Starting phenix.real_space_refine on Thu Mar 6 04:57:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vh7_21200/03_2025/6vh7_21200.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vh7_21200/03_2025/6vh7_21200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vh7_21200/03_2025/6vh7_21200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vh7_21200/03_2025/6vh7_21200.map" model { file = "/net/cci-nas-00/data/ceres_data/6vh7_21200/03_2025/6vh7_21200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vh7_21200/03_2025/6vh7_21200.cif" } resolution = 3.8 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= 0.000 sd= 0.001 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 12 5.16 5 C 3042 2.51 5 N 906 2.21 5 O 918 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4878 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Restraints were copied for chains: C, B, E, G, F Time building chain proxies: 2.71, per 1000 atoms: 0.56 Number of scatterers: 4878 At special positions: 0 Unit cell: (103.222, 193.718, 31.108, 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 12 16.00 O 918 8.00 N 906 7.00 C 3042 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: 1.25 Conformation dependent library (CDL) restraints added in 858.1 milliseconds 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1128 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 67.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 275 through 282 removed outlier: 6.993A pdb=" N GLN A 276 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE B 277 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE A 278 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN B 279 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS A 280 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS B 281 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLN B 276 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE C 277 " --> pdb=" O GLN B 276 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE B 278 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN C 279 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LYS B 280 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS C 281 " --> pdb=" O LYS B 280 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 285 through 299 removed outlier: 8.876A pdb=" N ASN A 286 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 9.875A pdb=" N SER B 289 " --> pdb=" O ASN A 286 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N GLN A 288 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N CYS B 291 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS A 290 " --> pdb=" O CYS B 291 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N SER B 293 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N GLY A 292 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N ASP B 295 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS A 294 " --> pdb=" O ASP B 295 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE B 297 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASN A 296 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N HIS B 299 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS A 298 " --> pdb=" O HIS B 299 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN B 286 " --> pdb=" O SER C 285 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL C 287 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLN B 288 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N SER C 289 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS B 290 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N SER C 293 " --> pdb=" O GLY B 292 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS B 294 " --> pdb=" O SER C 293 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 303 through 310 removed outlier: 6.740A pdb=" N GLY A 304 " --> pdb=" O SER B 305 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N GLN B 307 " --> pdb=" O GLY A 304 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL A 306 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL B 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE A 308 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLY B 304 " --> pdb=" O SER C 305 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N GLN C 307 " --> pdb=" O GLY B 304 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL B 306 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N VAL C 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE B 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 313 through 321 removed outlier: 6.272A pdb=" N ASP A 314 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N LYS B 317 " --> pdb=" O ASP A 314 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER A 316 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N THR B 319 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL A 318 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LYS B 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N SER A 320 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASP B 314 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N LYS C 317 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER B 316 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N THR C 319 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL B 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LYS C 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N SER B 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 327 through 330 removed outlier: 6.547A pdb=" N ILE A 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE B 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 336 through 346 removed outlier: 6.801A pdb=" N VAL B 337 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU A 338 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL B 339 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS A 340 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER B 341 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU A 342 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LYS B 343 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU C 344 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASP B 345 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N PHE C 346 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 349 through 362 removed outlier: 6.433A pdb=" N VAL A 350 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N LYS B 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N SER A 352 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLY B 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ILE A 354 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU B 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N SER A 356 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ASN B 359 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP A 358 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR B 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE A 360 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N SER B 356 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU C 357 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASP B 358 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 379 removed outlier: 6.034A pdb=" N LYS A 370 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR B 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLU A 372 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LYS B 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N HIS A 374 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N THR B 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU A 376 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ARG B 379 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE A 378 " --> pdb=" O ARG B 379 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LYS B 370 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR C 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLU B 372 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LYS C 375 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N HIS B 374 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N THR C 377 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LEU B 376 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ARG C 379 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE B 378 " --> pdb=" O ARG C 379 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 275 through 282 removed outlier: 6.993A pdb=" N GLN E 276 " --> pdb=" O VAL F 275 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE F 277 " --> pdb=" O GLN E 276 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE E 278 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN F 279 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS E 280 " --> pdb=" O ASN F 279 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS F 281 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLN F 276 " --> pdb=" O VAL G 275 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE G 277 " --> pdb=" O GLN F 276 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE F 278 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN G 279 " --> pdb=" O ILE F 278 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS F 280 " --> pdb=" O ASN G 279 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS G 281 " --> pdb=" O LYS F 280 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 285 through 299 removed outlier: 8.876A pdb=" N ASN E 286 " --> pdb=" O VAL F 287 " (cutoff:3.500A) removed outlier: 9.874A pdb=" N SER F 289 " --> pdb=" O ASN E 286 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N GLN E 288 " --> pdb=" O SER F 289 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N CYS F 291 " --> pdb=" O GLN E 288 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS E 290 " --> pdb=" O CYS F 291 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N SER F 293 " --> pdb=" O LYS E 290 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N GLY E 292 " --> pdb=" O SER F 293 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N ASP F 295 " --> pdb=" O GLY E 292 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS E 294 " --> pdb=" O ASP F 295 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE F 297 " --> pdb=" O LYS E 294 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASN E 296 " --> pdb=" O ILE F 297 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N HIS F 299 " --> pdb=" O ASN E 296 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS E 298 " --> pdb=" O HIS F 299 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN F 286 " --> pdb=" O SER G 285 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL G 287 " --> pdb=" O ASN F 286 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLN F 288 " --> pdb=" O VAL G 287 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N SER G 289 " --> pdb=" O GLN F 288 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS F 290 " --> pdb=" O SER G 289 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER G 293 " --> pdb=" O GLY F 292 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS F 294 " --> pdb=" O SER G 293 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 303 through 310 removed outlier: 6.741A pdb=" N GLY E 304 " --> pdb=" O SER F 305 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N GLN F 307 " --> pdb=" O GLY E 304 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL E 306 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N VAL F 309 " --> pdb=" O VAL E 306 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE E 308 " --> pdb=" O VAL F 309 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLY F 304 " --> pdb=" O SER G 305 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N GLN G 307 " --> pdb=" O GLY F 304 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL F 306 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N VAL G 309 " --> pdb=" O VAL F 306 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE F 308 " --> pdb=" O VAL G 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 313 through 321 removed outlier: 6.272A pdb=" N ASP E 314 " --> pdb=" O LEU F 315 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LYS F 317 " --> pdb=" O ASP E 314 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER E 316 " --> pdb=" O LYS F 317 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N THR F 319 " --> pdb=" O SER E 316 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL E 318 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LYS F 321 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N SER E 320 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASP F 314 " --> pdb=" O LEU G 315 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N LYS G 317 " --> pdb=" O ASP F 314 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER F 316 " --> pdb=" O LYS G 317 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N THR G 319 " --> pdb=" O SER F 316 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL F 318 " --> pdb=" O THR G 319 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LYS G 321 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N SER F 320 " --> pdb=" O LYS G 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 327 through 330 removed outlier: 6.546A pdb=" N ILE E 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE F 328 " --> pdb=" O HIS G 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 336 through 346 removed outlier: 6.800A pdb=" N VAL F 337 " --> pdb=" O GLN E 336 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU E 338 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL F 339 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS E 340 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER F 341 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLU E 342 " --> pdb=" O SER F 341 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS F 343 " --> pdb=" O GLU G 342 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU G 344 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASP F 345 " --> pdb=" O LEU G 344 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N PHE G 346 " --> pdb=" O ASP F 345 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 349 through 362 removed outlier: 6.432A pdb=" N VAL E 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LYS F 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N SER E 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLY F 355 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ILE E 354 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU F 357 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N SER E 356 " --> pdb=" O LEU F 357 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ASN F 359 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASP E 358 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR F 361 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE E 360 " --> pdb=" O THR F 361 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER F 356 " --> pdb=" O GLY G 355 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU G 357 " --> pdb=" O SER F 356 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASP F 358 " --> pdb=" O LEU G 357 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 369 through 379 removed outlier: 6.035A pdb=" N LYS E 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR F 373 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLU E 372 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LYS F 375 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N HIS E 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N THR F 377 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU E 376 " --> pdb=" O THR F 377 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ARG F 379 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE E 378 " --> pdb=" O ARG F 379 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LYS F 370 " --> pdb=" O ILE G 371 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR G 373 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLU F 372 " --> pdb=" O THR G 373 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LYS G 375 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N HIS F 374 " --> pdb=" O LYS G 375 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N THR G 377 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU F 376 " --> pdb=" O THR G 377 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ARG G 379 " --> pdb=" O LEU F 376 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE F 378 " --> pdb=" O ARG G 379 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 58 hydrogen bonds defined for protein. 174 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1626 1.34 - 1.46: 626 1.46 - 1.57: 2680 1.57 - 1.69: 0 1.69 - 1.80: 12 Bond restraints: 4944 Sorted by residual: bond pdb=" CA LYS G 353 " pdb=" CB LYS G 353 " ideal model delta sigma weight residual 1.529 1.499 0.030 1.38e-02 5.25e+03 4.69e+00 bond pdb=" CA LYS C 353 " pdb=" CB LYS C 353 " ideal model delta sigma weight residual 1.529 1.499 0.030 1.38e-02 5.25e+03 4.66e+00 bond pdb=" CA LYS E 353 " pdb=" CB LYS E 353 " ideal model delta sigma weight residual 1.529 1.499 0.030 1.38e-02 5.25e+03 4.58e+00 bond pdb=" CA LYS A 353 " pdb=" CB LYS A 353 " ideal model delta sigma weight residual 1.529 1.500 0.029 1.38e-02 5.25e+03 4.53e+00 bond pdb=" CA LYS F 353 " pdb=" CB LYS F 353 " ideal model delta sigma weight residual 1.529 1.500 0.029 1.38e-02 5.25e+03 4.52e+00 ... (remaining 4939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 5735 1.38 - 2.77: 724 2.77 - 4.15: 111 4.15 - 5.53: 24 5.53 - 6.92: 12 Bond angle restraints: 6606 Sorted by residual: angle pdb=" C LYS E 347 " pdb=" N ASP E 348 " pdb=" CA ASP E 348 " ideal model delta sigma weight residual 122.17 115.25 6.92 1.54e+00 4.22e-01 2.02e+01 angle pdb=" C LYS G 347 " pdb=" N ASP G 348 " pdb=" CA ASP G 348 " ideal model delta sigma weight residual 122.17 115.28 6.89 1.54e+00 4.22e-01 2.00e+01 angle pdb=" C LYS B 347 " pdb=" N ASP B 348 " pdb=" CA ASP B 348 " ideal model delta sigma weight residual 122.17 115.28 6.89 1.54e+00 4.22e-01 2.00e+01 angle pdb=" C LYS F 347 " pdb=" N ASP F 348 " pdb=" CA ASP F 348 " ideal model delta sigma weight residual 122.17 115.29 6.88 1.54e+00 4.22e-01 2.00e+01 angle pdb=" C LYS C 347 " pdb=" N ASP C 348 " pdb=" CA ASP C 348 " ideal model delta sigma weight residual 122.17 115.30 6.87 1.54e+00 4.22e-01 1.99e+01 ... (remaining 6601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 2654 16.26 - 32.52: 317 32.52 - 48.77: 53 48.77 - 65.03: 24 65.03 - 81.29: 6 Dihedral angle restraints: 3054 sinusoidal: 1284 harmonic: 1770 Sorted by residual: dihedral pdb=" CA VAL G 313 " pdb=" C VAL G 313 " pdb=" N ASP G 314 " pdb=" CA ASP G 314 " ideal model delta harmonic sigma weight residual -180.00 -159.23 -20.77 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA VAL A 313 " pdb=" C VAL A 313 " pdb=" N ASP A 314 " pdb=" CA ASP A 314 " ideal model delta harmonic sigma weight residual -180.00 -159.25 -20.75 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA VAL B 313 " pdb=" C VAL B 313 " pdb=" N ASP B 314 " pdb=" CA ASP B 314 " ideal model delta harmonic sigma weight residual -180.00 -159.25 -20.75 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 3051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 394 0.036 - 0.073: 219 0.073 - 0.109: 92 0.109 - 0.145: 27 0.145 - 0.181: 12 Chirality restraints: 744 Sorted by residual: chirality pdb=" CB ILE B 277 " pdb=" CA ILE B 277 " pdb=" CG1 ILE B 277 " pdb=" CG2 ILE B 277 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.21e-01 chirality pdb=" CB ILE A 277 " pdb=" CA ILE A 277 " pdb=" CG1 ILE A 277 " pdb=" CG2 ILE A 277 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" CB ILE C 277 " pdb=" CA ILE C 277 " pdb=" CG1 ILE C 277 " pdb=" CG2 ILE C 277 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.79e-01 ... (remaining 741 not shown) Planarity restraints: 846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 363 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.30e+00 pdb=" N PRO G 364 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO G 364 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 364 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 363 " -0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO A 364 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 364 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 364 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 363 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO F 364 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO F 364 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 364 " 0.029 5.00e-02 4.00e+02 ... (remaining 843 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1567 2.83 - 3.35: 4573 3.35 - 3.87: 8817 3.87 - 4.38: 8741 4.38 - 4.90: 16812 Nonbonded interactions: 40510 Sorted by model distance: nonbonded pdb=" N GLU C 380 " pdb=" OE1 GLU C 380 " model vdw 2.318 3.120 nonbonded pdb=" N GLU E 380 " pdb=" OE1 GLU E 380 " model vdw 2.319 3.120 nonbonded pdb=" N GLU B 380 " pdb=" OE1 GLU B 380 " model vdw 2.319 3.120 nonbonded pdb=" N GLU A 380 " pdb=" OE1 GLU A 380 " model vdw 2.319 3.120 nonbonded pdb=" N GLU F 380 " pdb=" OE1 GLU F 380 " model vdw 2.319 3.120 ... (remaining 40505 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'G' selection = chain 'F' } 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 group one per residue 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: 12.030 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.150 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 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 0.039 4944 Z= 0.493 Angle : 1.025 6.915 6606 Z= 0.590 Chirality : 0.054 0.181 744 Planarity : 0.006 0.052 846 Dihedral : 15.142 81.287 1926 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 28.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer: Outliers : 2.13 % Allowed : 10.64 % Favored : 87.23 % 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: -4.78 (0.23), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.18), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 374 PHE 0.003 0.001 PHE E 378 TYR 0.004 0.002 TYR E 310 ARG 0.001 0.000 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 285 SER cc_start: 0.7274 (t) cc_final: 0.7066 (t) REVERT: B 277 ILE cc_start: 0.8449 (tp) cc_final: 0.8052 (mp) REVERT: B 278 ILE cc_start: 0.7470 (mt) cc_final: 0.7263 (mp) REVERT: B 345 ASP cc_start: 0.7908 (p0) cc_final: 0.7590 (p0) REVERT: C 278 ILE cc_start: 0.5867 (mt) cc_final: 0.5593 (mp) REVERT: F 277 ILE cc_start: 0.8529 (tp) cc_final: 0.8186 (mp) REVERT: F 278 ILE cc_start: 0.7084 (mt) cc_final: 0.6817 (mp) REVERT: F 338 GLU cc_start: 0.6168 (mm-30) cc_final: 0.5582 (mm-30) REVERT: F 345 ASP cc_start: 0.7216 (p0) cc_final: 0.6890 (p0) REVERT: G 278 ILE cc_start: 0.5385 (mt) cc_final: 0.5111 (mp) REVERT: G 370 LYS cc_start: 0.6726 (mttt) cc_final: 0.6511 (pptt) outliers start: 12 outliers final: 3 residues processed: 174 average time/residue: 0.1808 time to fit residues: 38.8653 Evaluate side-chains 93 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain G residue 356 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 HIS C 279 ASN ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS C 368 ASN C 374 HIS ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 HIS ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 HIS G 279 ASN G 362 HIS G 374 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5030 r_free = 0.5030 target = 0.170210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.148292 restraints weight = 13566.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.146531 restraints weight = 10843.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.146981 restraints weight = 9611.745| |-----------------------------------------------------------------------------| r_work (final): 0.4658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4944 Z= 0.271 Angle : 0.788 7.324 6606 Z= 0.401 Chirality : 0.052 0.147 744 Planarity : 0.005 0.037 846 Dihedral : 7.820 59.092 658 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.26 % Allowed : 18.44 % Favored : 77.30 % 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: -4.53 (0.24), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.18), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.002 HIS C 374 PHE 0.010 0.001 PHE G 378 TYR 0.010 0.002 TYR E 310 ARG 0.002 0.001 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.602 Fit side-chains REVERT: A 277 ILE cc_start: 0.8599 (mp) cc_final: 0.8300 (tp) REVERT: A 285 SER cc_start: 0.8341 (t) cc_final: 0.8138 (m) REVERT: G 317 LYS cc_start: 0.7122 (mttm) cc_final: 0.6815 (mttm) REVERT: G 370 LYS cc_start: 0.6680 (mttt) cc_final: 0.6404 (pptt) REVERT: G 378 PHE cc_start: 0.6320 (m-80) cc_final: 0.6112 (m-80) outliers start: 24 outliers final: 13 residues processed: 129 average time/residue: 0.1436 time to fit residues: 24.1198 Evaluate side-chains 101 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain G residue 356 SER Chi-restraints excluded: chain G residue 368 ASN Chi-restraints excluded: chain G residue 374 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 HIS A 330 HIS B 329 HIS C 329 HIS ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 HIS E 330 HIS ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 HIS G 329 HIS G 374 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.161549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.131572 restraints weight = 12179.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.132682 restraints weight = 8735.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.133256 restraints weight = 7154.062| |-----------------------------------------------------------------------------| r_work (final): 0.4513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4944 Z= 0.357 Angle : 0.802 7.230 6606 Z= 0.412 Chirality : 0.052 0.141 744 Planarity : 0.005 0.042 846 Dihedral : 7.125 23.653 656 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 3.90 % Allowed : 21.99 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.56 (0.23), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.17), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.002 HIS G 374 PHE 0.009 0.002 PHE B 346 TYR 0.009 0.002 TYR E 310 ARG 0.002 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.610 Fit side-chains REVERT: A 277 ILE cc_start: 0.8666 (mp) cc_final: 0.8353 (tp) REVERT: G 317 LYS cc_start: 0.7458 (mttm) cc_final: 0.7219 (mttt) REVERT: G 370 LYS cc_start: 0.6734 (mttt) cc_final: 0.6423 (pptt) outliers start: 22 outliers final: 18 residues processed: 116 average time/residue: 0.1495 time to fit residues: 22.6229 Evaluate side-chains 107 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain G residue 314 ASP Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 358 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 GLN ** 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 = 0.4965 r_free = 0.4965 target = 0.165969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.139289 restraints weight = 13954.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.140640 restraints weight = 8799.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.141473 restraints weight = 6903.321| |-----------------------------------------------------------------------------| r_work (final): 0.4590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4944 Z= 0.237 Angle : 0.710 7.672 6606 Z= 0.359 Chirality : 0.051 0.130 744 Planarity : 0.004 0.040 846 Dihedral : 6.452 21.798 654 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 4.26 % Allowed : 21.99 % Favored : 73.76 % 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: -4.48 (0.23), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.18), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 362 PHE 0.018 0.002 PHE C 378 TYR 0.011 0.002 TYR A 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.594 Fit side-chains REVERT: F 315 LEU cc_start: 0.8019 (mp) cc_final: 0.7376 (tt) REVERT: G 315 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7257 (tt) REVERT: G 370 LYS cc_start: 0.6645 (mttt) cc_final: 0.6345 (pptt) outliers start: 24 outliers final: 12 residues processed: 117 average time/residue: 0.1753 time to fit residues: 27.4643 Evaluate side-chains 102 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain G residue 314 ASP Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 368 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 0.0970 chunk 19 optimal weight: 2.9990 chunk 43 optimal weight: 0.0030 chunk 46 optimal weight: 1.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** 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 = 0.4973 r_free = 0.4973 target = 0.168432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.141226 restraints weight = 11812.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.141354 restraints weight = 7971.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.142060 restraints weight = 6743.507| |-----------------------------------------------------------------------------| r_work (final): 0.4645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.5730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4944 Z= 0.187 Angle : 0.656 6.400 6606 Z= 0.330 Chirality : 0.052 0.175 744 Planarity : 0.004 0.032 846 Dihedral : 5.988 20.848 654 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 2.30 % Allowed : 25.53 % Favored : 72.16 % 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: -4.35 (0.24), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.18), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.016 0.001 PHE B 378 TYR 0.007 0.002 TYR B 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.559 Fit side-chains REVERT: E 285 SER cc_start: 0.8228 (OUTLIER) cc_final: 0.8018 (p) REVERT: G 315 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7520 (tt) REVERT: G 370 LYS cc_start: 0.6657 (mttt) cc_final: 0.6316 (pptt) outliers start: 13 outliers final: 6 residues processed: 109 average time/residue: 0.1441 time to fit residues: 20.5231 Evaluate side-chains 97 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 368 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 59 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 GLN ** 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 = 0.4982 r_free = 0.4982 target = 0.169770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.147966 restraints weight = 13817.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.147196 restraints weight = 11184.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.147888 restraints weight = 9263.716| |-----------------------------------------------------------------------------| r_work (final): 0.4653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.5982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4944 Z= 0.193 Angle : 0.671 6.647 6606 Z= 0.336 Chirality : 0.052 0.192 744 Planarity : 0.004 0.033 846 Dihedral : 5.876 20.541 654 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 3.01 % Allowed : 25.18 % Favored : 71.81 % 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: -4.34 (0.24), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.18), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 330 PHE 0.019 0.002 PHE G 378 TYR 0.018 0.002 TYR E 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.593 Fit side-chains REVERT: A 372 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8256 (mm-30) REVERT: B 372 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7686 (mm-30) REVERT: E 372 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8145 (mm-30) REVERT: F 317 LYS cc_start: 0.8007 (mttm) cc_final: 0.7752 (mttm) REVERT: G 370 LYS cc_start: 0.6660 (mttt) cc_final: 0.6281 (pptt) REVERT: G 373 THR cc_start: 0.7157 (m) cc_final: 0.6900 (p) outliers start: 17 outliers final: 11 residues processed: 106 average time/residue: 0.1536 time to fit residues: 21.1693 Evaluate side-chains 98 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain G residue 314 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 23 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** 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 = 0.4926 r_free = 0.4926 target = 0.167400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.137917 restraints weight = 11589.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.139063 restraints weight = 8642.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.139705 restraints weight = 7089.620| |-----------------------------------------------------------------------------| r_work (final): 0.4578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.6226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4944 Z= 0.210 Angle : 0.696 9.175 6606 Z= 0.346 Chirality : 0.053 0.223 744 Planarity : 0.004 0.034 846 Dihedral : 5.842 20.931 654 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 2.66 % Allowed : 26.60 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.33 (0.24), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.18), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 330 PHE 0.019 0.002 PHE G 378 TYR 0.021 0.003 TYR E 310 ARG 0.004 0.001 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.555 Fit side-chains REVERT: A 315 LEU cc_start: 0.7654 (mp) cc_final: 0.7405 (tt) REVERT: A 372 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8009 (mm-30) REVERT: B 315 LEU cc_start: 0.7742 (mp) cc_final: 0.7060 (tp) REVERT: B 372 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7526 (mm-30) REVERT: E 372 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7986 (mm-30) REVERT: F 315 LEU cc_start: 0.7814 (mp) cc_final: 0.7166 (tp) REVERT: G 370 LYS cc_start: 0.6721 (mttt) cc_final: 0.6336 (pptt) REVERT: G 373 THR cc_start: 0.7003 (m) cc_final: 0.6758 (p) outliers start: 15 outliers final: 14 residues processed: 108 average time/residue: 0.1978 time to fit residues: 27.7009 Evaluate side-chains 105 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 314 ASP Chi-restraints excluded: chain G residue 368 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 5 optimal weight: 0.0040 chunk 56 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** 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 = 0.4947 r_free = 0.4947 target = 0.169681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.140461 restraints weight = 11789.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.141611 restraints weight = 8359.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.142208 restraints weight = 6911.451| |-----------------------------------------------------------------------------| r_work (final): 0.4616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.6466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4944 Z= 0.181 Angle : 0.674 7.906 6606 Z= 0.336 Chirality : 0.052 0.215 744 Planarity : 0.004 0.038 846 Dihedral : 5.618 19.265 654 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.01 % Allowed : 26.06 % Favored : 70.92 % 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: -4.30 (0.24), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.18), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.018 0.002 PHE G 378 TYR 0.023 0.002 TYR A 310 ARG 0.002 0.000 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.632 Fit side-chains REVERT: A 344 LEU cc_start: 0.8965 (mp) cc_final: 0.8748 (mt) REVERT: A 349 ARG cc_start: 0.6815 (mtt-85) cc_final: 0.5505 (ptt-90) REVERT: A 372 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8197 (mm-30) REVERT: B 372 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7537 (mm-30) REVERT: E 349 ARG cc_start: 0.6828 (mtt-85) cc_final: 0.5452 (ptt-90) REVERT: E 372 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8113 (mp0) REVERT: G 370 LYS cc_start: 0.6801 (mttt) cc_final: 0.6402 (pptt) REVERT: G 373 THR cc_start: 0.6922 (m) cc_final: 0.6687 (p) outliers start: 17 outliers final: 14 residues processed: 108 average time/residue: 0.2038 time to fit residues: 28.1942 Evaluate side-chains 107 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 314 ASP Chi-restraints excluded: chain G residue 368 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 40 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.0040 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** 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 = 0.4941 r_free = 0.4941 target = 0.169650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.140017 restraints weight = 11478.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.141113 restraints weight = 8481.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.141759 restraints weight = 7011.729| |-----------------------------------------------------------------------------| r_work (final): 0.4613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.6621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4944 Z= 0.186 Angle : 0.676 7.747 6606 Z= 0.337 Chirality : 0.052 0.205 744 Planarity : 0.004 0.041 846 Dihedral : 5.593 19.332 654 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 2.66 % Allowed : 26.42 % Favored : 70.92 % 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: -4.28 (0.24), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.18), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 330 PHE 0.017 0.002 PHE G 378 TYR 0.019 0.002 TYR A 310 ARG 0.002 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.689 Fit side-chains REVERT: A 315 LEU cc_start: 0.7579 (mp) cc_final: 0.7370 (tt) REVERT: A 349 ARG cc_start: 0.6844 (mtt-85) cc_final: 0.5488 (ptt-90) REVERT: A 372 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8257 (mm-30) REVERT: E 315 LEU cc_start: 0.7229 (mp) cc_final: 0.6992 (mp) REVERT: E 349 ARG cc_start: 0.6842 (mtt-85) cc_final: 0.5422 (ptt-90) REVERT: E 372 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8015 (mp0) REVERT: G 368 ASN cc_start: 0.7170 (OUTLIER) cc_final: 0.6864 (m110) REVERT: G 370 LYS cc_start: 0.6803 (mttt) cc_final: 0.6428 (pptt) REVERT: G 373 THR cc_start: 0.6928 (m) cc_final: 0.6708 (p) outliers start: 15 outliers final: 13 residues processed: 107 average time/residue: 0.2108 time to fit residues: 28.7862 Evaluate side-chains 110 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain G residue 314 ASP Chi-restraints excluded: chain G residue 368 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 276 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4878 r_free = 0.4878 target = 0.164924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.135402 restraints weight = 12347.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.136441 restraints weight = 9721.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.137038 restraints weight = 8248.028| |-----------------------------------------------------------------------------| r_work (final): 0.4538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.6760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4944 Z= 0.309 Angle : 0.777 8.789 6606 Z= 0.391 Chirality : 0.054 0.210 744 Planarity : 0.005 0.038 846 Dihedral : 6.329 21.579 654 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.75 % Favored : 88.25 % Rotamer: Outliers : 2.84 % Allowed : 26.60 % Favored : 70.57 % 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: -4.42 (0.24), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.18), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 374 PHE 0.017 0.002 PHE G 378 TYR 0.031 0.003 TYR A 310 ARG 0.006 0.001 ARG C 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.555 Fit side-chains REVERT: A 349 ARG cc_start: 0.6967 (mtt-85) cc_final: 0.5551 (ptt-90) REVERT: A 372 GLU cc_start: 0.8434 (mm-30) cc_final: 0.7887 (mp0) REVERT: E 349 ARG cc_start: 0.6932 (mtt-85) cc_final: 0.5539 (ptt-90) REVERT: E 372 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7831 (mp0) REVERT: G 370 LYS cc_start: 0.6796 (mttt) cc_final: 0.6408 (pptt) outliers start: 16 outliers final: 15 residues processed: 109 average time/residue: 0.1702 time to fit residues: 23.3476 Evaluate side-chains 110 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 288 GLN Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain G residue 314 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 16 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 8 optimal weight: 0.0270 chunk 47 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 13 optimal weight: 0.0670 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** 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 = 0.4950 r_free = 0.4950 target = 0.171134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.141509 restraints weight = 11654.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.143074 restraints weight = 7787.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.143981 restraints weight = 6209.865| |-----------------------------------------------------------------------------| r_work (final): 0.4628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.6900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4944 Z= 0.185 Angle : 0.729 9.131 6606 Z= 0.353 Chirality : 0.052 0.158 744 Planarity : 0.004 0.043 846 Dihedral : 5.732 21.386 654 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 2.13 % Allowed : 27.66 % Favored : 70.21 % 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: -4.28 (0.24), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.18), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.017 0.002 PHE G 378 TYR 0.030 0.002 TYR A 310 ARG 0.002 0.000 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2122.61 seconds wall clock time: 39 minutes 10.19 seconds (2350.19 seconds total)