Starting phenix.real_space_refine on Wed Mar 12 17:06:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p68_13221/03_2025/7p68_13221.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p68_13221/03_2025/7p68_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7p68_13221/03_2025/7p68_13221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p68_13221/03_2025/7p68_13221.map" model { file = "/net/cci-nas-00/data/ceres_data/7p68_13221/03_2025/7p68_13221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p68_13221/03_2025/7p68_13221.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.80, per 1000 atoms: 0.71 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: 1.91 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.27 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: 2.22 Time building geometry restraints manager: 2.26 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: 0.02 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: 2.600 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: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.840 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.450 ------------------------------------------------------------------------------- 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= 0.362 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.21), 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 HIS 0.004 0.001 HIS H 329 PHE 0.080 0.009 PHE F 346 TYR 0.009 0.002 TYR H 310 ARG 0.003 0.001 ARG B 379 *********************** 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 : 0.929 Fit side-chains 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: 0.9777 time to fit residues: 311.4746 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 : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 90 optimal weight: 0.2980 overall best weight: 5.4588 ------------------------------------------------------------------------------- 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 C 329 HIS ** G 307 GLN ** 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 ** J 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.117041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.098832 restraints weight = 12690.740| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.35 r_work: 0.3716 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 8230 Z= 0.527 Angle : 0.739 8.130 10990 Z= 0.373 Chirality : 0.052 0.139 1230 Planarity : 0.004 0.034 1410 Dihedral : 5.550 19.574 1100 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 5.48 % Allowed : 18.49 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.21), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS A 362 PHE 0.018 0.002 PHE J 378 TYR 0.016 0.003 TYR G 310 ARG 0.003 0.000 ARG F 349 *********************** 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 288 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 237 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 ASP cc_start: 0.8567 (m-30) cc_final: 0.8361 (m-30) REVERT: A 351 GLN cc_start: 0.8545 (tt0) cc_final: 0.8114 (tt0) REVERT: B 320 SER cc_start: 0.9308 (t) cc_final: 0.9049 (p) REVERT: B 345 ASP cc_start: 0.8210 (t0) cc_final: 0.7945 (t0) REVERT: B 347 LYS cc_start: 0.8623 (mttt) cc_final: 0.8316 (tppt) REVERT: B 349 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7535 (tmt170) REVERT: B 351 GLN cc_start: 0.8145 (tt0) cc_final: 0.7806 (tm-30) REVERT: B 379 ARG cc_start: 0.6136 (mmm-85) cc_final: 0.5905 (tmm160) REVERT: C 342 GLU cc_start: 0.4872 (pm20) cc_final: 0.4255 (pm20) REVERT: C 379 ARG cc_start: 0.4632 (tpm170) cc_final: 0.4420 (tpm170) REVERT: E 295 ASP cc_start: 0.8317 (m-30) cc_final: 0.8034 (m-30) REVERT: E 379 ARG cc_start: 0.6406 (tpm170) cc_final: 0.5216 (tpm170) REVERT: G 351 GLN cc_start: 0.8049 (mt0) cc_final: 0.7848 (mt0) REVERT: G 353 LYS cc_start: 0.5117 (pmtt) cc_final: 0.4850 (pptt) REVERT: G 379 ARG cc_start: 0.4699 (tmm160) cc_final: 0.4456 (tmm160) REVERT: I 337 VAL cc_start: 0.8155 (OUTLIER) cc_final: 0.7911 (t) REVERT: I 347 LYS cc_start: 0.8637 (ttmt) cc_final: 0.8292 (tttm) REVERT: D 320 SER cc_start: 0.9301 (t) cc_final: 0.8977 (p) REVERT: D 342 GLU cc_start: 0.7620 (tm-30) cc_final: 0.6372 (tm-30) REVERT: D 344 LEU cc_start: 0.9337 (mm) cc_final: 0.8811 (mm) REVERT: D 345 ASP cc_start: 0.8351 (t0) cc_final: 0.7935 (t0) REVERT: F 324 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.7889 (p) REVERT: F 342 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7489 (tm-30) REVERT: F 379 ARG cc_start: 0.6593 (mmt90) cc_final: 0.5133 (ptp90) REVERT: H 345 ASP cc_start: 0.8184 (t0) cc_final: 0.7744 (t0) REVERT: H 347 LYS cc_start: 0.8765 (mttt) cc_final: 0.8458 (ttmm) REVERT: H 349 ARG cc_start: 0.7945 (ttm110) cc_final: 0.7188 (ttt90) REVERT: H 359 ASN cc_start: 0.8609 (t0) cc_final: 0.8356 (t0) REVERT: J 320 SER cc_start: 0.9210 (t) cc_final: 0.8582 (p) REVERT: J 345 ASP cc_start: 0.7480 (m-30) cc_final: 0.7151 (m-30) REVERT: J 347 LYS cc_start: 0.8718 (mttt) cc_final: 0.8463 (mmmt) REVERT: J 349 ARG cc_start: 0.5436 (tpm170) cc_final: 0.5153 (tpp-160) REVERT: J 368 ASN cc_start: 0.8074 (m-40) cc_final: 0.7774 (m-40) REVERT: J 379 ARG cc_start: 0.6387 (mmm-85) cc_final: 0.6114 (tpt90) outliers start: 51 outliers final: 31 residues processed: 269 average time/residue: 1.0059 time to fit residues: 289.2487 Evaluate side-chains 247 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 213 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 349 ARG Chi-restraints excluded: chain B residue 357 LEU 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 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 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 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 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 36 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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** A 288 GLN ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 GLN ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 279 ASN ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 GLN D 351 GLN F 276 GLN F 351 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.117787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.099523 restraints weight = 12895.710| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.35 r_work: 0.3734 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 8230 Z= 0.398 Angle : 0.675 7.324 10990 Z= 0.336 Chirality : 0.051 0.138 1230 Planarity : 0.004 0.033 1410 Dihedral : 5.357 20.264 1100 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 6.99 % Allowed : 19.57 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.21), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 362 PHE 0.015 0.002 PHE D 346 TYR 0.015 0.002 TYR E 310 ARG 0.004 0.001 ARG F 349 *********************** 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 290 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 225 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 295 ASP cc_start: 0.8549 (m-30) cc_final: 0.8282 (m-30) REVERT: A 349 ARG cc_start: 0.8632 (ttp-110) cc_final: 0.8335 (ttp-110) REVERT: A 351 GLN cc_start: 0.8453 (tt0) cc_final: 0.7993 (tt0) REVERT: B 320 SER cc_start: 0.9377 (t) cc_final: 0.9123 (p) REVERT: B 345 ASP cc_start: 0.8357 (t0) cc_final: 0.8062 (t0) REVERT: B 351 GLN cc_start: 0.8447 (tt0) cc_final: 0.7818 (tm-30) REVERT: B 379 ARG cc_start: 0.6286 (mmm-85) cc_final: 0.5975 (tmm160) REVERT: C 345 ASP cc_start: 0.8105 (t0) cc_final: 0.7669 (t0) REVERT: E 295 ASP cc_start: 0.8335 (m-30) cc_final: 0.8063 (m-30) REVERT: E 349 ARG cc_start: 0.8511 (ttp-110) cc_final: 0.8211 (mtm110) REVERT: G 351 GLN cc_start: 0.8095 (mt0) cc_final: 0.7851 (mt0) REVERT: G 379 ARG cc_start: 0.4886 (tmm160) cc_final: 0.4666 (ttp-110) REVERT: I 337 VAL cc_start: 0.8221 (OUTLIER) cc_final: 0.8002 (t) REVERT: I 347 LYS cc_start: 0.8655 (ttmt) cc_final: 0.8315 (tttm) REVERT: D 342 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7375 (tm-30) REVERT: D 344 LEU cc_start: 0.9410 (mm) cc_final: 0.8982 (mm) REVERT: D 345 ASP cc_start: 0.8463 (t0) cc_final: 0.7939 (t0) REVERT: D 349 ARG cc_start: 0.7753 (tmt170) cc_final: 0.7539 (tmt170) REVERT: D 379 ARG cc_start: 0.6800 (tmm160) cc_final: 0.6341 (tmm160) REVERT: F 311 LYS cc_start: 0.9388 (OUTLIER) cc_final: 0.9127 (tppp) REVERT: F 324 SER cc_start: 0.9049 (OUTLIER) cc_final: 0.8377 (p) REVERT: F 342 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7507 (tm-30) REVERT: F 344 LEU cc_start: 0.9140 (mm) cc_final: 0.8468 (mm) REVERT: F 348 ASP cc_start: 0.7795 (t0) cc_final: 0.7571 (t0) REVERT: F 349 ARG cc_start: 0.5711 (OUTLIER) cc_final: 0.4210 (ppt90) REVERT: F 379 ARG cc_start: 0.6628 (mmt90) cc_final: 0.5395 (ptp90) REVERT: H 345 ASP cc_start: 0.8268 (t0) cc_final: 0.7849 (OUTLIER) REVERT: H 349 ARG cc_start: 0.7916 (ttm110) cc_final: 0.7067 (ttt90) REVERT: H 359 ASN cc_start: 0.8601 (t0) cc_final: 0.8317 (t0) REVERT: H 379 ARG cc_start: 0.6814 (tmm160) cc_final: 0.6364 (tmm160) REVERT: J 347 LYS cc_start: 0.8792 (mttt) cc_final: 0.8498 (mmmt) REVERT: J 349 ARG cc_start: 0.5626 (tpm170) cc_final: 0.5410 (tpp-160) REVERT: J 368 ASN cc_start: 0.8141 (m-40) cc_final: 0.7865 (m-40) REVERT: J 378 PHE cc_start: 0.7488 (m-80) cc_final: 0.7245 (m-10) REVERT: J 379 ARG cc_start: 0.6618 (mmm-85) cc_final: 0.6083 (tpt90) outliers start: 65 outliers final: 44 residues processed: 257 average time/residue: 1.0293 time to fit residues: 282.1882 Evaluate side-chains 255 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 207 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 344 LEU 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 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 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 311 LYS Chi-restraints excluded: chain F residue 319 THR 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 341 SER Chi-restraints excluded: chain J residue 311 LYS Chi-restraints excluded: chain J residue 319 THR 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 79 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 GLN E 351 GLN ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 329 HIS D 276 GLN F 351 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.118872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.100805 restraints weight = 12785.740| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.34 r_work: 0.3758 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3575 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= 0.331 Angle : 0.655 7.213 10990 Z= 0.322 Chirality : 0.050 0.137 1230 Planarity : 0.003 0.030 1410 Dihedral : 5.186 20.418 1100 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 7.53 % Allowed : 20.75 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.21), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.013 0.002 PHE H 346 TYR 0.014 0.002 TYR E 310 ARG 0.003 0.000 ARG F 349 *********************** 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 292 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 222 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.8595 (ttp-110) cc_final: 0.8284 (ttp-110) REVERT: A 351 GLN cc_start: 0.8479 (tt0) cc_final: 0.7969 (tt0) REVERT: B 320 SER cc_start: 0.9309 (t) cc_final: 0.9076 (p) REVERT: B 342 GLU cc_start: 0.7296 (tm-30) cc_final: 0.6687 (tm-30) REVERT: B 345 ASP cc_start: 0.8292 (t0) cc_final: 0.7687 (t0) REVERT: B 347 LYS cc_start: 0.8543 (mttt) cc_final: 0.7741 (mttp) REVERT: B 349 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7689 (tmt170) REVERT: B 351 GLN cc_start: 0.8380 (tt0) cc_final: 0.7845 (tm-30) REVERT: B 379 ARG cc_start: 0.6404 (mmm-85) cc_final: 0.6087 (tmm160) REVERT: C 295 ASP cc_start: 0.7800 (m-30) cc_final: 0.7565 (m-30) REVERT: C 345 ASP cc_start: 0.8010 (t0) cc_final: 0.7583 (t0) REVERT: E 295 ASP cc_start: 0.8352 (m-30) cc_final: 0.8025 (m-30) REVERT: E 349 ARG cc_start: 0.8480 (ttp-110) cc_final: 0.8150 (mtm110) REVERT: E 351 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7674 (mt0) REVERT: G 349 ARG cc_start: 0.5663 (OUTLIER) cc_final: 0.4443 (pmt-80) REVERT: G 351 GLN cc_start: 0.8086 (mt0) cc_final: 0.7886 (mt0) REVERT: G 379 ARG cc_start: 0.4830 (OUTLIER) cc_final: 0.4571 (ttp80) REVERT: I 290 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8477 (mmtm) REVERT: I 347 LYS cc_start: 0.8651 (ttmt) cc_final: 0.8358 (tttm) REVERT: I 350 VAL cc_start: 0.9356 (t) cc_final: 0.9151 (m) REVERT: D 342 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7569 (tm-30) REVERT: D 344 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9008 (mm) REVERT: D 345 ASP cc_start: 0.8391 (t0) cc_final: 0.7861 (t0) REVERT: D 347 LYS cc_start: 0.8668 (mttt) cc_final: 0.7951 (mmtt) REVERT: D 349 ARG cc_start: 0.7727 (tmt170) cc_final: 0.7468 (tmt170) REVERT: D 351 GLN cc_start: 0.8379 (tt0) cc_final: 0.8029 (tm130) REVERT: D 379 ARG cc_start: 0.6914 (tmm160) cc_final: 0.6361 (tmm160) REVERT: F 311 LYS cc_start: 0.9392 (OUTLIER) cc_final: 0.9142 (tppp) REVERT: F 324 SER cc_start: 0.9008 (OUTLIER) cc_final: 0.8212 (p) REVERT: F 342 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7613 (tm-30) REVERT: F 344 LEU cc_start: 0.9128 (mm) cc_final: 0.8431 (mm) REVERT: F 345 ASP cc_start: 0.7868 (t0) cc_final: 0.7508 (t0) REVERT: F 347 LYS cc_start: 0.8327 (mttt) cc_final: 0.7525 (pmtt) REVERT: F 348 ASP cc_start: 0.7766 (t0) cc_final: 0.7547 (t0) REVERT: F 349 ARG cc_start: 0.5690 (OUTLIER) cc_final: 0.4182 (ppt90) REVERT: F 379 ARG cc_start: 0.6755 (mmt90) cc_final: 0.5459 (ptp90) REVERT: H 345 ASP cc_start: 0.8327 (t0) cc_final: 0.7637 (t0) REVERT: H 359 ASN cc_start: 0.8592 (t0) cc_final: 0.8267 (t0) REVERT: H 379 ARG cc_start: 0.6665 (tmm160) cc_final: 0.6186 (tmm160) REVERT: J 347 LYS cc_start: 0.8813 (mttt) cc_final: 0.8554 (mmpt) REVERT: J 378 PHE cc_start: 0.7546 (m-80) cc_final: 0.7265 (m-10) REVERT: J 379 ARG cc_start: 0.6597 (mmm-85) cc_final: 0.6081 (tpt90) outliers start: 70 outliers final: 43 residues processed: 257 average time/residue: 1.0140 time to fit residues: 278.4001 Evaluate side-chains 257 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 204 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 289 SER Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 344 LEU 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 351 GLN Chi-restraints excluded: chain E residue 360 ILE 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 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 341 SER 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 320 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 344 LEU 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 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 341 SER Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 311 LYS 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 12 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 86 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 89 optimal weight: 0.0670 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.3324 ------------------------------------------------------------------------------- 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 E 307 GLN G 307 GLN I 307 GLN D 299 HIS F 351 GLN H 299 HIS J 276 GLN J 299 HIS J 359 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.122854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.104701 restraints weight = 12379.969| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.35 r_work: 0.3816 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8230 Z= 0.203 Angle : 0.622 7.802 10990 Z= 0.298 Chirality : 0.050 0.147 1230 Planarity : 0.003 0.027 1410 Dihedral : 4.862 19.791 1100 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 5.81 % Allowed : 22.15 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.21), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 330 PHE 0.011 0.002 PHE B 378 TYR 0.013 0.001 TYR E 310 ARG 0.002 0.000 ARG F 349 *********************** 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 282 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 228 time to evaluate : 1.059 Fit side-chains REVERT: A 351 GLN cc_start: 0.8323 (tt0) cc_final: 0.8037 (mt0) REVERT: B 342 GLU cc_start: 0.7432 (tm-30) cc_final: 0.6469 (tm-30) REVERT: B 344 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8364 (mm) REVERT: B 345 ASP cc_start: 0.8228 (t0) cc_final: 0.7391 (t0) REVERT: B 349 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7336 (tmt170) REVERT: B 351 GLN cc_start: 0.8410 (tt0) cc_final: 0.8049 (tm-30) REVERT: B 379 ARG cc_start: 0.6260 (mmm-85) cc_final: 0.6014 (tmm160) REVERT: C 295 ASP cc_start: 0.7769 (m-30) cc_final: 0.7538 (m-30) REVERT: C 345 ASP cc_start: 0.8019 (t0) cc_final: 0.7554 (t0) REVERT: E 288 GLN cc_start: 0.8815 (mt0) cc_final: 0.8354 (pm20) REVERT: E 295 ASP cc_start: 0.8208 (m-30) cc_final: 0.7948 (m-30) REVERT: G 336 GLN cc_start: 0.8801 (mp10) cc_final: 0.8382 (mp10) REVERT: G 338 GLU cc_start: 0.8057 (mp0) cc_final: 0.7836 (mp0) REVERT: G 347 LYS cc_start: 0.7751 (pmtt) cc_final: 0.7040 (ttpt) REVERT: G 349 ARG cc_start: 0.5360 (OUTLIER) cc_final: 0.4181 (pmt-80) REVERT: G 360 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.8879 (tp) REVERT: G 379 ARG cc_start: 0.4889 (OUTLIER) cc_final: 0.4653 (ttp80) REVERT: I 290 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8356 (mmtm) REVERT: I 338 GLU cc_start: 0.8081 (mp0) cc_final: 0.7881 (mp0) REVERT: I 347 LYS cc_start: 0.8666 (ttmt) cc_final: 0.8303 (tttm) REVERT: I 350 VAL cc_start: 0.9373 (t) cc_final: 0.9130 (m) REVERT: D 342 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7444 (tm-30) REVERT: D 344 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9007 (mm) REVERT: D 345 ASP cc_start: 0.8199 (t0) cc_final: 0.7587 (t0) REVERT: D 347 LYS cc_start: 0.8592 (mttt) cc_final: 0.7847 (mptp) REVERT: D 349 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7304 (tmt170) REVERT: D 351 GLN cc_start: 0.8297 (tt0) cc_final: 0.7944 (tm130) REVERT: D 379 ARG cc_start: 0.6932 (tmm160) cc_final: 0.6404 (tmm160) REVERT: F 311 LYS cc_start: 0.9356 (OUTLIER) cc_final: 0.9118 (tppt) REVERT: F 324 SER cc_start: 0.8921 (OUTLIER) cc_final: 0.8169 (p) REVERT: F 342 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7734 (pp20) REVERT: F 343 LYS cc_start: 0.5427 (pmtt) cc_final: 0.5184 (pmtt) REVERT: F 344 LEU cc_start: 0.9168 (mm) cc_final: 0.8730 (mm) REVERT: F 348 ASP cc_start: 0.7702 (t70) cc_final: 0.7470 (t0) REVERT: F 379 ARG cc_start: 0.6809 (mmt90) cc_final: 0.5388 (ptp-170) REVERT: H 345 ASP cc_start: 0.8248 (t0) cc_final: 0.7955 (t0) REVERT: H 379 ARG cc_start: 0.6686 (tmm160) cc_final: 0.6170 (tmm160) REVERT: J 347 LYS cc_start: 0.8820 (mttt) cc_final: 0.8435 (mmpt) REVERT: J 378 PHE cc_start: 0.7475 (m-80) cc_final: 0.7117 (m-10) REVERT: J 379 ARG cc_start: 0.6594 (mmm-85) cc_final: 0.6076 (tpt90) outliers start: 54 outliers final: 25 residues processed: 253 average time/residue: 1.1053 time to fit residues: 297.8765 Evaluate side-chains 244 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR 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 344 LEU 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 285 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 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 290 LYS Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 324 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 351 GLN ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 GLN J 327 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.115214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.097416 restraints weight = 12941.514| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.31 r_work: 0.3704 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3942 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= 0.548 Angle : 0.769 9.335 10990 Z= 0.384 Chirality : 0.053 0.139 1230 Planarity : 0.004 0.034 1410 Dihedral : 5.548 21.308 1100 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 7.63 % Allowed : 22.58 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 362 PHE 0.019 0.003 PHE H 346 TYR 0.014 0.002 TYR A 310 ARG 0.010 0.001 ARG E 349 *********************** 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 284 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 213 time to evaluate : 1.060 Fit side-chains REVERT: A 350 VAL cc_start: 0.9486 (OUTLIER) cc_final: 0.9210 (m) REVERT: A 351 GLN cc_start: 0.8334 (tt0) cc_final: 0.8021 (mt0) REVERT: B 342 GLU cc_start: 0.7481 (tm-30) cc_final: 0.5859 (tm-30) REVERT: B 344 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8189 (mm) REVERT: B 345 ASP cc_start: 0.8253 (t0) cc_final: 0.7767 (t0) REVERT: B 347 LYS cc_start: 0.8592 (mttt) cc_final: 0.7703 (mttp) REVERT: B 351 GLN cc_start: 0.8393 (tt0) cc_final: 0.7761 (tm-30) REVERT: C 342 GLU cc_start: 0.4054 (pm20) cc_final: 0.3826 (pm20) REVERT: E 295 ASP cc_start: 0.8384 (m-30) cc_final: 0.8159 (m-30) REVERT: E 351 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7698 (mm-40) REVERT: G 286 ASN cc_start: 0.8869 (t0) cc_final: 0.8628 (t0) REVERT: G 338 GLU cc_start: 0.8078 (mp0) cc_final: 0.7829 (mp0) REVERT: G 379 ARG cc_start: 0.4754 (OUTLIER) cc_final: 0.1440 (tmm160) REVERT: I 347 LYS cc_start: 0.8774 (ttmt) cc_final: 0.8430 (tttm) REVERT: I 351 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8172 (mt0) REVERT: D 342 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7447 (tm-30) REVERT: D 344 LEU cc_start: 0.9424 (mm) cc_final: 0.8785 (mm) REVERT: D 345 ASP cc_start: 0.8300 (t0) cc_final: 0.7834 (t0) REVERT: D 347 LYS cc_start: 0.8723 (mttt) cc_final: 0.8205 (mttm) REVERT: D 349 ARG cc_start: 0.7824 (tmt170) cc_final: 0.7467 (tmt170) REVERT: D 351 GLN cc_start: 0.8457 (tt0) cc_final: 0.7759 (tm-30) REVERT: D 379 ARG cc_start: 0.7052 (tmm160) cc_final: 0.6302 (tmm160) REVERT: F 311 LYS cc_start: 0.9407 (OUTLIER) cc_final: 0.9158 (tppp) REVERT: F 324 SER cc_start: 0.9042 (OUTLIER) cc_final: 0.8392 (p) REVERT: F 342 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7589 (tm-30) REVERT: F 343 LYS cc_start: 0.5349 (pmtt) cc_final: 0.4538 (pmtt) REVERT: F 344 LEU cc_start: 0.9160 (mm) cc_final: 0.8543 (mm) REVERT: F 347 LYS cc_start: 0.8310 (mttt) cc_final: 0.7439 (pptt) REVERT: F 349 ARG cc_start: 0.5636 (OUTLIER) cc_final: 0.4284 (ppt90) REVERT: F 379 ARG cc_start: 0.6827 (mmt90) cc_final: 0.5544 (ptp90) REVERT: H 342 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7578 (tp30) REVERT: H 344 LEU cc_start: 0.9473 (mp) cc_final: 0.9260 (mp) REVERT: H 345 ASP cc_start: 0.8443 (t0) cc_final: 0.7743 (t0) REVERT: H 349 ARG cc_start: 0.7997 (ttp-110) cc_final: 0.7182 (ttt90) REVERT: H 379 ARG cc_start: 0.6766 (tmm160) cc_final: 0.6348 (tmm160) REVERT: J 347 LYS cc_start: 0.8840 (mttt) cc_final: 0.8572 (mmpt) REVERT: J 378 PHE cc_start: 0.7561 (m-80) cc_final: 0.7316 (m-80) REVERT: J 379 ARG cc_start: 0.6641 (mmm-85) cc_final: 0.6105 (tpt90) outliers start: 71 outliers final: 51 residues processed: 251 average time/residue: 1.0878 time to fit residues: 291.6931 Evaluate side-chains 261 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 200 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 350 VAL 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 344 LEU Chi-restraints excluded: chain B residue 357 LEU 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 342 GLU Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 377 THR 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 354 ILE 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 319 THR 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 305 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain F residue 284 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 307 GLN ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 GLN J 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.118920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.100956 restraints weight = 12681.383| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.33 r_work: 0.3759 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3640 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8230 Z= 0.299 Angle : 0.689 8.309 10990 Z= 0.333 Chirality : 0.051 0.137 1230 Planarity : 0.003 0.046 1410 Dihedral : 5.229 19.646 1100 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 6.77 % Allowed : 24.84 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 374 PHE 0.015 0.003 PHE D 346 TYR 0.012 0.002 TYR E 310 ARG 0.012 0.001 ARG E 349 *********************** 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 276 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 213 time to evaluate : 1.358 Fit side-chains REVERT: A 350 VAL cc_start: 0.9380 (t) cc_final: 0.9074 (m) REVERT: A 351 GLN cc_start: 0.8110 (tt0) cc_final: 0.7850 (mt0) REVERT: A 357 LEU cc_start: 0.9166 (tp) cc_final: 0.8762 (tp) REVERT: B 342 GLU cc_start: 0.7371 (tm-30) cc_final: 0.5692 (tm-30) REVERT: B 344 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8190 (mm) REVERT: B 345 ASP cc_start: 0.8294 (t0) cc_final: 0.7708 (t0) REVERT: B 347 LYS cc_start: 0.8574 (mttt) cc_final: 0.7781 (mttp) REVERT: B 349 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7438 (tmt170) REVERT: B 351 GLN cc_start: 0.8391 (tt0) cc_final: 0.8055 (tm-30) REVERT: C 288 GLN cc_start: 0.8792 (mt0) cc_final: 0.8492 (mp-120) REVERT: C 345 ASP cc_start: 0.8026 (t0) cc_final: 0.7532 (t0) REVERT: C 347 LYS cc_start: 0.4883 (OUTLIER) cc_final: 0.4466 (mmpt) REVERT: E 288 GLN cc_start: 0.8817 (mt0) cc_final: 0.8161 (mp10) REVERT: G 349 ARG cc_start: 0.5188 (OUTLIER) cc_final: 0.3894 (pmt-80) REVERT: G 379 ARG cc_start: 0.4833 (OUTLIER) cc_final: 0.4524 (ttp80) REVERT: I 290 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8481 (mmtm) REVERT: I 347 LYS cc_start: 0.8732 (ttmt) cc_final: 0.8339 (mtpp) REVERT: I 350 VAL cc_start: 0.9374 (t) cc_final: 0.9043 (m) REVERT: D 342 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7495 (tm-30) REVERT: D 344 LEU cc_start: 0.9417 (mm) cc_final: 0.8913 (mm) REVERT: D 345 ASP cc_start: 0.8203 (t0) cc_final: 0.7645 (t0) REVERT: D 347 LYS cc_start: 0.8704 (mttt) cc_final: 0.8237 (mttm) REVERT: D 349 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7252 (tmt170) REVERT: D 351 GLN cc_start: 0.8388 (tt0) cc_final: 0.7737 (tm-30) REVERT: D 379 ARG cc_start: 0.6807 (tmm160) cc_final: 0.6476 (tmm160) REVERT: F 311 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.9134 (tppt) REVERT: F 324 SER cc_start: 0.9022 (OUTLIER) cc_final: 0.8359 (p) REVERT: F 342 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: F 343 LYS cc_start: 0.4997 (OUTLIER) cc_final: 0.4293 (pmtt) REVERT: F 344 LEU cc_start: 0.9196 (mm) cc_final: 0.8602 (mm) REVERT: F 345 ASP cc_start: 0.7747 (t0) cc_final: 0.7456 (t0) REVERT: F 347 LYS cc_start: 0.8341 (mttt) cc_final: 0.7635 (pptt) REVERT: F 349 ARG cc_start: 0.5441 (OUTLIER) cc_final: 0.4010 (ppt90) REVERT: F 379 ARG cc_start: 0.6782 (mmt90) cc_final: 0.5473 (ptp90) REVERT: H 320 SER cc_start: 0.9251 (t) cc_final: 0.9036 (p) REVERT: H 345 ASP cc_start: 0.8304 (t0) cc_final: 0.7657 (t0) REVERT: H 349 ARG cc_start: 0.8023 (ttp-110) cc_final: 0.7183 (ttt180) REVERT: H 379 ARG cc_start: 0.6785 (tmm160) cc_final: 0.6463 (tmm160) REVERT: J 342 GLU cc_start: 0.5131 (pm20) cc_final: 0.4659 (pm20) REVERT: J 347 LYS cc_start: 0.8838 (mttt) cc_final: 0.8556 (mmpt) REVERT: J 378 PHE cc_start: 0.7625 (m-80) cc_final: 0.7361 (m-10) REVERT: J 379 ARG cc_start: 0.6592 (mmm-85) cc_final: 0.6063 (tpt90) outliers start: 63 outliers final: 45 residues processed: 244 average time/residue: 1.2774 time to fit residues: 333.0755 Evaluate side-chains 259 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 202 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 342 GLU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain B residue 357 LEU 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 343 LYS Chi-restraints excluded: chain C residue 347 LYS 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 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 G residue 360 ILE Chi-restraints excluded: chain G residue 379 ARG Chi-restraints excluded: chain I residue 290 LYS Chi-restraints excluded: chain I residue 319 THR 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 319 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 349 ARG 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 343 LYS 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 373 THR 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 325 LEU 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 49 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 98 optimal weight: 0.0370 chunk 54 optimal weight: 6.9990 chunk 63 optimal weight: 0.5980 chunk 55 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 overall best weight: 3.1264 ------------------------------------------------------------------------------- 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 ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 GLN J 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.118078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.099926 restraints weight = 12779.447| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.36 r_work: 0.3736 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8230 Z= 0.336 Angle : 0.715 8.479 10990 Z= 0.346 Chirality : 0.051 0.197 1230 Planarity : 0.003 0.048 1410 Dihedral : 5.241 21.023 1100 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 7.31 % Allowed : 24.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.014 0.003 PHE B 346 TYR 0.010 0.002 TYR G 310 ARG 0.012 0.001 ARG E 349 *********************** 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 277 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 209 time to evaluate : 0.960 Fit side-chains REVERT: A 350 VAL cc_start: 0.9391 (t) cc_final: 0.9115 (m) REVERT: A 351 GLN cc_start: 0.8089 (tt0) cc_final: 0.7845 (mt0) REVERT: A 357 LEU cc_start: 0.9190 (tp) cc_final: 0.8839 (tp) REVERT: B 342 GLU cc_start: 0.7303 (tm-30) cc_final: 0.6531 (tm-30) REVERT: B 344 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8176 (mm) REVERT: B 345 ASP cc_start: 0.8291 (t0) cc_final: 0.7496 (t0) REVERT: B 347 LYS cc_start: 0.8589 (mttt) cc_final: 0.7774 (mttp) REVERT: B 349 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7492 (tmt170) REVERT: B 351 GLN cc_start: 0.8392 (tt0) cc_final: 0.7998 (tm-30) REVERT: C 288 GLN cc_start: 0.8842 (mt0) cc_final: 0.8539 (mp-120) REVERT: C 347 LYS cc_start: 0.4843 (OUTLIER) cc_final: 0.4438 (mmpt) REVERT: E 288 GLN cc_start: 0.8841 (mt0) cc_final: 0.8233 (mp-120) REVERT: G 349 ARG cc_start: 0.5300 (OUTLIER) cc_final: 0.4043 (pmt-80) REVERT: G 379 ARG cc_start: 0.4901 (OUTLIER) cc_final: 0.4542 (ttp80) REVERT: I 290 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8524 (mmtm) REVERT: I 347 LYS cc_start: 0.8715 (ttmt) cc_final: 0.8284 (mtpp) REVERT: I 349 ARG cc_start: 0.8480 (ttp80) cc_final: 0.8273 (ttp-110) REVERT: I 350 VAL cc_start: 0.9421 (t) cc_final: 0.9110 (m) REVERT: D 342 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7437 (tm-30) REVERT: D 344 LEU cc_start: 0.9400 (mm) cc_final: 0.8764 (mm) REVERT: D 345 ASP cc_start: 0.8173 (t0) cc_final: 0.7457 (t0) REVERT: D 347 LYS cc_start: 0.8712 (mttt) cc_final: 0.7952 (ttmm) REVERT: D 349 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7349 (tmt170) REVERT: D 351 GLN cc_start: 0.8377 (tt0) cc_final: 0.7702 (tm-30) REVERT: D 379 ARG cc_start: 0.6815 (tmm160) cc_final: 0.6574 (tmm160) REVERT: F 311 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.9112 (tppp) REVERT: F 324 SER cc_start: 0.9021 (OUTLIER) cc_final: 0.8334 (p) REVERT: F 342 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7719 (tm-30) REVERT: F 344 LEU cc_start: 0.9175 (mm) cc_final: 0.8567 (mm) REVERT: F 347 LYS cc_start: 0.8321 (mttt) cc_final: 0.7784 (mttp) REVERT: F 349 ARG cc_start: 0.5444 (OUTLIER) cc_final: 0.4060 (ppt90) REVERT: F 379 ARG cc_start: 0.6911 (mmt90) cc_final: 0.5411 (ptp90) REVERT: H 345 ASP cc_start: 0.8290 (t0) cc_final: 0.7654 (t0) REVERT: H 349 ARG cc_start: 0.7944 (ttp-110) cc_final: 0.7112 (ttt180) REVERT: H 379 ARG cc_start: 0.6862 (tmm160) cc_final: 0.6427 (tmm160) REVERT: J 342 GLU cc_start: 0.4834 (pm20) cc_final: 0.4409 (pm20) REVERT: J 347 LYS cc_start: 0.8860 (mttt) cc_final: 0.8543 (mmpt) REVERT: J 378 PHE cc_start: 0.7624 (m-80) cc_final: 0.7377 (m-10) REVERT: J 379 ARG cc_start: 0.6549 (mmm-85) cc_final: 0.6056 (tpt90) outliers start: 68 outliers final: 47 residues processed: 244 average time/residue: 1.0400 time to fit residues: 270.6422 Evaluate side-chains 262 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 203 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 319 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain B residue 357 LEU 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 343 LYS Chi-restraints excluded: chain C residue 347 LYS 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 342 GLU 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 347 LYS 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 290 LYS Chi-restraints excluded: chain I residue 319 THR 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 315 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 349 ARG 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 373 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 6 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 90 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 overall best weight: 4.6586 ------------------------------------------------------------------------------- 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 ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 GLN J 351 GLN J 374 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.117039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.099032 restraints weight = 13050.138| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.34 r_work: 0.3727 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 8230 Z= 0.458 Angle : 0.776 9.459 10990 Z= 0.381 Chirality : 0.052 0.141 1230 Planarity : 0.004 0.032 1410 Dihedral : 5.511 22.329 1100 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 7.85 % Allowed : 24.09 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 362 PHE 0.025 0.004 PHE H 346 TYR 0.018 0.003 TYR E 310 ARG 0.007 0.001 ARG E 349 *********************** 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 280 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 207 time to evaluate : 1.018 Fit side-chains REVERT: A 350 VAL cc_start: 0.9411 (t) cc_final: 0.9113 (m) REVERT: A 351 GLN cc_start: 0.8179 (tt0) cc_final: 0.7888 (mt0) REVERT: B 342 GLU cc_start: 0.7630 (tm-30) cc_final: 0.6884 (tm-30) REVERT: B 344 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8278 (mm) REVERT: B 345 ASP cc_start: 0.8251 (t0) cc_final: 0.7422 (t0) REVERT: B 347 LYS cc_start: 0.8623 (mttt) cc_final: 0.7691 (mttp) REVERT: B 351 GLN cc_start: 0.8406 (tt0) cc_final: 0.7943 (tm-30) REVERT: C 347 LYS cc_start: 0.4614 (OUTLIER) cc_final: 0.4069 (mmpt) REVERT: E 288 GLN cc_start: 0.8870 (mt0) cc_final: 0.8252 (mp10) REVERT: G 286 ASN cc_start: 0.8921 (t0) cc_final: 0.8612 (t0) REVERT: G 349 ARG cc_start: 0.5333 (OUTLIER) cc_final: 0.3995 (pmt-80) REVERT: G 379 ARG cc_start: 0.4641 (OUTLIER) cc_final: 0.3029 (ttm110) REVERT: I 290 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8620 (mmtm) REVERT: I 347 LYS cc_start: 0.8738 (ttmt) cc_final: 0.8318 (mtpp) REVERT: I 350 VAL cc_start: 0.9442 (t) cc_final: 0.9107 (m) REVERT: D 342 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7646 (tm-30) REVERT: D 344 LEU cc_start: 0.9388 (mm) cc_final: 0.8848 (mm) REVERT: D 345 ASP cc_start: 0.8283 (t0) cc_final: 0.7463 (t0) REVERT: D 347 LYS cc_start: 0.8712 (mttt) cc_final: 0.7931 (ttmm) REVERT: D 351 GLN cc_start: 0.8442 (tt0) cc_final: 0.7670 (tm-30) REVERT: D 379 ARG cc_start: 0.6909 (tmm160) cc_final: 0.6646 (tmm160) REVERT: F 311 LYS cc_start: 0.9383 (OUTLIER) cc_final: 0.9144 (tppp) REVERT: F 324 SER cc_start: 0.9054 (OUTLIER) cc_final: 0.8370 (p) REVERT: F 342 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7882 (tm-30) REVERT: F 343 LYS cc_start: 0.5130 (pmtt) cc_final: 0.4550 (pmtt) REVERT: F 344 LEU cc_start: 0.9168 (mm) cc_final: 0.8652 (mm) REVERT: F 347 LYS cc_start: 0.8316 (mttt) cc_final: 0.7750 (mttp) REVERT: F 349 ARG cc_start: 0.5724 (OUTLIER) cc_final: 0.4262 (ppt90) REVERT: F 379 ARG cc_start: 0.6837 (mmt90) cc_final: 0.5373 (ptp90) REVERT: H 310 TYR cc_start: 0.8569 (t80) cc_final: 0.8345 (t80) REVERT: H 342 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7182 (tm-30) REVERT: H 345 ASP cc_start: 0.8285 (t0) cc_final: 0.7493 (t0) REVERT: H 379 ARG cc_start: 0.6851 (tmm160) cc_final: 0.6439 (tmm160) REVERT: J 347 LYS cc_start: 0.8928 (mttt) cc_final: 0.8667 (mmpt) REVERT: J 378 PHE cc_start: 0.7627 (m-80) cc_final: 0.7388 (m-80) REVERT: J 379 ARG cc_start: 0.6612 (mmm-85) cc_final: 0.6114 (tpt90) outliers start: 73 outliers final: 53 residues processed: 246 average time/residue: 1.0272 time to fit residues: 269.8114 Evaluate side-chains 264 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 200 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 325 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 357 LEU 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 343 LYS Chi-restraints excluded: chain C residue 347 LYS 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 342 GLU Chi-restraints excluded: chain E residue 360 ILE 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 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 341 SER 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 315 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 342 GLU 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 F residue 356 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 342 GLU Chi-restraints excluded: chain H residue 373 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 96 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 48 optimal weight: 0.0020 chunk 21 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 overall best weight: 1.2592 ------------------------------------------------------------------------------- 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 307 GLN ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 GLN J 351 GLN J 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.122352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.104027 restraints weight = 12399.849| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.38 r_work: 0.3797 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8230 Z= 0.212 Angle : 0.708 8.566 10990 Z= 0.337 Chirality : 0.051 0.152 1230 Planarity : 0.003 0.032 1410 Dihedral : 5.022 21.872 1100 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 5.59 % Allowed : 26.24 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 374 PHE 0.019 0.003 PHE B 346 TYR 0.014 0.002 TYR C 310 ARG 0.008 0.001 ARG E 349 ********************** 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 266 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 214 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 350 VAL cc_start: 0.9310 (t) cc_final: 0.9033 (m) REVERT: A 351 GLN cc_start: 0.8068 (tt0) cc_final: 0.7788 (mt0) REVERT: A 357 LEU cc_start: 0.9046 (tp) cc_final: 0.8810 (tp) REVERT: B 342 GLU cc_start: 0.7536 (tm-30) cc_final: 0.6763 (tm-30) REVERT: B 344 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8333 (mm) REVERT: B 345 ASP cc_start: 0.8184 (t0) cc_final: 0.7321 (t0) REVERT: B 347 LYS cc_start: 0.8523 (mttt) cc_final: 0.7598 (mptp) REVERT: B 349 ARG cc_start: 0.7828 (tmt170) cc_final: 0.7500 (tmt170) REVERT: B 351 GLN cc_start: 0.8363 (tt0) cc_final: 0.7863 (tm-30) REVERT: C 288 GLN cc_start: 0.9007 (mt0) cc_final: 0.8595 (mp-120) REVERT: C 314 ASP cc_start: 0.8576 (t70) cc_final: 0.7967 (t0) REVERT: C 345 ASP cc_start: 0.7928 (t0) cc_final: 0.7451 (t0) REVERT: C 348 ASP cc_start: 0.6966 (t0) cc_final: 0.6663 (t0) REVERT: C 379 ARG cc_start: 0.4400 (tpm170) cc_final: 0.3963 (mmp80) REVERT: E 348 ASP cc_start: 0.7631 (t0) cc_final: 0.7415 (t0) REVERT: G 347 LYS cc_start: 0.7935 (pptt) cc_final: 0.7448 (ttmm) REVERT: G 349 ARG cc_start: 0.5278 (OUTLIER) cc_final: 0.4069 (pmt-80) REVERT: G 351 GLN cc_start: 0.7765 (mt0) cc_final: 0.6981 (pm20) REVERT: G 360 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.8811 (tp) REVERT: G 379 ARG cc_start: 0.4561 (OUTLIER) cc_final: 0.4207 (mtm110) REVERT: I 290 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8461 (mmtm) REVERT: I 347 LYS cc_start: 0.8665 (ttmt) cc_final: 0.7904 (mtpp) REVERT: I 350 VAL cc_start: 0.9417 (t) cc_final: 0.9110 (m) REVERT: D 342 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: D 344 LEU cc_start: 0.9367 (mm) cc_final: 0.8986 (mm) REVERT: D 347 LYS cc_start: 0.8681 (mttt) cc_final: 0.7876 (mttm) REVERT: D 349 ARG cc_start: 0.7737 (tmt170) cc_final: 0.7431 (tmt170) REVERT: D 351 GLN cc_start: 0.8272 (tt0) cc_final: 0.7904 (tm130) REVERT: D 379 ARG cc_start: 0.6893 (tmm160) cc_final: 0.6643 (tmm160) REVERT: F 324 SER cc_start: 0.8922 (OUTLIER) cc_final: 0.8314 (p) REVERT: F 342 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7862 (tm-30) REVERT: F 347 LYS cc_start: 0.8023 (mttt) cc_final: 0.7695 (mttp) REVERT: F 379 ARG cc_start: 0.6747 (mmt90) cc_final: 0.5231 (ptp90) REVERT: H 310 TYR cc_start: 0.8480 (t80) cc_final: 0.8267 (t80) REVERT: H 345 ASP cc_start: 0.7974 (t0) cc_final: 0.7170 (t0) REVERT: H 349 ARG cc_start: 0.7941 (ttp-110) cc_final: 0.7111 (ttt180) REVERT: H 379 ARG cc_start: 0.6792 (tmm160) cc_final: 0.6411 (tmm160) REVERT: J 342 GLU cc_start: 0.4924 (pm20) cc_final: 0.4568 (pm20) REVERT: J 347 LYS cc_start: 0.8911 (mttt) cc_final: 0.8625 (mmpt) REVERT: J 378 PHE cc_start: 0.7564 (m-80) cc_final: 0.7284 (m-10) REVERT: J 379 ARG cc_start: 0.6510 (mmm-85) cc_final: 0.6076 (tpt90) outliers start: 52 outliers final: 33 residues processed: 239 average time/residue: 1.0988 time to fit residues: 280.3164 Evaluate side-chains 247 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 206 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 341 SER Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 344 LEU 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 E residue 342 GLU 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 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 290 LYS Chi-restraints excluded: chain I residue 319 THR 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 284 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain F residue 305 SER 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 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 373 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 86 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 99 optimal weight: 0.5980 overall best weight: 3.4786 ------------------------------------------------------------------------------- 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** A 307 GLN G 307 GLN I 279 ASN ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 GLN J 351 GLN J 374 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.119498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.101504 restraints weight = 12771.422| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.31 r_work: 0.3741 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8230 Z= 0.366 Angle : 0.757 9.555 10990 Z= 0.367 Chirality : 0.052 0.163 1230 Planarity : 0.003 0.031 1410 Dihedral : 5.241 22.053 1100 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 5.59 % Allowed : 26.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.023 0.004 PHE E 346 TYR 0.015 0.002 TYR E 310 ARG 0.008 0.001 ARG E 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7143.36 seconds wall clock time: 125 minutes 13.73 seconds (7513.73 seconds total)