Starting phenix.real_space_refine on Sat Dec 28 08:15:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p68_13221/12_2024/7p68_13221.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p68_13221/12_2024/7p68_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_13221/12_2024/7p68_13221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p68_13221/12_2024/7p68_13221.map" model { file = "/net/cci-nas-00/data/ceres_data/7p68_13221/12_2024/7p68_13221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p68_13221/12_2024/7p68_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-5532/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: 5.67, per 1000 atoms: 0.70 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: 1.72 Conformation dependent library (CDL) restraints added in 1.3 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: 1.34 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: 2.10 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2637 1.34 - 1.46: 877 1.46 - 1.57: 4696 1.57 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 8230 Sorted by residual: bond pdb=" N GLY H 273 " pdb=" CA GLY H 273 " ideal model delta sigma weight residual 1.444 1.477 -0.033 1.06e-02 8.90e+03 9.79e+00 bond pdb=" N GLY F 273 " pdb=" CA GLY F 273 " ideal model delta sigma weight residual 1.444 1.477 -0.032 1.06e-02 8.90e+03 9.40e+00 bond pdb=" N GLY B 273 " pdb=" CA GLY B 273 " ideal model delta sigma weight residual 1.444 1.477 -0.032 1.06e-02 8.90e+03 9.38e+00 bond pdb=" N GLY D 273 " pdb=" CA GLY D 273 " ideal model delta sigma weight residual 1.444 1.476 -0.032 1.06e-02 8.90e+03 9.29e+00 bond pdb=" N GLY J 273 " pdb=" CA GLY J 273 " ideal model delta sigma weight residual 1.444 1.476 -0.032 1.06e-02 8.90e+03 9.18e+00 ... (remaining 8225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 10232 1.57 - 3.15: 575 3.15 - 4.72: 123 4.72 - 6.29: 45 6.29 - 7.87: 15 Bond angle restraints: 10990 Sorted by residual: angle pdb=" CA HIS F 299 " pdb=" C HIS F 299 " pdb=" O HIS F 299 " ideal model delta sigma weight residual 122.44 117.94 4.50 1.32e+00 5.74e-01 1.16e+01 angle pdb=" CA HIS H 299 " pdb=" C HIS H 299 " pdb=" O HIS H 299 " ideal model delta sigma weight residual 122.44 117.96 4.48 1.32e+00 5.74e-01 1.15e+01 angle pdb=" CA HIS J 299 " pdb=" C HIS J 299 " pdb=" O HIS J 299 " ideal model delta sigma weight residual 122.44 117.98 4.46 1.32e+00 5.74e-01 1.14e+01 angle pdb=" CA HIS B 299 " pdb=" C HIS B 299 " pdb=" O HIS B 299 " ideal model delta sigma weight residual 122.44 117.99 4.45 1.32e+00 5.74e-01 1.14e+01 angle pdb=" CA ASN I 286 " pdb=" C ASN I 286 " pdb=" O ASN I 286 " ideal model delta sigma weight residual 122.14 117.96 4.18 1.24e+00 6.50e-01 1.14e+01 ... (remaining 10985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.70: 4283 11.70 - 23.41: 507 23.41 - 35.11: 170 35.11 - 46.81: 55 46.81 - 58.52: 35 Dihedral angle restraints: 5050 sinusoidal: 2110 harmonic: 2940 Sorted by residual: dihedral pdb=" CA GLN J 351 " pdb=" C GLN J 351 " pdb=" N SER J 352 " pdb=" CA SER J 352 " ideal model delta harmonic sigma weight residual 180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA GLN D 351 " pdb=" C GLN D 351 " pdb=" N SER D 352 " pdb=" CA SER D 352 " ideal model delta harmonic sigma weight residual 180.00 -159.60 -20.40 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA GLN F 351 " pdb=" C GLN F 351 " pdb=" N SER F 352 " pdb=" CA SER F 352 " ideal model delta harmonic sigma weight residual -180.00 -159.60 -20.40 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 5047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 935 0.079 - 0.158: 266 0.158 - 0.236: 14 0.236 - 0.315: 5 0.315 - 0.394: 10 Chirality restraints: 1230 Sorted by residual: chirality pdb=" CB THR D 377 " pdb=" CA THR D 377 " pdb=" OG1 THR D 377 " pdb=" CG2 THR D 377 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CB THR F 377 " pdb=" CA THR F 377 " pdb=" OG1 THR F 377 " pdb=" CG2 THR F 377 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CB THR H 377 " pdb=" CA THR H 377 " pdb=" OG1 THR H 377 " pdb=" CG2 THR H 377 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.39 2.00e-01 2.50e+01 3.82e+00 ... (remaining 1227 not shown) Planarity restraints: 1410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 346 " 0.039 2.00e-02 2.50e+03 3.58e-02 2.24e+01 pdb=" CG PHE F 346 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE F 346 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE F 346 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE F 346 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE F 346 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 346 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 346 " 0.040 2.00e-02 2.50e+03 3.57e-02 2.23e+01 pdb=" CG PHE D 346 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE D 346 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE D 346 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE D 346 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE D 346 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 346 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 346 " 0.040 2.00e-02 2.50e+03 3.56e-02 2.21e+01 pdb=" CG PHE H 346 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE H 346 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE H 346 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE H 346 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE H 346 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE H 346 " -0.000 2.00e-02 2.50e+03 ... (remaining 1407 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 3144 2.92 - 3.42: 6994 3.42 - 3.91: 14499 3.91 - 4.41: 15011 4.41 - 4.90: 30338 Nonbonded interactions: 69986 Sorted by model distance: nonbonded pdb=" NZ LYS B 340 " pdb=" OE2 GLU B 342 " model vdw 2.430 3.120 nonbonded pdb=" NZ LYS J 340 " pdb=" OE2 GLU J 342 " model vdw 2.430 3.120 nonbonded pdb=" NZ LYS D 340 " pdb=" OE2 GLU D 342 " model vdw 2.430 3.120 nonbonded pdb=" NZ LYS H 340 " pdb=" OE2 GLU H 342 " model vdw 2.430 3.120 nonbonded pdb=" NZ LYS F 340 " pdb=" OE2 GLU F 342 " model vdw 2.430 3.120 ... (remaining 69981 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.000 Find NCS groups from input model: 0.260 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:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.830 ------------------------------------------------------------------------------- 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 : 0.935 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: 1.0292 time to fit residues: 327.4936 Evaluate side-chains 217 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 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 : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 379 ARG cc_start: 0.7071 (mmm-85) cc_final: 0.6745 (tmm160) REVERT: C 342 GLU cc_start: 0.4716 (pm20) cc_final: 0.4178 (pm20) REVERT: E 379 ARG cc_start: 0.6127 (tpm170) cc_final: 0.5501 (tpm170) REVERT: D 276 GLN cc_start: 0.8168 (mt0) cc_final: 0.7916 (mt0) REVERT: D 342 GLU cc_start: 0.6585 (tm-30) cc_final: 0.6038 (tm-30) REVERT: D 344 LEU cc_start: 0.8810 (mm) cc_final: 0.8524 (mm) REVERT: F 379 ARG cc_start: 0.6374 (mmt90) cc_final: 0.5863 (ptp90) REVERT: H 345 ASP cc_start: 0.7782 (t0) cc_final: 0.7578 (t0) REVERT: H 379 ARG cc_start: 0.6723 (mmm-85) cc_final: 0.6517 (tmm160) outliers start: 51 outliers final: 31 residues processed: 269 average time/residue: 1.0484 time to fit residues: 300.9264 Evaluate side-chains 238 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 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 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 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 50 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 351 GLN F 276 GLN F 351 GLN ** J 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 359 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8230 Z= 0.417 Angle : 0.691 7.454 10990 Z= 0.344 Chirality : 0.051 0.149 1230 Planarity : 0.004 0.034 1410 Dihedral : 5.406 20.649 1100 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 7.42 % Allowed : 20.11 % Favored : 72.47 % 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: -3.32 (0.21), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (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 0.016 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 288 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 219 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 379 ARG cc_start: 0.7086 (mmm-85) cc_final: 0.6792 (tmm160) REVERT: G 353 LYS cc_start: 0.4889 (OUTLIER) cc_final: 0.4431 (pmtt) REVERT: F 311 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8457 (tppp) REVERT: F 349 ARG cc_start: 0.6186 (OUTLIER) cc_final: 0.4718 (ppt90) REVERT: F 379 ARG cc_start: 0.6631 (mmt90) cc_final: 0.6166 (ptp90) outliers start: 69 outliers final: 46 residues processed: 253 average time/residue: 1.0634 time to fit residues: 286.6942 Evaluate side-chains 250 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 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 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 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 353 LYS 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 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 291 CYS Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 344 LEU 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 H residue 345 ASP 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 348 ASP Chi-restraints excluded: chain J residue 373 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 26 optimal weight: 0.0000 chunk 80 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 overall best weight: 1.7390 ------------------------------------------------------------------------------- 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** ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 GLN F 351 GLN ** J 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 299 HIS J 359 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8230 Z= 0.233 Angle : 0.644 7.333 10990 Z= 0.312 Chirality : 0.050 0.147 1230 Planarity : 0.003 0.029 1410 Dihedral : 5.056 20.431 1100 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 6.13 % Allowed : 22.15 % 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: -3.31 (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 0.015 0.002 PHE H 346 TYR 0.012 0.002 TYR E 310 ARG 0.005 0.001 ARG I 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 278 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 221 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 GLU cc_start: 0.6195 (tm-30) cc_final: 0.5608 (tm-30) REVERT: B 379 ARG cc_start: 0.7030 (mmm-85) cc_final: 0.6802 (tmm160) REVERT: C 379 ARG cc_start: 0.5148 (tpm170) cc_final: 0.4735 (mmp80) REVERT: E 347 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7663 (mtpm) REVERT: G 349 ARG cc_start: 0.5470 (OUTLIER) cc_final: 0.4581 (pmt-80) REVERT: G 353 LYS cc_start: 0.5372 (OUTLIER) cc_final: 0.3317 (pptt) REVERT: F 311 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8332 (tppt) REVERT: F 379 ARG cc_start: 0.6666 (mmt90) cc_final: 0.6208 (ptp90) outliers start: 57 outliers final: 30 residues processed: 250 average time/residue: 1.0879 time to fit residues: 289.5505 Evaluate side-chains 232 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 198 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 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 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 347 LYS 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 353 LYS Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain I residue 319 THR 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 311 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 341 SER Chi-restraints excluded: chain J residue 311 LYS Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 373 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 66 optimal weight: 0.2980 chunk 0 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 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 279 ASN A 351 GLN C 276 GLN C 351 GLN E 351 GLN ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 8230 Z= 0.522 Angle : 0.762 9.333 10990 Z= 0.382 Chirality : 0.052 0.144 1230 Planarity : 0.004 0.034 1410 Dihedral : 5.546 21.245 1100 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 7.31 % Allowed : 22.58 % Favored : 70.11 % 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 : -2.61 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 362 PHE 0.022 0.003 PHE J 378 TYR 0.017 0.002 TYR E 310 ARG 0.006 0.001 ARG A 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 275 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 207 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 342 GLU cc_start: 0.6342 (tm-30) cc_final: 0.5845 (tm-30) REVERT: B 344 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8252 (mm) REVERT: E 347 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7913 (ttpp) REVERT: G 353 LYS cc_start: 0.5134 (OUTLIER) cc_final: 0.4570 (pptt) REVERT: F 349 ARG cc_start: 0.6091 (OUTLIER) cc_final: 0.4568 (ppt90) REVERT: F 379 ARG cc_start: 0.6766 (mmt90) cc_final: 0.6230 (ptp90) outliers start: 68 outliers final: 47 residues processed: 244 average time/residue: 1.1280 time to fit residues: 293.3031 Evaluate side-chains 242 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 191 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 345 ASP 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 347 LYS Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 341 SER Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 349 ARG Chi-restraints excluded: chain G residue 353 LYS 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 341 SER Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 344 LEU 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 H residue 344 LEU Chi-restraints excluded: chain J residue 311 LYS Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 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 19 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 I 307 GLN D 299 HIS F 276 GLN F 351 GLN H 351 GLN ** J 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 351 GLN J 374 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8230 Z= 0.242 Angle : 0.681 7.858 10990 Z= 0.330 Chirality : 0.051 0.136 1230 Planarity : 0.003 0.028 1410 Dihedral : 5.108 20.580 1100 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 6.67 % Allowed : 24.41 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.37 (0.21), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS J 374 PHE 0.020 0.002 PHE B 346 TYR 0.013 0.002 TYR E 310 ARG 0.004 0.001 ARG B 379 *********************** 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 271 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 209 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: B 342 GLU cc_start: 0.6338 (OUTLIER) cc_final: 0.6087 (tm-30) REVERT: B 344 LEU cc_start: 0.8763 (mm) cc_final: 0.8340 (mm) REVERT: G 349 ARG cc_start: 0.5388 (OUTLIER) cc_final: 0.4381 (pmt-80) REVERT: G 353 LYS cc_start: 0.5475 (OUTLIER) cc_final: 0.3434 (pptt) REVERT: G 379 ARG cc_start: 0.4902 (OUTLIER) cc_final: 0.3144 (ttp80) REVERT: I 307 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7923 (mt0) REVERT: F 349 ARG cc_start: 0.6225 (OUTLIER) cc_final: 0.4798 (ppt90) REVERT: F 379 ARG cc_start: 0.6707 (mmt90) cc_final: 0.6236 (ptp90) REVERT: J 342 GLU cc_start: 0.4787 (pm20) cc_final: 0.4192 (pm20) outliers start: 62 outliers final: 37 residues processed: 242 average time/residue: 1.1704 time to fit residues: 301.4858 Evaluate side-chains 239 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 196 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain E residue 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 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 353 LYS Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain G residue 379 ARG Chi-restraints excluded: chain I residue 307 GLN 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 324 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 320 SER 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 344 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN A 351 GLN E 276 GLN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 GLN G 288 GLN ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 351 GLN ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 351 GLN D 276 GLN F 276 GLN F 351 GLN H 351 GLN ** J 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 327 ASN J 351 GLN ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 374 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 8230 Z= 0.475 Angle : 0.793 9.359 10990 Z= 0.393 Chirality : 0.052 0.171 1230 Planarity : 0.004 0.033 1410 Dihedral : 5.549 22.724 1100 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 7.53 % Allowed : 24.84 % Favored : 67.63 % 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: -3.51 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 362 PHE 0.024 0.004 PHE H 346 TYR 0.014 0.002 TYR I 310 ARG 0.006 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 274 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 204 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: B 342 GLU cc_start: 0.6389 (OUTLIER) cc_final: 0.6162 (tm-30) REVERT: B 344 LEU cc_start: 0.8752 (mm) cc_final: 0.8319 (mm) REVERT: G 286 ASN cc_start: 0.8146 (t0) cc_final: 0.7904 (t0) REVERT: G 349 ARG cc_start: 0.5593 (OUTLIER) cc_final: 0.4491 (pmt-80) REVERT: G 353 LYS cc_start: 0.5284 (OUTLIER) cc_final: 0.4764 (pptt) REVERT: G 379 ARG cc_start: 0.5042 (OUTLIER) cc_final: 0.3485 (ttp80) REVERT: F 349 ARG cc_start: 0.6216 (OUTLIER) cc_final: 0.4802 (ppt90) REVERT: F 379 ARG cc_start: 0.6903 (mmt90) cc_final: 0.6291 (ptp90) outliers start: 70 outliers final: 46 residues processed: 238 average time/residue: 1.0494 time to fit residues: 266.3335 Evaluate side-chains 245 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 194 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 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 342 GLU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain E residue 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 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 353 LYS 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 360 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 344 LEU 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 344 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 87 optimal weight: 0.0770 chunk 92 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- 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** C 288 GLN E 307 GLN G 307 GLN G 351 GLN I 307 GLN ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 GLN H 351 GLN ** J 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 351 GLN J 374 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4140 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 : 0.757 9.845 10990 Z= 0.368 Chirality : 0.052 0.244 1230 Planarity : 0.003 0.031 1410 Dihedral : 5.370 20.818 1100 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 6.67 % Allowed : 25.16 % 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: -3.48 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.021 0.003 PHE F 346 TYR 0.015 0.002 TYR C 310 ARG 0.007 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 262 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 200 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: G 286 ASN cc_start: 0.8054 (t0) cc_final: 0.7786 (t0) REVERT: G 349 ARG cc_start: 0.5405 (OUTLIER) cc_final: 0.4457 (pmt-80) REVERT: G 353 LYS cc_start: 0.5238 (OUTLIER) cc_final: 0.3307 (pptt) REVERT: F 349 ARG cc_start: 0.6005 (OUTLIER) cc_final: 0.4664 (ppt90) REVERT: F 379 ARG cc_start: 0.6837 (mmt90) cc_final: 0.6253 (ptp90) REVERT: J 374 HIS cc_start: 0.6199 (OUTLIER) cc_final: 0.5642 (t-170) outliers start: 62 outliers final: 42 residues processed: 232 average time/residue: 1.0876 time to fit residues: 269.2742 Evaluate side-chains 239 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 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 377 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain 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 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 353 LYS 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 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 324 SER Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 320 SER 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 J residue 319 THR Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain J residue 374 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 351 GLN C 288 GLN G 307 GLN ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 GLN H 299 HIS H 351 GLN J 276 GLN J 351 GLN J 359 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8230 Z= 0.219 Angle : 0.742 10.343 10990 Z= 0.354 Chirality : 0.051 0.155 1230 Planarity : 0.003 0.029 1410 Dihedral : 5.029 22.381 1100 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.95 % Allowed : 27.10 % Favored : 67.96 % 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: -3.40 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS J 374 PHE 0.025 0.003 PHE H 346 TYR 0.013 0.002 TYR C 310 ARG 0.008 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 248 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 1.039 Fit side-chains REVERT: B 342 GLU cc_start: 0.6362 (tm-30) cc_final: 0.5194 (tp30) REVERT: G 349 ARG cc_start: 0.5338 (OUTLIER) cc_final: 0.4582 (pmt-80) REVERT: G 353 LYS cc_start: 0.5298 (OUTLIER) cc_final: 0.3381 (pptt) REVERT: D 342 GLU cc_start: 0.6973 (tm-30) cc_final: 0.6619 (tm-30) REVERT: F 349 ARG cc_start: 0.6109 (OUTLIER) cc_final: 0.4531 (ppt90) REVERT: F 379 ARG cc_start: 0.6792 (mmt90) cc_final: 0.6129 (ptp90) REVERT: J 342 GLU cc_start: 0.4957 (pm20) cc_final: 0.4462 (pm20) outliers start: 46 outliers final: 28 residues processed: 227 average time/residue: 1.0710 time to fit residues: 259.2612 Evaluate side-chains 223 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 342 GLU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 360 ILE 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 353 LYS Chi-restraints excluded: chain G residue 360 ILE 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 324 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 320 SER 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 J residue 319 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 48 optimal weight: 0.2980 chunk 63 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 overall best weight: 4.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN C 288 GLN G 307 GLN I 279 ASN ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 GLN H 351 GLN J 351 GLN ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 374 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 8230 Z= 0.468 Angle : 0.850 10.336 10990 Z= 0.414 Chirality : 0.054 0.305 1230 Planarity : 0.004 0.031 1410 Dihedral : 5.523 20.409 1100 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 4.62 % Allowed : 27.63 % Favored : 67.74 % 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 0.006 0.001 HIS A 362 PHE 0.023 0.004 PHE D 346 TYR 0.015 0.002 TYR G 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 245 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 202 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: C 379 ARG cc_start: 0.5176 (tpm170) cc_final: 0.4744 (mmp80) REVERT: G 349 ARG cc_start: 0.5525 (OUTLIER) cc_final: 0.4570 (pmt-80) REVERT: G 353 LYS cc_start: 0.5280 (OUTLIER) cc_final: 0.3413 (pptt) REVERT: I 288 GLN cc_start: 0.7668 (mp-120) cc_final: 0.7394 (mp10) REVERT: F 349 ARG cc_start: 0.6137 (OUTLIER) cc_final: 0.4777 (ppt90) REVERT: F 379 ARG cc_start: 0.6733 (mmt90) cc_final: 0.6090 (ptp90) REVERT: H 379 ARG cc_start: 0.6943 (tmm160) cc_final: 0.6664 (tpt90) outliers start: 43 outliers final: 32 residues processed: 226 average time/residue: 1.0973 time to fit residues: 264.0849 Evaluate side-chains 234 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 311 LYS Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain 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 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 353 LYS 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 342 GLU Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 320 SER 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 J residue 319 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 307 GLN I 307 GLN ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 GLN J 359 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.126337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.107504 restraints weight = 12154.833| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.32 r_work: 0.3873 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8230 Z= 0.223 Angle : 0.778 10.586 10990 Z= 0.370 Chirality : 0.052 0.136 1230 Planarity : 0.003 0.031 1410 Dihedral : 4.989 19.135 1100 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.55 % Allowed : 28.82 % Favored : 67.63 % 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: -3.40 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 330 PHE 0.016 0.002 PHE E 346 TYR 0.015 0.001 TYR C 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: 4355.01 seconds wall clock time: 79 minutes 12.83 seconds (4752.83 seconds total)