Starting phenix.real_space_refine on Tue Mar 3 18:56:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p67_13220/03_2026/7p67_13220.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p67_13220/03_2026/7p67_13220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p67_13220/03_2026/7p67_13220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p67_13220/03_2026/7p67_13220.map" model { file = "/net/cci-nas-00/data/ceres_data/7p67_13220/03_2026/7p67_13220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p67_13220/03_2026/7p67_13220.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 5060 2.51 5 N 1520 2.21 5 O 1520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8120 Number of models: 1 Model: "" Number of chains: 1 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} Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 1.00, per 1000 atoms: 0.12 Number of scatterers: 8120 At special positions: 0 Unit cell: (120.75, 151.8, 51.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 1520 8.00 N 1520 7.00 C 5060 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 383.2 milliseconds 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1860 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 27 sheets defined 0.0% alpha, 47.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 274 through 284 removed outlier: 9.175A pdb=" N LYS B 274 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 9.874A pdb=" N ILE C 277 " --> pdb=" O LYS B 274 " (cutoff:3.500A) removed outlier: 9.026A pdb=" N GLN B 276 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 10.182A pdb=" N ASN C 279 " --> pdb=" O GLN B 276 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N ILE B 278 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N LYS C 281 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LYS B 280 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ASP C 283 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU B 282 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N LYS A 274 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 9.883A pdb=" N ILE B 277 " --> pdb=" O LYS A 274 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N GLN A 276 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N ASN B 279 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N ILE A 278 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 10.141A pdb=" N LYS B 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LYS A 280 " --> pdb=" O LYS B 281 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ASP B 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU A 282 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A 275 " --> pdb=" O LYS D 274 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLN D 276 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE A 277 " --> pdb=" O GLN D 276 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE D 278 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN A 279 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS D 280 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LYS A 281 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL D 275 " --> pdb=" O LYS E 274 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLN E 276 " --> pdb=" O VAL D 275 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE D 277 " --> pdb=" O GLN E 276 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE E 278 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASN D 279 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS E 280 " --> pdb=" O ASN D 279 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYS D 281 " --> pdb=" O LYS E 280 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 287 through 290 removed outlier: 6.750A pdb=" N GLN A 288 " --> pdb=" O SER D 289 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLN D 288 " --> pdb=" O SER E 289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 297 through 298 removed outlier: 6.530A pdb=" N ILE B 297 " --> pdb=" O LYS C 298 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE A 297 " --> pdb=" O LYS B 298 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.374A pdb=" N VAL A 306 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL D 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE A 308 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL D 306 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL E 309 " --> pdb=" O VAL D 306 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE D 308 " --> pdb=" O VAL E 309 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.794A pdb=" N VAL A 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL D 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.488A pdb=" N VAL B 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LYS C 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N SER B 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL A 318 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N LYS B 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N SER A 320 " --> pdb=" O LYS B 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.700A pdb=" N ILE B 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE A 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 337 through 341 removed outlier: 6.171A pdb=" N VAL A 337 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LYS B 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 339 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N GLU B 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N SER A 341 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N LEU B 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS A 343 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLU A 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N SER D 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LYS A 340 " --> pdb=" O SER D 341 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLU D 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N SER E 341 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LYS D 340 " --> pdb=" O SER E 341 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 344 through 345 removed outlier: 7.839A pdb=" N LEU C 344 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LYS B 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL A 337 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LYS B 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 339 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N GLU B 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N SER A 341 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N LEU B 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS A 343 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ASP D 345 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 344 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU D 344 " --> pdb=" O ASP E 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 348 through 350 removed outlier: 6.823A pdb=" N ASP A 348 " --> pdb=" O ARG D 349 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASP D 348 " --> pdb=" O ARG E 349 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 353 through 357 removed outlier: 6.834A pdb=" N ILE B 354 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY C 355 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE A 354 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLY B 355 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N LYS A 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N SER D 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLY A 355 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N LYS D 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N SER E 356 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY D 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.511A pdb=" N THR B 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR A 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 369 through 371 removed outlier: 6.770A pdb=" N ILE C 371 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE B 371 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N LYS A 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N LYS D 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 374 through 378 removed outlier: 6.366A pdb=" N LYS B 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N PHE C 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR B 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LYS A 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N PHE B 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N THR A 377 " --> pdb=" O PHE B 378 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 274 through 284 removed outlier: 9.179A pdb=" N LYS G 274 " --> pdb=" O VAL H 275 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N ILE H 277 " --> pdb=" O LYS G 274 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N GLN G 276 " --> pdb=" O ILE H 277 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N ASN H 279 " --> pdb=" O GLN G 276 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N ILE G 278 " --> pdb=" O ASN H 279 " (cutoff:3.500A) removed outlier: 10.170A pdb=" N LYS H 281 " --> pdb=" O ILE G 278 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LYS G 280 " --> pdb=" O LYS H 281 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ASP H 283 " --> pdb=" O LYS G 280 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU G 282 " --> pdb=" O ASP H 283 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N LYS F 274 " --> pdb=" O VAL G 275 " (cutoff:3.500A) removed outlier: 9.882A pdb=" N ILE G 277 " --> pdb=" O LYS F 274 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N GLN F 276 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 10.182A pdb=" N ASN G 279 " --> pdb=" O GLN F 276 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N ILE F 278 " --> pdb=" O ASN G 279 " (cutoff:3.500A) removed outlier: 10.124A pdb=" N LYS G 281 " --> pdb=" O ILE F 278 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LYS F 280 " --> pdb=" O LYS G 281 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N ASP G 283 " --> pdb=" O LYS F 280 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU F 282 " --> pdb=" O ASP G 283 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL F 275 " --> pdb=" O LYS I 274 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLN I 276 " --> pdb=" O VAL F 275 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE F 277 " --> pdb=" O GLN I 276 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE I 278 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ASN F 279 " --> pdb=" O ILE I 278 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LYS I 280 " --> pdb=" O ASN F 279 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LYS F 281 " --> pdb=" O LYS I 280 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL I 275 " --> pdb=" O LYS J 274 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLN J 276 " --> pdb=" O VAL I 275 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE I 277 " --> pdb=" O GLN J 276 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE J 278 " --> pdb=" O ILE I 277 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ASN I 279 " --> pdb=" O ILE J 278 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LYS J 280 " --> pdb=" O ASN I 279 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LYS I 281 " --> pdb=" O LYS J 280 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 287 through 290 removed outlier: 6.792A pdb=" N GLN F 288 " --> pdb=" O SER I 289 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLN I 288 " --> pdb=" O SER J 289 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 297 through 298 removed outlier: 6.520A pdb=" N ILE G 297 " --> pdb=" O LYS H 298 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE F 297 " --> pdb=" O LYS G 298 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 306 through 310 removed outlier: 6.395A pdb=" N VAL F 306 " --> pdb=" O GLN I 307 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N VAL I 309 " --> pdb=" O VAL F 306 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE F 308 " --> pdb=" O VAL I 309 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL I 306 " --> pdb=" O GLN J 307 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL J 309 " --> pdb=" O VAL I 306 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE I 308 " --> pdb=" O VAL J 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 313 through 314 removed outlier: 6.819A pdb=" N VAL F 313 " --> pdb=" O ASP I 314 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL I 313 " --> pdb=" O ASP J 314 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 317 through 322 removed outlier: 6.504A pdb=" N VAL G 318 " --> pdb=" O THR H 319 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LYS H 321 " --> pdb=" O VAL G 318 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N SER G 320 " --> pdb=" O LYS H 321 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL F 318 " --> pdb=" O THR G 319 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LYS G 321 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N SER F 320 " --> pdb=" O LYS G 321 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 328 through 330 removed outlier: 6.716A pdb=" N ILE G 328 " --> pdb=" O HIS H 329 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE F 328 " --> pdb=" O HIS G 329 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 337 through 345 removed outlier: 6.146A pdb=" N VAL G 337 " --> pdb=" O GLU H 338 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LYS H 340 " --> pdb=" O VAL G 337 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL G 339 " --> pdb=" O LYS H 340 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLU H 342 " --> pdb=" O VAL G 339 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N SER G 341 " --> pdb=" O GLU H 342 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU H 344 " --> pdb=" O SER G 341 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LYS G 343 " --> pdb=" O LEU H 344 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL F 337 " --> pdb=" O GLU G 338 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LYS G 340 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL F 339 " --> pdb=" O LYS G 340 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N GLU G 342 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER F 341 " --> pdb=" O GLU G 342 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU G 344 " --> pdb=" O SER F 341 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LYS F 343 " --> pdb=" O LEU G 344 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 348 through 350 removed outlier: 6.815A pdb=" N ASP F 348 " --> pdb=" O ARG I 349 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASP I 348 " --> pdb=" O ARG J 349 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 353 through 357 removed outlier: 6.819A pdb=" N ILE G 354 " --> pdb=" O LYS H 353 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLY H 355 " --> pdb=" O ILE G 354 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE F 354 " --> pdb=" O LYS G 353 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY G 355 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N LYS F 353 " --> pdb=" O ILE I 354 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N SER I 356 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLY F 355 " --> pdb=" O SER I 356 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N LYS I 353 " --> pdb=" O ILE J 354 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N SER J 356 " --> pdb=" O LYS I 353 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY I 355 " --> pdb=" O SER J 356 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 360 through 362 removed outlier: 6.502A pdb=" N THR G 361 " --> pdb=" O HIS H 362 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR F 361 " --> pdb=" O HIS G 362 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 369 through 371 removed outlier: 6.807A pdb=" N ILE H 371 " --> pdb=" O LYS G 370 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLU G 372 " --> pdb=" O ILE H 371 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYS F 369 " --> pdb=" O LYS G 370 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N GLU G 372 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE F 371 " --> pdb=" O GLU G 372 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N HIS G 374 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N THR F 373 " --> pdb=" O HIS G 374 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N LEU G 376 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS F 375 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N PHE G 378 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR F 377 " --> pdb=" O PHE G 378 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS F 370 " --> pdb=" O LYS I 369 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N LYS I 369 " --> pdb=" O LYS J 370 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 374 through 378 removed outlier: 7.975A pdb=" N HIS H 374 " --> pdb=" O ILE G 371 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N THR G 373 " --> pdb=" O HIS H 374 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LEU H 376 " --> pdb=" O THR G 373 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LYS G 375 " --> pdb=" O LEU H 376 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N PHE H 378 " --> pdb=" O LYS G 375 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N THR G 377 " --> pdb=" O PHE H 378 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYS F 369 " --> pdb=" O LYS G 370 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N GLU G 372 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE F 371 " --> pdb=" O GLU G 372 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N HIS G 374 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N THR F 373 " --> pdb=" O HIS G 374 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N LEU G 376 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS F 375 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N PHE G 378 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR F 377 " --> pdb=" O PHE G 378 " (cutoff:3.500A) 141 hydrogen bonds defined for protein. 423 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2465 1.33 - 1.45: 844 1.45 - 1.57: 4891 1.57 - 1.69: 10 1.69 - 1.81: 20 Bond restraints: 8230 Sorted by residual: bond pdb=" N VAL J 313 " pdb=" CA VAL J 313 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.24e-02 6.50e+03 8.63e+00 bond pdb=" N VAL I 313 " pdb=" CA VAL I 313 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.24e-02 6.50e+03 8.50e+00 bond pdb=" N VAL E 313 " pdb=" CA VAL E 313 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.24e-02 6.50e+03 8.30e+00 bond pdb=" N VAL F 313 " pdb=" CA VAL F 313 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.24e-02 6.50e+03 8.25e+00 bond pdb=" N VAL D 313 " pdb=" CA VAL D 313 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.24e-02 6.50e+03 8.16e+00 ... (remaining 8225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 9961 1.65 - 3.31: 814 3.31 - 4.96: 152 4.96 - 6.62: 53 6.62 - 8.27: 10 Bond angle restraints: 10990 Sorted by residual: angle pdb=" CA ASN F 286 " pdb=" C ASN F 286 " pdb=" O ASN F 286 " ideal model delta sigma weight residual 122.14 117.56 4.58 1.24e+00 6.50e-01 1.36e+01 angle pdb=" CA ASN J 286 " pdb=" C ASN J 286 " pdb=" O ASN J 286 " ideal model delta sigma weight residual 122.14 117.57 4.57 1.24e+00 6.50e-01 1.36e+01 angle pdb=" CA ASN I 286 " pdb=" C ASN I 286 " pdb=" O ASN I 286 " ideal model delta sigma weight residual 122.14 117.59 4.55 1.24e+00 6.50e-01 1.35e+01 angle pdb=" CA ASN A 286 " pdb=" C ASN A 286 " pdb=" O ASN A 286 " ideal model delta sigma weight residual 122.14 117.60 4.54 1.24e+00 6.50e-01 1.34e+01 angle pdb=" CA ASN D 286 " pdb=" C ASN D 286 " pdb=" O ASN D 286 " ideal model delta sigma weight residual 122.14 117.62 4.52 1.24e+00 6.50e-01 1.33e+01 ... (remaining 10985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.66: 4206 9.66 - 19.33: 484 19.33 - 28.99: 200 28.99 - 38.66: 130 38.66 - 48.32: 30 Dihedral angle restraints: 5050 sinusoidal: 2110 harmonic: 2940 Sorted by residual: dihedral pdb=" CA ILE G 360 " pdb=" C ILE G 360 " pdb=" N THR G 361 " pdb=" CA THR G 361 " ideal model delta harmonic sigma weight residual 180.00 164.81 15.19 0 5.00e+00 4.00e-02 9.23e+00 dihedral pdb=" CA ILE D 360 " pdb=" C ILE D 360 " pdb=" N THR D 361 " pdb=" CA THR D 361 " ideal model delta harmonic sigma weight residual 180.00 164.83 15.17 0 5.00e+00 4.00e-02 9.20e+00 dihedral pdb=" CA ILE I 360 " pdb=" C ILE I 360 " pdb=" N THR I 361 " pdb=" CA THR I 361 " ideal model delta harmonic sigma weight residual 180.00 164.86 15.14 0 5.00e+00 4.00e-02 9.17e+00 ... (remaining 5047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 1093 0.117 - 0.235: 107 0.235 - 0.352: 20 0.352 - 0.470: 0 0.470 - 0.587: 10 Chirality restraints: 1230 Sorted by residual: chirality pdb=" CB ILE G 360 " pdb=" CA ILE G 360 " pdb=" CG1 ILE G 360 " pdb=" CG2 ILE G 360 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.59 2.00e-01 2.50e+01 8.61e+00 chirality pdb=" CB ILE J 360 " pdb=" CA ILE J 360 " pdb=" CG1 ILE J 360 " pdb=" CG2 ILE J 360 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.58 2.00e-01 2.50e+01 8.52e+00 chirality pdb=" CB ILE B 360 " pdb=" CA ILE B 360 " pdb=" CG1 ILE B 360 " pdb=" CG2 ILE B 360 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.58 2.00e-01 2.50e+01 8.51e+00 ... (remaining 1227 not shown) Planarity restraints: 1410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 358 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" C ASP C 358 " -0.036 2.00e-02 2.50e+03 pdb=" O ASP C 358 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN C 359 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 358 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" C ASP B 358 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP B 358 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN B 359 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 358 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.19e+00 pdb=" C ASP D 358 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP D 358 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN D 359 " 0.012 2.00e-02 2.50e+03 ... (remaining 1407 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 2358 2.85 - 3.36: 7035 3.36 - 3.88: 13884 3.88 - 4.39: 15362 4.39 - 4.90: 30345 Nonbonded interactions: 68984 Sorted by model distance: nonbonded pdb=" OD2 ASP A 348 " pdb=" NZ LYS D 311 " model vdw 2.338 3.120 nonbonded pdb=" NZ LYS B 311 " pdb=" OD2 ASP C 348 " model vdw 2.342 3.120 nonbonded pdb=" NZ LYS G 311 " pdb=" OD2 ASP H 348 " model vdw 2.344 3.120 nonbonded pdb=" OD2 ASP D 348 " pdb=" NZ LYS E 311 " model vdw 2.348 3.120 nonbonded pdb=" OD2 ASP F 348 " pdb=" NZ LYS I 311 " model vdw 2.354 3.120 ... (remaining 68979 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: 0.03 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: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.660 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 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 : 0.007 0.048 8230 Z= 0.470 Angle : 1.057 8.269 10990 Z= 0.654 Chirality : 0.093 0.587 1230 Planarity : 0.005 0.027 1410 Dihedral : 11.976 48.319 3190 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.19 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 379 TYR 0.007 0.002 TYR I 310 PHE 0.003 0.001 PHE G 346 HIS 0.003 0.001 HIS J 299 Details of bonding type rmsd covalent geometry : bond 0.00700 ( 8230) covalent geometry : angle 1.05727 (10990) hydrogen bonds : bond 0.10185 ( 141) hydrogen bonds : angle 6.93944 ( 423) *********************** 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 306 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.340 Fit side-chains REVERT: C 316 SER cc_start: 0.9184 (p) cc_final: 0.8978 (p) REVERT: C 349 ARG cc_start: 0.7451 (mtp180) cc_final: 0.6853 (pmt-80) REVERT: C 358 ASP cc_start: 0.8164 (p0) cc_final: 0.7863 (p0) REVERT: D 276 GLN cc_start: 0.7539 (tt0) cc_final: 0.7162 (tt0) REVERT: D 316 SER cc_start: 0.8989 (p) cc_final: 0.8693 (p) REVERT: E 359 ASN cc_start: 0.8018 (t0) cc_final: 0.7800 (t0) REVERT: F 316 SER cc_start: 0.9026 (p) cc_final: 0.8718 (p) REVERT: G 316 SER cc_start: 0.8892 (p) cc_final: 0.8686 (p) REVERT: I 357 LEU cc_start: 0.8655 (tp) cc_final: 0.8350 (tp) REVERT: J 316 SER cc_start: 0.9076 (p) cc_final: 0.8866 (p) REVERT: J 351 GLN cc_start: 0.8216 (pt0) cc_final: 0.7839 (mm-40) REVERT: J 357 LEU cc_start: 0.8725 (tp) cc_final: 0.8282 (tp) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.0802 time to fit residues: 34.6739 Evaluate side-chains 259 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 279 ASN J 279 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.129051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.110382 restraints weight = 11728.409| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.35 r_work: 0.3694 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8230 Z= 0.134 Angle : 0.541 6.454 10990 Z= 0.274 Chirality : 0.049 0.123 1230 Planarity : 0.003 0.021 1410 Dihedral : 5.066 14.937 1100 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.15 % Allowed : 10.00 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 349 TYR 0.013 0.002 TYR C 310 PHE 0.005 0.001 PHE D 346 HIS 0.003 0.001 HIS E 299 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8230) covalent geometry : angle 0.54065 (10990) hydrogen bonds : bond 0.01908 ( 141) hydrogen bonds : angle 4.62638 ( 423) *********************** 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 283 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 263 time to evaluate : 0.356 Fit side-chains REVERT: A 295 ASP cc_start: 0.8640 (m-30) cc_final: 0.8213 (m-30) REVERT: A 345 ASP cc_start: 0.8510 (t0) cc_final: 0.8264 (t0) REVERT: A 358 ASP cc_start: 0.9024 (p0) cc_final: 0.8742 (p0) REVERT: B 279 ASN cc_start: 0.9117 (m-40) cc_final: 0.8900 (m110) REVERT: B 345 ASP cc_start: 0.8507 (t0) cc_final: 0.8192 (t0) REVERT: B 349 ARG cc_start: 0.8140 (mtp180) cc_final: 0.7869 (ttm110) REVERT: B 358 ASP cc_start: 0.8932 (p0) cc_final: 0.8300 (p0) REVERT: C 338 GLU cc_start: 0.8161 (tt0) cc_final: 0.7953 (tt0) REVERT: C 349 ARG cc_start: 0.8525 (mtp180) cc_final: 0.8134 (ttm110) REVERT: C 358 ASP cc_start: 0.8865 (p0) cc_final: 0.8601 (p0) REVERT: C 379 ARG cc_start: 0.7093 (mtt180) cc_final: 0.5893 (pmt-80) REVERT: D 276 GLN cc_start: 0.8330 (tt0) cc_final: 0.8074 (tt0) REVERT: D 316 SER cc_start: 0.9243 (p) cc_final: 0.8927 (p) REVERT: D 345 ASP cc_start: 0.8616 (t0) cc_final: 0.8376 (t0) REVERT: E 345 ASP cc_start: 0.8572 (t0) cc_final: 0.8372 (t0) REVERT: E 351 GLN cc_start: 0.4684 (mm110) cc_final: 0.4404 (mm-40) REVERT: F 295 ASP cc_start: 0.8661 (m-30) cc_final: 0.8154 (m-30) REVERT: F 314 ASP cc_start: 0.9247 (t0) cc_final: 0.8930 (t0) REVERT: F 336 GLN cc_start: 0.8867 (mp10) cc_final: 0.8649 (mp10) REVERT: F 345 ASP cc_start: 0.8589 (t0) cc_final: 0.8360 (t0) REVERT: F 349 ARG cc_start: 0.8249 (mtp180) cc_final: 0.7918 (ttp-110) REVERT: F 359 ASN cc_start: 0.8904 (t0) cc_final: 0.8672 (t0) REVERT: G 295 ASP cc_start: 0.8619 (m-30) cc_final: 0.8185 (m-30) REVERT: G 306 VAL cc_start: 0.9116 (t) cc_final: 0.8859 (p) REVERT: G 345 ASP cc_start: 0.8596 (t0) cc_final: 0.8302 (t0) REVERT: G 358 ASP cc_start: 0.8691 (p0) cc_final: 0.8077 (p0) REVERT: H 295 ASP cc_start: 0.8725 (m-30) cc_final: 0.8458 (m-30) REVERT: H 336 GLN cc_start: 0.8725 (mp10) cc_final: 0.8509 (mp10) REVERT: H 345 ASP cc_start: 0.8404 (t0) cc_final: 0.8158 (t0) REVERT: H 358 ASP cc_start: 0.8968 (p0) cc_final: 0.8314 (p0) REVERT: I 286 ASN cc_start: 0.8663 (t0) cc_final: 0.8378 (t0) REVERT: I 338 GLU cc_start: 0.8260 (tt0) cc_final: 0.7891 (mp0) REVERT: I 359 ASN cc_start: 0.9065 (t0) cc_final: 0.8522 (t0) REVERT: J 316 SER cc_start: 0.9143 (p) cc_final: 0.8864 (p) REVERT: J 338 GLU cc_start: 0.8353 (mp0) cc_final: 0.8005 (mp0) REVERT: J 349 ARG cc_start: 0.8198 (mtp180) cc_final: 0.6847 (mmt-90) REVERT: J 351 GLN cc_start: 0.8980 (pt0) cc_final: 0.7341 (mm-40) outliers start: 20 outliers final: 16 residues processed: 275 average time/residue: 0.0791 time to fit residues: 30.9031 Evaluate side-chains 254 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 238 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain I residue 344 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 43 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 359 ASN ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 279 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.120337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.101844 restraints weight = 11953.258| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.28 r_work: 0.3571 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 8230 Z= 0.309 Angle : 0.622 5.823 10990 Z= 0.320 Chirality : 0.051 0.125 1230 Planarity : 0.004 0.026 1410 Dihedral : 5.647 17.003 1100 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.69 % Allowed : 12.58 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 349 TYR 0.011 0.002 TYR C 310 PHE 0.012 0.001 PHE J 378 HIS 0.005 0.001 HIS G 299 Details of bonding type rmsd covalent geometry : bond 0.00734 ( 8230) covalent geometry : angle 0.62194 (10990) hydrogen bonds : bond 0.02200 ( 141) hydrogen bonds : angle 4.71865 ( 423) *********************** 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 283 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 258 time to evaluate : 0.408 Fit side-chains REVERT: A 338 GLU cc_start: 0.7934 (tt0) cc_final: 0.7733 (mp0) REVERT: A 345 ASP cc_start: 0.8544 (t0) cc_final: 0.8290 (t0) REVERT: A 358 ASP cc_start: 0.8998 (p0) cc_final: 0.8430 (p0) REVERT: B 338 GLU cc_start: 0.8191 (tt0) cc_final: 0.7990 (mp0) REVERT: B 349 ARG cc_start: 0.8148 (mtp180) cc_final: 0.7870 (ttm110) REVERT: B 358 ASP cc_start: 0.9089 (p0) cc_final: 0.8468 (p0) REVERT: C 336 GLN cc_start: 0.8712 (mp10) cc_final: 0.8333 (mp10) REVERT: C 349 ARG cc_start: 0.8562 (mtp180) cc_final: 0.6530 (ppt170) REVERT: C 358 ASP cc_start: 0.8783 (p0) cc_final: 0.8515 (p0) REVERT: D 276 GLN cc_start: 0.8444 (tt0) cc_final: 0.8239 (tt0) REVERT: D 295 ASP cc_start: 0.8490 (m-30) cc_final: 0.7898 (m-30) REVERT: D 358 ASP cc_start: 0.8620 (p0) cc_final: 0.7973 (p0) REVERT: E 295 ASP cc_start: 0.8162 (m-30) cc_final: 0.7828 (m-30) REVERT: E 314 ASP cc_start: 0.9199 (t0) cc_final: 0.8997 (t0) REVERT: E 338 GLU cc_start: 0.8302 (mp0) cc_final: 0.7972 (mp0) REVERT: E 342 GLU cc_start: 0.4835 (pm20) cc_final: 0.4335 (pm20) REVERT: F 279 ASN cc_start: 0.9148 (m-40) cc_final: 0.8930 (m110) REVERT: F 295 ASP cc_start: 0.8612 (m-30) cc_final: 0.8059 (m-30) REVERT: F 349 ARG cc_start: 0.8260 (mtp180) cc_final: 0.7892 (ttp-110) REVERT: F 358 ASP cc_start: 0.8733 (p0) cc_final: 0.8067 (p0) REVERT: G 345 ASP cc_start: 0.8588 (t0) cc_final: 0.8302 (t0) REVERT: G 356 SER cc_start: 0.8295 (t) cc_final: 0.7636 (m) REVERT: G 358 ASP cc_start: 0.8673 (p0) cc_final: 0.7791 (p0) REVERT: H 336 GLN cc_start: 0.8696 (mp10) cc_final: 0.8296 (mp10) REVERT: H 358 ASP cc_start: 0.9100 (p0) cc_final: 0.8464 (p0) REVERT: H 379 ARG cc_start: 0.7215 (mtt180) cc_final: 0.6859 (pmt-80) REVERT: I 314 ASP cc_start: 0.9281 (t0) cc_final: 0.8966 (t0) REVERT: I 338 GLU cc_start: 0.8179 (tt0) cc_final: 0.7846 (mp0) REVERT: J 338 GLU cc_start: 0.8424 (mp0) cc_final: 0.8038 (mp0) REVERT: J 345 ASP cc_start: 0.8391 (t0) cc_final: 0.8088 (t0) REVERT: J 349 ARG cc_start: 0.8230 (mtp180) cc_final: 0.6810 (mmt-90) REVERT: J 351 GLN cc_start: 0.9024 (pt0) cc_final: 0.7014 (tp-100) outliers start: 25 outliers final: 21 residues processed: 274 average time/residue: 0.0920 time to fit residues: 34.2676 Evaluate side-chains 259 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 238 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 342 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.122980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.104600 restraints weight = 12008.186| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.32 r_work: 0.3612 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8230 Z= 0.208 Angle : 0.583 7.343 10990 Z= 0.288 Chirality : 0.050 0.122 1230 Planarity : 0.003 0.027 1410 Dihedral : 5.348 15.960 1100 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.01 % Allowed : 12.47 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.28 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 349 TYR 0.013 0.001 TYR C 310 PHE 0.010 0.001 PHE E 378 HIS 0.003 0.001 HIS E 299 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 8230) covalent geometry : angle 0.58250 (10990) hydrogen bonds : bond 0.01719 ( 141) hydrogen bonds : angle 4.46167 ( 423) *********************** 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 281 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 253 time to evaluate : 0.335 Fit side-chains REVERT: A 338 GLU cc_start: 0.7917 (tt0) cc_final: 0.7698 (mp0) REVERT: A 358 ASP cc_start: 0.8855 (p0) cc_final: 0.8134 (p0) REVERT: B 338 GLU cc_start: 0.8046 (tt0) cc_final: 0.7806 (mp0) REVERT: B 348 ASP cc_start: 0.8557 (m-30) cc_final: 0.8331 (m-30) REVERT: B 349 ARG cc_start: 0.8166 (mtp180) cc_final: 0.7855 (ttm110) REVERT: B 358 ASP cc_start: 0.9148 (p0) cc_final: 0.8325 (p0) REVERT: C 336 GLN cc_start: 0.8815 (mp10) cc_final: 0.8179 (mp10) REVERT: C 338 GLU cc_start: 0.8106 (mp0) cc_final: 0.7889 (mp0) REVERT: C 349 ARG cc_start: 0.8533 (mtp180) cc_final: 0.6543 (ppt170) REVERT: C 358 ASP cc_start: 0.8688 (p0) cc_final: 0.8463 (p0) REVERT: D 295 ASP cc_start: 0.8447 (m-30) cc_final: 0.8139 (m-30) REVERT: D 349 ARG cc_start: 0.8759 (ttp-110) cc_final: 0.8473 (ttp-110) REVERT: D 358 ASP cc_start: 0.8727 (p0) cc_final: 0.8085 (p0) REVERT: E 295 ASP cc_start: 0.8184 (m-30) cc_final: 0.7922 (m-30) REVERT: E 342 GLU cc_start: 0.4945 (pm20) cc_final: 0.4307 (pm20) REVERT: E 351 GLN cc_start: 0.5571 (mm110) cc_final: 0.4282 (pt0) REVERT: F 295 ASP cc_start: 0.8595 (m-30) cc_final: 0.8392 (m-30) REVERT: F 336 GLN cc_start: 0.9048 (mp10) cc_final: 0.8432 (mp10) REVERT: F 349 ARG cc_start: 0.8221 (mtp180) cc_final: 0.7861 (ttp-110) REVERT: F 358 ASP cc_start: 0.8866 (p0) cc_final: 0.8216 (p0) REVERT: G 336 GLN cc_start: 0.8980 (mp10) cc_final: 0.8431 (mp10) REVERT: G 345 ASP cc_start: 0.8639 (t0) cc_final: 0.8428 (t0) REVERT: G 358 ASP cc_start: 0.8765 (p0) cc_final: 0.7978 (p0) REVERT: H 295 ASP cc_start: 0.8592 (m-30) cc_final: 0.8109 (m-30) REVERT: H 336 GLN cc_start: 0.8772 (mp10) cc_final: 0.8245 (mp10) REVERT: H 358 ASP cc_start: 0.9039 (p0) cc_final: 0.8348 (p0) REVERT: I 314 ASP cc_start: 0.9306 (t0) cc_final: 0.9081 (t0) REVERT: I 338 GLU cc_start: 0.8140 (tt0) cc_final: 0.7859 (mp0) REVERT: I 358 ASP cc_start: 0.8855 (p0) cc_final: 0.8279 (p0) REVERT: J 338 GLU cc_start: 0.8449 (mp0) cc_final: 0.8044 (mp0) REVERT: J 345 ASP cc_start: 0.8459 (t0) cc_final: 0.8052 (t0) REVERT: J 349 ARG cc_start: 0.8277 (mtp180) cc_final: 0.6874 (mmt-90) REVERT: J 351 GLN cc_start: 0.9012 (pt0) cc_final: 0.7007 (tp-100) outliers start: 28 outliers final: 26 residues processed: 270 average time/residue: 0.0881 time to fit residues: 32.1425 Evaluate side-chains 268 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 242 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 348 ASP Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 342 GLU Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 38 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 85 optimal weight: 20.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.123920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.105360 restraints weight = 11828.650| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.28 r_work: 0.3623 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8230 Z= 0.195 Angle : 0.590 8.127 10990 Z= 0.288 Chirality : 0.050 0.121 1230 Planarity : 0.003 0.027 1410 Dihedral : 5.258 15.063 1100 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.90 % Allowed : 13.76 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 349 TYR 0.005 0.001 TYR A 310 PHE 0.021 0.001 PHE G 378 HIS 0.003 0.001 HIS E 299 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 8230) covalent geometry : angle 0.58995 (10990) hydrogen bonds : bond 0.01609 ( 141) hydrogen bonds : angle 4.35566 ( 423) *********************** 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 272 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 245 time to evaluate : 0.346 Fit side-chains REVERT: A 338 GLU cc_start: 0.7863 (tt0) cc_final: 0.7656 (mp0) REVERT: A 345 ASP cc_start: 0.8548 (t0) cc_final: 0.8313 (t0) REVERT: A 358 ASP cc_start: 0.8885 (p0) cc_final: 0.8133 (p0) REVERT: B 338 GLU cc_start: 0.8029 (tt0) cc_final: 0.7804 (mp0) REVERT: B 349 ARG cc_start: 0.8211 (mtp180) cc_final: 0.7887 (ttm110) REVERT: B 358 ASP cc_start: 0.9046 (p0) cc_final: 0.8220 (p0) REVERT: C 336 GLN cc_start: 0.8789 (mp10) cc_final: 0.8070 (mp10) REVERT: C 338 GLU cc_start: 0.8043 (mp0) cc_final: 0.7741 (mp0) REVERT: C 349 ARG cc_start: 0.8524 (mtp180) cc_final: 0.6554 (ppt170) REVERT: C 358 ASP cc_start: 0.8674 (p0) cc_final: 0.8446 (p0) REVERT: D 295 ASP cc_start: 0.8414 (m-30) cc_final: 0.8109 (m-30) REVERT: D 349 ARG cc_start: 0.8741 (ttp-110) cc_final: 0.8473 (ttp-110) REVERT: D 358 ASP cc_start: 0.8739 (p0) cc_final: 0.8096 (p0) REVERT: E 295 ASP cc_start: 0.8163 (m-30) cc_final: 0.7905 (m-30) REVERT: E 338 GLU cc_start: 0.8259 (mp0) cc_final: 0.7905 (mp0) REVERT: E 342 GLU cc_start: 0.4418 (pm20) cc_final: 0.3812 (pm20) REVERT: E 351 GLN cc_start: 0.5699 (mm110) cc_final: 0.4269 (pt0) REVERT: F 336 GLN cc_start: 0.9032 (mp10) cc_final: 0.8749 (mp10) REVERT: F 349 ARG cc_start: 0.8197 (mtp180) cc_final: 0.7786 (mtm-85) REVERT: F 358 ASP cc_start: 0.8823 (p0) cc_final: 0.8172 (p0) REVERT: G 345 ASP cc_start: 0.8621 (t0) cc_final: 0.8364 (t0) REVERT: G 358 ASP cc_start: 0.8793 (p0) cc_final: 0.7969 (p0) REVERT: H 295 ASP cc_start: 0.8602 (m-30) cc_final: 0.8122 (m-30) REVERT: H 336 GLN cc_start: 0.8754 (mp10) cc_final: 0.8225 (mp10) REVERT: H 358 ASP cc_start: 0.9039 (p0) cc_final: 0.8357 (p0) REVERT: I 295 ASP cc_start: 0.8670 (m-30) cc_final: 0.8466 (m-30) REVERT: I 338 GLU cc_start: 0.8125 (tt0) cc_final: 0.7864 (mp0) REVERT: I 358 ASP cc_start: 0.8830 (p0) cc_final: 0.8266 (p0) REVERT: J 338 GLU cc_start: 0.8416 (mp0) cc_final: 0.8012 (mp0) REVERT: J 345 ASP cc_start: 0.8569 (t0) cc_final: 0.8143 (t0) REVERT: J 349 ARG cc_start: 0.8279 (mtp180) cc_final: 0.6863 (mmp-170) REVERT: J 351 GLN cc_start: 0.8950 (pt0) cc_final: 0.6974 (tp-100) REVERT: J 379 ARG cc_start: 0.6798 (tpt90) cc_final: 0.5737 (tpp-160) outliers start: 27 outliers final: 26 residues processed: 262 average time/residue: 0.0909 time to fit residues: 32.4334 Evaluate side-chains 266 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 240 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 342 GLU Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 34 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 78 optimal weight: 0.2980 chunk 23 optimal weight: 0.7980 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.121599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.103218 restraints weight = 11866.973| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.27 r_work: 0.3593 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 8230 Z= 0.256 Angle : 0.627 8.454 10990 Z= 0.309 Chirality : 0.051 0.126 1230 Planarity : 0.003 0.030 1410 Dihedral : 5.431 15.894 1100 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.33 % Allowed : 13.76 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 379 TYR 0.015 0.001 TYR C 310 PHE 0.023 0.001 PHE G 378 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00601 ( 8230) covalent geometry : angle 0.62704 (10990) hydrogen bonds : bond 0.01769 ( 141) hydrogen bonds : angle 4.45823 ( 423) *********************** 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 273 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 242 time to evaluate : 0.342 Fit side-chains REVERT: A 338 GLU cc_start: 0.7897 (tt0) cc_final: 0.7654 (mp0) REVERT: A 358 ASP cc_start: 0.8880 (p0) cc_final: 0.8172 (p0) REVERT: B 338 GLU cc_start: 0.8037 (tt0) cc_final: 0.7823 (mp0) REVERT: B 349 ARG cc_start: 0.8212 (mtp180) cc_final: 0.7891 (ttm110) REVERT: B 358 ASP cc_start: 0.8989 (p0) cc_final: 0.8163 (p0) REVERT: C 336 GLN cc_start: 0.8749 (mp10) cc_final: 0.8382 (mp10) REVERT: C 338 GLU cc_start: 0.8158 (mp0) cc_final: 0.7792 (mp0) REVERT: C 349 ARG cc_start: 0.8556 (mtp180) cc_final: 0.6371 (ppt170) REVERT: C 358 ASP cc_start: 0.8700 (p0) cc_final: 0.8481 (p0) REVERT: D 295 ASP cc_start: 0.8426 (m-30) cc_final: 0.8121 (m-30) REVERT: D 358 ASP cc_start: 0.8675 (p0) cc_final: 0.8018 (p0) REVERT: D 379 ARG cc_start: 0.7041 (mtt180) cc_final: 0.6743 (tpt90) REVERT: E 295 ASP cc_start: 0.8163 (m-30) cc_final: 0.7880 (m-30) REVERT: E 338 GLU cc_start: 0.8389 (mp0) cc_final: 0.7961 (mp0) REVERT: E 351 GLN cc_start: 0.5804 (mm110) cc_final: 0.4114 (pt0) REVERT: F 336 GLN cc_start: 0.9061 (mp10) cc_final: 0.8756 (mp10) REVERT: F 349 ARG cc_start: 0.8207 (mtp180) cc_final: 0.7795 (mtm-85) REVERT: F 358 ASP cc_start: 0.8825 (p0) cc_final: 0.8096 (p0) REVERT: G 288 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.7810 (mm-40) REVERT: G 336 GLN cc_start: 0.9007 (mp10) cc_final: 0.8601 (mp10) REVERT: G 345 ASP cc_start: 0.8765 (t0) cc_final: 0.8461 (t0) REVERT: G 358 ASP cc_start: 0.8799 (p0) cc_final: 0.8009 (p0) REVERT: H 336 GLN cc_start: 0.8683 (mp10) cc_final: 0.8306 (mp10) REVERT: H 358 ASP cc_start: 0.9043 (p0) cc_final: 0.8356 (p0) REVERT: I 338 GLU cc_start: 0.8140 (tt0) cc_final: 0.7870 (mp0) REVERT: I 345 ASP cc_start: 0.8500 (t0) cc_final: 0.8294 (t0) REVERT: I 358 ASP cc_start: 0.8981 (p0) cc_final: 0.8444 (p0) REVERT: J 338 GLU cc_start: 0.8431 (mp0) cc_final: 0.8029 (mp0) REVERT: J 345 ASP cc_start: 0.8596 (t0) cc_final: 0.8153 (t0) REVERT: J 349 ARG cc_start: 0.8283 (mtp180) cc_final: 0.6765 (mmp-170) REVERT: J 351 GLN cc_start: 0.9051 (pt0) cc_final: 0.7172 (tp-100) REVERT: J 379 ARG cc_start: 0.6800 (tpt90) cc_final: 0.5993 (tpp-160) outliers start: 31 outliers final: 29 residues processed: 261 average time/residue: 0.0915 time to fit residues: 32.5661 Evaluate side-chains 268 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 238 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain G residue 288 GLN Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain I residue 348 ASP Chi-restraints excluded: chain I residue 351 GLN Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 30 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 96 optimal weight: 0.0980 chunk 33 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 65 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.124250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.106044 restraints weight = 11991.510| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.29 r_work: 0.3640 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8230 Z= 0.174 Angle : 0.601 8.825 10990 Z= 0.290 Chirality : 0.050 0.123 1230 Planarity : 0.003 0.027 1410 Dihedral : 5.183 14.949 1100 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.23 % Allowed : 14.09 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 379 TYR 0.014 0.001 TYR C 310 PHE 0.018 0.001 PHE G 378 HIS 0.003 0.001 HIS E 299 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 8230) covalent geometry : angle 0.60066 (10990) hydrogen bonds : bond 0.01488 ( 141) hydrogen bonds : angle 4.25124 ( 423) *********************** 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 277 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 247 time to evaluate : 0.334 Fit side-chains REVERT: A 338 GLU cc_start: 0.7890 (tt0) cc_final: 0.7641 (mp0) REVERT: A 358 ASP cc_start: 0.8888 (p0) cc_final: 0.8112 (p0) REVERT: B 288 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.7771 (mm-40) REVERT: B 338 GLU cc_start: 0.8064 (tt0) cc_final: 0.7861 (mp0) REVERT: B 349 ARG cc_start: 0.8199 (mtp180) cc_final: 0.7872 (ttm110) REVERT: B 358 ASP cc_start: 0.8986 (p0) cc_final: 0.8179 (p0) REVERT: C 336 GLN cc_start: 0.8773 (mp10) cc_final: 0.8399 (mp10) REVERT: C 338 GLU cc_start: 0.8129 (mp0) cc_final: 0.7755 (mp0) REVERT: C 349 ARG cc_start: 0.8527 (mtp180) cc_final: 0.6376 (ppt170) REVERT: C 358 ASP cc_start: 0.8650 (p0) cc_final: 0.8431 (p0) REVERT: D 295 ASP cc_start: 0.8416 (m-30) cc_final: 0.8123 (m-30) REVERT: D 358 ASP cc_start: 0.8834 (p0) cc_final: 0.8182 (p0) REVERT: D 379 ARG cc_start: 0.7006 (mtt180) cc_final: 0.6729 (tpt90) REVERT: E 295 ASP cc_start: 0.8181 (m-30) cc_final: 0.7925 (m-30) REVERT: E 351 GLN cc_start: 0.5760 (mm110) cc_final: 0.4014 (pt0) REVERT: F 336 GLN cc_start: 0.9040 (mp10) cc_final: 0.8695 (mp10) REVERT: F 349 ARG cc_start: 0.8224 (mtp180) cc_final: 0.7825 (mtm-85) REVERT: F 358 ASP cc_start: 0.8827 (p0) cc_final: 0.8093 (p0) REVERT: G 288 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.7812 (mm-40) REVERT: G 336 GLN cc_start: 0.8984 (mp10) cc_final: 0.8392 (mp10) REVERT: G 345 ASP cc_start: 0.8576 (t0) cc_final: 0.8257 (t0) REVERT: G 358 ASP cc_start: 0.8796 (p0) cc_final: 0.7947 (p0) REVERT: H 295 ASP cc_start: 0.8616 (m-30) cc_final: 0.8159 (m-30) REVERT: H 336 GLN cc_start: 0.8738 (mp10) cc_final: 0.8133 (mp10) REVERT: H 358 ASP cc_start: 0.9009 (p0) cc_final: 0.8315 (p0) REVERT: I 338 GLU cc_start: 0.8100 (tt0) cc_final: 0.7873 (mp0) REVERT: I 345 ASP cc_start: 0.8473 (t0) cc_final: 0.8250 (t0) REVERT: I 358 ASP cc_start: 0.8983 (p0) cc_final: 0.8438 (p0) REVERT: J 338 GLU cc_start: 0.8395 (mp0) cc_final: 0.8039 (mp0) REVERT: J 345 ASP cc_start: 0.8582 (t0) cc_final: 0.8107 (t0) REVERT: J 349 ARG cc_start: 0.8276 (mtp180) cc_final: 0.6748 (mmp-170) REVERT: J 351 GLN cc_start: 0.9005 (pt0) cc_final: 0.6957 (tp-100) outliers start: 30 outliers final: 27 residues processed: 266 average time/residue: 0.0887 time to fit residues: 32.1769 Evaluate side-chains 266 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 237 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain G residue 288 GLN Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain I residue 351 GLN Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 342 GLU Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 90 optimal weight: 10.0000 chunk 80 optimal weight: 0.4980 chunk 9 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.123864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.105708 restraints weight = 11832.114| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.27 r_work: 0.3638 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8230 Z= 0.184 Angle : 0.620 8.513 10990 Z= 0.299 Chirality : 0.050 0.123 1230 Planarity : 0.003 0.027 1410 Dihedral : 5.172 14.907 1100 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.44 % Allowed : 14.84 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.33 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 379 TYR 0.005 0.001 TYR A 310 PHE 0.017 0.001 PHE G 378 HIS 0.003 0.001 HIS E 299 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 8230) covalent geometry : angle 0.62040 (10990) hydrogen bonds : bond 0.01505 ( 141) hydrogen bonds : angle 4.21687 ( 423) *********************** 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 269 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 237 time to evaluate : 0.344 Fit side-chains REVERT: A 338 GLU cc_start: 0.7867 (tt0) cc_final: 0.7649 (mp0) REVERT: A 358 ASP cc_start: 0.8898 (p0) cc_final: 0.8107 (p0) REVERT: B 288 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.7771 (mm-40) REVERT: B 349 ARG cc_start: 0.8210 (mtp180) cc_final: 0.7870 (ttm110) REVERT: B 358 ASP cc_start: 0.8997 (p0) cc_final: 0.8188 (p0) REVERT: C 336 GLN cc_start: 0.8789 (mp10) cc_final: 0.8410 (mp10) REVERT: C 338 GLU cc_start: 0.8147 (mp0) cc_final: 0.7768 (mp0) REVERT: C 349 ARG cc_start: 0.8536 (mtp180) cc_final: 0.6353 (ppt170) REVERT: C 358 ASP cc_start: 0.8648 (p0) cc_final: 0.8422 (p0) REVERT: D 295 ASP cc_start: 0.8407 (m-30) cc_final: 0.8110 (m-30) REVERT: D 351 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8554 (pt0) REVERT: D 358 ASP cc_start: 0.8826 (p0) cc_final: 0.8215 (p0) REVERT: D 379 ARG cc_start: 0.7083 (mtt180) cc_final: 0.6741 (tpt90) REVERT: E 295 ASP cc_start: 0.8179 (m-30) cc_final: 0.7932 (m-30) REVERT: E 338 GLU cc_start: 0.8363 (mp0) cc_final: 0.8140 (mp0) REVERT: E 351 GLN cc_start: 0.5844 (mm110) cc_final: 0.3979 (pt0) REVERT: F 336 GLN cc_start: 0.9039 (mp10) cc_final: 0.8704 (mp10) REVERT: F 345 ASP cc_start: 0.8508 (t0) cc_final: 0.8269 (t0) REVERT: F 349 ARG cc_start: 0.8228 (mtp180) cc_final: 0.7826 (mtm-85) REVERT: F 358 ASP cc_start: 0.8838 (p0) cc_final: 0.8107 (p0) REVERT: G 288 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.7823 (mm-40) REVERT: G 345 ASP cc_start: 0.8584 (t0) cc_final: 0.8239 (t0) REVERT: G 358 ASP cc_start: 0.8817 (p0) cc_final: 0.7956 (p0) REVERT: G 379 ARG cc_start: 0.6973 (mtt180) cc_final: 0.6666 (tpt90) REVERT: H 295 ASP cc_start: 0.8791 (m-30) cc_final: 0.8350 (m-30) REVERT: H 336 GLN cc_start: 0.8742 (mp10) cc_final: 0.8148 (mp10) REVERT: H 358 ASP cc_start: 0.9017 (p0) cc_final: 0.8269 (p0) REVERT: I 338 GLU cc_start: 0.8102 (tt0) cc_final: 0.7860 (mp0) REVERT: I 345 ASP cc_start: 0.8484 (t0) cc_final: 0.8235 (t0) REVERT: I 358 ASP cc_start: 0.8992 (p0) cc_final: 0.8445 (p0) REVERT: J 338 GLU cc_start: 0.8380 (mp0) cc_final: 0.8023 (mp0) REVERT: J 345 ASP cc_start: 0.8583 (t0) cc_final: 0.8119 (t0) REVERT: J 349 ARG cc_start: 0.8279 (mtp180) cc_final: 0.6750 (mmp-170) REVERT: J 351 GLN cc_start: 0.8996 (pt0) cc_final: 0.7123 (tp-100) outliers start: 32 outliers final: 26 residues processed: 257 average time/residue: 0.0860 time to fit residues: 30.3210 Evaluate side-chains 263 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 234 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain G residue 288 GLN Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 351 GLN Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 342 GLU Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 30 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.124839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.106691 restraints weight = 11820.208| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.27 r_work: 0.3653 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8230 Z= 0.166 Angle : 0.626 8.697 10990 Z= 0.301 Chirality : 0.050 0.123 1230 Planarity : 0.003 0.026 1410 Dihedral : 5.100 14.784 1100 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.90 % Allowed : 15.27 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.33 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 379 TYR 0.015 0.001 TYR C 310 PHE 0.017 0.001 PHE D 378 HIS 0.003 0.001 HIS E 299 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 8230) covalent geometry : angle 0.62631 (10990) hydrogen bonds : bond 0.01429 ( 141) hydrogen bonds : angle 4.13007 ( 423) *********************** 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 272 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 245 time to evaluate : 0.336 Fit side-chains REVERT: A 338 GLU cc_start: 0.7877 (tt0) cc_final: 0.7633 (mp0) REVERT: A 358 ASP cc_start: 0.8892 (p0) cc_final: 0.8095 (p0) REVERT: B 279 ASN cc_start: 0.9088 (m-40) cc_final: 0.8843 (m110) REVERT: B 288 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.7784 (mm-40) REVERT: B 349 ARG cc_start: 0.8197 (mtp180) cc_final: 0.7855 (ttm110) REVERT: B 358 ASP cc_start: 0.8993 (p0) cc_final: 0.8187 (p0) REVERT: C 336 GLN cc_start: 0.8786 (mp10) cc_final: 0.8049 (mp10) REVERT: C 338 GLU cc_start: 0.8122 (mp0) cc_final: 0.7767 (mp0) REVERT: C 349 ARG cc_start: 0.8534 (mtp180) cc_final: 0.6350 (ppt170) REVERT: C 358 ASP cc_start: 0.8473 (p0) cc_final: 0.8268 (p0) REVERT: D 295 ASP cc_start: 0.8401 (m-30) cc_final: 0.8126 (m-30) REVERT: D 358 ASP cc_start: 0.8828 (p0) cc_final: 0.8213 (p0) REVERT: D 379 ARG cc_start: 0.7093 (mtt180) cc_final: 0.6736 (tpt90) REVERT: E 295 ASP cc_start: 0.7644 (m-30) cc_final: 0.7412 (m-30) REVERT: E 338 GLU cc_start: 0.8387 (mp0) cc_final: 0.8067 (mp0) REVERT: E 351 GLN cc_start: 0.5840 (mm110) cc_final: 0.3913 (pt0) REVERT: F 336 GLN cc_start: 0.9035 (mp10) cc_final: 0.8679 (mp10) REVERT: F 349 ARG cc_start: 0.8220 (mtp180) cc_final: 0.7971 (ttp-170) REVERT: F 358 ASP cc_start: 0.8842 (p0) cc_final: 0.8093 (p0) REVERT: G 288 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.7797 (mm-40) REVERT: G 306 VAL cc_start: 0.9140 (t) cc_final: 0.8887 (p) REVERT: G 336 GLN cc_start: 0.8921 (mp10) cc_final: 0.8440 (mp10) REVERT: G 345 ASP cc_start: 0.8582 (t0) cc_final: 0.8213 (t0) REVERT: G 358 ASP cc_start: 0.8820 (p0) cc_final: 0.7936 (p0) REVERT: G 379 ARG cc_start: 0.6930 (mtt180) cc_final: 0.6660 (tpt90) REVERT: H 295 ASP cc_start: 0.8620 (m-30) cc_final: 0.8162 (m-30) REVERT: H 336 GLN cc_start: 0.8718 (mp10) cc_final: 0.8086 (mp10) REVERT: H 358 ASP cc_start: 0.9006 (p0) cc_final: 0.8298 (p0) REVERT: I 338 GLU cc_start: 0.8063 (tt0) cc_final: 0.7836 (mp0) REVERT: I 345 ASP cc_start: 0.8495 (t0) cc_final: 0.8216 (t0) REVERT: I 358 ASP cc_start: 0.8993 (p0) cc_final: 0.8450 (p0) REVERT: J 338 GLU cc_start: 0.8397 (mp0) cc_final: 0.8034 (mp0) REVERT: J 345 ASP cc_start: 0.8580 (t0) cc_final: 0.8091 (t0) REVERT: J 349 ARG cc_start: 0.8273 (mtp180) cc_final: 0.6818 (tpm170) REVERT: J 351 GLN cc_start: 0.8932 (pt0) cc_final: 0.7101 (tp-100) outliers start: 27 outliers final: 24 residues processed: 263 average time/residue: 0.0875 time to fit residues: 31.6326 Evaluate side-chains 268 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 242 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain G residue 288 GLN Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 351 GLN Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 342 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 13 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN D 351 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.118668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.100470 restraints weight = 12117.410| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.25 r_work: 0.3555 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.058 8230 Z= 0.390 Angle : 0.732 8.229 10990 Z= 0.366 Chirality : 0.053 0.131 1230 Planarity : 0.004 0.037 1410 Dihedral : 5.661 17.089 1100 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.90 % Allowed : 15.38 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.48 (0.19), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 379 TYR 0.006 0.002 TYR C 310 PHE 0.024 0.002 PHE G 378 HIS 0.005 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00910 ( 8230) covalent geometry : angle 0.73184 (10990) hydrogen bonds : bond 0.02072 ( 141) hydrogen bonds : angle 4.59659 ( 423) ********************** 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 269 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 242 time to evaluate : 0.398 Fit side-chains REVERT: A 358 ASP cc_start: 0.8890 (p0) cc_final: 0.8259 (p0) REVERT: B 279 ASN cc_start: 0.9157 (m-40) cc_final: 0.8882 (m110) REVERT: B 288 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.7853 (mm-40) REVERT: B 358 ASP cc_start: 0.8928 (p0) cc_final: 0.8091 (p0) REVERT: C 336 GLN cc_start: 0.8809 (mp10) cc_final: 0.8414 (mp10) REVERT: C 349 ARG cc_start: 0.8502 (mtp180) cc_final: 0.6253 (ppt170) REVERT: C 358 ASP cc_start: 0.8744 (p0) cc_final: 0.8507 (p0) REVERT: D 295 ASP cc_start: 0.8449 (m-30) cc_final: 0.8155 (m-30) REVERT: D 351 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8541 (pt0) REVERT: D 358 ASP cc_start: 0.8752 (p0) cc_final: 0.8072 (p0) REVERT: D 379 ARG cc_start: 0.7028 (mtt180) cc_final: 0.6701 (tpt90) REVERT: F 336 GLN cc_start: 0.9026 (mp10) cc_final: 0.8693 (mp10) REVERT: F 349 ARG cc_start: 0.8271 (mtp180) cc_final: 0.7830 (mtm-85) REVERT: F 358 ASP cc_start: 0.8665 (p0) cc_final: 0.7909 (p0) REVERT: G 288 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.7805 (mm-40) REVERT: G 336 GLN cc_start: 0.9015 (mp10) cc_final: 0.8647 (mp10) REVERT: G 345 ASP cc_start: 0.8776 (t0) cc_final: 0.8387 (t0) REVERT: G 356 SER cc_start: 0.8383 (t) cc_final: 0.7671 (m) REVERT: G 358 ASP cc_start: 0.8812 (p0) cc_final: 0.7905 (p0) REVERT: G 379 ARG cc_start: 0.7058 (mtt180) cc_final: 0.6832 (tpt90) REVERT: H 336 GLN cc_start: 0.8633 (mp10) cc_final: 0.8167 (mp10) REVERT: H 358 ASP cc_start: 0.9008 (p0) cc_final: 0.8343 (p0) REVERT: I 338 GLU cc_start: 0.8165 (tt0) cc_final: 0.7868 (mp0) REVERT: I 358 ASP cc_start: 0.9065 (p0) cc_final: 0.8554 (p0) REVERT: J 338 GLU cc_start: 0.8434 (mp0) cc_final: 0.8011 (mp0) REVERT: J 345 ASP cc_start: 0.8605 (t0) cc_final: 0.8187 (t0) REVERT: J 349 ARG cc_start: 0.8256 (mtp180) cc_final: 0.6743 (mmp-170) REVERT: J 351 GLN cc_start: 0.9085 (pt0) cc_final: 0.7190 (tp-100) outliers start: 27 outliers final: 22 residues processed: 261 average time/residue: 0.0872 time to fit residues: 31.2840 Evaluate side-chains 264 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 239 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain G residue 288 GLN Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 51 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN D 279 ASN D 351 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.123234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.105247 restraints weight = 11954.042| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.26 r_work: 0.3627 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8230 Z= 0.183 Angle : 0.657 8.549 10990 Z= 0.317 Chirality : 0.050 0.124 1230 Planarity : 0.003 0.030 1410 Dihedral : 5.272 14.879 1100 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.01 % Allowed : 15.27 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.42 (0.19), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 379 TYR 0.004 0.001 TYR C 310 PHE 0.020 0.001 PHE G 378 HIS 0.003 0.001 HIS E 299 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 8230) covalent geometry : angle 0.65733 (10990) hydrogen bonds : bond 0.01510 ( 141) hydrogen bonds : angle 4.24698 ( 423) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2159.42 seconds wall clock time: 38 minutes 2.35 seconds (2282.35 seconds total)