Starting phenix.real_space_refine on Fri Dec 8 09:20:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsh_22454/12_2023/7jsh_22454.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsh_22454/12_2023/7jsh_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsh_22454/12_2023/7jsh_22454.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsh_22454/12_2023/7jsh_22454.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsh_22454/12_2023/7jsh_22454.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsh_22454/12_2023/7jsh_22454.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 5.69, per 1000 atoms: 0.72 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 - 3.50 Amino acid : False - 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: 3.46 Conformation dependent library (CDL) restraints added in 2.5 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: 1.18 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: 2.08 Time building geometry restraints manager: 3.66 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: 101.19 - 106.98: 88 106.98 - 112.76: 1766 112.76 - 118.55: 2204 118.55 - 124.34: 5920 124.34 - 130.13: 31 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 2.520 nonbonded pdb=" O TRP A 331 " pdb=" N PHE A 448 " model vdw 2.596 2.520 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 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: 0.840 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: 3.910 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 27.120 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.390 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** 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 fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.888 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0651 time to fit residues: 6.4515 Evaluate side-chains 42 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.895 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1290 ------------------------------------------------------------------------------- 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: 10.0000 chunk 79 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 40.0000 chunk 76 optimal weight: 30.0000 chunk 148 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 110 optimal weight: 40.0000 chunk 172 optimal weight: 30.0000 overall best weight: 15.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3812 moved from start: 1.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 7942 Z= 0.474 Angle : 1.363 13.470 10009 Z= 0.811 Chirality : 0.035 0.134 60 Planarity : 0.008 0.032 1912 Dihedral : 13.763 68.524 2044 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.90 % Allowed : 13.86 % Favored : 85.24 % 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 : 1.09 % 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: -4.34 (0.16), residues: 1890 helix: -1.85 (0.16), residues: 746 sheet: -3.04 (0.69), residues: 47 loop : -3.85 (0.15), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** 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 fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.953 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0703 time to fit residues: 7.0499 Evaluate side-chains 42 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.912 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 0.0020 chunk 53 optimal weight: 30.0000 chunk 143 optimal weight: 10.0000 chunk 117 optimal weight: 40.0000 chunk 47 optimal weight: 20.0000 chunk 172 optimal weight: 8.9990 chunk 186 optimal weight: 8.9990 chunk 153 optimal weight: 40.0000 chunk 171 optimal weight: 7.9990 chunk 58 optimal weight: 30.0000 chunk 138 optimal weight: 50.0000 overall best weight: 7.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3776 moved from start: 1.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7942 Z= 0.229 Angle : 0.760 8.204 10009 Z= 0.449 Chirality : 0.025 0.062 60 Planarity : 0.004 0.020 1912 Dihedral : 11.182 74.914 2044 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.42 % Allowed : 13.17 % Favored : 86.40 % 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 : 0.11 % 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: -3.48 (0.17), residues: 1890 helix: -0.67 (0.17), residues: 780 sheet: -3.81 (0.60), residues: 58 loop : -3.74 (0.16), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** 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 fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.944 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0669 time to fit residues: 6.7930 Evaluate side-chains 42 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.980 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 20.0000 chunk 129 optimal weight: 0.1980 chunk 89 optimal weight: 20.0000 chunk 19 optimal weight: 30.0000 chunk 82 optimal weight: 50.0000 chunk 116 optimal weight: 20.0000 chunk 173 optimal weight: 50.0000 chunk 183 optimal weight: 40.0000 chunk 90 optimal weight: 8.9990 chunk 164 optimal weight: 9.9990 chunk 49 optimal weight: 50.0000 overall best weight: 11.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4380 moved from start: 1.9453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7942 Z= 0.386 Angle : 1.180 12.410 10009 Z= 0.699 Chirality : 0.038 0.121 60 Planarity : 0.006 0.036 1912 Dihedral : 13.531 85.944 2044 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 23.73 Ramachandran Plot: Outliers : 0.85 % Allowed : 19.89 % Favored : 79.26 % 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 : 0.44 % 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: -4.69 (0.16), residues: 1890 helix: -1.85 (0.16), residues: 740 sheet: -3.79 (0.54), residues: 64 loop : -4.23 (0.15), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** 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 fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.995 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0689 time to fit residues: 6.9183 Evaluate side-chains 42 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.039 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 136 optimal weight: 40.0000 chunk 75 optimal weight: 30.0000 chunk 156 optimal weight: 3.9990 chunk 126 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 93 optimal weight: 9.9990 chunk 164 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4180 moved from start: 1.9199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7942 Z= 0.188 Angle : 0.695 9.617 10009 Z= 0.409 Chirality : 0.027 0.083 60 Planarity : 0.003 0.017 1912 Dihedral : 11.698 87.324 2044 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 14.07 % Favored : 85.71 % 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: -3.76 (0.17), residues: 1890 helix: -0.75 (0.17), residues: 766 sheet: -3.94 (0.49), residues: 75 loop : -3.97 (0.16), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** 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 fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.917 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1069 time to fit residues: 11.1298 Evaluate side-chains 42 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.470 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 20.0000 chunk 165 optimal weight: 50.0000 chunk 36 optimal weight: 7.9990 chunk 107 optimal weight: 0.3980 chunk 45 optimal weight: 0.4980 chunk 183 optimal weight: 20.0000 chunk 152 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 96 optimal weight: 0.7980 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4127 moved from start: 1.9570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7942 Z= 0.148 Angle : 0.551 7.036 10009 Z= 0.324 Chirality : 0.024 0.070 60 Planarity : 0.002 0.013 1912 Dihedral : 10.962 86.809 2044 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.21 % Allowed : 16.46 % Favored : 83.33 % 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 : 0.00 % 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: -2.82 (0.19), residues: 1890 helix: 0.44 (0.18), residues: 799 sheet: -4.40 (0.41), residues: 73 loop : -3.85 (0.17), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** 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 fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.939 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0663 time to fit residues: 6.7023 Evaluate side-chains 42 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.981 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 30.0000 chunk 20 optimal weight: 20.0000 chunk 104 optimal weight: 0.9990 chunk 134 optimal weight: 30.0000 chunk 154 optimal weight: 40.0000 chunk 102 optimal weight: 40.0000 chunk 183 optimal weight: 50.0000 chunk 114 optimal weight: 40.0000 chunk 111 optimal weight: 50.0000 chunk 84 optimal weight: 50.0000 chunk 113 optimal weight: 40.0000 overall best weight: 24.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4909 moved from start: 2.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 7942 Z= 0.590 Angle : 1.528 15.894 10009 Z= 0.927 Chirality : 0.057 0.155 60 Planarity : 0.009 0.045 1912 Dihedral : 15.301 117.923 2044 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 52.77 Ramachandran Plot: Outliers : 1.90 % Allowed : 28.47 % Favored : 69.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.04 % 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: -5.76 (0.15), residues: 1890 helix: -2.98 (0.15), residues: 692 sheet: -4.79 (0.52), residues: 47 loop : -4.62 (0.15), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** 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 fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.981 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0693 time to fit residues: 6.8168 Evaluate side-chains 42 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.960 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 0.0980 chunk 109 optimal weight: 50.0000 chunk 55 optimal weight: 50.0000 chunk 35 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 124 optimal weight: 40.0000 chunk 90 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 143 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 175 optimal weight: 10.0000 overall best weight: 6.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4523 moved from start: 2.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7942 Z= 0.210 Angle : 0.784 8.690 10009 Z= 0.465 Chirality : 0.032 0.088 60 Planarity : 0.004 0.022 1912 Dihedral : 12.906 123.187 2044 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 19.68 % Favored : 80.11 % 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: -4.89 (0.16), residues: 1890 helix: -1.86 (0.16), residues: 758 sheet: -5.18 (0.39), residues: 51 loop : -4.46 (0.16), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** 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 fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.006 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0712 time to fit residues: 7.1516 Evaluate side-chains 42 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.986 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 7.9990 chunk 170 optimal weight: 10.0000 chunk 175 optimal weight: 30.0000 chunk 102 optimal weight: 40.0000 chunk 74 optimal weight: 0.9990 chunk 134 optimal weight: 30.0000 chunk 52 optimal weight: 40.0000 chunk 154 optimal weight: 30.0000 chunk 161 optimal weight: 50.0000 chunk 112 optimal weight: 50.0000 chunk 180 optimal weight: 30.0000 overall best weight: 15.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4884 moved from start: 2.6233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 7942 Z= 0.435 Angle : 1.194 13.496 10009 Z= 0.717 Chirality : 0.047 0.140 60 Planarity : 0.006 0.034 1912 Dihedral : 14.232 125.061 2044 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 35.25 Ramachandran Plot: Outliers : 0.79 % Allowed : 31.53 % Favored : 67.67 % 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: -5.58 (0.15), residues: 1890 helix: -2.61 (0.16), residues: 718 sheet: -4.98 (0.58), residues: 40 loop : -4.71 (0.15), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** 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 fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.977 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0716 time to fit residues: 7.1318 Evaluate side-chains 42 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.974 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 50.0000 chunk 85 optimal weight: 30.0000 chunk 125 optimal weight: 20.0000 chunk 189 optimal weight: 20.0000 chunk 174 optimal weight: 20.0000 chunk 150 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 92 optimal weight: 40.0000 chunk 119 optimal weight: 50.0000 chunk 160 optimal weight: 30.0000 overall best weight: 15.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4892 moved from start: 2.7488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7942 Z= 0.390 Angle : 1.104 10.410 10009 Z= 0.665 Chirality : 0.045 0.135 60 Planarity : 0.006 0.032 1912 Dihedral : 13.971 120.370 2044 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 30.32 Ramachandran Plot: Outliers : 0.21 % Allowed : 28.73 % Favored : 71.06 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % Rama-Z (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: -5.62 (0.15), residues: 1890 helix: -2.58 (0.16), residues: 723 sheet: -5.60 (0.40), residues: 53 loop : -4.73 (0.15), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ********************** 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 fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.871 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0687 time to fit residues: 6.7713 Evaluate side-chains 42 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.965 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 40.0000 chunk 138 optimal weight: 30.0000 chunk 22 optimal weight: 30.0000 chunk 41 optimal weight: 0.9990 chunk 150 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 155 optimal weight: 30.0000 chunk 19 optimal weight: 30.0000 chunk 27 optimal weight: 50.0000 chunk 132 optimal weight: 30.0000 chunk 8 optimal weight: 0.0670 overall best weight: 12.2130 ------------------------------------------------------------------------------- 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 = 0.3074 r_free = 0.3074 target = 0.041646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.038729 restraints weight = 163809.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.038729 restraints weight = 211269.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.038729 restraints weight = 211269.468| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 2.8179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 7942 Z= 0.338 Angle : 1.009 10.972 10009 Z= 0.603 Chirality : 0.045 0.151 60 Planarity : 0.005 0.031 1912 Dihedral : 13.691 123.913 2044 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 27.17 Ramachandran Plot: Outliers : 0.32 % Allowed : 31.69 % Favored : 67.99 % 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 : 0.44 % 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: -5.48 (0.16), residues: 1890 helix: -2.40 (0.16), residues: 720 sheet: -5.33 (0.50), residues: 51 loop : -4.71 (0.15), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1184.40 seconds wall clock time: 21 minutes 58.55 seconds (1318.55 seconds total)