Starting phenix.real_space_refine on Wed Mar 12 17:24:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p67_13220/03_2025/7p67_13220.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p67_13220/03_2025/7p67_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_2025/7p67_13220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p67_13220/03_2025/7p67_13220.map" model { file = "/net/cci-nas-00/data/ceres_data/7p67_13220/03_2025/7p67_13220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p67_13220/03_2025/7p67_13220.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 5060 2.51 5 N 1520 2.21 5 O 1520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8120 Number of models: 1 Model: "" Number of chains: 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: C, B, E, D, G, F, I, H, J Time building chain proxies: 3.19, per 1000 atoms: 0.39 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: 1.75 Conformation dependent library (CDL) restraints added in 1.2 seconds 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1860 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 27 sheets defined 0.0% alpha, 47.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 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: 2.24 Time building geometry restraints manager: 2.12 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' 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: 4.230 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.120 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.070 ------------------------------------------------------------------------------- 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= 0.472 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 : 3.61 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (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 HIS 0.003 0.001 HIS J 299 PHE 0.003 0.001 PHE G 346 TYR 0.007 0.002 TYR I 310 ARG 0.001 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.986 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: 0.7799 (t0) REVERT: F 316 SER cc_start: 0.9026 (p) cc_final: 0.8717 (p) REVERT: G 316 SER cc_start: 0.8892 (p) cc_final: 0.8687 (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: 0.8217 (pt0) cc_final: 0.7838 (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: 0.1762 time to fit residues: 75.5477 Evaluate side-chains 261 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 90 optimal weight: 0.3980 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN ** F 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 = 0.4010 r_free = 0.4010 target = 0.124785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.106061 restraints weight = 11744.465| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.32 r_work: 0.3627 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8230 Z= 0.345 Angle : 0.579 6.311 10990 Z= 0.297 Chirality : 0.050 0.122 1230 Planarity : 0.003 0.021 1410 Dihedral : 5.367 16.280 1100 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.26 % Allowed : 10.11 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (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 HIS 0.004 0.001 HIS F 299 PHE 0.007 0.001 PHE B 346 TYR 0.012 0.002 TYR C 310 ARG 0.003 0.000 ARG I 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 268 time to evaluate : 0.955 Fit side-chains REVERT: A 295 ASP cc_start: 0.8598 (m-30) cc_final: 0.8214 (m-30) REVERT: A 336 GLN cc_start: 0.8740 (mp10) cc_final: 0.8392 (mp10) REVERT: A 345 ASP cc_start: 0.8528 (t0) cc_final: 0.8282 (t0) REVERT: A 358 ASP cc_start: 0.9060 (p0) cc_final: 0.8680 (p0) REVERT: B 336 GLN cc_start: 0.8629 (mp10) cc_final: 0.8386 (mp10) REVERT: B 345 ASP cc_start: 0.8544 (t0) cc_final: 0.8227 (t0) REVERT: B 358 ASP cc_start: 0.9025 (p0) cc_final: 0.8403 (p0) REVERT: C 336 GLN cc_start: 0.8771 (mp10) cc_final: 0.8515 (mp10) REVERT: C 338 GLU cc_start: 0.8232 (tt0) cc_final: 0.8026 (tt0) REVERT: C 349 ARG cc_start: 0.8590 (mtp180) cc_final: 0.6477 (ppt170) REVERT: C 358 ASP cc_start: 0.8926 (p0) cc_final: 0.8659 (p0) REVERT: C 379 ARG cc_start: 0.7342 (mtt180) cc_final: 0.6284 (pmt-80) REVERT: D 276 GLN cc_start: 0.8421 (tt0) cc_final: 0.8186 (tt0) REVERT: D 316 SER cc_start: 0.9228 (p) cc_final: 0.8882 (p) REVERT: D 338 GLU cc_start: 0.8016 (tt0) cc_final: 0.7787 (mp0) REVERT: D 345 ASP cc_start: 0.8663 (t0) cc_final: 0.8422 (t0) REVERT: D 358 ASP cc_start: 0.8663 (p0) cc_final: 0.8077 (p0) REVERT: E 351 GLN cc_start: 0.4688 (mm110) cc_final: 0.4330 (tp-100) REVERT: F 295 ASP cc_start: 0.8621 (m-30) cc_final: 0.8071 (m-30) REVERT: F 314 ASP cc_start: 0.9220 (t0) cc_final: 0.8932 (t0) REVERT: F 316 SER cc_start: 0.9371 (p) cc_final: 0.9159 (p) REVERT: F 336 GLN cc_start: 0.8950 (mp10) cc_final: 0.8705 (mp10) REVERT: F 345 ASP cc_start: 0.8550 (t0) cc_final: 0.8323 (t0) REVERT: F 349 ARG cc_start: 0.8224 (mtp180) cc_final: 0.7872 (ttp-110) REVERT: F 359 ASN cc_start: 0.8964 (t0) cc_final: 0.8588 (t0) REVERT: G 295 ASP cc_start: 0.8572 (m-30) cc_final: 0.8172 (m-30) REVERT: G 306 VAL cc_start: 0.9127 (t) cc_final: 0.8893 (p) REVERT: G 345 ASP cc_start: 0.8576 (t0) cc_final: 0.8294 (t0) REVERT: G 356 SER cc_start: 0.8268 (t) cc_final: 0.7618 (m) REVERT: G 358 ASP cc_start: 0.8763 (p0) cc_final: 0.8043 (p0) REVERT: H 295 ASP cc_start: 0.8694 (m-30) cc_final: 0.8441 (m-30) REVERT: H 336 GLN cc_start: 0.8658 (mp10) cc_final: 0.8361 (mp10) REVERT: H 358 ASP cc_start: 0.9004 (p0) cc_final: 0.8287 (p0) REVERT: H 379 ARG cc_start: 0.6876 (mtt180) cc_final: 0.6052 (pmt-80) REVERT: I 295 ASP cc_start: 0.8595 (m-30) cc_final: 0.8299 (m-30) REVERT: I 338 GLU cc_start: 0.8170 (tt0) cc_final: 0.7815 (mp0) REVERT: J 316 SER cc_start: 0.9177 (p) cc_final: 0.8894 (p) REVERT: J 338 GLU cc_start: 0.8384 (mp0) cc_final: 0.8030 (mp0) REVERT: J 349 ARG cc_start: 0.8198 (mtp180) cc_final: 0.6801 (mmt-90) REVERT: J 351 GLN cc_start: 0.9005 (pt0) cc_final: 0.7269 (mm-40) outliers start: 21 outliers final: 18 residues processed: 281 average time/residue: 0.1917 time to fit residues: 72.6800 Evaluate side-chains 260 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 242 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 344 LEU 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 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 36 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 40 optimal weight: 0.0570 chunk 93 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 overall best weight: 0.7504 ------------------------------------------------------------------------------- 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 ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 279 ASN J 279 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.132385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.114057 restraints weight = 11751.873| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.34 r_work: 0.3756 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8230 Z= 0.137 Angle : 0.515 5.725 10990 Z= 0.254 Chirality : 0.050 0.122 1230 Planarity : 0.002 0.018 1410 Dihedral : 4.801 13.725 1100 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.29 % Allowed : 12.90 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (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 HIS 0.003 0.001 HIS E 299 PHE 0.010 0.001 PHE I 378 TYR 0.015 0.001 TYR C 310 ARG 0.003 0.000 ARG I 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 268 time to evaluate : 0.979 Fit side-chains REVERT: A 295 ASP cc_start: 0.8714 (m-30) cc_final: 0.8324 (m-30) REVERT: A 345 ASP cc_start: 0.8593 (t0) cc_final: 0.8151 (t0) REVERT: A 358 ASP cc_start: 0.9132 (p0) cc_final: 0.8571 (p0) REVERT: B 345 ASP cc_start: 0.8544 (t0) cc_final: 0.8197 (t0) REVERT: B 349 ARG cc_start: 0.8142 (mtp180) cc_final: 0.7866 (ttm110) REVERT: B 358 ASP cc_start: 0.8996 (p0) cc_final: 0.8163 (p0) REVERT: C 336 GLN cc_start: 0.8858 (mp10) cc_final: 0.8387 (mp10) REVERT: C 349 ARG cc_start: 0.8516 (mtp180) cc_final: 0.6239 (pmt-80) REVERT: C 358 ASP cc_start: 0.8405 (p0) cc_final: 0.8159 (p0) REVERT: C 379 ARG cc_start: 0.7075 (mtt180) cc_final: 0.6522 (pmt-80) REVERT: D 316 SER cc_start: 0.9268 (p) cc_final: 0.8994 (p) REVERT: E 338 GLU cc_start: 0.8146 (mp0) cc_final: 0.7877 (mp0) REVERT: E 351 GLN cc_start: 0.4672 (mm110) cc_final: 0.4368 (mm-40) REVERT: F 314 ASP cc_start: 0.9278 (t0) cc_final: 0.8967 (t0) REVERT: F 336 GLN cc_start: 0.8870 (mp10) cc_final: 0.8402 (mp10) REVERT: F 345 ASP cc_start: 0.8576 (t0) cc_final: 0.8343 (t0) REVERT: F 349 ARG cc_start: 0.8132 (mtp180) cc_final: 0.7839 (ttp-110) REVERT: F 358 ASP cc_start: 0.8652 (p0) cc_final: 0.8039 (p0) REVERT: F 359 ASN cc_start: 0.9009 (t0) cc_final: 0.8652 (t0) REVERT: G 295 ASP cc_start: 0.8796 (m-30) cc_final: 0.8248 (m-30) REVERT: G 306 VAL cc_start: 0.9134 (t) cc_final: 0.8869 (p) REVERT: G 314 ASP cc_start: 0.9135 (t0) cc_final: 0.8812 (t0) REVERT: G 316 SER cc_start: 0.9157 (p) cc_final: 0.8857 (p) REVERT: G 345 ASP cc_start: 0.8633 (t0) cc_final: 0.8200 (t0) REVERT: G 358 ASP cc_start: 0.8845 (p0) cc_final: 0.7992 (p0) REVERT: H 288 GLN cc_start: 0.7476 (mm-40) cc_final: 0.7102 (mt0) REVERT: H 295 ASP cc_start: 0.8838 (m-30) cc_final: 0.8605 (m-30) REVERT: H 336 GLN cc_start: 0.8668 (mp10) cc_final: 0.8383 (mp10) REVERT: H 358 ASP cc_start: 0.9010 (p0) cc_final: 0.8332 (p0) REVERT: H 379 ARG cc_start: 0.6846 (mtt180) cc_final: 0.6531 (pmt-80) REVERT: I 286 ASN cc_start: 0.8701 (t0) cc_final: 0.8473 (t0) REVERT: I 338 GLU cc_start: 0.8143 (tt0) cc_final: 0.7859 (mp0) REVERT: I 345 ASP cc_start: 0.8414 (t0) cc_final: 0.8146 (t0) REVERT: J 314 ASP cc_start: 0.9119 (t0) cc_final: 0.8909 (t0) REVERT: J 316 SER cc_start: 0.9112 (p) cc_final: 0.8902 (p) REVERT: J 338 GLU cc_start: 0.8297 (mp0) cc_final: 0.7927 (mp0) REVERT: J 345 ASP cc_start: 0.8500 (t0) cc_final: 0.8222 (t0) REVERT: J 349 ARG cc_start: 0.8191 (mtp180) cc_final: 0.6913 (mmt-90) REVERT: J 351 GLN cc_start: 0.9008 (pt0) cc_final: 0.7036 (tp-100) outliers start: 12 outliers final: 11 residues processed: 273 average time/residue: 0.1981 time to fit residues: 72.8152 Evaluate side-chains 254 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 243 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 319 THR Chi-restraints excluded: chain C 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 360 ILE Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain I residue 360 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 79 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 63 optimal weight: 0.1980 chunk 36 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 98 optimal weight: 0.0470 overall best weight: 3.4484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 279 ASN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.123013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.104530 restraints weight = 11846.509| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.28 r_work: 0.3612 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8230 Z= 0.355 Angle : 0.578 6.249 10990 Z= 0.288 Chirality : 0.050 0.125 1230 Planarity : 0.003 0.022 1410 Dihedral : 5.270 15.945 1100 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.80 % Allowed : 13.23 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 299 PHE 0.003 0.001 PHE G 346 TYR 0.008 0.001 TYR D 310 ARG 0.002 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 255 time to evaluate : 1.037 Fit side-chains REVERT: A 338 GLU cc_start: 0.7943 (tt0) cc_final: 0.7740 (mp0) REVERT: A 358 ASP cc_start: 0.8930 (p0) cc_final: 0.8239 (p0) REVERT: B 338 GLU cc_start: 0.8173 (tt0) cc_final: 0.7972 (mp0) REVERT: B 358 ASP cc_start: 0.9129 (p0) cc_final: 0.8272 (p0) REVERT: C 336 GLN cc_start: 0.8772 (mp10) cc_final: 0.8456 (mp10) REVERT: C 349 ARG cc_start: 0.8515 (mtp180) cc_final: 0.6504 (ppt170) REVERT: C 358 ASP cc_start: 0.8720 (p0) cc_final: 0.8452 (p0) REVERT: D 295 ASP cc_start: 0.8494 (m-30) cc_final: 0.7950 (m-30) REVERT: D 358 ASP cc_start: 0.8707 (p0) cc_final: 0.8085 (p0) REVERT: F 295 ASP cc_start: 0.8651 (m-30) cc_final: 0.8120 (m-30) REVERT: F 336 GLN cc_start: 0.9024 (mp10) cc_final: 0.8640 (mp10) REVERT: F 349 ARG cc_start: 0.8238 (mtp180) cc_final: 0.7876 (ttp-110) REVERT: F 358 ASP cc_start: 0.8711 (p0) cc_final: 0.7986 (p0) REVERT: G 295 ASP cc_start: 0.8572 (m-30) cc_final: 0.8230 (m-30) REVERT: G 306 VAL cc_start: 0.9103 (t) cc_final: 0.8823 (p) REVERT: G 336 GLN cc_start: 0.8979 (mp10) cc_final: 0.8494 (mp10) REVERT: G 345 ASP cc_start: 0.8616 (t0) cc_final: 0.8412 (t0) REVERT: G 358 ASP cc_start: 0.8921 (p0) cc_final: 0.8118 (p0) REVERT: H 295 ASP cc_start: 0.8705 (m-30) cc_final: 0.8449 (m-30) REVERT: H 336 GLN cc_start: 0.8774 (mp10) cc_final: 0.8301 (mp10) REVERT: H 358 ASP cc_start: 0.9179 (p0) cc_final: 0.8483 (p0) REVERT: H 379 ARG cc_start: 0.7290 (mtt180) cc_final: 0.6932 (pmt-80) REVERT: I 295 ASP cc_start: 0.8551 (m-30) cc_final: 0.8166 (m-30) REVERT: I 338 GLU cc_start: 0.8142 (tt0) cc_final: 0.7859 (mp0) REVERT: J 316 SER cc_start: 0.9203 (p) cc_final: 0.8971 (p) REVERT: J 338 GLU cc_start: 0.8402 (mp0) cc_final: 0.7995 (mp0) REVERT: J 345 ASP cc_start: 0.8608 (t0) cc_final: 0.8310 (t0) REVERT: J 349 ARG cc_start: 0.8229 (mtp180) cc_final: 0.6798 (mmt-90) REVERT: J 351 GLN cc_start: 0.9023 (pt0) cc_final: 0.7007 (tp-100) outliers start: 26 outliers final: 22 residues processed: 271 average time/residue: 0.1914 time to fit residues: 70.1202 Evaluate side-chains 267 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 245 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 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 360 ILE Chi-restraints excluded: chain J residue 342 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 46 optimal weight: 0.3980 chunk 24 optimal weight: 6.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 276 GLN D 279 ASN ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 276 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.126227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.107917 restraints weight = 11661.228| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.28 r_work: 0.3667 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8230 Z= 0.236 Angle : 0.566 8.870 10990 Z= 0.274 Chirality : 0.050 0.122 1230 Planarity : 0.002 0.020 1410 Dihedral : 5.014 14.773 1100 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.04 % Allowed : 14.95 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 299 PHE 0.015 0.001 PHE A 378 TYR 0.005 0.001 TYR D 310 ARG 0.002 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 247 time to evaluate : 1.026 Fit side-chains REVERT: A 289 SER cc_start: 0.9309 (p) cc_final: 0.9107 (p) REVERT: A 345 ASP cc_start: 0.8574 (t0) cc_final: 0.8236 (t0) REVERT: A 358 ASP cc_start: 0.8971 (p0) cc_final: 0.8213 (p0) REVERT: B 338 GLU cc_start: 0.8084 (tt0) cc_final: 0.7800 (mp0) REVERT: B 349 ARG cc_start: 0.8176 (mtp180) cc_final: 0.7892 (ttm110) REVERT: B 358 ASP cc_start: 0.8980 (p0) cc_final: 0.8105 (p0) REVERT: C 288 GLN cc_start: 0.7640 (mm-40) cc_final: 0.7299 (mt0) REVERT: C 336 GLN cc_start: 0.8277 (mp10) cc_final: 0.7940 (mp10) REVERT: C 349 ARG cc_start: 0.8495 (mtp180) cc_final: 0.6553 (ppt170) REVERT: C 358 ASP cc_start: 0.8470 (p0) cc_final: 0.8219 (p0) REVERT: D 295 ASP cc_start: 0.8402 (m-30) cc_final: 0.8141 (m-30) REVERT: D 358 ASP cc_start: 0.8722 (p0) cc_final: 0.8096 (p0) REVERT: E 338 GLU cc_start: 0.8177 (mp0) cc_final: 0.7881 (mp0) REVERT: E 342 GLU cc_start: 0.4744 (pm20) cc_final: 0.4265 (pm20) REVERT: F 295 ASP cc_start: 0.8717 (m-30) cc_final: 0.8277 (m-30) REVERT: F 336 GLN cc_start: 0.8982 (mp10) cc_final: 0.8613 (mp10) REVERT: F 345 ASP cc_start: 0.8555 (t0) cc_final: 0.8244 (t0) REVERT: F 349 ARG cc_start: 0.8178 (mtp180) cc_final: 0.7795 (ttm110) REVERT: F 358 ASP cc_start: 0.8821 (p0) cc_final: 0.8094 (p0) REVERT: G 295 ASP cc_start: 0.8675 (m-30) cc_final: 0.8343 (m-30) REVERT: G 306 VAL cc_start: 0.9095 (t) cc_final: 0.8812 (p) REVERT: G 345 ASP cc_start: 0.8635 (t0) cc_final: 0.8339 (t0) REVERT: G 358 ASP cc_start: 0.8779 (p0) cc_final: 0.7896 (p0) REVERT: H 295 ASP cc_start: 0.8591 (m-30) cc_final: 0.8322 (m-30) REVERT: H 336 GLN cc_start: 0.8826 (mp10) cc_final: 0.8320 (mp10) REVERT: H 358 ASP cc_start: 0.9112 (p0) cc_final: 0.8389 (p0) REVERT: I 314 ASP cc_start: 0.9228 (t0) cc_final: 0.8988 (t0) REVERT: I 338 GLU cc_start: 0.8108 (tt0) cc_final: 0.7860 (mp0) REVERT: I 345 ASP cc_start: 0.8435 (t0) cc_final: 0.8218 (t0) REVERT: J 316 SER cc_start: 0.9204 (p) cc_final: 0.8949 (p) REVERT: J 338 GLU cc_start: 0.8397 (mp0) cc_final: 0.8001 (mp0) REVERT: J 345 ASP cc_start: 0.8612 (t0) cc_final: 0.8216 (t0) REVERT: J 349 ARG cc_start: 0.8222 (mtp180) cc_final: 0.6836 (mmt-90) REVERT: J 351 GLN cc_start: 0.8955 (pt0) cc_final: 0.7056 (mm-40) outliers start: 19 outliers final: 18 residues processed: 257 average time/residue: 0.2018 time to fit residues: 69.7793 Evaluate side-chains 258 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 240 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 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 360 ILE Chi-restraints excluded: chain E residue 360 ILE 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 I residue 360 ILE Chi-restraints excluded: chain J residue 342 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** 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 = 0.4051 r_free = 0.4051 target = 0.127191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.108812 restraints weight = 11654.740| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.27 r_work: 0.3681 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3309 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= 0.219 Angle : 0.576 9.718 10990 Z= 0.276 Chirality : 0.050 0.122 1230 Planarity : 0.002 0.021 1410 Dihedral : 4.920 14.376 1100 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.69 % Allowed : 13.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 299 PHE 0.019 0.001 PHE G 378 TYR 0.015 0.001 TYR C 310 ARG 0.002 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 248 time to evaluate : 1.715 Fit side-chains REVERT: A 345 ASP cc_start: 0.8608 (t0) cc_final: 0.8395 (t0) REVERT: A 358 ASP cc_start: 0.8982 (p0) cc_final: 0.8220 (p0) REVERT: B 338 GLU cc_start: 0.8123 (tt0) cc_final: 0.7851 (mp0) REVERT: B 349 ARG cc_start: 0.8178 (mtp180) cc_final: 0.7885 (ttm110) REVERT: B 358 ASP cc_start: 0.8983 (p0) cc_final: 0.8102 (p0) REVERT: C 288 GLN cc_start: 0.7635 (mm-40) cc_final: 0.7313 (mt0) REVERT: C 336 GLN cc_start: 0.8417 (mp10) cc_final: 0.8072 (mp10) REVERT: C 349 ARG cc_start: 0.8491 (mtp180) cc_final: 0.6571 (ppt170) REVERT: C 358 ASP cc_start: 0.8435 (p0) cc_final: 0.8181 (p0) REVERT: C 379 ARG cc_start: 0.5045 (pmt-80) cc_final: 0.4360 (pmt-80) REVERT: D 295 ASP cc_start: 0.8369 (m-30) cc_final: 0.8129 (m-30) REVERT: D 358 ASP cc_start: 0.8740 (p0) cc_final: 0.8100 (p0) REVERT: E 336 GLN cc_start: 0.8828 (mp10) cc_final: 0.7988 (mp10) REVERT: E 342 GLU cc_start: 0.4758 (pm20) cc_final: 0.4337 (pm20) REVERT: E 351 GLN cc_start: 0.5528 (mm110) cc_final: 0.4217 (pt0) REVERT: E 378 PHE cc_start: 0.8503 (m-80) cc_final: 0.8172 (m-80) REVERT: E 379 ARG cc_start: 0.6798 (mtt180) cc_final: 0.6539 (mmp-170) REVERT: F 295 ASP cc_start: 0.8715 (m-30) cc_final: 0.8290 (m-30) REVERT: F 336 GLN cc_start: 0.8977 (mp10) cc_final: 0.8543 (mp10) REVERT: F 349 ARG cc_start: 0.8215 (mtp180) cc_final: 0.7840 (ttm110) REVERT: F 358 ASP cc_start: 0.8847 (p0) cc_final: 0.8091 (p0) REVERT: G 295 ASP cc_start: 0.8683 (m-30) cc_final: 0.8350 (m-30) REVERT: G 306 VAL cc_start: 0.9066 (t) cc_final: 0.8785 (p) REVERT: G 336 GLN cc_start: 0.8873 (mp10) cc_final: 0.8278 (mp10) REVERT: G 345 ASP cc_start: 0.8611 (t0) cc_final: 0.8305 (t0) REVERT: G 358 ASP cc_start: 0.8790 (p0) cc_final: 0.7879 (p0) REVERT: H 288 GLN cc_start: 0.7713 (mm-40) cc_final: 0.7359 (mt0) REVERT: H 295 ASP cc_start: 0.8610 (m-30) cc_final: 0.8340 (m-30) REVERT: H 336 GLN cc_start: 0.8778 (mp10) cc_final: 0.8254 (mp10) REVERT: H 358 ASP cc_start: 0.9101 (p0) cc_final: 0.8347 (p0) REVERT: I 314 ASP cc_start: 0.9250 (t0) cc_final: 0.9036 (t0) REVERT: I 338 GLU cc_start: 0.8050 (tt0) cc_final: 0.7838 (mp0) REVERT: I 345 ASP cc_start: 0.8442 (t0) cc_final: 0.8231 (t0) REVERT: J 316 SER cc_start: 0.9213 (p) cc_final: 0.8957 (p) REVERT: J 338 GLU cc_start: 0.8401 (mp0) cc_final: 0.8000 (mp0) REVERT: J 345 ASP cc_start: 0.8601 (t0) cc_final: 0.8182 (t0) REVERT: J 349 ARG cc_start: 0.8243 (mtp180) cc_final: 0.6828 (mmt-90) REVERT: J 351 GLN cc_start: 0.8961 (pt0) cc_final: 0.6987 (tp-100) outliers start: 25 outliers final: 24 residues processed: 263 average time/residue: 0.2297 time to fit residues: 81.8303 Evaluate side-chains 263 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 239 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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 351 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.121052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.102527 restraints weight = 11905.750| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.26 r_work: 0.3576 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3469 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= 0.471 Angle : 0.657 9.272 10990 Z= 0.326 Chirality : 0.051 0.127 1230 Planarity : 0.003 0.028 1410 Dihedral : 5.464 16.852 1100 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.12 % Allowed : 13.87 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 299 PHE 0.012 0.001 PHE A 378 TYR 0.005 0.001 TYR I 310 ARG 0.002 0.001 ARG J 379 *********************** 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 272 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 243 time to evaluate : 0.990 Fit side-chains REVERT: A 345 ASP cc_start: 0.8574 (t0) cc_final: 0.8351 (t0) REVERT: A 358 ASP cc_start: 0.8867 (p0) cc_final: 0.8180 (p0) REVERT: B 338 GLU cc_start: 0.8094 (tt0) cc_final: 0.7834 (mp0) REVERT: B 358 ASP cc_start: 0.9061 (p0) cc_final: 0.8228 (p0) REVERT: C 336 GLN cc_start: 0.8818 (mp10) cc_final: 0.8423 (mp10) REVERT: C 349 ARG cc_start: 0.8542 (mtp180) cc_final: 0.6318 (ppt170) REVERT: C 358 ASP cc_start: 0.8712 (p0) cc_final: 0.8471 (p0) REVERT: D 295 ASP cc_start: 0.8375 (m-30) cc_final: 0.8096 (m-30) REVERT: D 351 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8674 (pt0) REVERT: D 358 ASP cc_start: 0.8676 (p0) cc_final: 0.8019 (p0) REVERT: D 379 ARG cc_start: 0.6935 (mtt180) cc_final: 0.6703 (tpt90) REVERT: E 342 GLU cc_start: 0.4492 (pm20) cc_final: 0.3846 (pm20) REVERT: E 351 GLN cc_start: 0.5816 (mm110) cc_final: 0.4131 (pt0) REVERT: F 295 ASP cc_start: 0.8631 (m-30) cc_final: 0.8089 (m-30) REVERT: F 336 GLN cc_start: 0.9052 (mp10) cc_final: 0.8637 (mp10) REVERT: F 349 ARG cc_start: 0.8200 (mtp180) cc_final: 0.7781 (mtm-85) REVERT: F 358 ASP cc_start: 0.8709 (p0) cc_final: 0.8007 (p0) REVERT: G 295 ASP cc_start: 0.8548 (m-30) cc_final: 0.8263 (m-30) REVERT: G 336 GLN cc_start: 0.9014 (mp10) cc_final: 0.8534 (mp10) REVERT: G 345 ASP cc_start: 0.8782 (t0) cc_final: 0.8449 (t0) REVERT: G 356 SER cc_start: 0.8320 (t) cc_final: 0.7655 (m) REVERT: G 358 ASP cc_start: 0.8820 (p0) cc_final: 0.7936 (p0) REVERT: H 295 ASP cc_start: 0.8659 (m-30) cc_final: 0.8414 (m-30) REVERT: H 336 GLN cc_start: 0.8715 (mp10) cc_final: 0.8343 (mp10) REVERT: H 358 ASP cc_start: 0.9038 (p0) cc_final: 0.8356 (p0) REVERT: I 295 ASP cc_start: 0.8538 (m-30) cc_final: 0.8166 (m-30) REVERT: I 338 GLU cc_start: 0.8140 (tt0) cc_final: 0.7870 (mp0) REVERT: J 338 GLU cc_start: 0.8449 (mp0) cc_final: 0.8064 (mp0) REVERT: J 345 ASP cc_start: 0.8579 (t0) cc_final: 0.8164 (t0) REVERT: J 349 ARG cc_start: 0.8274 (mtp180) cc_final: 0.6754 (mmp-170) REVERT: J 351 GLN cc_start: 0.9036 (pt0) cc_final: 0.6977 (tp-100) outliers start: 29 outliers final: 25 residues processed: 261 average time/residue: 0.2091 time to fit residues: 73.1640 Evaluate side-chains 264 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 238 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 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 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 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 360 ILE 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 49 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 overall best weight: 2.7184 ------------------------------------------------------------------------------- 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 351 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.124202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.105985 restraints weight = 11899.581| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.27 r_work: 0.3639 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3628 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= 0.295 Angle : 0.628 9.377 10990 Z= 0.301 Chirality : 0.050 0.124 1230 Planarity : 0.003 0.026 1410 Dihedral : 5.194 15.716 1100 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.01 % Allowed : 14.52 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 299 PHE 0.009 0.001 PHE A 378 TYR 0.004 0.001 TYR D 310 ARG 0.005 0.001 ARG F 379 *********************** 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 267 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 239 time to evaluate : 1.032 Fit side-chains REVERT: A 345 ASP cc_start: 0.8540 (t0) cc_final: 0.8299 (t0) REVERT: A 358 ASP cc_start: 0.8867 (p0) cc_final: 0.8098 (p0) REVERT: A 379 ARG cc_start: 0.7094 (tpt90) cc_final: 0.6756 (mtt180) REVERT: B 338 GLU cc_start: 0.8027 (tt0) cc_final: 0.7822 (mp0) REVERT: B 358 ASP cc_start: 0.9049 (p0) cc_final: 0.8245 (p0) REVERT: C 336 GLN cc_start: 0.8574 (mp10) cc_final: 0.8186 (mp10) REVERT: C 349 ARG cc_start: 0.8524 (mtp180) cc_final: 0.6313 (ppt170) REVERT: C 358 ASP cc_start: 0.8661 (p0) cc_final: 0.8422 (p0) REVERT: D 295 ASP cc_start: 0.8384 (m-30) cc_final: 0.8121 (m-30) REVERT: D 349 ARG cc_start: 0.8635 (ttp-110) cc_final: 0.8092 (mtm-85) REVERT: D 351 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8478 (pt0) REVERT: D 358 ASP cc_start: 0.8820 (p0) cc_final: 0.8180 (p0) REVERT: D 379 ARG cc_start: 0.7061 (mtt180) cc_final: 0.6758 (tpt90) REVERT: E 336 GLN cc_start: 0.8873 (mp10) cc_final: 0.8340 (mp10) REVERT: E 338 GLU cc_start: 0.8325 (mp0) cc_final: 0.8089 (mp0) REVERT: E 351 GLN cc_start: 0.5759 (mm110) cc_final: 0.4075 (pt0) REVERT: F 295 ASP cc_start: 0.8717 (m-30) cc_final: 0.8283 (m-30) REVERT: F 336 GLN cc_start: 0.9005 (mp10) cc_final: 0.8603 (mp10) REVERT: F 349 ARG cc_start: 0.8162 (mtp180) cc_final: 0.7753 (mtm-85) REVERT: F 358 ASP cc_start: 0.8661 (p0) cc_final: 0.7929 (p0) REVERT: G 295 ASP cc_start: 0.8691 (m-30) cc_final: 0.8410 (m-30) REVERT: G 345 ASP cc_start: 0.8641 (t0) cc_final: 0.8287 (t0) REVERT: G 358 ASP cc_start: 0.8867 (p0) cc_final: 0.8031 (p0) REVERT: H 295 ASP cc_start: 0.8569 (m-30) cc_final: 0.8309 (m-30) REVERT: H 336 GLN cc_start: 0.8742 (mp10) cc_final: 0.8173 (mp10) REVERT: H 358 ASP cc_start: 0.9053 (p0) cc_final: 0.8345 (p0) REVERT: I 338 GLU cc_start: 0.8095 (tt0) cc_final: 0.7877 (mp0) REVERT: I 345 ASP cc_start: 0.8426 (t0) cc_final: 0.8210 (t0) REVERT: I 358 ASP cc_start: 0.8792 (p0) cc_final: 0.8279 (p0) REVERT: J 338 GLU cc_start: 0.8416 (mp0) cc_final: 0.8048 (mp0) REVERT: J 345 ASP cc_start: 0.8567 (t0) cc_final: 0.8129 (t0) REVERT: J 349 ARG cc_start: 0.8285 (mtp180) cc_final: 0.6793 (mmt-90) REVERT: J 351 GLN cc_start: 0.9012 (pt0) cc_final: 0.6942 (tp-100) outliers start: 28 outliers final: 27 residues processed: 256 average time/residue: 0.1989 time to fit residues: 68.7534 Evaluate side-chains 263 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 235 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 305 SER Chi-restraints excluded: chain B residue 351 GLN 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 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 351 GLN Chi-restraints excluded: chain I residue 360 ILE 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 6 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 63 optimal weight: 0.0670 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 overall best weight: 3.1724 ------------------------------------------------------------------------------- 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** ** E 276 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.122989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.104691 restraints weight = 12025.803| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.28 r_work: 0.3618 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8230 Z= 0.337 Angle : 0.648 9.887 10990 Z= 0.311 Chirality : 0.050 0.126 1230 Planarity : 0.003 0.027 1410 Dihedral : 5.250 16.000 1100 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.01 % Allowed : 14.62 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.20), residues: 1060 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 299 PHE 0.017 0.001 PHE D 378 TYR 0.015 0.001 TYR C 310 ARG 0.003 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 235 time to evaluate : 1.768 Fit side-chains REVERT: A 345 ASP cc_start: 0.8557 (t0) cc_final: 0.8331 (t0) REVERT: A 358 ASP cc_start: 0.8881 (p0) cc_final: 0.8112 (p0) REVERT: B 358 ASP cc_start: 0.8993 (p0) cc_final: 0.8172 (p0) REVERT: C 336 GLN cc_start: 0.8724 (mp10) cc_final: 0.8319 (mp10) REVERT: C 349 ARG cc_start: 0.8525 (mtp180) cc_final: 0.6311 (ppt170) REVERT: C 358 ASP cc_start: 0.8668 (p0) cc_final: 0.8434 (p0) REVERT: D 295 ASP cc_start: 0.8397 (m-30) cc_final: 0.8128 (m-30) REVERT: D 349 ARG cc_start: 0.8607 (ttp-110) cc_final: 0.8322 (ttp-110) REVERT: D 351 GLN cc_start: 0.9026 (pt0) cc_final: 0.8758 (pt0) REVERT: D 358 ASP cc_start: 0.8830 (p0) cc_final: 0.8219 (p0) REVERT: D 379 ARG cc_start: 0.7076 (mtt180) cc_final: 0.6750 (tpt90) REVERT: E 336 GLN cc_start: 0.8877 (mp10) cc_final: 0.8253 (mp10) REVERT: E 338 GLU cc_start: 0.8351 (mp0) cc_final: 0.7909 (mp0) REVERT: E 351 GLN cc_start: 0.5827 (mm110) cc_final: 0.4015 (pt0) REVERT: F 295 ASP cc_start: 0.8687 (m-30) cc_final: 0.8190 (m-30) REVERT: F 336 GLN cc_start: 0.9011 (mp10) cc_final: 0.8585 (mp10) REVERT: F 349 ARG cc_start: 0.8203 (mtp180) cc_final: 0.7788 (mtm-85) REVERT: F 358 ASP cc_start: 0.8665 (p0) cc_final: 0.7948 (p0) REVERT: G 295 ASP cc_start: 0.8649 (m-30) cc_final: 0.8365 (m-30) REVERT: G 336 GLN cc_start: 0.8911 (mp10) cc_final: 0.8427 (mp10) REVERT: G 345 ASP cc_start: 0.8658 (t0) cc_final: 0.8296 (t0) REVERT: G 358 ASP cc_start: 0.8963 (p0) cc_final: 0.8189 (p0) REVERT: G 379 ARG cc_start: 0.6894 (mtt180) cc_final: 0.6667 (tpt90) REVERT: H 295 ASP cc_start: 0.8730 (m-30) cc_final: 0.8485 (m-30) REVERT: H 336 GLN cc_start: 0.8727 (mp10) cc_final: 0.8118 (mp10) REVERT: H 358 ASP cc_start: 0.9065 (p0) cc_final: 0.8366 (p0) REVERT: I 338 GLU cc_start: 0.8114 (tt0) cc_final: 0.7872 (mp0) REVERT: I 345 ASP cc_start: 0.8433 (t0) cc_final: 0.8206 (t0) REVERT: I 358 ASP cc_start: 0.8831 (p0) cc_final: 0.8293 (p0) REVERT: J 338 GLU cc_start: 0.8441 (mp0) cc_final: 0.8073 (mp0) REVERT: J 345 ASP cc_start: 0.8581 (t0) cc_final: 0.8129 (t0) REVERT: J 349 ARG cc_start: 0.8288 (mtp180) cc_final: 0.6847 (tpm170) REVERT: J 351 GLN cc_start: 0.9013 (pt0) cc_final: 0.6938 (tp-100) outliers start: 28 outliers final: 28 residues processed: 252 average time/residue: 0.2736 time to fit residues: 94.3340 Evaluate side-chains 261 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 233 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 351 GLN 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 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 351 GLN 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 1 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 96 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- 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 351 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.125497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.107344 restraints weight = 11690.587| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.26 r_work: 0.3659 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8230 Z= 0.264 Angle : 0.639 10.219 10990 Z= 0.304 Chirality : 0.050 0.122 1230 Planarity : 0.002 0.024 1410 Dihedral : 5.076 14.983 1100 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.01 % Allowed : 14.52 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (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 HIS 0.003 0.001 HIS E 299 PHE 0.015 0.001 PHE D 378 TYR 0.005 0.001 TYR D 310 ARG 0.003 0.000 ARG D 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 239 time to evaluate : 0.931 Fit side-chains REVERT: A 345 ASP cc_start: 0.8541 (t0) cc_final: 0.8323 (t0) REVERT: A 358 ASP cc_start: 0.8874 (p0) cc_final: 0.8100 (p0) REVERT: B 358 ASP cc_start: 0.9053 (p0) cc_final: 0.8247 (p0) REVERT: C 336 GLN cc_start: 0.8573 (mp10) cc_final: 0.7900 (mp10) REVERT: C 349 ARG cc_start: 0.8518 (mtp180) cc_final: 0.6020 (pmt-80) REVERT: C 358 ASP cc_start: 0.8477 (p0) cc_final: 0.8264 (p0) REVERT: D 295 ASP cc_start: 0.8391 (m-30) cc_final: 0.8131 (m-30) REVERT: D 351 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8691 (pt0) REVERT: D 358 ASP cc_start: 0.8834 (p0) cc_final: 0.8220 (p0) REVERT: D 379 ARG cc_start: 0.7050 (mtt180) cc_final: 0.6734 (tpt90) REVERT: E 336 GLN cc_start: 0.8856 (mp10) cc_final: 0.8281 (mp10) REVERT: E 338 GLU cc_start: 0.8326 (mp0) cc_final: 0.8098 (mp0) REVERT: E 351 GLN cc_start: 0.5839 (mm110) cc_final: 0.3925 (pt0) REVERT: F 336 GLN cc_start: 0.9008 (mp10) cc_final: 0.8560 (mp10) REVERT: F 345 ASP cc_start: 0.8451 (t0) cc_final: 0.8217 (t0) REVERT: F 349 ARG cc_start: 0.8217 (mtp180) cc_final: 0.7813 (mtm-85) REVERT: F 358 ASP cc_start: 0.8626 (p0) cc_final: 0.7867 (p0) REVERT: G 295 ASP cc_start: 0.8678 (m-30) cc_final: 0.8225 (m-30) REVERT: G 336 GLN cc_start: 0.8899 (mp10) cc_final: 0.8396 (mp10) REVERT: G 345 ASP cc_start: 0.8598 (t0) cc_final: 0.8217 (t0) REVERT: G 358 ASP cc_start: 0.8858 (p0) cc_final: 0.8004 (p0) REVERT: G 379 ARG cc_start: 0.6997 (mtt180) cc_final: 0.6725 (tpt90) REVERT: H 295 ASP cc_start: 0.8597 (m-30) cc_final: 0.8343 (m-30) REVERT: H 336 GLN cc_start: 0.8740 (mp10) cc_final: 0.8145 (mp10) REVERT: H 358 ASP cc_start: 0.9056 (p0) cc_final: 0.8368 (p0) REVERT: I 338 GLU cc_start: 0.8097 (tt0) cc_final: 0.7864 (mp0) REVERT: I 345 ASP cc_start: 0.8406 (t0) cc_final: 0.8145 (t0) REVERT: I 358 ASP cc_start: 0.8820 (p0) cc_final: 0.8284 (p0) REVERT: J 316 SER cc_start: 0.9241 (p) cc_final: 0.8996 (p) REVERT: J 338 GLU cc_start: 0.8427 (mp0) cc_final: 0.8066 (mp0) REVERT: J 345 ASP cc_start: 0.8566 (t0) cc_final: 0.8092 (t0) REVERT: J 349 ARG cc_start: 0.8286 (mtp180) cc_final: 0.6827 (tpm170) REVERT: J 351 GLN cc_start: 0.8997 (pt0) cc_final: 0.6932 (tp-100) outliers start: 28 outliers final: 27 residues processed: 255 average time/residue: 0.2046 time to fit residues: 70.4061 Evaluate side-chains 264 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 236 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 305 SER Chi-restraints excluded: chain B residue 351 GLN 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 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 351 GLN 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 86 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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** ** E 276 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.125022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.106809 restraints weight = 11932.298| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.28 r_work: 0.3651 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.117 8230 Z= 0.450 Angle : 1.002 59.200 10990 Z= 0.558 Chirality : 0.054 0.354 1230 Planarity : 0.003 0.025 1410 Dihedral : 5.085 14.902 1100 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.23 % Allowed : 14.52 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.20), 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 HIS 0.003 0.001 HIS E 374 PHE 0.014 0.001 PHE D 378 TYR 0.008 0.002 TYR C 310 ARG 0.002 0.000 ARG H 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4645.79 seconds wall clock time: 82 minutes 14.16 seconds (4934.16 seconds total)