Starting phenix.real_space_refine on Thu Jul 2 08:32:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jsh_22454/07_2026/7jsh_22454.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jsh_22454/07_2026/7jsh_22454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jsh_22454/07_2026/7jsh_22454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jsh_22454/07_2026/7jsh_22454.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jsh_22454/07_2026/7jsh_22454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jsh_22454/07_2026/7jsh_22454.map" } resolution = 4.4 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= -0.002 sd= 0.090 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians P 15 5.49 5 C 3950 2.51 5 N 1954 2.21 5 O 1997 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7916 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 1088 Classifications: {'peptide': 272} Incomplete info: {'backbone_only': 255} Link IDs: {'PTRANS': 9, 'TRANS': 262} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1130 Unresolved non-hydrogen angles: 1634 Unresolved non-hydrogen dihedrals: 753 Unresolved non-hydrogen chiralities: 325 Planarities with less than four sites: {'ARG:plan': 9, 'TYR:plan': 8, 'GLU:plan': 16, 'TRP:plan': 8, 'ASP:plan': 16, 'GLN:plan1': 13, 'PHE:plan': 14, 'ASN:plan1': 14, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 553 Chain: "B" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 1088 Classifications: {'peptide': 272} Incomplete info: {'backbone_only': 255} Link IDs: {'PTRANS': 9, 'TRANS': 262} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1130 Unresolved non-hydrogen angles: 1634 Unresolved non-hydrogen dihedrals: 753 Unresolved non-hydrogen chiralities: 325 Planarities with less than four sites: {'ARG:plan': 9, 'TYR:plan': 8, 'GLU:plan': 16, 'TRP:plan': 8, 'ASP:plan': 16, 'GLN:plan1': 13, 'PHE:plan': 14, 'ASN:plan1': 14, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 553 Chain: "C" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 1088 Classifications: {'peptide': 272} Incomplete info: {'backbone_only': 255} Link IDs: {'PTRANS': 9, 'TRANS': 262} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1130 Unresolved non-hydrogen angles: 1634 Unresolved non-hydrogen dihedrals: 753 Unresolved non-hydrogen chiralities: 325 Planarities with less than four sites: {'ARG:plan': 9, 'TYR:plan': 8, 'GLU:plan': 16, 'TRP:plan': 8, 'ASP:plan': 16, 'GLN:plan1': 13, 'PHE:plan': 14, 'ASN:plan1': 14, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 553 Chain: "D" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 1088 Classifications: {'peptide': 272} Incomplete info: {'backbone_only': 255} Link IDs: {'PTRANS': 9, 'TRANS': 262} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1130 Unresolved non-hydrogen angles: 1634 Unresolved non-hydrogen dihedrals: 753 Unresolved non-hydrogen chiralities: 325 Planarities with less than four sites: {'ARG:plan': 9, 'TYR:plan': 8, 'GLU:plan': 16, 'TRP:plan': 8, 'ASP:plan': 16, 'GLN:plan1': 13, 'PHE:plan': 14, 'ASN:plan1': 14, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 553 Chain: "E" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 1088 Classifications: {'peptide': 272} Incomplete info: {'backbone_only': 255} Link IDs: {'PTRANS': 9, 'TRANS': 262} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1130 Unresolved non-hydrogen angles: 1634 Unresolved non-hydrogen dihedrals: 753 Unresolved non-hydrogen chiralities: 325 Planarities with less than four sites: {'ARG:plan': 9, 'TYR:plan': 8, 'GLU:plan': 16, 'TRP:plan': 8, 'ASP:plan': 16, 'GLN:plan1': 13, 'PHE:plan': 14, 'ASN:plan1': 14, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 553 Chain: "F" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 1088 Classifications: {'peptide': 272} Incomplete info: {'backbone_only': 255} Link IDs: {'PTRANS': 9, 'TRANS': 262} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1130 Unresolved non-hydrogen angles: 1634 Unresolved non-hydrogen dihedrals: 753 Unresolved non-hydrogen chiralities: 325 Planarities with less than four sites: {'ARG:plan': 9, 'TYR:plan': 8, 'GLU:plan': 16, 'TRP:plan': 8, 'ASP:plan': 16, 'GLN:plan1': 13, 'PHE:plan': 14, 'ASN:plan1': 14, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 553 Chain: "G" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 1088 Classifications: {'peptide': 272} Incomplete info: {'backbone_only': 255} Link IDs: {'PTRANS': 9, 'TRANS': 262} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1130 Unresolved non-hydrogen angles: 1634 Unresolved non-hydrogen dihedrals: 753 Unresolved non-hydrogen chiralities: 325 Planarities with less than four sites: {'ARG:plan': 9, 'TYR:plan': 8, 'GLU:plan': 16, 'TRP:plan': 8, 'ASP:plan': 16, 'GLN:plan1': 13, 'PHE:plan': 14, 'ASN:plan1': 14, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 553 Chain: "N" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 300 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Time building chain proxies: 2.82, per 1000 atoms: 0.36 Number of scatterers: 7916 At special positions: 0 Unit cell: (99.0388, 132.995, 138.654, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) P 15 15.00 O 1997 8.00 N 1954 7.00 C 3950 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: 1.09 Conformation dependent library (CDL) restraints added in 585.0 milliseconds 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 17 sheets defined 46.6% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 219 through 233 Processing helix chain 'A' and resid 238 through 245 removed outlier: 3.508A pdb=" N TRP A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 256 Processing helix chain 'A' and resid 260 through 276 Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 296 through 306 removed outlier: 3.662A pdb=" N LYS A 300 " --> pdb=" O ASN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 322 removed outlier: 3.578A pdb=" N LYS A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 351 removed outlier: 3.943A pdb=" N VAL A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 394 removed outlier: 3.731A pdb=" N LYS A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 444 removed outlier: 3.924A pdb=" N LEU A 441 " --> pdb=" O HIS A 437 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG A 444 " --> pdb=" O PRO A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 476 removed outlier: 3.580A pdb=" N HIS A 476 " --> pdb=" O TRP A 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 233 Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'B' and resid 247 through 256 removed outlier: 4.256A pdb=" N ILE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 276 removed outlier: 3.932A pdb=" N ILE B 263 " --> pdb=" O SER B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 Processing helix chain 'B' and resid 296 through 306 removed outlier: 3.547A pdb=" N LYS B 300 " --> pdb=" O ASN B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 322 Processing helix chain 'B' and resid 339 through 351 removed outlier: 4.114A pdb=" N VAL B 351 " --> pdb=" O ILE B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 392 removed outlier: 3.731A pdb=" N ALA B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 444 Processing helix chain 'B' and resid 462 through 476 removed outlier: 3.921A pdb=" N VAL B 466 " --> pdb=" O THR B 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 233 Processing helix chain 'C' and resid 238 through 246 removed outlier: 3.568A pdb=" N TRP C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP C 246 " --> pdb=" O TRP C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 257 removed outlier: 3.973A pdb=" N TYR C 250 " --> pdb=" O ASP C 246 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 251 " --> pdb=" O GLN C 247 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER C 257 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 278 Processing helix chain 'C' and resid 279 through 285 removed outlier: 3.578A pdb=" N TYR C 283 " --> pdb=" O THR C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 306 Processing helix chain 'C' and resid 308 through 320 Processing helix chain 'C' and resid 335 through 338 removed outlier: 3.775A pdb=" N THR C 338 " --> pdb=" O PRO C 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 335 through 338' Processing helix chain 'C' and resid 339 through 351 removed outlier: 3.842A pdb=" N VAL C 351 " --> pdb=" O ILE C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 395 Processing helix chain 'C' and resid 438 through 444 Processing helix chain 'C' and resid 462 through 476 removed outlier: 3.929A pdb=" N VAL C 466 " --> pdb=" O THR C 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 233 Processing helix chain 'D' and resid 238 through 245 Processing helix chain 'D' and resid 247 through 256 removed outlier: 4.004A pdb=" N ILE D 251 " --> pdb=" O GLN D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 278 removed outlier: 3.702A pdb=" N LYS D 278 " --> pdb=" O MET D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 295 removed outlier: 3.687A pdb=" N SER D 295 " --> pdb=" O ASP D 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 292 through 295' Processing helix chain 'D' and resid 296 through 306 removed outlier: 3.571A pdb=" N LYS D 300 " --> pdb=" O ASN D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 335 through 338 removed outlier: 3.682A pdb=" N THR D 338 " --> pdb=" O PRO D 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 335 through 338' Processing helix chain 'D' and resid 339 through 350 removed outlier: 3.702A pdb=" N ILE D 343 " --> pdb=" O GLY D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 394 removed outlier: 3.710A pdb=" N ALA D 392 " --> pdb=" O GLU D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 444 removed outlier: 3.842A pdb=" N LEU D 441 " --> pdb=" O HIS D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 476 Processing helix chain 'E' and resid 220 through 235 Processing helix chain 'E' and resid 238 through 245 Processing helix chain 'E' and resid 247 through 256 Processing helix chain 'E' and resid 260 through 276 Processing helix chain 'E' and resid 281 through 285 removed outlier: 3.549A pdb=" N LEU E 284 " --> pdb=" O PRO E 281 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL E 285 " --> pdb=" O ASP E 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 281 through 285' Processing helix chain 'E' and resid 296 through 306 removed outlier: 3.907A pdb=" N LYS E 300 " --> pdb=" O ASN E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 322 Processing helix chain 'E' and resid 340 through 351 removed outlier: 3.921A pdb=" N VAL E 351 " --> pdb=" O ILE E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 396 removed outlier: 3.611A pdb=" N ALA E 392 " --> pdb=" O GLU E 388 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY E 395 " --> pdb=" O LYS E 391 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY E 396 " --> pdb=" O ALA E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 444 removed outlier: 3.783A pdb=" N LEU E 441 " --> pdb=" O HIS E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 476 removed outlier: 3.606A pdb=" N VAL E 466 " --> pdb=" O THR E 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 233 Processing helix chain 'F' and resid 238 through 246 Processing helix chain 'F' and resid 247 through 256 removed outlier: 4.434A pdb=" N ILE F 251 " --> pdb=" O GLN F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 276 Processing helix chain 'F' and resid 280 through 285 removed outlier: 3.711A pdb=" N TYR F 283 " --> pdb=" O ALA F 280 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU F 284 " --> pdb=" O PRO F 281 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL F 285 " --> pdb=" O ASP F 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 280 through 285' Processing helix chain 'F' and resid 296 through 306 Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 339 through 350 removed outlier: 3.703A pdb=" N ILE F 343 " --> pdb=" O GLY F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 395 removed outlier: 3.771A pdb=" N ALA F 392 " --> pdb=" O GLU F 388 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE F 393 " --> pdb=" O SER F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 444 Processing helix chain 'F' and resid 463 through 476 Processing helix chain 'G' and resid 220 through 235 Processing helix chain 'G' and resid 239 through 245 Processing helix chain 'G' and resid 246 through 256 removed outlier: 4.331A pdb=" N TYR G 250 " --> pdb=" O ASP G 246 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE G 251 " --> pdb=" O GLN G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 277 removed outlier: 3.971A pdb=" N ILE G 263 " --> pdb=" O SER G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 306 Processing helix chain 'G' and resid 308 through 320 Processing helix chain 'G' and resid 340 through 351 removed outlier: 3.989A pdb=" N VAL G 351 " --> pdb=" O ILE G 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 394 removed outlier: 3.634A pdb=" N ALA G 392 " --> pdb=" O GLU G 388 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 444 removed outlier: 4.334A pdb=" N LEU G 441 " --> pdb=" O HIS G 437 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 476 Processing sheet with id=AA1, first strand: chain 'A' and resid 375 through 377 removed outlier: 6.490A pdb=" N ILE A 375 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N THR A 419 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N TRP A 377 " --> pdb=" O THR A 419 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ILE A 330 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR A 329 " --> pdb=" O PHE A 446 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N PHE A 448 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TRP A 331 " --> pdb=" O PHE A 448 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 332 removed outlier: 6.327A pdb=" N ILE B 330 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY B 355 " --> pdb=" O TRP B 376 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 428 through 429 removed outlier: 4.208A pdb=" N SER B 432 " --> pdb=" O ASP B 429 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 331 through 332 removed outlier: 6.439A pdb=" N TRP C 331 " --> pdb=" O PHE C 448 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LYS C 447 " --> pdb=" O VAL C 486 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 354 through 356 removed outlier: 5.970A pdb=" N ILE C 375 " --> pdb=" O ILE C 417 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 354 through 358 removed outlier: 4.574A pdb=" N GLU D 378 " --> pdb=" O VAL D 357 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE D 417 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP D 377 " --> pdb=" O ILE D 417 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILE D 330 " --> pdb=" O VAL D 418 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N PHE D 448 " --> pdb=" O THR D 329 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TRP D 331 " --> pdb=" O PHE D 448 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 399 through 402 removed outlier: 3.504A pdb=" N VAL D 399 " --> pdb=" O ILE D 411 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 428 through 429 removed outlier: 3.579A pdb=" N SER D 432 " --> pdb=" O ASP D 429 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 416 through 418 removed outlier: 5.867A pdb=" N ILE E 330 " --> pdb=" O VAL E 418 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 354 through 357 Processing sheet with id=AB2, first strand: chain 'E' and resid 399 through 400 removed outlier: 3.794A pdb=" N VAL E 399 " --> pdb=" O ILE E 411 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 354 through 356 removed outlier: 5.976A pdb=" N ILE F 375 " --> pdb=" O ILE F 417 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N THR F 419 " --> pdb=" O ILE F 375 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N TRP F 377 " --> pdb=" O THR F 419 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE F 330 " --> pdb=" O VAL F 418 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE F 448 " --> pdb=" O TRP F 331 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 399 through 402 removed outlier: 4.179A pdb=" N VAL F 399 " --> pdb=" O ILE F 411 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL F 401 " --> pdb=" O ALA F 409 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA F 409 " --> pdb=" O VAL F 401 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 428 through 429 Processing sheet with id=AB6, first strand: chain 'G' and resid 416 through 418 removed outlier: 6.046A pdb=" N ILE G 330 " --> pdb=" O VAL G 418 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 355 through 356 removed outlier: 7.400A pdb=" N GLY G 355 " --> pdb=" O TRP G 376 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'G' and resid 427 through 428 removed outlier: 4.116A pdb=" N VAL G 427 " --> pdb=" O THR G 434 " (cutoff:3.500A) 555 hydrogen bonds defined for protein. 1659 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: 1.23 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.30: 1922 1.30 - 1.37: 1961 1.37 - 1.45: 209 1.45 - 1.53: 3793 1.53 - 1.61: 57 Bond restraints: 7942 Sorted by residual: bond pdb=" C1' DT N 8 " pdb=" N1 DT N 8 " ideal model delta sigma weight residual 1.468 1.492 -0.024 1.40e-02 5.10e+03 2.99e+00 bond pdb=" C1' DT N 4 " pdb=" N1 DT N 4 " ideal model delta sigma weight residual 1.468 1.492 -0.024 1.40e-02 5.10e+03 2.92e+00 bond pdb=" C1' DT N 12 " pdb=" N1 DT N 12 " ideal model delta sigma weight residual 1.468 1.491 -0.023 1.40e-02 5.10e+03 2.80e+00 bond pdb=" C1' DC N 5 " pdb=" N1 DC N 5 " ideal model delta sigma weight residual 1.468 1.491 -0.023 1.40e-02 5.10e+03 2.69e+00 bond pdb=" C1' DC N 1 " pdb=" N1 DC N 1 " ideal model delta sigma weight residual 1.468 1.491 -0.023 1.40e-02 5.10e+03 2.64e+00 ... (remaining 7937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.77: 9797 0.77 - 1.55: 146 1.55 - 2.32: 53 2.32 - 3.09: 10 3.09 - 3.86: 3 Bond angle restraints: 10009 Sorted by residual: angle pdb=" N3 DT N 8 " pdb=" C4 DT N 8 " pdb=" O4 DT N 8 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT N 4 " pdb=" C4 DT N 4 " pdb=" O4 DT N 4 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT N 12 " pdb=" C4 DT N 12 " pdb=" O4 DT N 12 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 angle pdb=" O4 DT N 8 " pdb=" C4 DT N 8 " pdb=" C5 DT N 8 " ideal model delta sigma weight residual 124.90 122.32 2.58 7.00e-01 2.04e+00 1.36e+01 angle pdb=" O4 DT N 12 " pdb=" C4 DT N 12 " pdb=" C5 DT N 12 " ideal model delta sigma weight residual 124.90 122.35 2.55 7.00e-01 2.04e+00 1.33e+01 ... (remaining 10004 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.82: 1952 11.82 - 23.64: 13 23.64 - 35.46: 20 35.46 - 47.28: 22 47.28 - 59.09: 37 Dihedral angle restraints: 2044 sinusoidal: 147 harmonic: 1897 Sorted by residual: dihedral pdb=" C3' DG N 2 " pdb=" O3' DG N 2 " pdb=" P DC N 3 " pdb=" O5' DC N 3 " ideal model delta sinusoidal sigma weight residual 172.00 -128.91 -59.09 3 3.00e+01 1.11e-03 2.37e+00 dihedral pdb=" C3' DC N 5 " pdb=" O3' DC N 5 " pdb=" P DG N 6 " pdb=" O5' DG N 6 " ideal model delta sinusoidal sigma weight residual 172.00 -130.76 -57.24 3 3.00e+01 1.11e-03 2.36e+00 dihedral pdb=" C3' DT N 4 " pdb=" O3' DT N 4 " pdb=" P DC N 5 " pdb=" O5' DC N 5 " ideal model delta sinusoidal sigma weight residual 172.00 -131.21 -56.79 3 3.00e+01 1.11e-03 2.35e+00 ... (remaining 2041 not shown) Histogram of chiral volume deviations from ideal: 0.008 - 0.023: 6 0.023 - 0.039: 35 0.039 - 0.055: 5 0.055 - 0.071: 7 0.071 - 0.086: 7 Chirality restraints: 60 Sorted by residual: chirality pdb=" C3' DC N 7 " pdb=" C4' DC N 7 " pdb=" O3' DC N 7 " pdb=" C2' DC N 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.64 -0.09 2.00e-01 2.50e+01 1.86e-01 chirality pdb=" C3' DG N 14 " pdb=" C4' DG N 14 " pdb=" O3' DG N 14 " pdb=" C2' DG N 14 " both_signs ideal model delta sigma weight residual False -2.73 -2.65 -0.08 2.00e-01 2.50e+01 1.67e-01 chirality pdb=" C3' DC N 3 " pdb=" C4' DC N 3 " pdb=" O3' DC N 3 " pdb=" C2' DC N 3 " both_signs ideal model delta sigma weight residual False -2.73 -2.65 -0.08 2.00e-01 2.50e+01 1.50e-01 ... (remaining 57 not shown) Planarity restraints: 1912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC N 9 " 0.002 2.00e-02 2.50e+03 1.30e-03 3.83e-02 pdb=" N1 DC N 9 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DC N 9 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DC N 9 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DC N 9 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DC N 9 " -0.000 2.00e-02 2.50e+03 pdb=" N4 DC N 9 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DC N 9 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DC N 9 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT N 8 " 0.002 2.00e-02 2.50e+03 1.13e-03 3.20e-02 pdb=" N1 DT N 8 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DT N 8 " -0.000 2.00e-02 2.50e+03 pdb=" O2 DT N 8 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DT N 8 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT N 8 " -0.000 2.00e-02 2.50e+03 pdb=" O4 DT N 8 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DT N 8 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT N 8 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DT N 8 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 300 " -0.001 2.00e-02 2.50e+03 1.72e-03 2.97e-02 pdb=" C LYS B 300 " 0.003 2.00e-02 2.50e+03 pdb=" O LYS B 300 " -0.001 2.00e-02 2.50e+03 pdb=" N ILE B 301 " -0.001 2.00e-02 2.50e+03 ... (remaining 1909 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.04: 4797 3.04 - 3.51: 5816 3.51 - 3.97: 8507 3.97 - 4.44: 8124 4.44 - 4.90: 13550 Nonbonded interactions: 40794 Sorted by model distance: nonbonded pdb=" N TRP C 331 " pdb=" O PHE C 446 " model vdw 2.581 3.120 nonbonded pdb=" O TRP A 331 " pdb=" N PHE A 448 " model vdw 2.596 3.120 nonbonded pdb=" N1 DG N 14 " pdb=" C4 DG N 14 " model vdw 2.602 2.672 nonbonded pdb=" N1 DG N 2 " pdb=" C4 DG N 2 " model vdw 2.603 2.672 nonbonded pdb=" N1 DG N 10 " pdb=" C4 DG N 10 " model vdw 2.603 2.672 ... (remaining 40789 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.090 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2458 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 : 0.002 0.024 7942 Z= 0.141 Angle : 0.248 3.863 10009 Z= 0.211 Chirality : 0.045 0.086 60 Planarity : 0.000 0.002 1912 Dihedral : 8.813 59.094 2044 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 3.23 % Allowed : 13.12 % Favored : 83.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.27 (0.17), residues: 1890 helix: -0.27 (0.18), residues: 830 sheet: -2.57 (0.44), residues: 108 loop : -4.10 (0.14), residues: 952 Details of bonding type rmsd/Z covalent geometry : bond 0.00157 / 0.14 ( 7942) covalent geometry : angle 0.24792 / 0.21 (10009) hydrogen bonds : bond 0.14316 / 11.20 ( 555) hydrogen bonds : angle 5.20654 / 3.97 ( 1659) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.323 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0308 time to fit residues: 2.9036 Evaluate side-chains 42 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 40.0000 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 0.6980 overall best weight: 10.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.072008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.059525 restraints weight = 77730.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.058716 restraints weight = 89890.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.058494 restraints weight = 106538.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.058483 restraints weight = 107745.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.058457 restraints weight = 107915.972| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4773 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7942 Z= 0.366 Angle : 1.069 11.708 10009 Z= 0.641 Chirality : 0.043 0.096 60 Planarity : 0.006 0.034 1912 Dihedral : 11.390 59.403 2044 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.30 % Favored : 92.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.31 (0.17), residues: 1890 helix: -0.88 (0.16), residues: 834 sheet: -1.95 (0.50), residues: 104 loop : -3.60 (0.15), residues: 952 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.37 ( 7942) covalent geometry : angle 1.06906 / 0.64 (10009) hydrogen bonds : bond 0.06277 / 4.94 ( 555) hydrogen bonds : angle 6.44776 / 4.97 ( 1659) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.338 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0340 time to fit residues: 3.1488 Evaluate side-chains 42 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 7 optimal weight: 8.9990 chunk 83 optimal weight: 40.0000 chunk 125 optimal weight: 30.0000 chunk 18 optimal weight: 50.0000 chunk 142 optimal weight: 0.0000 chunk 156 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 146 optimal weight: 40.0000 chunk 137 optimal weight: 30.0000 chunk 45 optimal weight: 30.0000 overall best weight: 13.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.063227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.049964 restraints weight = 78923.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.049911 restraints weight = 82054.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.049868 restraints weight = 81569.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.049887 restraints weight = 79310.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.049887 restraints weight = 78602.032| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5438 moved from start: 1.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 7942 Z= 0.413 Angle : 1.256 14.636 10009 Z= 0.747 Chirality : 0.057 0.176 60 Planarity : 0.007 0.031 1912 Dihedral : 12.817 66.674 2044 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 1.64 % Allowed : 14.76 % Favored : 83.60 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.60 % 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: -4.05 (0.16), residues: 1890 helix: -1.60 (0.16), residues: 759 sheet: -2.52 (0.59), residues: 68 loop : -3.73 (0.16), residues: 1063 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.41 ( 7942) covalent geometry : angle 1.25561 / 0.75 (10009) hydrogen bonds : bond 0.08594 / 6.72 ( 555) hydrogen bonds : angle 9.21863 / 7.05 ( 1659) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.334 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0341 time to fit residues: 3.1924 Evaluate side-chains 42 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 186 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 159 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 74 optimal weight: 30.0000 chunk 139 optimal weight: 30.0000 chunk 148 optimal weight: 0.6980 chunk 65 optimal weight: 20.0000 chunk 48 optimal weight: 30.0000 chunk 123 optimal weight: 7.9990 overall best weight: 6.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.058682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.047417 restraints weight = 85882.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.047417 restraints weight = 86163.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.047416 restraints weight = 86163.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.047416 restraints weight = 86163.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.047416 restraints weight = 86163.867| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3305 moved from start: 1.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7942 Z= 0.194 Angle : 0.719 9.474 10009 Z= 0.424 Chirality : 0.031 0.086 60 Planarity : 0.003 0.020 1912 Dihedral : 11.302 64.720 2044 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.69 % Favored : 88.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.33 (0.17), residues: 1890 helix: -0.82 (0.17), residues: 791 sheet: -2.40 (0.72), residues: 50 loop : -3.51 (0.17), residues: 1049 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.19 ( 7942) covalent geometry : angle 0.71941 / 0.42 (10009) hydrogen bonds : bond 0.04734 / 3.69 ( 555) hydrogen bonds : angle 7.56106 / 5.80 ( 1659) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.349 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0341 time to fit residues: 3.1646 Evaluate side-chains 42 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 156 optimal weight: 30.0000 chunk 38 optimal weight: 50.0000 chunk 187 optimal weight: 20.0000 chunk 92 optimal weight: 40.0000 chunk 85 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 21 optimal weight: 50.0000 chunk 132 optimal weight: 30.0000 chunk 109 optimal weight: 50.0000 chunk 8 optimal weight: 0.0970 overall best weight: 9.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.059158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.046457 restraints weight = 84831.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.046056 restraints weight = 87492.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.045927 restraints weight = 92925.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.045900 restraints weight = 95052.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.045927 restraints weight = 91606.465| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5740 moved from start: 1.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 7942 Z= 0.307 Angle : 0.965 11.968 10009 Z= 0.569 Chirality : 0.042 0.125 60 Planarity : 0.005 0.025 1912 Dihedral : 11.800 74.299 2044 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.90 % Allowed : 18.47 % Favored : 80.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -3.67 (0.17), residues: 1890 helix: -1.01 (0.17), residues: 776 sheet: -2.81 (0.58), residues: 71 loop : -3.75 (0.17), residues: 1043 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.31 ( 7942) covalent geometry : angle 0.96520 / 0.57 (10009) hydrogen bonds : bond 0.06459 / 5.05 ( 555) hydrogen bonds : angle 8.30957 / 6.40 ( 1659) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.338 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0339 time to fit residues: 3.1623 Evaluate side-chains 42 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 157 optimal weight: 40.0000 chunk 48 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 145 optimal weight: 50.0000 chunk 90 optimal weight: 40.0000 chunk 60 optimal weight: 20.0000 chunk 160 optimal weight: 30.0000 chunk 130 optimal weight: 40.0000 chunk 1 optimal weight: 50.0000 chunk 183 optimal weight: 30.0000 chunk 18 optimal weight: 8.9990 overall best weight: 17.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.052936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.041268 restraints weight = 94199.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.041097 restraints weight = 93993.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.041000 restraints weight = 94082.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.041054 restraints weight = 93111.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.041037 restraints weight = 92640.802| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 moved from start: 1.8142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 7942 Z= 0.478 Angle : 1.427 14.216 10009 Z= 0.854 Chirality : 0.058 0.143 60 Planarity : 0.008 0.034 1912 Dihedral : 14.135 81.957 2044 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 1.06 % Allowed : 20.53 % Favored : 78.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.93 % 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: -5.15 (0.15), residues: 1890 helix: -2.68 (0.15), residues: 714 sheet: -2.41 (1.35), residues: 10 loop : -4.19 (0.15), residues: 1166 Details of bonding type rmsd/Z covalent geometry : bond 0.00651 / 0.48 ( 7942) covalent geometry : angle 1.42723 / 0.85 (10009) hydrogen bonds : bond 0.09858 / 7.66 ( 555) hydrogen bonds : angle 11.60647 / 8.89 ( 1659) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.318 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0309 time to fit residues: 2.8906 Evaluate side-chains 42 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 33 optimal weight: 10.0000 chunk 156 optimal weight: 30.0000 chunk 79 optimal weight: 9.9990 chunk 133 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 chunk 58 optimal weight: 30.0000 chunk 184 optimal weight: 7.9990 chunk 3 optimal weight: 50.0000 chunk 87 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.054255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.042411 restraints weight = 90012.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.041921 restraints weight = 90043.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.041858 restraints weight = 93612.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.041826 restraints weight = 96187.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.041852 restraints weight = 91277.844| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 moved from start: 1.7827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7942 Z= 0.211 Angle : 0.825 10.859 10009 Z= 0.483 Chirality : 0.048 0.138 60 Planarity : 0.004 0.021 1912 Dihedral : 12.296 84.208 2044 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.37 % Allowed : 18.68 % Favored : 80.95 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -4.43 (0.17), residues: 1890 helix: -1.75 (0.16), residues: 737 sheet: -3.75 (0.66), residues: 36 loop : -4.00 (0.16), residues: 1117 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.21 ( 7942) covalent geometry : angle 0.82507 / 0.48 (10009) hydrogen bonds : bond 0.05759 / 4.46 ( 555) hydrogen bonds : angle 9.18699 / 7.02 ( 1659) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.332 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0339 time to fit residues: 3.1334 Evaluate side-chains 42 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 0 optimal weight: 50.0000 chunk 23 optimal weight: 40.0000 chunk 96 optimal weight: 50.0000 chunk 184 optimal weight: 20.0000 chunk 50 optimal weight: 30.0000 chunk 56 optimal weight: 30.0000 chunk 7 optimal weight: 30.0000 chunk 98 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 37 optimal weight: 40.0000 chunk 48 optimal weight: 20.0000 overall best weight: 19.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.045650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.042897 restraints weight = 154100.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.042669 restraints weight = 241953.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.042634 restraints weight = 253725.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.042634 restraints weight = 257637.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.042634 restraints weight = 257478.196| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5717 moved from start: 2.0336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 7942 Z= 0.515 Angle : 1.379 15.432 10009 Z= 0.831 Chirality : 0.061 0.138 60 Planarity : 0.008 0.038 1912 Dihedral : 14.136 90.496 2044 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 1.32 % Allowed : 28.47 % Favored : 70.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.15 % 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: -5.48 (0.15), residues: 1890 helix: -2.91 (0.15), residues: 709 sheet: -2.51 (1.16), residues: 15 loop : -4.42 (0.15), residues: 1166 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.52 ( 7942) covalent geometry : angle 1.37862 / 0.83 (10009) hydrogen bonds : bond 0.10254 / 7.97 ( 555) hydrogen bonds : angle 11.85189 / 9.06 ( 1659) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.379 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0338 time to fit residues: 3.2008 Evaluate side-chains 42 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 45 optimal weight: 30.0000 chunk 92 optimal weight: 5.9990 chunk 117 optimal weight: 30.0000 chunk 120 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 53 optimal weight: 40.0000 chunk 66 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 153 optimal weight: 20.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.051975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.039679 restraints weight = 92882.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.039776 restraints weight = 86688.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.039895 restraints weight = 82451.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.039895 restraints weight = 79204.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.039895 restraints weight = 79204.025| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 moved from start: 1.9946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7942 Z= 0.212 Angle : 0.846 12.097 10009 Z= 0.496 Chirality : 0.053 0.176 60 Planarity : 0.004 0.022 1912 Dihedral : 12.703 96.932 2044 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.26 % Allowed : 19.58 % Favored : 80.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -4.80 (0.16), residues: 1890 helix: -2.03 (0.16), residues: 739 sheet: -3.38 (0.79), residues: 30 loop : -4.27 (0.16), residues: 1121 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.21 ( 7942) covalent geometry : angle 0.84599 / 0.50 (10009) hydrogen bonds : bond 0.05746 / 4.45 ( 555) hydrogen bonds : angle 9.76448 / 7.45 ( 1659) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.331 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0342 time to fit residues: 3.1711 Evaluate side-chains 42 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 156 optimal weight: 50.0000 chunk 30 optimal weight: 50.0000 chunk 136 optimal weight: 50.0000 chunk 84 optimal weight: 50.0000 chunk 115 optimal weight: 20.0000 chunk 143 optimal weight: 5.9990 chunk 158 optimal weight: 50.0000 chunk 14 optimal weight: 40.0000 chunk 32 optimal weight: 9.9990 chunk 38 optimal weight: 0.0980 chunk 170 optimal weight: 10.0000 overall best weight: 9.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.046630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.043613 restraints weight = 148135.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.043396 restraints weight = 167964.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.043309 restraints weight = 197811.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.043277 restraints weight = 207468.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.043274 restraints weight = 208360.063| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5631 moved from start: 2.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7942 Z= 0.272 Angle : 0.908 11.106 10009 Z= 0.532 Chirality : 0.047 0.141 60 Planarity : 0.005 0.025 1912 Dihedral : 12.627 97.237 2044 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.37 % Allowed : 26.03 % Favored : 73.60 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -4.71 (0.16), residues: 1890 helix: -1.77 (0.16), residues: 749 sheet: -2.41 (1.37), residues: 10 loop : -4.40 (0.15), residues: 1131 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.27 ( 7942) covalent geometry : angle 0.90816 / 0.53 (10009) hydrogen bonds : bond 0.06020 / 4.68 ( 555) hydrogen bonds : angle 9.62538 / 7.35 ( 1659) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.342 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0337 time to fit residues: 3.1296 Evaluate side-chains 42 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 0.0980 chunk 186 optimal weight: 5.9990 chunk 124 optimal weight: 30.0000 chunk 83 optimal weight: 50.0000 chunk 158 optimal weight: 40.0000 chunk 81 optimal weight: 40.0000 chunk 38 optimal weight: 30.0000 chunk 61 optimal weight: 0.0870 chunk 136 optimal weight: 50.0000 chunk 176 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 overall best weight: 3.6364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.047887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.043006 restraints weight = 173360.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.042253 restraints weight = 251044.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 91)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.042035 restraints weight = 267297.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.041851 restraints weight = 308103.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.041840 restraints weight = 306373.298| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4365 moved from start: 2.0493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7942 Z= 0.146 Angle : 0.673 9.993 10009 Z= 0.390 Chirality : 0.045 0.173 60 Planarity : 0.003 0.016 1912 Dihedral : 12.083 100.355 2044 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.26 % Allowed : 17.20 % Favored : 82.54 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.91 (0.17), residues: 1890 helix: -0.78 (0.17), residues: 757 sheet: -4.16 (0.59), residues: 42 loop : -4.15 (0.16), residues: 1091 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.15 ( 7942) covalent geometry : angle 0.67264 / 0.39 (10009) hydrogen bonds : bond 0.04465 / 3.46 ( 555) hydrogen bonds : angle 8.43131 / 6.42 ( 1659) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1318.97 seconds wall clock time: 23 minutes 17.28 seconds (1397.28 seconds total)