Starting phenix.real_space_refine on Wed Mar 12 13:02:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jsh_22454/03_2025/7jsh_22454.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jsh_22454/03_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_22454/03_2025/7jsh_22454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jsh_22454/03_2025/7jsh_22454.map" model { file = "/net/cci-nas-00/data/ceres_data/7jsh_22454/03_2025/7jsh_22454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jsh_22454/03_2025/7jsh_22454.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 13, 'HIS:plan': 5, 'TYR:plan': 8, 'ASN:plan1': 14, 'TRP:plan': 8, 'ASP:plan': 16, 'PHE:plan': 14, 'GLU:plan': 16, 'ARG:plan': 9} 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: {'GLN:plan1': 13, 'HIS:plan': 5, 'TYR:plan': 8, 'ASN:plan1': 14, 'TRP:plan': 8, 'ASP:plan': 16, 'PHE:plan': 14, 'GLU:plan': 16, 'ARG:plan': 9} 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: {'GLN:plan1': 13, 'HIS:plan': 5, 'TYR:plan': 8, 'ASN:plan1': 14, 'TRP:plan': 8, 'ASP:plan': 16, 'PHE:plan': 14, 'GLU:plan': 16, 'ARG:plan': 9} 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: {'GLN:plan1': 13, 'HIS:plan': 5, 'TYR:plan': 8, 'ASN:plan1': 14, 'TRP:plan': 8, 'ASP:plan': 16, 'PHE:plan': 14, 'GLU:plan': 16, 'ARG:plan': 9} 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: {'GLN:plan1': 13, 'HIS:plan': 5, 'TYR:plan': 8, 'ASN:plan1': 14, 'TRP:plan': 8, 'ASP:plan': 16, 'PHE:plan': 14, 'GLU:plan': 16, 'ARG:plan': 9} 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: {'GLN:plan1': 13, 'HIS:plan': 5, 'TYR:plan': 8, 'ASN:plan1': 14, 'TRP:plan': 8, 'ASP:plan': 16, 'PHE:plan': 14, 'GLU:plan': 16, 'ARG:plan': 9} 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: {'GLN:plan1': 13, 'HIS:plan': 5, 'TYR:plan': 8, 'ASN:plan1': 14, 'TRP:plan': 8, 'ASP:plan': 16, 'PHE:plan': 14, 'GLU:plan': 16, 'ARG:plan': 9} 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: 6.19, per 1000 atoms: 0.78 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: 2.43 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.10 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: 2.15 Time building geometry restraints manager: 2.75 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: 0.710 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.950 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.390 ------------------------------------------------------------------------------- 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= 0.070 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 *********************** 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 : 0.872 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0671 time to fit residues: 6.5327 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 : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 30.0000 chunk 144 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 49 optimal weight: 30.0000 chunk 97 optimal weight: 40.0000 chunk 76 optimal weight: 20.0000 chunk 148 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 90 optimal weight: 8.9990 chunk 110 optimal weight: 40.0000 chunk 172 optimal weight: 30.0000 overall best weight: 13.7994 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.063064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.050432 restraints weight = 79767.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.050002 restraints weight = 81627.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.049937 restraints weight = 84029.414| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5540 moved from start: 1.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 7942 Z= 0.446 Angle : 1.314 14.590 10009 Z= 0.780 Chirality : 0.034 0.122 60 Planarity : 0.007 0.029 1912 Dihedral : 13.478 67.253 2044 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.85 % Allowed : 12.91 % Favored : 86.24 % 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 : 0.76 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.16), residues: 1890 helix: -1.52 (0.16), residues: 758 sheet: -3.29 (0.59), residues: 57 loop : -3.82 (0.15), residues: 1075 *********************** 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 : 0.856 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0639 time to fit residues: 6.3213 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 : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 103 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 chunk 21 optimal weight: 30.0000 chunk 12 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 115 optimal weight: 0.0370 chunk 140 optimal weight: 30.0000 chunk 144 optimal weight: 9.9990 chunk 7 optimal weight: 0.5980 overall best weight: 5.5264 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.061730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.048589 restraints weight = 86421.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.048385 restraints weight = 85201.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.048324 restraints weight = 85579.396| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5730 moved from start: 1.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7942 Z= 0.187 Angle : 0.669 10.429 10009 Z= 0.391 Chirality : 0.023 0.052 60 Planarity : 0.003 0.013 1912 Dihedral : 10.823 69.209 2044 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.37 % Allowed : 11.53 % Favored : 88.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.18), residues: 1890 helix: -0.31 (0.18), residues: 802 sheet: -2.79 (0.72), residues: 53 loop : -3.63 (0.16), residues: 1035 *********************** 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 : 1.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0669 time to fit residues: 6.6483 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 : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 116 optimal weight: 20.0000 chunk 139 optimal weight: 30.0000 chunk 68 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 15 optimal weight: 30.0000 chunk 183 optimal weight: 40.0000 chunk 98 optimal weight: 30.0000 chunk 6 optimal weight: 10.0000 chunk 114 optimal weight: 0.0270 chunk 175 optimal weight: 20.0000 chunk 163 optimal weight: 50.0000 overall best weight: 12.0052 ------------------------------------------------------------------------------- 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 = 0.3467 r_free = 0.3467 target = 0.053559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.041716 restraints weight = 92449.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.041357 restraints weight = 92831.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.041196 restraints weight = 100232.316| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6092 moved from start: 1.8276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7942 Z= 0.373 Angle : 1.134 11.255 10009 Z= 0.672 Chirality : 0.037 0.115 60 Planarity : 0.006 0.028 1912 Dihedral : 13.288 81.847 2044 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.90 % Allowed : 18.52 % Favored : 80.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.50 (0.16), residues: 1890 helix: -1.67 (0.16), residues: 750 sheet: -3.75 (0.66), residues: 46 loop : -4.18 (0.16), residues: 1094 *********************** 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 : 0.979 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0681 time to fit residues: 6.7800 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 : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 26 optimal weight: 30.0000 chunk 123 optimal weight: 30.0000 chunk 8 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 187 optimal weight: 40.0000 chunk 163 optimal weight: 20.0000 chunk 7 optimal weight: 0.0010 chunk 141 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 119 optimal weight: 50.0000 overall best weight: 12.0002 ------------------------------------------------------------------------------- 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 = 0.3419 r_free = 0.3419 target = 0.051376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.039457 restraints weight = 92326.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.039574 restraints weight = 87131.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.039574 restraints weight = 82907.242| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 moved from start: 2.0684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 7942 Z= 0.322 Angle : 0.974 10.568 10009 Z= 0.581 Chirality : 0.034 0.091 60 Planarity : 0.005 0.026 1912 Dihedral : 12.753 94.822 2044 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.32 % Allowed : 17.78 % Favored : 81.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.48 (0.16), residues: 1890 helix: -1.63 (0.16), residues: 738 sheet: -4.52 (0.55), residues: 42 loop : -4.13 (0.15), residues: 1110 *********************** 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 : 0.924 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0639 time to fit residues: 6.2689 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 : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 96 optimal weight: 0.0670 chunk 163 optimal weight: 50.0000 chunk 56 optimal weight: 20.0000 chunk 97 optimal weight: 0.0670 chunk 20 optimal weight: 30.0000 chunk 29 optimal weight: 30.0000 chunk 157 optimal weight: 30.0000 chunk 65 optimal weight: 30.0000 chunk 38 optimal weight: 20.0000 chunk 17 optimal weight: 40.0000 chunk 71 optimal weight: 10.0000 overall best weight: 10.0268 ------------------------------------------------------------------------------- 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 = 0.3379 r_free = 0.3379 target = 0.049526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.038028 restraints weight = 93842.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.038162 restraints weight = 87895.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.038213 restraints weight = 83697.803| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 2.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7942 Z= 0.301 Angle : 0.945 10.249 10009 Z= 0.559 Chirality : 0.032 0.087 60 Planarity : 0.005 0.023 1912 Dihedral : 13.107 118.500 2044 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.48 % Allowed : 21.53 % Favored : 77.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.60 (0.16), residues: 1890 helix: -1.51 (0.16), residues: 740 sheet: -4.84 (0.45), residues: 61 loop : -4.33 (0.16), residues: 1089 *********************** 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 : 0.951 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0686 time to fit residues: 6.7783 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 : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 167 optimal weight: 30.0000 chunk 156 optimal weight: 0.4980 chunk 170 optimal weight: 20.0000 chunk 84 optimal weight: 50.0000 chunk 7 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 131 optimal weight: 30.0000 chunk 121 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 chunk 82 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 overall best weight: 5.2786 ------------------------------------------------------------------------------- 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 = 0.3207 r_free = 0.3207 target = 0.047156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.045095 restraints weight = 184053.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.044924 restraints weight = 217204.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.044922 restraints weight = 239983.620| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5309 moved from start: 2.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7942 Z= 0.180 Angle : 0.676 8.933 10009 Z= 0.396 Chirality : 0.028 0.084 60 Planarity : 0.003 0.016 1912 Dihedral : 12.106 118.317 2044 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.32 % Allowed : 16.88 % Favored : 82.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.17), residues: 1890 helix: -0.60 (0.17), residues: 769 sheet: -4.85 (0.45), residues: 57 loop : -4.23 (0.16), residues: 1064 *********************** 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 : 0.878 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0672 time to fit residues: 6.5519 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 : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 162 optimal weight: 50.0000 chunk 184 optimal weight: 50.0000 chunk 122 optimal weight: 30.0000 chunk 114 optimal weight: 6.9990 chunk 74 optimal weight: 0.0020 chunk 98 optimal weight: 10.0000 chunk 126 optimal weight: 40.0000 chunk 179 optimal weight: 6.9990 chunk 161 optimal weight: 40.0000 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 overall best weight: 3.9794 ------------------------------------------------------------------------------- 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 = 0.3292 r_free = 0.3292 target = 0.054368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.049451 restraints weight = 84993.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.048909 restraints weight = 158262.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.048686 restraints weight = 212774.087| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5451 moved from start: 2.2729 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= 0.151 Angle : 0.582 8.597 10009 Z= 0.339 Chirality : 0.025 0.083 60 Planarity : 0.002 0.014 1912 Dihedral : 11.626 117.734 2044 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.26 % Allowed : 18.04 % Favored : 81.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.19), residues: 1890 helix: 0.23 (0.18), residues: 789 sheet: -4.62 (0.48), residues: 60 loop : -4.08 (0.17), residues: 1041 *********************** 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 : 0.921 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0702 time to fit residues: 6.9313 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 : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 144 optimal weight: 2.9990 chunk 118 optimal weight: 0.0020 chunk 175 optimal weight: 40.0000 chunk 142 optimal weight: 0.2980 chunk 150 optimal weight: 40.0000 chunk 160 optimal weight: 10.0000 chunk 75 optimal weight: 50.0000 chunk 35 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 overall best weight: 3.4594 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.051696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.039809 restraints weight = 91628.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.039865 restraints weight = 86750.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 13)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.039865 restraints weight = 83728.766| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6175 moved from start: 2.2869 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= 0.135 Angle : 0.523 7.602 10009 Z= 0.304 Chirality : 0.024 0.083 60 Planarity : 0.002 0.013 1912 Dihedral : 11.338 114.989 2044 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.26 % Allowed : 14.34 % Favored : 85.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.19), residues: 1890 helix: 0.85 (0.19), residues: 804 sheet: -4.05 (0.57), residues: 48 loop : -3.95 (0.17), residues: 1038 *********************** 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 : 0.879 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0682 time to fit residues: 6.6523 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 : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 153 optimal weight: 40.0000 chunk 69 optimal weight: 50.0000 chunk 73 optimal weight: 20.0000 chunk 6 optimal weight: 50.0000 chunk 15 optimal weight: 30.0000 chunk 135 optimal weight: 50.0000 chunk 45 optimal weight: 30.0000 chunk 176 optimal weight: 0.3980 chunk 17 optimal weight: 40.0000 chunk 154 optimal weight: 50.0000 chunk 40 optimal weight: 30.0000 overall best weight: 22.0796 ------------------------------------------------------------------------------- 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 = 0.3329 r_free = 0.3329 target = 0.046564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.035986 restraints weight = 102730.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.036161 restraints weight = 94018.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.036161 restraints weight = 86575.309| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 2.6515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 7942 Z= 0.544 Angle : 1.349 14.806 10009 Z= 0.813 Chirality : 0.051 0.162 60 Planarity : 0.008 0.038 1912 Dihedral : 14.190 120.991 2044 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 1.06 % Allowed : 29.10 % Favored : 69.84 % 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 : 0.65 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.47 (0.15), residues: 1890 helix: -2.36 (0.16), residues: 700 sheet: -4.66 (0.59), residues: 44 loop : -4.75 (0.15), residues: 1146 ********************** 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 : 1.057 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0692 time to fit residues: 6.7236 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 : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 171 optimal weight: 20.0000 chunk 46 optimal weight: 30.0000 chunk 124 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 45 optimal weight: 40.0000 chunk 25 optimal weight: 8.9990 chunk 186 optimal weight: 30.0000 chunk 66 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 overall best weight: 10.3992 ------------------------------------------------------------------------------- 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 = 0.3347 r_free = 0.3347 target = 0.047304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.036351 restraints weight = 97439.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.036351 restraints weight = 89600.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.036351 restraints weight = 89600.499| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 2.6293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7942 Z= 0.290 Angle : 0.907 9.597 10009 Z= 0.540 Chirality : 0.035 0.105 60 Planarity : 0.005 0.026 1912 Dihedral : 13.140 122.178 2044 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.26 % Allowed : 23.49 % Favored : 76.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.02 (0.16), residues: 1890 helix: -1.84 (0.17), residues: 733 sheet: -5.52 (0.64), residues: 28 loop : -4.63 (0.15), residues: 1129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2247.93 seconds wall clock time: 39 minutes 5.21 seconds (2345.21 seconds total)