight = 62841.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.063638 restraints weight = 35393.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.064886 restraints weight = 25010.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.065670 restraints weight = 20168.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.066035 restraints weight = 17644.487| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14943 Z= 0.103 Angle : 0.505 10.612 20257 Z= 0.251 Chirality : 0.037 0.140 2247 Planarity : 0.003 0.047 2621 Dihedral : 7.169 88.571 2151 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.31 % Allowed : 12.14 % Favored : 86.55 % 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: 0.93 (0.20), residues: 1855 helix: 2.20 (0.18), residues: 886 sheet: -0.37 (0.38), residues: 192 loop : -1.04 (0.22), residues: 777 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 0.008 0.001 TRP B 15 HIS 0.003 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00234 (14943) covalent geometry : angle 0.50542 (20257) hydrogen bonds : bond 0.02750 ( 694) hydrogen bonds : angle 3.55555 ( 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 104 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 287 ASN cc_start: 0.8337 (t0) cc_final: 0.8110 (t0) REVERT: A 358 LEU cc_start: 0.8406 (pp) cc_final: 0.8176 (pp) REVERT: C 142 ASP cc_start: 0.7949 (t0) cc_final: 0.7741 (t0) REVERT: C 231 HIS cc_start: 0.7900 (OUTLIER) cc_final: 0.7490 (t-90) REVERT: D 170 MET cc_start: 0.8505 (tpt) cc_final: 0.8155 (tpt) REVERT: D 320 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7589 (tpp) outliers start: 20 outliers final: 18 residues processed: 97 average time/residue: 0.0984 time to fit residues: 15.7489 Evaluate side-chains 102 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 143 LEU 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 320 MET 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: 1.9990 chunk 156 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 139 optimal weight: 0.3980 chunk 145 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.081118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.061952 restraints weight = 62371.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.063791 restraints weight = 35262.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.065065 restraints weight = 24772.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.065772 restraints weight = 19998.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.066303 restraints weight = 17646.954| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14943 Z= 0.099 Angle : 0.505 11.441 20257 Z= 0.249 Chirality : 0.037 0.147 2247 Planarity : 0.003 0.047 2621 Dihedral : 7.144 88.039 2151 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % 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: 1.00 (0.20), residues: 1855 helix: 2.22 (0.18), residues: 886 sheet: -0.23 (0.37), residues: 204 loop : -0.98 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 213 TYR 0.007 0.001 TYR D 172 PHE 0.011 0.001 PHE D 268 TRP 0.008 0.001 TRP B 15 HIS 0.006 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00225 (14943) covalent geometry : angle 0.50459 (20257) hydrogen bonds : bond 0.02689 ( 694) hydrogen bonds : angle 3.53629 ( 2001) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2537.60 seconds wall clock time: 44 minutes 43.06 seconds (2683.06 seconds total)