Starting phenix.real_space_refine on Wed Feb 12 12:36:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jsh_22454/02_2025/7jsh_22454.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jsh_22454/02_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_22454/02_2025/7jsh_22454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jsh_22454/02_2025/7jsh_22454.map" model { file = "/net/cci-nas-00/data/ceres_data/7jsh_22454/02_2025/7jsh_22454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jsh_22454/02_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-5592/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: 2.87 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: 1.17 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: 2.33 Time building geometry restraints manager: 2.90 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: 0.700 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.990 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.540 ------------------------------------------------------------------------------- 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 : 0.969 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0706 time to fit residues: 7.0246 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 : 0.906 ------------------------------------------------------------------------------- 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 = 0.050434 restraints weight = 79767.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.049998 restraints weight = 81751.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.049937 restraints weight = 84109.421| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5541 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 : 0.906 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0694 time to fit residues: 6.8284 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 : 1.105 ------------------------------------------------------------------------------- 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: 8.9990 chunk 116 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 21 optimal weight: 40.0000 chunk 12 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 115 optimal weight: 0.0670 chunk 140 optimal weight: 30.0000 chunk 144 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 overall best weight: 5.2126 ------------------------------------------------------------------------------- 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 = 0.3570 r_free = 0.3570 target = 0.061997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.048884 restraints weight = 86248.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.048705 restraints weight = 82729.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.048644 restraints weight = 83559.681| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5695 moved from start: 1.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7942 Z= 0.187 Angle : 0.647 10.353 10009 Z= 0.380 Chirality : 0.023 0.050 60 Planarity : 0.003 0.015 1912 Dihedral : 10.658 68.609 2044 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.06 % Favored : 88.62 % 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: -2.95 (0.18), residues: 1890 helix: -0.22 (0.18), residues: 807 sheet: -2.57 (0.74), residues: 51 loop : -3.60 (0.16), residues: 1032 *********************** 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 : 0.933 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0762 time to fit residues: 7.4818 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 : 1.165 ------------------------------------------------------------------------------- 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: 20.0000 chunk 70 optimal weight: 30.0000 chunk 15 optimal weight: 30.0000 chunk 183 optimal weight: 50.0000 chunk 98 optimal weight: 30.0000 chunk 6 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 175 optimal weight: 30.0000 chunk 163 optimal weight: 50.0000 overall best weight: 17.1998 ------------------------------------------------------------------------------- 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 = 0.051419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.040150 restraints weight = 94969.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.040031 restraints weight = 88748.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.039942 restraints weight = 88464.626| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6216 moved from start: 2.0018 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= 0.480 Angle : 1.384 15.049 10009 Z= 0.827 Chirality : 0.045 0.122 60 Planarity : 0.008 0.038 1912 Dihedral : 14.392 93.378 2044 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 1.27 % Allowed : 21.43 % Favored : 77.30 % 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 : 1.31 % 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: -5.20 (0.15), residues: 1890 helix: -2.55 (0.15), residues: 717 sheet: -4.55 (0.55), residues: 50 loop : -4.28 (0.15), residues: 1123 *********************** 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 : 0.928 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0681 time to fit residues: 6.7196 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 : 1.011 ------------------------------------------------------------------------------- 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: 40.0000 chunk 123 optimal weight: 40.0000 chunk 8 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 chunk 187 optimal weight: 10.0000 chunk 163 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 chunk 141 optimal weight: 20.0000 chunk 71 optimal weight: 8.9990 chunk 119 optimal weight: 40.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.052299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.040039 restraints weight = 90991.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.040139 restraints weight = 86433.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.040234 restraints weight = 82724.085| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 1.9960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7942 Z= 0.238 Angle : 0.793 8.172 10009 Z= 0.472 Chirality : 0.029 0.083 60 Planarity : 0.004 0.020 1912 Dihedral : 12.251 95.314 2044 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.32 % Allowed : 15.24 % Favored : 84.44 % 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: -4.37 (0.16), residues: 1890 helix: -1.56 (0.16), residues: 733 sheet: -4.38 (0.57), residues: 46 loop : -4.03 (0.16), residues: 1111 *********************** 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 : 0.894 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0718 time to fit residues: 6.9657 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 ------------------------------------------------------------------------------- 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: 7.9990 chunk 163 optimal weight: 50.0000 chunk 56 optimal weight: 30.0000 chunk 97 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 29 optimal weight: 50.0000 chunk 157 optimal weight: 0.7980 chunk 65 optimal weight: 40.0000 chunk 38 optimal weight: 50.0000 chunk 17 optimal weight: 50.0000 chunk 71 optimal weight: 10.0000 overall best weight: 9.7594 ------------------------------------------------------------------------------- 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 = 0.3394 r_free = 0.3394 target = 0.050171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.038471 restraints weight = 94348.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.038626 restraints weight = 87365.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.038778 restraints weight = 82172.673| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 moved from start: 2.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7942 Z= 0.296 Angle : 0.907 9.774 10009 Z= 0.538 Chirality : 0.033 0.088 60 Planarity : 0.004 0.025 1912 Dihedral : 12.864 110.369 2044 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.37 % Allowed : 22.43 % Favored : 77.20 % 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: -4.65 (0.16), residues: 1890 helix: -1.66 (0.16), residues: 750 sheet: -4.70 (0.49), residues: 54 loop : -4.32 (0.16), residues: 1086 *********************** 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 : 0.907 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0680 time to fit residues: 6.6696 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 : 0.890 ------------------------------------------------------------------------------- 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: 20.0000 chunk 170 optimal weight: 9.9990 chunk 84 optimal weight: 50.0000 chunk 7 optimal weight: 0.0470 chunk 120 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 0 optimal weight: 50.0000 overall best weight: 2.6084 ------------------------------------------------------------------------------- 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 = 0.3229 r_free = 0.3229 target = 0.047660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.045993 restraints weight = 171123.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.045828 restraints weight = 198891.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.045831 restraints weight = 225137.700| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4888 moved from start: 2.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7942 Z= 0.128 Angle : 0.535 7.527 10009 Z= 0.313 Chirality : 0.025 0.077 60 Planarity : 0.002 0.013 1912 Dihedral : 11.577 111.940 2044 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.59 % 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: -3.30 (0.18), residues: 1890 helix: -0.05 (0.18), residues: 790 sheet: -4.94 (0.44), residues: 56 loop : -4.02 (0.17), residues: 1044 *********************** 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 : 1.192 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0737 time to fit residues: 7.5357 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 : 0.968 ------------------------------------------------------------------------------- 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: 20.0000 chunk 122 optimal weight: 30.0000 chunk 114 optimal weight: 0.0010 chunk 74 optimal weight: 50.0000 chunk 98 optimal weight: 30.0000 chunk 126 optimal weight: 40.0000 chunk 179 optimal weight: 20.0000 chunk 161 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 21 optimal weight: 30.0000 overall best weight: 16.0002 ------------------------------------------------------------------------------- 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 = 0.3356 r_free = 0.3356 target = 0.048281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.037198 restraints weight = 97530.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.037317 restraints weight = 89198.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.037481 restraints weight = 83813.335| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 2.4180 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= 0.407 Angle : 1.089 11.680 10009 Z= 0.656 Chirality : 0.040 0.112 60 Planarity : 0.005 0.029 1912 Dihedral : 13.427 119.878 2044 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.74 % Allowed : 25.93 % 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 : 0.27 % 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: -5.06 (0.16), residues: 1890 helix: -1.93 (0.16), residues: 727 sheet: -4.74 (0.57), residues: 39 loop : -4.61 (0.15), residues: 1124 *********************** 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 : 0.968 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0698 time to fit residues: 6.8292 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 : 0.986 ------------------------------------------------------------------------------- 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: 10.0000 chunk 118 optimal weight: 10.0000 chunk 175 optimal weight: 30.0000 chunk 142 optimal weight: 20.0000 chunk 150 optimal weight: 30.0000 chunk 160 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 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: 8.1994 ------------------------------------------------------------------------------- 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 = 0.3167 r_free = 0.3167 target = 0.046022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.042513 restraints weight = 156388.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.042305 restraints weight = 220396.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.042235 restraints weight = 256267.143| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5910 moved from start: 2.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7942 Z= 0.241 Angle : 0.792 8.763 10009 Z= 0.471 Chirality : 0.030 0.090 60 Planarity : 0.004 0.021 1912 Dihedral : 12.592 121.289 2044 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.26 % Allowed : 20.21 % Favored : 79.52 % 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: -4.46 (0.17), residues: 1890 helix: -1.27 (0.17), residues: 752 sheet: -4.74 (0.73), residues: 30 loop : -4.43 (0.15), residues: 1108 *********************** 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 : 0.956 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0834 time to fit residues: 7.9409 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 : 0.852 ------------------------------------------------------------------------------- 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: 50.0000 chunk 69 optimal weight: 50.0000 chunk 73 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 135 optimal weight: 50.0000 chunk 45 optimal weight: 50.0000 chunk 176 optimal weight: 2.9990 chunk 17 optimal weight: 40.0000 chunk 154 optimal weight: 30.0000 chunk 40 optimal weight: 20.0000 overall best weight: 9.7992 ------------------------------------------------------------------------------- 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 = 0.3348 r_free = 0.3348 target = 0.047559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.036653 restraints weight = 96337.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.036840 restraints weight = 88578.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.036985 restraints weight = 82867.929| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 2.5942 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= 0.296 Angle : 0.918 11.068 10009 Z= 0.546 Chirality : 0.036 0.113 60 Planarity : 0.004 0.023 1912 Dihedral : 13.011 119.945 2044 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.26 % Allowed : 26.98 % Favored : 72.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (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: -4.83 (0.16), residues: 1890 helix: -1.53 (0.17), residues: 750 sheet: -5.03 (0.80), residues: 22 loop : -4.70 (0.15), residues: 1118 ********************** 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 : 0.916 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0725 time to fit residues: 7.1065 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 : 0.925 ------------------------------------------------------------------------------- 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: 30.0000 chunk 46 optimal weight: 30.0000 chunk 124 optimal weight: 40.0000 chunk 11 optimal weight: 40.0000 chunk 65 optimal weight: 30.0000 chunk 45 optimal weight: 40.0000 chunk 25 optimal weight: 50.0000 chunk 186 optimal weight: 40.0000 chunk 66 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 overall best weight: 19.1998 ------------------------------------------------------------------------------- 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 = 0.3304 r_free = 0.3304 target = 0.045775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.035449 restraints weight = 105163.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.035599 restraints weight = 95997.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.035776 restraints weight = 90048.701| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 2.8214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 7942 Z= 0.492 Angle : 1.278 14.119 10009 Z= 0.771 Chirality : 0.057 0.185 60 Planarity : 0.007 0.038 1912 Dihedral : 14.485 122.989 2044 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.42 % Allowed : 30.16 % Favored : 69.42 % 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 : 0.71 % 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: -5.64 (0.15), residues: 1890 helix: -2.57 (0.17), residues: 664 sheet: -5.67 (0.47), residues: 28 loop : -4.74 (0.14), residues: 1198 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2230.24 seconds wall clock time: 40 minutes 7.49 seconds (2407.49 seconds total)