Starting phenix.real_space_refine on Fri Aug 22 20:59:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jsh_22454/08_2025/7jsh_22454.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jsh_22454/08_2025/7jsh_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7jsh_22454/08_2025/7jsh_22454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jsh_22454/08_2025/7jsh_22454.map" model { file = "/net/cci-nas-00/data/ceres_data/7jsh_22454/08_2025/7jsh_22454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jsh_22454/08_2025/7jsh_22454.cif" } 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-2.0-5787/lib/python3.9/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: 2.71, per 1000 atoms: 0.34 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: 0.92 Conformation dependent library (CDL) restraints added in 472.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.37 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: 1.11 Time building geometry restraints manager: 1.13 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=" C SER F 257 " pdb=" N ASN F 258 " ideal model delta sigma weight residual 1.329 1.342 -0.013 1.23e-02 6.61e+03 1.10e+00 bond pdb=" N VAL F 357 " pdb=" CA VAL F 357 " ideal model delta sigma weight residual 1.474 1.459 0.016 1.57e-02 4.06e+03 1.00e+00 bond pdb=" C VAL E 351 " pdb=" O VAL E 351 " ideal model delta sigma weight residual 1.232 1.239 -0.007 8.90e-03 1.26e+04 5.60e-01 bond pdb=" C4' DT N 8 " pdb=" C3' DT N 8 " ideal model delta sigma weight residual 1.523 1.535 -0.012 2.00e-02 2.50e+03 3.37e-01 bond pdb=" N THR C 277 " pdb=" CA THR C 277 " ideal model delta sigma weight residual 1.463 1.457 0.006 1.08e-02 8.57e+03 3.21e-01 ... (remaining 7937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.77: 9888 0.77 - 1.55: 90 1.55 - 2.32: 24 2.32 - 3.09: 4 3.09 - 3.86: 3 Bond angle restraints: 10009 Sorted by residual: angle pdb=" N LYS F 234 " pdb=" CA LYS F 234 " pdb=" C LYS F 234 " ideal model delta sigma weight residual 114.62 110.76 3.86 1.14e+00 7.69e-01 1.15e+01 angle pdb=" N THR E 451 " pdb=" CA THR E 451 " pdb=" C THR E 451 " ideal model delta sigma weight residual 114.56 110.76 3.80 1.27e+00 6.20e-01 8.96e+00 angle pdb=" N VAL F 357 " pdb=" CA VAL F 357 " pdb=" C VAL F 357 " ideal model delta sigma weight residual 106.21 109.35 -3.14 1.07e+00 8.73e-01 8.64e+00 angle pdb=" CA LYS F 234 " pdb=" C LYS F 234 " pdb=" N GLY F 235 " ideal model delta sigma weight residual 119.71 116.86 2.85 1.17e+00 7.31e-01 5.92e+00 angle pdb=" CA VAL F 357 " pdb=" C VAL F 357 " pdb=" O VAL F 357 " ideal model delta sigma weight residual 122.63 120.78 1.85 8.70e-01 1.32e+00 4.50e+00 ... (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: 0.000 - 0.007: 23 0.007 - 0.015: 6 0.015 - 0.022: 13 0.022 - 0.030: 16 0.030 - 0.037: 2 Chirality restraints: 60 Sorted by residual: chirality pdb=" P DC N 9 " pdb=" OP1 DC N 9 " pdb=" OP2 DC N 9 " pdb=" O5' DC N 9 " both_signs ideal model delta sigma weight residual True 2.35 -2.38 -0.04 2.00e-01 2.50e+01 3.42e-02 chirality pdb=" P DG N 10 " pdb=" OP1 DG N 10 " pdb=" OP2 DG N 10 " pdb=" O5' DG N 10 " both_signs ideal model delta sigma weight residual True 2.35 -2.38 -0.03 2.00e-01 2.50e+01 2.57e-02 chirality pdb=" P DG N 14 " pdb=" OP1 DG N 14 " pdb=" OP2 DG N 14 " pdb=" O5' DG N 14 " both_signs ideal model delta sigma weight residual True 2.35 -2.37 -0.03 2.00e-01 2.50e+01 2.16e-02 ... (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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.950 Find NCS groups from input model: 0.180 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:1.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2484 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 : 0.001 0.016 7942 Z= 0.063 Angle : 0.202 3.863 10009 Z= 0.145 Chirality : 0.018 0.037 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 aren 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 covalent geometry : bond 0.00092 ( 7942) covalent geometry : angle 0.20213 (10009) hydrogen bonds : bond 0.14316 ( 555) hydrogen bonds : angle 5.20654 ( 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 : 0.310 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0321 time to fit residues: 2.9599 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 : 0.307 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.094678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.090169 restraints weight = 106291.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.088976 restraints weight = 201231.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.088774 restraints weight = 271108.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.088627 restraints weight = 274901.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.088603 restraints weight = 254979.164| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5071 moved from start: 0.9956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 7942 Z= 0.383 Angle : 1.124 15.202 10009 Z= 0.666 Chirality : 0.027 0.081 60 Planarity : 0.006 0.030 1912 Dihedral : 12.569 62.432 2044 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.53 % Allowed : 11.06 % Favored : 88.41 % 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 : 0.00 % Twisted General : 0.49 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.68 (0.16), residues: 1890 helix: -1.10 (0.17), residues: 793 sheet: -2.81 (0.52), residues: 84 loop : -3.72 (0.15), residues: 1013 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 7942) covalent geometry : angle 1.12436 (10009) hydrogen bonds : bond 0.06839 ( 555) hydrogen bonds : angle 8.70190 ( 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 : 0.330 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0284 time to fit residues: 2.6854 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 : 0.292 ------------------------------------------------------------------------------- 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: 0.0050 chunk 83 optimal weight: 50.0000 chunk 125 optimal weight: 9.9990 chunk 18 optimal weight: 40.0000 chunk 142 optimal weight: 0.0070 chunk 156 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 chunk 78 optimal weight: 30.0000 chunk 146 optimal weight: 20.0000 chunk 137 optimal weight: 0.0470 chunk 45 optimal weight: 0.5980 overall best weight: 1.9312 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.067710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.054594 restraints weight = 74939.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.053708 restraints weight = 87143.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.053681 restraints weight = 96328.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.053698 restraints weight = 93634.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.053690 restraints weight = 91058.868| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5106 moved from start: 0.9428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.020 7942 Z= 0.099 Angle : 0.457 5.789 10009 Z= 0.263 Chirality : 0.021 0.044 60 Planarity : 0.002 0.012 1912 Dihedral : 9.778 59.976 2044 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 0.10 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.73 % Favored : 90.95 % 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 : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.14 (0.19), residues: 1890 helix: 0.61 (0.18), residues: 836 sheet: -2.29 (0.53), residues: 99 loop : -3.40 (0.17), residues: 955 Details of bonding type rmsd covalent geometry : bond 0.00146 ( 7942) covalent geometry : angle 0.45678 (10009) hydrogen bonds : bond 0.02670 ( 555) hydrogen bonds : angle 4.70341 ( 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 : 0.377 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0331 time to fit residues: 3.1224 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 186 optimal weight: 50.0000 chunk 122 optimal weight: 30.0000 chunk 159 optimal weight: 20.0000 chunk 149 optimal weight: 9.9990 chunk 52 optimal weight: 30.0000 chunk 74 optimal weight: 50.0000 chunk 139 optimal weight: 20.0000 chunk 148 optimal weight: 20.0000 chunk 65 optimal weight: 30.0000 chunk 48 optimal weight: 0.0170 chunk 123 optimal weight: 40.0000 overall best weight: 14.0032 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.055038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.043063 restraints weight = 91246.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.042682 restraints weight = 88025.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.042542 restraints weight = 93679.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.042592 restraints weight = 95565.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.042604 restraints weight = 92514.590| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5997 moved from start: 1.7028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 7942 Z= 0.416 Angle : 1.232 15.521 10009 Z= 0.739 Chirality : 0.037 0.102 60 Planarity : 0.007 0.037 1912 Dihedral : 13.396 78.124 2044 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 1.01 % Allowed : 17.99 % Favored : 81.01 % 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 : 0.55 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.50 (0.16), residues: 1890 helix: -1.83 (0.16), residues: 752 sheet: -3.45 (0.61), residues: 54 loop : -4.06 (0.15), residues: 1084 Details of bonding type rmsd covalent geometry : bond 0.00578 ( 7942) covalent geometry : angle 1.23230 (10009) hydrogen bonds : bond 0.08708 ( 555) hydrogen bonds : angle 10.60124 ( 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 : 0.225 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0272 time to fit residues: 2.4999 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 : 0.311 ------------------------------------------------------------------------------- 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: 0.0270 chunk 38 optimal weight: 30.0000 chunk 187 optimal weight: 40.0000 chunk 92 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 94 optimal weight: 20.0000 chunk 168 optimal weight: 7.9990 chunk 21 optimal weight: 50.0000 chunk 132 optimal weight: 0.0170 chunk 109 optimal weight: 50.0000 chunk 8 optimal weight: 10.0000 overall best weight: 5.0082 ------------------------------------------------------------------------------- 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 = 0.3283 r_free = 0.3283 target = 0.052203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.042624 restraints weight = 103406.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.041740 restraints weight = 145876.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.041650 restraints weight = 166139.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.041455 restraints weight = 170625.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.041412 restraints weight = 166547.459| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3939 moved from start: 1.6791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7942 Z= 0.169 Angle : 0.654 8.903 10009 Z= 0.387 Chirality : 0.025 0.081 60 Planarity : 0.003 0.016 1912 Dihedral : 11.253 84.167 2044 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.80 % Favored : 86.88 % 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 aren not related in a simple way. whole: -3.48 (0.17), residues: 1890 helix: -0.50 (0.17), residues: 785 sheet: -3.96 (0.54), residues: 68 loop : -3.88 (0.16), residues: 1037 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 7942) covalent geometry : angle 0.65443 (10009) hydrogen bonds : bond 0.04499 ( 555) hydrogen bonds : angle 7.12652 ( 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 : 0.228 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0295 time to fit residues: 2.6999 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 : 0.311 ------------------------------------------------------------------------------- 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: 20.0000 chunk 48 optimal weight: 40.0000 chunk 72 optimal weight: 50.0000 chunk 145 optimal weight: 50.0000 chunk 90 optimal weight: 10.0000 chunk 60 optimal weight: 30.0000 chunk 160 optimal weight: 0.4980 chunk 130 optimal weight: 20.0000 chunk 1 optimal weight: 50.0000 chunk 183 optimal weight: 30.0000 chunk 18 optimal weight: 40.0000 overall best weight: 16.0996 ------------------------------------------------------------------------------- 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 = 0.3372 r_free = 0.3372 target = 0.049316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.038412 restraints weight = 97873.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.038503 restraints weight = 91256.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.038568 restraints weight = 83926.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.038579 restraints weight = 83851.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.038611 restraints weight = 78877.215| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 2.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 7942 Z= 0.441 Angle : 1.311 16.869 10009 Z= 0.784 Chirality : 0.052 0.134 60 Planarity : 0.007 0.038 1912 Dihedral : 14.282 103.179 2044 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 1.06 % Allowed : 24.60 % Favored : 74.34 % 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 : 0.65 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.19 (0.16), residues: 1890 helix: -2.50 (0.15), residues: 729 sheet: -4.65 (0.48), residues: 55 loop : -4.29 (0.16), residues: 1106 Details of bonding type rmsd covalent geometry : bond 0.00618 ( 7942) covalent geometry : angle 1.31057 (10009) hydrogen bonds : bond 0.09417 ( 555) hydrogen bonds : angle 12.06519 ( 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 : 0.342 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0328 time to fit residues: 3.0464 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 : 0.289 ------------------------------------------------------------------------------- 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: 1.9990 chunk 156 optimal weight: 9.9990 chunk 79 optimal weight: 30.0000 chunk 133 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 58 optimal weight: 20.0000 chunk 184 optimal weight: 30.0000 chunk 3 optimal weight: 50.0000 chunk 87 optimal weight: 30.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- 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 = 0.3192 r_free = 0.3192 target = 0.046680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.044609 restraints weight = 166218.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.044527 restraints weight = 181868.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.044526 restraints weight = 183178.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.044526 restraints weight = 182517.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.044526 restraints weight = 182517.494| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5451 moved from start: 2.1512 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= 0.185 Angle : 0.725 7.734 10009 Z= 0.428 Chirality : 0.028 0.078 60 Planarity : 0.003 0.019 1912 Dihedral : 12.269 110.700 2044 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.32 % Allowed : 15.87 % Favored : 83.81 % 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 aren not related in a simple way. whole: -4.23 (0.17), residues: 1890 helix: -1.17 (0.17), residues: 754 sheet: -4.23 (0.54), residues: 58 loop : -4.21 (0.16), residues: 1078 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 7942) covalent geometry : angle 0.72500 (10009) hydrogen bonds : bond 0.04824 ( 555) hydrogen bonds : angle 8.61031 ( 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 : 0.320 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0315 time to fit residues: 2.9687 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 : 0.311 ------------------------------------------------------------------------------- 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: 0.7980 chunk 96 optimal weight: 0.8980 chunk 184 optimal weight: 50.0000 chunk 50 optimal weight: 30.0000 chunk 56 optimal weight: 50.0000 chunk 7 optimal weight: 8.9990 chunk 98 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 48 optimal weight: 50.0000 overall best weight: 8.1388 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.049932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.038197 restraints weight = 94327.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.038361 restraints weight = 86330.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.038559 restraints weight = 80458.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.038650 restraints weight = 75650.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.038753 restraints weight = 72636.385| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 2.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7942 Z= 0.244 Angle : 0.823 9.405 10009 Z= 0.488 Chirality : 0.032 0.089 60 Planarity : 0.004 0.020 1912 Dihedral : 12.590 119.864 2044 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.37 % Allowed : 23.97 % Favored : 75.66 % 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 aren not related in a simple way. whole: -4.39 (0.17), residues: 1890 helix: -1.16 (0.17), residues: 760 sheet: -4.54 (0.55), residues: 47 loop : -4.44 (0.16), residues: 1083 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 7942) covalent geometry : angle 0.82269 (10009) hydrogen bonds : bond 0.05636 ( 555) hydrogen bonds : angle 9.06178 ( 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 : 0.189 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0292 time to fit residues: 2.6727 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 : 0.319 ------------------------------------------------------------------------------- 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: 50.0000 chunk 92 optimal weight: 0.3980 chunk 117 optimal weight: 30.0000 chunk 120 optimal weight: 10.0000 chunk 115 optimal weight: 0.5980 chunk 17 optimal weight: 40.0000 chunk 53 optimal weight: 50.0000 chunk 66 optimal weight: 30.0000 chunk 46 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 153 optimal weight: 40.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3259 r_free = 0.3259 target = 0.048317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.045235 restraints weight = 158449.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.045235 restraints weight = 164285.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.045235 restraints weight = 164285.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.045235 restraints weight = 164285.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.045235 restraints weight = 164285.279| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5626 moved from start: 2.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7942 Z= 0.156 Angle : 0.631 6.422 10009 Z= 0.371 Chirality : 0.027 0.082 60 Planarity : 0.003 0.015 1912 Dihedral : 11.942 121.083 2044 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.26 % Allowed : 16.14 % 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 : 0.05 % 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 aren not related in a simple way. whole: -3.70 (0.18), residues: 1890 helix: -0.35 (0.18), residues: 784 sheet: -4.83 (0.59), residues: 39 loop : -4.31 (0.16), residues: 1067 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 7942) covalent geometry : angle 0.63075 (10009) hydrogen bonds : bond 0.04190 ( 555) hydrogen bonds : angle 7.62689 ( 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 : 0.319 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0267 time to fit residues: 2.4712 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 : 0.294 ------------------------------------------------------------------------------- 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: 20.0000 chunk 30 optimal weight: 50.0000 chunk 136 optimal weight: 50.0000 chunk 84 optimal weight: 50.0000 chunk 115 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 158 optimal weight: 50.0000 chunk 14 optimal weight: 50.0000 chunk 32 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 170 optimal weight: 9.9990 overall best weight: 10.3790 ------------------------------------------------------------------------------- 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 = 0.3152 r_free = 0.3152 target = 0.044629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.041852 restraints weight = 172336.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.041700 restraints weight = 227745.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.041655 restraints weight = 263025.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.041621 restraints weight = 262040.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.041614 restraints weight = 269140.316| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5961 moved from start: 2.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7942 Z= 0.279 Angle : 0.891 9.720 10009 Z= 0.532 Chirality : 0.034 0.102 60 Planarity : 0.004 0.024 1912 Dihedral : 12.786 120.740 2044 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.32 % Allowed : 26.35 % Favored : 73.33 % 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 aren not related in a simple way. whole: -4.41 (0.17), residues: 1890 helix: -1.13 (0.17), residues: 744 sheet: -4.85 (0.72), residues: 30 loop : -4.47 (0.16), residues: 1116 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 7942) covalent geometry : angle 0.89134 (10009) hydrogen bonds : bond 0.06587 ( 555) hydrogen bonds : angle 9.52919 ( 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 : 0.281 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0350 time to fit residues: 3.2666 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 : 0.434 ------------------------------------------------------------------------------- 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: 30.0000 chunk 186 optimal weight: 50.0000 chunk 124 optimal weight: 50.0000 chunk 83 optimal weight: 50.0000 chunk 158 optimal weight: 40.0000 chunk 81 optimal weight: 50.0000 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 136 optimal weight: 50.0000 chunk 176 optimal weight: 2.9990 chunk 44 optimal weight: 20.0000 overall best weight: 16.5996 ------------------------------------------------------------------------------- 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 = 0.3332 r_free = 0.3332 target = 0.046606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.035867 restraints weight = 101574.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.035995 restraints weight = 93608.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.035995 restraints weight = 87269.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.035995 restraints weight = 87269.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.035995 restraints weight = 87269.048| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 2.7030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 7942 Z= 0.412 Angle : 1.203 13.030 10009 Z= 0.721 Chirality : 0.046 0.148 60 Planarity : 0.006 0.034 1912 Dihedral : 14.010 122.147 2044 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.26 % Allowed : 27.04 % Favored : 72.70 % 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 : 0.71 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.52 (0.15), residues: 1890 helix: -2.38 (0.16), residues: 717 sheet: -5.88 (0.37), residues: 36 loop : -4.78 (0.14), residues: 1137 Details of bonding type rmsd covalent geometry : bond 0.00576 ( 7942) covalent geometry : angle 1.20253 (10009) hydrogen bonds : bond 0.09082 ( 555) hydrogen bonds : angle 11.58499 ( 1659) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1145.26 seconds wall clock time: 20 minutes 11.99 seconds (1211.99 seconds total)