Starting phenix.real_space_refine on Tue Mar 3 18:50:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p68_13221/03_2026/7p68_13221.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p68_13221/03_2026/7p68_13221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7p68_13221/03_2026/7p68_13221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p68_13221/03_2026/7p68_13221.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p68_13221/03_2026/7p68_13221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p68_13221/03_2026/7p68_13221.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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 S 20 5.16 5 C 5060 2.51 5 N 1520 2.21 5 O 1520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8120 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "B" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "C" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "E" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "G" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "I" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "D" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "F" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "H" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "J" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Time building chain proxies: 1.82, per 1000 atoms: 0.22 Number of scatterers: 8120 At special positions: 0 Unit cell: (140.3, 112.7, 55.2, 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) S 20 16.00 O 1520 8.00 N 1520 7.00 C 5060 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 243.4 milliseconds 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1860 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 22 sheets defined 0.0% alpha, 45.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 275 through 280 removed outlier: 6.225A pdb=" N VAL C 275 " --> pdb=" O GLN E 276 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE E 278 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE C 277 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LYS E 280 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASN C 279 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL A 275 " --> pdb=" O GLN I 276 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE I 278 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE A 277 " --> pdb=" O ILE I 278 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LYS I 280 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ASN A 279 " --> pdb=" O LYS I 280 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 283 through 284 removed outlier: 6.182A pdb=" N ASP A 283 " --> pdb=" O LEU E 284 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP G 283 " --> pdb=" O LEU I 284 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 287 through 290 removed outlier: 6.366A pdb=" N VAL C 287 " --> pdb=" O GLN E 288 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LYS E 290 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER C 289 " --> pdb=" O LYS E 290 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL A 287 " --> pdb=" O GLN I 288 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N LYS I 290 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER A 289 " --> pdb=" O LYS I 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 297 through 298 removed outlier: 6.423A pdb=" N ILE C 297 " --> pdb=" O LYS E 298 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE A 297 " --> pdb=" O LYS I 298 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 307 through 310 removed outlier: 6.697A pdb=" N ILE A 308 " --> pdb=" O VAL E 309 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE G 308 " --> pdb=" O VAL I 309 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.855A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL G 313 " --> pdb=" O ASP I 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.238A pdb=" N LYS A 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N SER E 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR A 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N CYS E 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LYS A 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LYS G 317 " --> pdb=" O VAL I 318 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N SER I 320 " --> pdb=" O LYS G 317 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR G 319 " --> pdb=" O SER I 320 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N CYS I 322 " --> pdb=" O THR G 319 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LYS G 321 " --> pdb=" O CYS I 322 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.636A pdb=" N ILE C 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE A 328 " --> pdb=" O HIS I 329 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 337 through 345 removed outlier: 6.649A pdb=" N VAL C 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N LYS E 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL C 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N GLU E 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N SER C 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU E 344 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LYS C 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL A 337 " --> pdb=" O GLU I 338 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LYS I 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 339 " --> pdb=" O LYS I 340 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N GLU I 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N SER A 341 " --> pdb=" O GLU I 342 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU I 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS A 343 " --> pdb=" O LEU I 344 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 348 through 350 removed outlier: 6.194A pdb=" N ARG C 349 " --> pdb=" O VAL E 350 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ARG A 349 " --> pdb=" O VAL I 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 354 through 362 removed outlier: 6.890A pdb=" N GLY E 355 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE C 360 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR E 361 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N HIS C 362 " --> pdb=" O THR E 361 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY A 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ASP E 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU A 357 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE E 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ASN A 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N HIS E 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 9.080A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE A 354 " --> pdb=" O GLY I 355 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N LEU I 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N SER A 356 " --> pdb=" O LEU I 357 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ASN I 359 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ASP A 358 " --> pdb=" O ASN I 359 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR I 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N ILE A 360 " --> pdb=" O THR I 361 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLY G 355 " --> pdb=" O SER I 356 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASP I 358 " --> pdb=" O GLY G 355 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU G 357 " --> pdb=" O ASP I 358 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE I 360 " --> pdb=" O LEU G 357 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ASN G 359 " --> pdb=" O ILE I 360 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N HIS I 362 " --> pdb=" O ASN G 359 " (cutoff:3.500A) removed outlier: 9.155A pdb=" N THR G 361 " --> pdb=" O HIS I 362 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 369 through 377 removed outlier: 6.301A pdb=" N LYS C 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N GLU E 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE C 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N HIS E 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR C 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU E 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LYS C 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYS A 370 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LYS A 369 " --> pdb=" O LYS I 370 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N GLU I 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A 371 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N HIS I 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR A 373 " --> pdb=" O HIS I 374 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N LEU I 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LYS A 375 " --> pdb=" O LEU I 376 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS G 370 " --> pdb=" O LYS I 369 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 274 through 289 removed outlier: 6.715A pdb=" N LEU F 282 " --> pdb=" O LYS D 281 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASP D 283 " --> pdb=" O LEU F 282 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU F 284 " --> pdb=" O ASP D 283 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER D 285 " --> pdb=" O LEU F 284 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN F 286 " --> pdb=" O SER D 285 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU D 282 " --> pdb=" O LYS B 281 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP B 283 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU D 284 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N SER B 285 " --> pdb=" O LEU D 284 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN D 286 " --> pdb=" O SER B 285 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS B 274 " --> pdb=" O VAL H 275 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE H 277 " --> pdb=" O LYS B 274 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN B 276 " --> pdb=" O ILE H 277 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASN H 279 " --> pdb=" O GLN B 276 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE B 278 " --> pdb=" O ASN H 279 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LYS H 281 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N LYS B 280 " --> pdb=" O LYS H 281 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ASP H 283 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N LEU B 282 " --> pdb=" O ASP H 283 " (cutoff:3.500A) removed outlier: 10.286A pdb=" N SER H 285 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N LEU B 284 " --> pdb=" O SER H 285 " (cutoff:3.500A) removed outlier: 9.375A pdb=" N VAL H 287 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN B 286 " --> pdb=" O VAL H 287 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N SER H 289 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLN B 288 " --> pdb=" O SER H 289 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LYS H 274 " --> pdb=" O VAL J 275 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ILE J 277 " --> pdb=" O LYS H 274 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLN H 276 " --> pdb=" O ILE J 277 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ASN J 279 " --> pdb=" O GLN H 276 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE H 278 " --> pdb=" O ASN J 279 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LYS J 281 " --> pdb=" O ILE H 278 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N LYS H 280 " --> pdb=" O LYS J 281 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ASP J 283 " --> pdb=" O LYS H 280 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N LEU H 282 " --> pdb=" O ASP J 283 " (cutoff:3.500A) removed outlier: 10.296A pdb=" N SER J 285 " --> pdb=" O LEU H 282 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N LEU H 284 " --> pdb=" O SER J 285 " (cutoff:3.500A) removed outlier: 9.392A pdb=" N VAL J 287 " --> pdb=" O LEU H 284 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASN H 286 " --> pdb=" O VAL J 287 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N SER J 289 " --> pdb=" O ASN H 286 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLN H 288 " --> pdb=" O SER J 289 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 297 through 298 removed outlier: 6.624A pdb=" N ILE D 297 " --> pdb=" O LYS F 298 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE B 297 " --> pdb=" O LYS D 298 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 306 through 310 removed outlier: 6.309A pdb=" N VAL B 306 " --> pdb=" O GLN H 307 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N VAL H 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE B 308 " --> pdb=" O VAL H 309 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL H 306 " --> pdb=" O GLN J 307 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL J 309 " --> pdb=" O VAL H 306 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE H 308 " --> pdb=" O VAL J 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 313 through 314 removed outlier: 6.806A pdb=" N VAL B 313 " --> pdb=" O ASP H 314 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL H 313 " --> pdb=" O ASP J 314 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 319 through 322 removed outlier: 5.984A pdb=" N SER D 320 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N SER B 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 328 through 330 removed outlier: 6.663A pdb=" N ILE D 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 337 through 345 removed outlier: 6.412A pdb=" N VAL D 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LYS F 340 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL D 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N GLU F 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N SER D 341 " --> pdb=" O GLU F 342 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU F 344 " --> pdb=" O SER D 341 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LYS D 343 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N GLU D 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N SER B 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU D 344 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS B 343 " --> pdb=" O LEU D 344 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 348 through 350 removed outlier: 6.383A pdb=" N ARG D 349 " --> pdb=" O VAL F 350 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ARG B 349 " --> pdb=" O VAL D 350 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 354 through 362 removed outlier: 6.867A pdb=" N GLY F 355 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE D 360 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR F 361 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N HIS D 362 " --> pdb=" O THR F 361 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY D 355 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE B 360 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR D 361 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N HIS B 362 " --> pdb=" O THR D 361 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY B 355 " --> pdb=" O SER H 356 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ASP H 358 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU B 357 " --> pdb=" O ASP H 358 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE H 360 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ASN B 359 " --> pdb=" O ILE H 360 " (cutoff:3.500A) removed outlier: 9.805A pdb=" N HIS H 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N THR B 361 " --> pdb=" O HIS H 362 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY H 355 " --> pdb=" O SER J 356 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ASP J 358 " --> pdb=" O GLY H 355 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU H 357 " --> pdb=" O ASP J 358 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE J 360 " --> pdb=" O LEU H 357 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ASN H 359 " --> pdb=" O ILE J 360 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N HIS J 362 " --> pdb=" O ASN H 359 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N THR H 361 " --> pdb=" O HIS J 362 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 369 through 377 removed outlier: 6.860A pdb=" N LYS F 370 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LYS D 370 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LYS B 370 " --> pdb=" O LYS H 369 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS H 370 " --> pdb=" O ILE J 371 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N THR J 373 " --> pdb=" O LYS H 370 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLU H 372 " --> pdb=" O THR J 373 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LYS J 375 " --> pdb=" O GLU H 372 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N HIS H 374 " --> pdb=" O LYS J 375 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N THR J 377 " --> pdb=" O HIS H 374 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU H 376 " --> pdb=" O THR J 377 " (cutoff:3.500A) 171 hydrogen bonds defined for protein. 513 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2637 1.34 - 1.46: 877 1.46 - 1.57: 4696 1.57 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 8230 Sorted by residual: bond pdb=" N GLY H 273 " pdb=" CA GLY H 273 " ideal model delta sigma weight residual 1.444 1.477 -0.033 1.06e-02 8.90e+03 9.79e+00 bond pdb=" N GLY F 273 " pdb=" CA GLY F 273 " ideal model delta sigma weight residual 1.444 1.477 -0.032 1.06e-02 8.90e+03 9.40e+00 bond pdb=" N GLY B 273 " pdb=" CA GLY B 273 " ideal model delta sigma weight residual 1.444 1.477 -0.032 1.06e-02 8.90e+03 9.38e+00 bond pdb=" N GLY D 273 " pdb=" CA GLY D 273 " ideal model delta sigma weight residual 1.444 1.476 -0.032 1.06e-02 8.90e+03 9.29e+00 bond pdb=" N GLY J 273 " pdb=" CA GLY J 273 " ideal model delta sigma weight residual 1.444 1.476 -0.032 1.06e-02 8.90e+03 9.18e+00 ... (remaining 8225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 10232 1.57 - 3.15: 575 3.15 - 4.72: 123 4.72 - 6.29: 45 6.29 - 7.87: 15 Bond angle restraints: 10990 Sorted by residual: angle pdb=" CA HIS F 299 " pdb=" C HIS F 299 " pdb=" O HIS F 299 " ideal model delta sigma weight residual 122.44 117.94 4.50 1.32e+00 5.74e-01 1.16e+01 angle pdb=" CA HIS H 299 " pdb=" C HIS H 299 " pdb=" O HIS H 299 " ideal model delta sigma weight residual 122.44 117.96 4.48 1.32e+00 5.74e-01 1.15e+01 angle pdb=" CA HIS J 299 " pdb=" C HIS J 299 " pdb=" O HIS J 299 " ideal model delta sigma weight residual 122.44 117.98 4.46 1.32e+00 5.74e-01 1.14e+01 angle pdb=" CA HIS B 299 " pdb=" C HIS B 299 " pdb=" O HIS B 299 " ideal model delta sigma weight residual 122.44 117.99 4.45 1.32e+00 5.74e-01 1.14e+01 angle pdb=" CA ASN I 286 " pdb=" C ASN I 286 " pdb=" O ASN I 286 " ideal model delta sigma weight residual 122.14 117.96 4.18 1.24e+00 6.50e-01 1.14e+01 ... (remaining 10985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.70: 4283 11.70 - 23.41: 507 23.41 - 35.11: 170 35.11 - 46.81: 55 46.81 - 58.52: 35 Dihedral angle restraints: 5050 sinusoidal: 2110 harmonic: 2940 Sorted by residual: dihedral pdb=" CA GLN J 351 " pdb=" C GLN J 351 " pdb=" N SER J 352 " pdb=" CA SER J 352 " ideal model delta harmonic sigma weight residual 180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA GLN D 351 " pdb=" C GLN D 351 " pdb=" N SER D 352 " pdb=" CA SER D 352 " ideal model delta harmonic sigma weight residual 180.00 -159.60 -20.40 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA GLN F 351 " pdb=" C GLN F 351 " pdb=" N SER F 352 " pdb=" CA SER F 352 " ideal model delta harmonic sigma weight residual -180.00 -159.60 -20.40 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 5047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 935 0.079 - 0.158: 266 0.158 - 0.236: 14 0.236 - 0.315: 5 0.315 - 0.394: 10 Chirality restraints: 1230 Sorted by residual: chirality pdb=" CB THR D 377 " pdb=" CA THR D 377 " pdb=" OG1 THR D 377 " pdb=" CG2 THR D 377 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CB THR F 377 " pdb=" CA THR F 377 " pdb=" OG1 THR F 377 " pdb=" CG2 THR F 377 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CB THR H 377 " pdb=" CA THR H 377 " pdb=" OG1 THR H 377 " pdb=" CG2 THR H 377 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.39 2.00e-01 2.50e+01 3.82e+00 ... (remaining 1227 not shown) Planarity restraints: 1410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 346 " 0.039 2.00e-02 2.50e+03 3.58e-02 2.24e+01 pdb=" CG PHE F 346 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE F 346 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE F 346 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE F 346 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE F 346 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 346 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 346 " 0.040 2.00e-02 2.50e+03 3.57e-02 2.23e+01 pdb=" CG PHE D 346 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE D 346 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE D 346 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE D 346 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE D 346 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 346 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 346 " 0.040 2.00e-02 2.50e+03 3.56e-02 2.21e+01 pdb=" CG PHE H 346 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE H 346 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE H 346 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE H 346 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE H 346 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE H 346 " -0.000 2.00e-02 2.50e+03 ... (remaining 1407 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 3144 2.92 - 3.42: 6994 3.42 - 3.91: 14499 3.91 - 4.41: 15011 4.41 - 4.90: 30338 Nonbonded interactions: 69986 Sorted by model distance: nonbonded pdb=" NZ LYS B 340 " pdb=" OE2 GLU B 342 " model vdw 2.430 3.120 nonbonded pdb=" NZ LYS J 340 " pdb=" OE2 GLU J 342 " model vdw 2.430 3.120 nonbonded pdb=" NZ LYS D 340 " pdb=" OE2 GLU D 342 " model vdw 2.430 3.120 nonbonded pdb=" NZ LYS H 340 " pdb=" OE2 GLU H 342 " model vdw 2.430 3.120 nonbonded pdb=" NZ LYS F 340 " pdb=" OE2 GLU F 342 " model vdw 2.430 3.120 ... (remaining 69981 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' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 individual isotropic 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: 3.590 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.990 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:9.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 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 : 0.006 0.060 8230 Z= 0.323 Angle : 0.903 7.868 10990 Z= 0.487 Chirality : 0.071 0.394 1230 Planarity : 0.005 0.036 1410 Dihedral : 12.923 58.516 3190 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.21), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 379 TYR 0.009 0.002 TYR H 310 PHE 0.080 0.009 PHE F 346 HIS 0.004 0.001 HIS H 329 Details of bonding type rmsd covalent geometry : bond 0.00550 ( 8230) covalent geometry : angle 0.90268 (10990) hydrogen bonds : bond 0.12338 ( 171) hydrogen bonds : angle 7.53207 ( 513) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 276 GLN cc_start: 0.8117 (mt0) cc_final: 0.7817 (mt0) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.4819 time to fit residues: 152.9522 Evaluate side-chains 217 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 0.1980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN B 327 ASN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 351 GLN D 351 GLN F 276 GLN F 351 GLN H 327 ASN ** H 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.120134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.101761 restraints weight = 12686.460| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.38 r_work: 0.3758 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8230 Z= 0.224 Angle : 0.670 8.097 10990 Z= 0.331 Chirality : 0.050 0.135 1230 Planarity : 0.004 0.030 1410 Dihedral : 5.239 19.225 1100 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 5.27 % Allowed : 17.53 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.21), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 349 TYR 0.013 0.002 TYR E 310 PHE 0.014 0.002 PHE J 378 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00538 ( 8230) covalent geometry : angle 0.67023 (10990) hydrogen bonds : bond 0.02210 ( 171) hydrogen bonds : angle 5.18313 ( 513) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 238 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 ASP cc_start: 0.8589 (m-30) cc_final: 0.8289 (m-30) REVERT: B 320 SER cc_start: 0.9263 (t) cc_final: 0.9056 (p) REVERT: B 342 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8327 (tm-30) REVERT: B 343 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.7865 (tmtt) REVERT: B 345 ASP cc_start: 0.8107 (t0) cc_final: 0.7900 (t0) REVERT: B 349 ARG cc_start: 0.7867 (tmt170) cc_final: 0.7563 (tmt170) REVERT: B 379 ARG cc_start: 0.6095 (mmm-85) cc_final: 0.5864 (tmm160) REVERT: C 342 GLU cc_start: 0.5172 (pm20) cc_final: 0.4716 (pm20) REVERT: E 295 ASP cc_start: 0.8224 (m-30) cc_final: 0.7917 (m-30) REVERT: E 338 GLU cc_start: 0.8042 (mp0) cc_final: 0.7782 (mp0) REVERT: G 293 SER cc_start: 0.9178 (p) cc_final: 0.8758 (p) REVERT: G 336 GLN cc_start: 0.8739 (mp10) cc_final: 0.8502 (mp10) REVERT: G 338 GLU cc_start: 0.8053 (mp0) cc_final: 0.7851 (mp0) REVERT: G 351 GLN cc_start: 0.8072 (mt0) cc_final: 0.7829 (mt0) REVERT: I 279 ASN cc_start: 0.8218 (m-40) cc_final: 0.7995 (m110) REVERT: I 337 VAL cc_start: 0.8072 (OUTLIER) cc_final: 0.7853 (t) REVERT: I 347 LYS cc_start: 0.8540 (ttmt) cc_final: 0.8269 (tttm) REVERT: D 320 SER cc_start: 0.9243 (t) cc_final: 0.9024 (m) REVERT: D 342 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8209 (tm-30) REVERT: D 345 ASP cc_start: 0.8120 (t0) cc_final: 0.7692 (t0) REVERT: F 342 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7267 (tm-30) REVERT: F 379 ARG cc_start: 0.6444 (mmt90) cc_final: 0.4997 (ptp90) REVERT: H 345 ASP cc_start: 0.8128 (t0) cc_final: 0.7870 (t0) REVERT: H 359 ASN cc_start: 0.8564 (t0) cc_final: 0.8321 (t0) REVERT: J 345 ASP cc_start: 0.7334 (m-30) cc_final: 0.7103 (m-30) REVERT: J 347 LYS cc_start: 0.8679 (mttt) cc_final: 0.8456 (mmmt) REVERT: J 349 ARG cc_start: 0.5255 (tpm170) cc_final: 0.5000 (tpp-160) REVERT: J 368 ASN cc_start: 0.8098 (m-40) cc_final: 0.7837 (m-40) REVERT: J 378 PHE cc_start: 0.7295 (m-80) cc_final: 0.7088 (m-10) outliers start: 49 outliers final: 31 residues processed: 266 average time/residue: 0.4781 time to fit residues: 135.6171 Evaluate side-chains 248 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain G residue 283 ASP Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 341 SER Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 349 ARG Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 337 VAL Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain H residue 311 LYS Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 341 SER Chi-restraints excluded: chain J residue 311 LYS Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 373 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 43 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 49 optimal weight: 0.0570 chunk 58 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 overall best weight: 4.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN A 288 GLN ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN C 329 HIS ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 288 GLN ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 GLN D 351 GLN F 276 GLN F 351 GLN H 276 GLN ** J 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.116916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.098669 restraints weight = 12791.874| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.32 r_work: 0.3718 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 8230 Z= 0.291 Angle : 0.705 8.337 10990 Z= 0.353 Chirality : 0.051 0.139 1230 Planarity : 0.004 0.031 1410 Dihedral : 5.427 19.956 1100 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 7.31 % Allowed : 18.82 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.27 (0.21), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 379 TYR 0.016 0.002 TYR E 310 PHE 0.017 0.002 PHE J 378 HIS 0.006 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00691 ( 8230) covalent geometry : angle 0.70493 (10990) hydrogen bonds : bond 0.02230 ( 171) hydrogen bonds : angle 5.05893 ( 513) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 227 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 ASP cc_start: 0.8533 (m-30) cc_final: 0.8310 (m-30) REVERT: A 349 ARG cc_start: 0.8596 (ttp-110) cc_final: 0.8364 (ttp-110) REVERT: A 351 GLN cc_start: 0.8561 (tt0) cc_final: 0.8128 (tt0) REVERT: B 320 SER cc_start: 0.9402 (t) cc_final: 0.9092 (p) REVERT: B 342 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8318 (tm-30) REVERT: B 343 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8580 (tptp) REVERT: B 345 ASP cc_start: 0.8441 (t0) cc_final: 0.7992 (t0) REVERT: B 347 LYS cc_start: 0.8684 (mttt) cc_final: 0.8093 (mptp) REVERT: B 349 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7461 (tmt170) REVERT: B 379 ARG cc_start: 0.6382 (mmm-85) cc_final: 0.6153 (tmm160) REVERT: C 295 ASP cc_start: 0.7775 (m-30) cc_final: 0.7524 (m-30) REVERT: C 345 ASP cc_start: 0.8110 (t0) cc_final: 0.7684 (t0) REVERT: E 295 ASP cc_start: 0.8322 (m-30) cc_final: 0.8027 (m-30) REVERT: G 288 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8495 (mt0) REVERT: G 336 GLN cc_start: 0.8820 (mp10) cc_final: 0.8602 (mp10) REVERT: G 337 VAL cc_start: 0.8577 (OUTLIER) cc_final: 0.8372 (t) REVERT: G 338 GLU cc_start: 0.8162 (mp0) cc_final: 0.7948 (mp0) REVERT: I 279 ASN cc_start: 0.8277 (m-40) cc_final: 0.8046 (m110) REVERT: I 347 LYS cc_start: 0.8586 (ttmt) cc_final: 0.8276 (tttm) REVERT: I 349 ARG cc_start: 0.8511 (ttp-110) cc_final: 0.8246 (ttp-110) REVERT: I 351 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8450 (mt0) REVERT: D 320 SER cc_start: 0.9304 (t) cc_final: 0.8933 (p) REVERT: D 345 ASP cc_start: 0.8441 (t0) cc_final: 0.8017 (t0) REVERT: D 349 ARG cc_start: 0.7837 (tmt170) cc_final: 0.7632 (tmt170) REVERT: D 379 ARG cc_start: 0.6735 (tmm160) cc_final: 0.6351 (tmm160) REVERT: F 311 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.9127 (tppp) REVERT: F 324 SER cc_start: 0.9074 (OUTLIER) cc_final: 0.8377 (p) REVERT: F 342 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7436 (tm-30) REVERT: F 379 ARG cc_start: 0.6695 (mmt90) cc_final: 0.5524 (ptp90) REVERT: H 345 ASP cc_start: 0.8291 (t0) cc_final: 0.7607 (t0) REVERT: H 347 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8000 (tppp) REVERT: H 379 ARG cc_start: 0.6555 (tmm160) cc_final: 0.6091 (tpt90) REVERT: J 347 LYS cc_start: 0.8728 (mttt) cc_final: 0.8208 (mmmt) REVERT: J 349 ARG cc_start: 0.5546 (tpm170) cc_final: 0.5344 (tpp-160) REVERT: J 368 ASN cc_start: 0.8112 (m-40) cc_final: 0.7887 (m-40) REVERT: J 378 PHE cc_start: 0.7581 (m-80) cc_final: 0.7320 (m-80) REVERT: J 379 ARG cc_start: 0.6299 (mmm160) cc_final: 0.5777 (tpt90) outliers start: 68 outliers final: 47 residues processed: 262 average time/residue: 0.4726 time to fit residues: 131.9660 Evaluate side-chains 268 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 213 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 288 GLN Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 341 SER Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 349 ARG Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 337 VAL Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain I residue 351 GLN Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain H residue 311 LYS Chi-restraints excluded: chain H residue 320 SER Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 341 SER Chi-restraints excluded: chain H residue 347 LYS Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 311 LYS Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 373 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 24 optimal weight: 0.0060 chunk 43 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN A 307 GLN B 351 GLN C 351 GLN E 351 GLN G 307 GLN I 307 GLN F 276 GLN F 351 GLN F 374 HIS J 276 GLN J 299 HIS J 359 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.123764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.105536 restraints weight = 12650.178| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.40 r_work: 0.3826 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8230 Z= 0.108 Angle : 0.600 7.149 10990 Z= 0.289 Chirality : 0.050 0.145 1230 Planarity : 0.003 0.026 1410 Dihedral : 4.799 19.538 1100 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 5.59 % Allowed : 21.40 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.21), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG J 379 TYR 0.010 0.001 TYR E 310 PHE 0.018 0.002 PHE B 346 HIS 0.002 0.000 HIS G 330 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8230) covalent geometry : angle 0.60015 (10990) hydrogen bonds : bond 0.01674 ( 171) hydrogen bonds : angle 4.73632 ( 513) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 231 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.8599 (ttp-110) cc_final: 0.8237 (ttp-110) REVERT: A 351 GLN cc_start: 0.8541 (tt0) cc_final: 0.8084 (tt0) REVERT: B 342 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8253 (tm-30) REVERT: B 345 ASP cc_start: 0.8462 (t0) cc_final: 0.7991 (t0) REVERT: B 349 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7110 (tmt170) REVERT: B 379 ARG cc_start: 0.6353 (mmm-85) cc_final: 0.6053 (tmm160) REVERT: C 345 ASP cc_start: 0.8010 (t0) cc_final: 0.7549 (t0) REVERT: C 379 ARG cc_start: 0.4086 (tpm170) cc_final: 0.3536 (mmp80) REVERT: E 288 GLN cc_start: 0.8784 (mt0) cc_final: 0.8356 (pm20) REVERT: E 295 ASP cc_start: 0.8261 (m-30) cc_final: 0.7943 (m-30) REVERT: E 349 ARG cc_start: 0.8461 (ttp-110) cc_final: 0.8128 (mtm110) REVERT: G 336 GLN cc_start: 0.8851 (mp10) cc_final: 0.8607 (mp10) REVERT: G 338 GLU cc_start: 0.8195 (mp0) cc_final: 0.7949 (mp0) REVERT: G 349 ARG cc_start: 0.5372 (OUTLIER) cc_final: 0.4377 (pmt-80) REVERT: G 360 ILE cc_start: 0.9419 (OUTLIER) cc_final: 0.8870 (tp) REVERT: I 290 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8356 (mmtm) REVERT: I 338 GLU cc_start: 0.7992 (mp0) cc_final: 0.7778 (mp0) REVERT: I 347 LYS cc_start: 0.8600 (ttmt) cc_final: 0.8281 (tttm) REVERT: D 311 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.9171 (mmtp) REVERT: D 342 GLU cc_start: 0.7667 (tm-30) cc_final: 0.6281 (tm-30) REVERT: D 344 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8888 (mm) REVERT: D 345 ASP cc_start: 0.8058 (t0) cc_final: 0.7348 (t0) REVERT: D 349 ARG cc_start: 0.7697 (tmt170) cc_final: 0.7370 (tmt170) REVERT: D 379 ARG cc_start: 0.6701 (tmm160) cc_final: 0.6171 (tmm160) REVERT: F 324 SER cc_start: 0.9029 (OUTLIER) cc_final: 0.8235 (p) REVERT: F 342 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7682 (tm-30) REVERT: F 379 ARG cc_start: 0.6789 (mmt90) cc_final: 0.5306 (ptp-170) REVERT: H 345 ASP cc_start: 0.8262 (t0) cc_final: 0.7828 (t0) REVERT: J 342 GLU cc_start: 0.4624 (pm20) cc_final: 0.4292 (pm20) REVERT: J 345 ASP cc_start: 0.7853 (t0) cc_final: 0.7273 (t0) REVERT: J 347 LYS cc_start: 0.8492 (mttt) cc_final: 0.8272 (mmpt) REVERT: J 368 ASN cc_start: 0.8102 (m-40) cc_final: 0.7867 (m-40) REVERT: J 378 PHE cc_start: 0.7410 (m-80) cc_final: 0.7148 (m-10) REVERT: J 379 ARG cc_start: 0.6450 (mmm160) cc_final: 0.5928 (tpt90) outliers start: 52 outliers final: 26 residues processed: 254 average time/residue: 0.4534 time to fit residues: 122.9525 Evaluate side-chains 238 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 341 SER Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 349 ARG Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain I residue 290 LYS Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 320 SER Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 341 SER Chi-restraints excluded: chain H residue 344 LEU Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 373 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 38 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 14 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN B 351 GLN C 351 GLN E 351 GLN ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 GLN F 276 GLN F 351 GLN J 327 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.115971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.098063 restraints weight = 12930.694| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.33 r_work: 0.3711 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 8230 Z= 0.323 Angle : 0.742 9.499 10990 Z= 0.370 Chirality : 0.052 0.142 1230 Planarity : 0.004 0.035 1410 Dihedral : 5.451 20.748 1100 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 7.63 % Allowed : 21.94 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.21), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 379 TYR 0.017 0.002 TYR E 310 PHE 0.020 0.003 PHE H 346 HIS 0.006 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00765 ( 8230) covalent geometry : angle 0.74175 (10990) hydrogen bonds : bond 0.02136 ( 171) hydrogen bonds : angle 4.96335 ( 513) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 214 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 349 ARG cc_start: 0.8599 (ttp-110) cc_final: 0.8332 (ttp-110) REVERT: A 351 GLN cc_start: 0.8371 (tt0) cc_final: 0.7945 (tt0) REVERT: B 314 ASP cc_start: 0.8919 (t0) cc_final: 0.8687 (t0) REVERT: B 345 ASP cc_start: 0.8379 (t0) cc_final: 0.7477 (t0) REVERT: B 347 LYS cc_start: 0.8634 (mttt) cc_final: 0.7879 (ttmm) REVERT: B 349 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7367 (tmt170) REVERT: B 351 GLN cc_start: 0.8191 (tt0) cc_final: 0.7606 (tm-30) REVERT: B 379 ARG cc_start: 0.6397 (mmm-85) cc_final: 0.6149 (tmm160) REVERT: C 295 ASP cc_start: 0.8608 (m-30) cc_final: 0.8388 (m-30) REVERT: C 351 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7207 (mt0) REVERT: E 347 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.7982 (mtpm) REVERT: E 349 ARG cc_start: 0.8503 (ttp-110) cc_final: 0.8201 (mtm110) REVERT: G 336 GLN cc_start: 0.8919 (mp10) cc_final: 0.8640 (mp10) REVERT: G 347 LYS cc_start: 0.8407 (ttmt) cc_final: 0.8163 (pmtt) REVERT: I 307 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8855 (mt0) REVERT: I 338 GLU cc_start: 0.8147 (mp0) cc_final: 0.7900 (mp0) REVERT: I 347 LYS cc_start: 0.8697 (ttmt) cc_final: 0.8377 (tttm) REVERT: I 350 VAL cc_start: 0.9355 (t) cc_final: 0.9081 (m) REVERT: D 311 LYS cc_start: 0.9420 (OUTLIER) cc_final: 0.9123 (tptm) REVERT: D 342 GLU cc_start: 0.7719 (tm-30) cc_final: 0.6351 (tm-30) REVERT: D 344 LEU cc_start: 0.9317 (mm) cc_final: 0.8870 (mm) REVERT: D 345 ASP cc_start: 0.8287 (t0) cc_final: 0.7734 (t0) REVERT: D 347 LYS cc_start: 0.8667 (mttt) cc_final: 0.7966 (mptp) REVERT: D 349 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7392 (tmt170) REVERT: D 351 GLN cc_start: 0.8411 (tt0) cc_final: 0.8040 (tm130) REVERT: D 379 ARG cc_start: 0.6883 (tmm160) cc_final: 0.6349 (tmm160) REVERT: F 311 LYS cc_start: 0.9407 (OUTLIER) cc_final: 0.9181 (tppt) REVERT: F 324 SER cc_start: 0.9041 (OUTLIER) cc_final: 0.8371 (p) REVERT: F 342 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7560 (tm-30) REVERT: F 344 LEU cc_start: 0.9197 (mm) cc_final: 0.8533 (mm) REVERT: F 347 LYS cc_start: 0.8382 (mttt) cc_final: 0.7569 (pptt) REVERT: F 349 ARG cc_start: 0.5537 (OUTLIER) cc_final: 0.4237 (ppt90) REVERT: F 379 ARG cc_start: 0.6775 (mmt90) cc_final: 0.5451 (ptp90) REVERT: H 320 SER cc_start: 0.9283 (OUTLIER) cc_final: 0.9062 (t) REVERT: H 345 ASP cc_start: 0.8431 (t0) cc_final: 0.7501 (t0) REVERT: H 379 ARG cc_start: 0.6839 (tmm160) cc_final: 0.6370 (tpt90) REVERT: J 342 GLU cc_start: 0.5243 (pm20) cc_final: 0.4921 (pm20) REVERT: J 345 ASP cc_start: 0.8059 (t0) cc_final: 0.7495 (t0) REVERT: J 379 ARG cc_start: 0.6426 (mmm160) cc_final: 0.5868 (tpt90) outliers start: 71 outliers final: 49 residues processed: 249 average time/residue: 0.4991 time to fit residues: 132.3976 Evaluate side-chains 259 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 199 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 341 SER Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 349 ARG Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 307 GLN Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 337 VAL Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain H residue 311 LYS Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 320 SER Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 341 SER Chi-restraints excluded: chain H residue 344 LEU Chi-restraints excluded: chain J residue 311 LYS Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 373 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 34 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 276 GLN F 351 GLN H 351 GLN J 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.118454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.100613 restraints weight = 12753.963| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.29 r_work: 0.3748 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8230 Z= 0.211 Angle : 0.687 8.452 10990 Z= 0.336 Chirality : 0.051 0.145 1230 Planarity : 0.003 0.030 1410 Dihedral : 5.267 20.352 1100 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 6.67 % Allowed : 23.87 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.21), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 379 TYR 0.015 0.002 TYR E 310 PHE 0.023 0.003 PHE H 346 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00503 ( 8230) covalent geometry : angle 0.68665 (10990) hydrogen bonds : bond 0.01931 ( 171) hydrogen bonds : angle 4.92329 ( 513) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 206 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: B 342 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7070 (tm-30) REVERT: B 344 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.8581 (mm) REVERT: B 345 ASP cc_start: 0.8273 (t0) cc_final: 0.7352 (t0) REVERT: B 347 LYS cc_start: 0.8565 (mttt) cc_final: 0.7797 (mptp) REVERT: B 349 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7569 (tmt170) REVERT: B 351 GLN cc_start: 0.8065 (tt0) cc_final: 0.7570 (tm-30) REVERT: E 288 GLN cc_start: 0.8852 (mt0) cc_final: 0.8311 (mp10) REVERT: E 347 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.7989 (mtpm) REVERT: E 349 ARG cc_start: 0.8562 (ttp-110) cc_final: 0.8341 (mtm110) REVERT: G 336 GLN cc_start: 0.8952 (mp10) cc_final: 0.8687 (mp10) REVERT: G 347 LYS cc_start: 0.8432 (ttmt) cc_final: 0.8162 (pmtt) REVERT: G 349 ARG cc_start: 0.5431 (OUTLIER) cc_final: 0.4185 (pmt-80) REVERT: G 379 ARG cc_start: 0.4244 (OUTLIER) cc_final: 0.2449 (ttp80) REVERT: I 290 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8540 (mmtm) REVERT: I 337 VAL cc_start: 0.8302 (OUTLIER) cc_final: 0.8083 (t) REVERT: I 338 GLU cc_start: 0.8136 (mp0) cc_final: 0.7820 (mp0) REVERT: I 347 LYS cc_start: 0.8751 (ttmt) cc_final: 0.8391 (mtpp) REVERT: I 350 VAL cc_start: 0.9421 (t) cc_final: 0.9161 (m) REVERT: D 344 LEU cc_start: 0.9352 (mm) cc_final: 0.9027 (mm) REVERT: D 345 ASP cc_start: 0.8054 (t0) cc_final: 0.7524 (t0) REVERT: D 347 LYS cc_start: 0.8633 (mttt) cc_final: 0.7876 (mptp) REVERT: D 349 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7337 (tmt170) REVERT: D 351 GLN cc_start: 0.8473 (tt0) cc_final: 0.8132 (tm130) REVERT: D 379 ARG cc_start: 0.6726 (tmm160) cc_final: 0.6041 (tmm160) REVERT: F 324 SER cc_start: 0.9069 (OUTLIER) cc_final: 0.8284 (p) REVERT: F 342 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7951 (tm-30) REVERT: F 345 ASP cc_start: 0.7755 (t0) cc_final: 0.7488 (t0) REVERT: F 347 LYS cc_start: 0.8356 (mttt) cc_final: 0.7633 (pptt) REVERT: F 349 ARG cc_start: 0.5643 (OUTLIER) cc_final: 0.4182 (ppt90) REVERT: F 379 ARG cc_start: 0.6800 (mmt90) cc_final: 0.5529 (ptp90) REVERT: H 320 SER cc_start: 0.9256 (OUTLIER) cc_final: 0.9052 (t) REVERT: H 345 ASP cc_start: 0.8407 (t0) cc_final: 0.7286 (t0) REVERT: H 379 ARG cc_start: 0.6896 (tmm160) cc_final: 0.6467 (tpt90) REVERT: J 342 GLU cc_start: 0.5240 (pm20) cc_final: 0.4985 (pm20) REVERT: J 345 ASP cc_start: 0.8022 (t0) cc_final: 0.7457 (t0) REVERT: J 378 PHE cc_start: 0.7513 (m-80) cc_final: 0.7289 (m-80) REVERT: J 379 ARG cc_start: 0.6616 (mmm160) cc_final: 0.5974 (tpt90) outliers start: 62 outliers final: 37 residues processed: 238 average time/residue: 0.5035 time to fit residues: 127.4864 Evaluate side-chains 247 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 197 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 341 SER Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 349 ARG Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain G residue 379 ARG Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 290 LYS Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 337 VAL Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 320 SER Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 373 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 30 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN C 276 GLN E 276 GLN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 GLN G 288 GLN ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 GLN H 351 GLN J 351 GLN J 374 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.116008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.097947 restraints weight = 13040.492| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.36 r_work: 0.3709 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 8230 Z= 0.294 Angle : 0.749 9.421 10990 Z= 0.371 Chirality : 0.052 0.138 1230 Planarity : 0.004 0.034 1410 Dihedral : 5.516 22.589 1100 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 8.06 % Allowed : 23.12 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.49 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 379 TYR 0.013 0.002 TYR G 310 PHE 0.013 0.003 PHE E 346 HIS 0.005 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00697 ( 8230) covalent geometry : angle 0.74915 (10990) hydrogen bonds : bond 0.02069 ( 171) hydrogen bonds : angle 4.99518 ( 513) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 206 time to evaluate : 0.330 Fit side-chains REVERT: A 351 GLN cc_start: 0.8094 (mt0) cc_final: 0.7892 (tp40) REVERT: B 342 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7184 (tm-30) REVERT: B 344 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.8618 (mm) REVERT: B 345 ASP cc_start: 0.8270 (t0) cc_final: 0.7767 (t0) REVERT: B 347 LYS cc_start: 0.8636 (mttt) cc_final: 0.7903 (mttp) REVERT: B 351 GLN cc_start: 0.8148 (tt0) cc_final: 0.7612 (tm-30) REVERT: C 288 GLN cc_start: 0.8864 (mt0) cc_final: 0.8520 (mp-120) REVERT: E 288 GLN cc_start: 0.8888 (mt0) cc_final: 0.8249 (mp10) REVERT: E 349 ARG cc_start: 0.8652 (ttp-110) cc_final: 0.8301 (mtm110) REVERT: G 286 ASN cc_start: 0.8900 (t0) cc_final: 0.8660 (t0) REVERT: G 336 GLN cc_start: 0.8970 (mp10) cc_final: 0.8697 (mp10) REVERT: G 347 LYS cc_start: 0.8566 (ttmt) cc_final: 0.8198 (pmtt) REVERT: G 349 ARG cc_start: 0.5358 (OUTLIER) cc_final: 0.4080 (pmt-80) REVERT: G 353 LYS cc_start: 0.5442 (pmtt) cc_final: 0.5010 (pmtt) REVERT: G 379 ARG cc_start: 0.4403 (OUTLIER) cc_final: 0.2771 (ttp80) REVERT: I 290 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8601 (mmtm) REVERT: I 338 GLU cc_start: 0.8241 (mp0) cc_final: 0.7920 (mp0) REVERT: I 347 LYS cc_start: 0.8764 (ttmt) cc_final: 0.8351 (mtpp) REVERT: I 350 VAL cc_start: 0.9392 (t) cc_final: 0.9060 (m) REVERT: D 342 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7098 (tm-30) REVERT: D 344 LEU cc_start: 0.9312 (mm) cc_final: 0.8781 (mm) REVERT: D 345 ASP cc_start: 0.8220 (t0) cc_final: 0.7442 (t0) REVERT: D 347 LYS cc_start: 0.8727 (mttt) cc_final: 0.8079 (mttm) REVERT: D 349 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7330 (tmt170) REVERT: D 351 GLN cc_start: 0.8457 (tt0) cc_final: 0.8079 (tm130) REVERT: F 311 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.9164 (tppp) REVERT: F 324 SER cc_start: 0.9028 (OUTLIER) cc_final: 0.8367 (p) REVERT: F 342 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7882 (tm-30) REVERT: F 344 LEU cc_start: 0.9182 (mm) cc_final: 0.8500 (mm) REVERT: F 347 LYS cc_start: 0.8329 (mttt) cc_final: 0.7787 (mttp) REVERT: F 349 ARG cc_start: 0.5436 (OUTLIER) cc_final: 0.3967 (ppt90) REVERT: F 379 ARG cc_start: 0.6733 (mmt90) cc_final: 0.5368 (ptp90) REVERT: H 342 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7153 (tm-30) REVERT: H 344 LEU cc_start: 0.9353 (mm) cc_final: 0.8722 (mm) REVERT: H 345 ASP cc_start: 0.8529 (t0) cc_final: 0.7404 (t0) REVERT: H 379 ARG cc_start: 0.6769 (OUTLIER) cc_final: 0.6308 (tpt90) REVERT: J 345 ASP cc_start: 0.8168 (t0) cc_final: 0.7552 (t0) REVERT: J 378 PHE cc_start: 0.7544 (m-80) cc_final: 0.7335 (m-80) REVERT: J 379 ARG cc_start: 0.6570 (mmm160) cc_final: 0.5959 (tpt90) outliers start: 75 outliers final: 49 residues processed: 248 average time/residue: 0.5017 time to fit residues: 132.3104 Evaluate side-chains 257 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 196 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 341 SER Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 349 ARG Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain G residue 379 ARG Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 290 LYS Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 337 VAL Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain H residue 311 LYS Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain H residue 379 ARG Chi-restraints excluded: chain J residue 311 LYS Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 347 LYS Chi-restraints excluded: chain J residue 373 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 90 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 GLN ** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 307 GLN I 307 GLN ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 HIS F 351 GLN H 299 HIS H 351 GLN J 351 GLN J 374 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.124084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.106128 restraints weight = 12452.105| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 2.36 r_work: 0.3835 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3715 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8230 Z= 0.115 Angle : 0.663 8.255 10990 Z= 0.315 Chirality : 0.051 0.137 1230 Planarity : 0.003 0.027 1410 Dihedral : 4.861 20.935 1100 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 5.70 % Allowed : 25.38 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (0.21), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 379 TYR 0.010 0.001 TYR C 310 PHE 0.023 0.003 PHE H 346 HIS 0.004 0.001 HIS J 374 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8230) covalent geometry : angle 0.66341 (10990) hydrogen bonds : bond 0.01549 ( 171) hydrogen bonds : angle 4.71151 ( 513) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 215 time to evaluate : 0.364 Fit side-chains REVERT: A 357 LEU cc_start: 0.9087 (tp) cc_final: 0.8867 (tp) REVERT: B 344 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8581 (mm) REVERT: B 345 ASP cc_start: 0.8156 (t0) cc_final: 0.7426 (t0) REVERT: B 347 LYS cc_start: 0.8485 (mttt) cc_final: 0.7668 (mptp) REVERT: B 349 ARG cc_start: 0.7909 (tmt170) cc_final: 0.7283 (tmt170) REVERT: B 351 GLN cc_start: 0.8115 (tt0) cc_final: 0.7760 (tm-30) REVERT: C 288 GLN cc_start: 0.8812 (mt0) cc_final: 0.8433 (mp10) REVERT: C 314 ASP cc_start: 0.8540 (t70) cc_final: 0.7904 (OUTLIER) REVERT: C 345 ASP cc_start: 0.7982 (t0) cc_final: 0.7519 (t0) REVERT: C 379 ARG cc_start: 0.4131 (tpm170) cc_final: 0.3680 (mmp80) REVERT: E 349 ARG cc_start: 0.8568 (ttp-110) cc_final: 0.8224 (mtm110) REVERT: G 290 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8701 (mppt) REVERT: G 336 GLN cc_start: 0.8930 (mp10) cc_final: 0.8612 (mp10) REVERT: G 347 LYS cc_start: 0.8469 (ttmt) cc_final: 0.8120 (pmtt) REVERT: G 349 ARG cc_start: 0.5375 (OUTLIER) cc_final: 0.4135 (pmt-80) REVERT: G 360 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.8772 (tp) REVERT: I 290 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8411 (mmtm) REVERT: I 338 GLU cc_start: 0.8105 (mp0) cc_final: 0.7789 (mp0) REVERT: I 347 LYS cc_start: 0.8754 (ttmt) cc_final: 0.8442 (mtpp) REVERT: I 349 ARG cc_start: 0.8327 (ttp80) cc_final: 0.8121 (ttp-110) REVERT: D 342 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7134 (tm-30) REVERT: D 344 LEU cc_start: 0.9325 (mm) cc_final: 0.8899 (mm) REVERT: D 347 LYS cc_start: 0.8635 (mttt) cc_final: 0.8032 (mttm) REVERT: D 349 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7241 (tmt170) REVERT: D 351 GLN cc_start: 0.8321 (tt0) cc_final: 0.7899 (tm130) REVERT: F 324 SER cc_start: 0.8945 (OUTLIER) cc_final: 0.8209 (p) REVERT: F 342 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7683 (tm-30) REVERT: F 344 LEU cc_start: 0.9010 (mm) cc_final: 0.8454 (mm) REVERT: F 345 ASP cc_start: 0.7416 (t0) cc_final: 0.7148 (t0) REVERT: F 347 LYS cc_start: 0.8291 (mttt) cc_final: 0.7585 (pptt) REVERT: F 349 ARG cc_start: 0.5618 (OUTLIER) cc_final: 0.4201 (ppt90) REVERT: F 379 ARG cc_start: 0.6674 (mmt90) cc_final: 0.5303 (ptp90) REVERT: H 345 ASP cc_start: 0.8189 (t0) cc_final: 0.7278 (t0) REVERT: H 379 ARG cc_start: 0.6438 (OUTLIER) cc_final: 0.5885 (tpt90) REVERT: J 342 GLU cc_start: 0.4735 (pm20) cc_final: 0.4375 (pm20) REVERT: J 345 ASP cc_start: 0.7947 (t0) cc_final: 0.7455 (t0) REVERT: J 379 ARG cc_start: 0.6539 (mmm160) cc_final: 0.5988 (tpt90) outliers start: 53 outliers final: 30 residues processed: 240 average time/residue: 0.4962 time to fit residues: 126.6193 Evaluate side-chains 240 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain G residue 290 LYS Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 349 ARG Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain I residue 290 LYS Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 337 VAL Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 373 THR Chi-restraints excluded: chain H residue 379 ARG Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 373 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 30 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 307 GLN I 279 ASN ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 GLN H 351 GLN ** H 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 351 GLN J 359 ASN J 374 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.116160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.098256 restraints weight = 12918.051| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.29 r_work: 0.3709 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 8230 Z= 0.303 Angle : 0.787 9.988 10990 Z= 0.386 Chirality : 0.053 0.187 1230 Planarity : 0.004 0.031 1410 Dihedral : 5.461 21.224 1100 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 5.70 % Allowed : 25.70 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.48 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 379 TYR 0.015 0.003 TYR G 310 PHE 0.024 0.004 PHE I 346 HIS 0.006 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00722 ( 8230) covalent geometry : angle 0.78707 (10990) hydrogen bonds : bond 0.02077 ( 171) hydrogen bonds : angle 4.89951 ( 513) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 210 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 351 GLN cc_start: 0.8007 (mt0) cc_final: 0.7662 (tp40) REVERT: B 342 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7148 (tp30) REVERT: B 344 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8747 (mm) REVERT: B 345 ASP cc_start: 0.8166 (t0) cc_final: 0.7596 (t0) REVERT: B 347 LYS cc_start: 0.8589 (mttt) cc_final: 0.7754 (mptp) REVERT: B 351 GLN cc_start: 0.8173 (tt0) cc_final: 0.7644 (tm-30) REVERT: C 379 ARG cc_start: 0.4688 (tpm170) cc_final: 0.4111 (mmp80) REVERT: E 288 GLN cc_start: 0.8858 (mt0) cc_final: 0.8479 (pm20) REVERT: E 349 ARG cc_start: 0.8547 (ttp-110) cc_final: 0.8342 (mtm110) REVERT: G 286 ASN cc_start: 0.8648 (t0) cc_final: 0.8412 (t0) REVERT: G 336 GLN cc_start: 0.8993 (mp10) cc_final: 0.8747 (mp10) REVERT: G 338 GLU cc_start: 0.8162 (mp0) cc_final: 0.7880 (mp0) REVERT: G 347 LYS cc_start: 0.8462 (ttmt) cc_final: 0.8211 (pmtt) REVERT: G 349 ARG cc_start: 0.5410 (OUTLIER) cc_final: 0.4106 (pmt-80) REVERT: G 353 LYS cc_start: 0.5638 (pmtt) cc_final: 0.2818 (pptt) REVERT: I 290 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8518 (mmtm) REVERT: I 338 GLU cc_start: 0.8274 (mp0) cc_final: 0.7941 (mp0) REVERT: I 347 LYS cc_start: 0.8742 (ttmt) cc_final: 0.8390 (mtpp) REVERT: I 349 ARG cc_start: 0.8376 (ttp80) cc_final: 0.8174 (ttp-110) REVERT: D 344 LEU cc_start: 0.9348 (mm) cc_final: 0.8850 (mm) REVERT: D 345 ASP cc_start: 0.8172 (t0) cc_final: 0.7372 (t0) REVERT: D 347 LYS cc_start: 0.8699 (mttt) cc_final: 0.7961 (mttm) REVERT: D 349 ARG cc_start: 0.7717 (tmt170) cc_final: 0.7356 (tmt170) REVERT: D 351 GLN cc_start: 0.8442 (tt0) cc_final: 0.8082 (tm130) REVERT: F 311 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.9152 (tppp) REVERT: F 324 SER cc_start: 0.9068 (OUTLIER) cc_final: 0.8373 (p) REVERT: F 342 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7823 (tm-30) REVERT: F 344 LEU cc_start: 0.9185 (mm) cc_final: 0.8477 (mm) REVERT: F 347 LYS cc_start: 0.8331 (mttt) cc_final: 0.7768 (mttp) REVERT: F 349 ARG cc_start: 0.5635 (OUTLIER) cc_final: 0.4164 (ppt90) REVERT: F 379 ARG cc_start: 0.6867 (mmt90) cc_final: 0.5436 (ptp90) REVERT: H 324 SER cc_start: 0.9140 (OUTLIER) cc_final: 0.8702 (p) REVERT: H 344 LEU cc_start: 0.9342 (mm) cc_final: 0.8873 (mm) REVERT: H 345 ASP cc_start: 0.8456 (t0) cc_final: 0.7157 (t0) REVERT: H 379 ARG cc_start: 0.6661 (OUTLIER) cc_final: 0.6272 (tpt90) REVERT: J 345 ASP cc_start: 0.8241 (t0) cc_final: 0.7828 (t0) REVERT: J 379 ARG cc_start: 0.6488 (mmm160) cc_final: 0.6008 (tpt90) outliers start: 53 outliers final: 36 residues processed: 237 average time/residue: 0.5048 time to fit residues: 127.0992 Evaluate side-chains 247 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 202 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain G residue 283 ASP Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 341 SER Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 349 ARG Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain I residue 290 LYS Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 337 VAL Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 373 THR Chi-restraints excluded: chain H residue 379 ARG Chi-restraints excluded: chain J residue 311 LYS Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 347 LYS Chi-restraints excluded: chain J residue 373 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 13 optimal weight: 0.0980 chunk 91 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 307 GLN ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 GLN H 351 GLN ** H 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 351 GLN J 359 ASN J 374 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.118974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.101002 restraints weight = 12759.185| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.29 r_work: 0.3754 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8230 Z= 0.189 Angle : 0.746 9.465 10990 Z= 0.357 Chirality : 0.052 0.166 1230 Planarity : 0.003 0.031 1410 Dihedral : 5.331 21.374 1100 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 5.16 % Allowed : 26.99 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.45 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 349 TYR 0.012 0.002 TYR C 310 PHE 0.031 0.004 PHE H 346 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 8230) covalent geometry : angle 0.74571 (10990) hydrogen bonds : bond 0.01850 ( 171) hydrogen bonds : angle 4.80432 ( 513) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 205 time to evaluate : 0.364 Fit side-chains REVERT: A 351 GLN cc_start: 0.7922 (mt0) cc_final: 0.7587 (tp40) REVERT: B 342 GLU cc_start: 0.7568 (tm-30) cc_final: 0.6480 (tp30) REVERT: B 344 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.8823 (mm) REVERT: B 345 ASP cc_start: 0.8152 (t0) cc_final: 0.7421 (t0) REVERT: B 347 LYS cc_start: 0.8499 (mttt) cc_final: 0.7700 (mptp) REVERT: B 351 GLN cc_start: 0.8195 (tt0) cc_final: 0.7707 (tm-30) REVERT: C 288 GLN cc_start: 0.8988 (mt0) cc_final: 0.8581 (mp-120) REVERT: C 345 ASP cc_start: 0.8059 (t0) cc_final: 0.7610 (t0) REVERT: E 288 GLN cc_start: 0.8845 (mt0) cc_final: 0.8427 (pm20) REVERT: E 349 ARG cc_start: 0.8570 (ttp-110) cc_final: 0.8303 (mtm110) REVERT: G 336 GLN cc_start: 0.8982 (mp10) cc_final: 0.8430 (mp10) REVERT: G 347 LYS cc_start: 0.8408 (ttmt) cc_final: 0.8171 (pmtt) REVERT: G 349 ARG cc_start: 0.5330 (OUTLIER) cc_final: 0.4047 (pmt-80) REVERT: G 351 GLN cc_start: 0.7869 (mt0) cc_final: 0.6976 (pm20) REVERT: I 290 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8487 (mmtm) REVERT: I 338 GLU cc_start: 0.8186 (mp0) cc_final: 0.7811 (mp0) REVERT: I 347 LYS cc_start: 0.8783 (ttmt) cc_final: 0.8441 (mtpp) REVERT: D 344 LEU cc_start: 0.9355 (mm) cc_final: 0.8924 (mm) REVERT: D 347 LYS cc_start: 0.8682 (mttt) cc_final: 0.7846 (mttm) REVERT: D 349 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7306 (tmt170) REVERT: D 351 GLN cc_start: 0.8440 (tt0) cc_final: 0.8079 (tm130) REVERT: F 324 SER cc_start: 0.9040 (OUTLIER) cc_final: 0.8378 (p) REVERT: F 342 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7865 (tm-30) REVERT: F 344 LEU cc_start: 0.9036 (mm) cc_final: 0.8411 (mm) REVERT: F 347 LYS cc_start: 0.8246 (mttt) cc_final: 0.7933 (mttp) REVERT: F 349 ARG cc_start: 0.5692 (OUTLIER) cc_final: 0.4207 (ppt90) REVERT: F 379 ARG cc_start: 0.6873 (mmt90) cc_final: 0.5435 (ptp90) REVERT: H 324 SER cc_start: 0.9099 (OUTLIER) cc_final: 0.8679 (p) REVERT: H 344 LEU cc_start: 0.9323 (mm) cc_final: 0.9052 (mm) REVERT: H 345 ASP cc_start: 0.8409 (t0) cc_final: 0.7234 (t0) REVERT: H 379 ARG cc_start: 0.6632 (OUTLIER) cc_final: 0.6186 (tpt90) REVERT: J 345 ASP cc_start: 0.8142 (t0) cc_final: 0.7753 (t0) REVERT: J 374 HIS cc_start: 0.6622 (OUTLIER) cc_final: 0.6371 (t-170) REVERT: J 379 ARG cc_start: 0.6434 (mmm160) cc_final: 0.5980 (tpt90) outliers start: 48 outliers final: 31 residues processed: 228 average time/residue: 0.5063 time to fit residues: 122.5870 Evaluate side-chains 242 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 349 ARG Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain I residue 290 LYS Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 337 VAL Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 373 THR Chi-restraints excluded: chain H residue 379 ARG Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain J residue 374 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 51 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 56 optimal weight: 0.4980 chunk 65 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 43 optimal weight: 0.0980 chunk 18 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 307 GLN I 279 ASN ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 GLN H 351 GLN J 351 GLN ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.121747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.103432 restraints weight = 12600.825| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.39 r_work: 0.3794 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8230 Z= 0.146 Angle : 0.732 9.465 10990 Z= 0.347 Chirality : 0.051 0.163 1230 Planarity : 0.003 0.030 1410 Dihedral : 5.138 21.928 1100 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.84 % Allowed : 27.31 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.40 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 349 TYR 0.013 0.002 TYR C 310 PHE 0.025 0.003 PHE H 346 HIS 0.006 0.001 HIS J 374 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8230) covalent geometry : angle 0.73199 (10990) hydrogen bonds : bond 0.01712 ( 171) hydrogen bonds : angle 4.76050 ( 513) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3306.66 seconds wall clock time: 57 minutes 15.20 seconds (3435.20 seconds total)