Starting phenix.real_space_refine on Wed Mar 4 10:22:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n7s_0362/03_2026/6n7s_0362.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n7s_0362/03_2026/6n7s_0362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n7s_0362/03_2026/6n7s_0362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n7s_0362/03_2026/6n7s_0362.map" model { file = "/net/cci-nas-00/data/ceres_data/6n7s_0362/03_2026/6n7s_0362.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n7s_0362/03_2026/6n7s_0362.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 25 5.49 5 Mg 4 5.21 5 S 78 5.16 5 C 7932 2.51 5 N 2253 2.21 5 O 2491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12783 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2093 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 4, 'TRANS': 266} Chain breaks: 3 Chain: "B" Number of atoms: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2105 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 4, 'TRANS': 268} Chain breaks: 3 Chain: "C" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2121 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 4, 'TRANS': 270} Chain breaks: 3 Chain: "D" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2086 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 266} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2003 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 254} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1995 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 253} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "T" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 260 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.24, per 1000 atoms: 0.18 Number of scatterers: 12783 At special positions: 0 Unit cell: (75.97, 129.47, 135.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 78 16.00 P 25 15.00 Mg 4 11.99 O 2491 8.00 N 2253 7.00 C 7932 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 570.7 milliseconds 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2864 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 11 sheets defined 33.5% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 272 through 280 removed outlier: 4.165A pdb=" N ARG A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 298 removed outlier: 3.971A pdb=" N ASN A 296 " --> pdb=" O CYS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 332 removed outlier: 3.942A pdb=" N GLY A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 348 removed outlier: 3.603A pdb=" N GLU A 348 " --> pdb=" O SER A 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 345 through 348' Processing helix chain 'A' and resid 349 through 358 removed outlier: 3.841A pdb=" N LEU A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 404 through 416 Processing helix chain 'A' and resid 425 through 430 removed outlier: 4.310A pdb=" N VAL A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 453 Processing helix chain 'A' and resid 474 through 478 removed outlier: 3.654A pdb=" N GLY A 478 " --> pdb=" O HIS A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 279 removed outlier: 4.076A pdb=" N ARG B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N HIS B 278 " --> pdb=" O ARG B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 298 removed outlier: 3.564A pdb=" N LYS B 298 " --> pdb=" O GLY B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 329 removed outlier: 3.795A pdb=" N GLN B 325 " --> pdb=" O PHE B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 removed outlier: 4.921A pdb=" N GLU B 351 " --> pdb=" O GLU B 347 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASP B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 353 " --> pdb=" O THR B 349 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY B 355 " --> pdb=" O GLU B 351 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN B 358 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 382 Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 404 through 415 removed outlier: 3.591A pdb=" N TYR B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 430 removed outlier: 4.427A pdb=" N VAL B 429 " --> pdb=" O HIS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 454 removed outlier: 3.618A pdb=" N ASP B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS B 448 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 486 removed outlier: 3.839A pdb=" N ASP B 485 " --> pdb=" O SER B 482 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU B 486 " --> pdb=" O ILE B 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 482 through 486' Processing helix chain 'C' and resid 272 through 277 removed outlier: 3.632A pdb=" N ARG C 276 " --> pdb=" O ARG C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 298 Processing helix chain 'C' and resid 324 through 329 removed outlier: 3.621A pdb=" N GLN C 328 " --> pdb=" O GLN C 324 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TRP C 329 " --> pdb=" O GLN C 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 324 through 329' Processing helix chain 'C' and resid 345 through 351 removed outlier: 3.915A pdb=" N THR C 349 " --> pdb=" O SER C 345 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU C 351 " --> pdb=" O GLU C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 358 Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.926A pdb=" N LYS C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 386 removed outlier: 3.887A pdb=" N LEU C 385 " --> pdb=" O TRP C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 415 removed outlier: 4.194A pdb=" N TYR C 411 " --> pdb=" O ALA C 407 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N MET C 412 " --> pdb=" O LYS C 408 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG C 413 " --> pdb=" O LEU C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 445 through 457 removed outlier: 3.786A pdb=" N THR C 456 " --> pdb=" O PHE C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 478 removed outlier: 3.581A pdb=" N GLY C 478 " --> pdb=" O HIS C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 486 removed outlier: 3.690A pdb=" N LEU C 486 " --> pdb=" O ILE C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 494 removed outlier: 3.633A pdb=" N ARG C 493 " --> pdb=" O GLY C 490 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN C 494 " --> pdb=" O ALA C 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 490 through 494' Processing helix chain 'D' and resid 272 through 277 Processing helix chain 'D' and resid 294 through 299 Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 347 through 358 removed outlier: 3.832A pdb=" N ASP D 352 " --> pdb=" O GLU D 348 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU D 353 " --> pdb=" O THR D 349 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N HIS D 357 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN D 358 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 372 removed outlier: 3.784A pdb=" N ILE D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 384 removed outlier: 4.119A pdb=" N GLN D 380 " --> pdb=" O GLY D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 415 removed outlier: 3.733A pdb=" N ALA D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA D 410 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N MET D 412 " --> pdb=" O LYS D 408 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG D 413 " --> pdb=" O LEU D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 457 removed outlier: 3.692A pdb=" N MET D 446 " --> pdb=" O ILE D 442 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS D 448 " --> pdb=" O ASN D 444 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA D 453 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 478 removed outlier: 3.966A pdb=" N GLU D 477 " --> pdb=" O ALA D 474 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY D 478 " --> pdb=" O HIS D 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 474 through 478' Processing helix chain 'D' and resid 490 through 494 removed outlier: 3.614A pdb=" N ARG D 493 " --> pdb=" O GLY D 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 271 No H-bonds generated for 'chain 'E' and resid 269 through 271' Processing helix chain 'E' and resid 272 through 277 Processing helix chain 'E' and resid 324 through 332 removed outlier: 3.885A pdb=" N GLY E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA E 332 " --> pdb=" O GLN E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 358 removed outlier: 4.866A pdb=" N ASP E 352 " --> pdb=" O GLU E 348 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU E 353 " --> pdb=" O THR E 349 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE E 354 " --> pdb=" O ALA E 350 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY E 355 " --> pdb=" O GLU E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 365 removed outlier: 3.986A pdb=" N GLN E 364 " --> pdb=" O ARG E 361 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER E 365 " --> pdb=" O LEU E 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 361 through 365' Processing helix chain 'E' and resid 367 through 372 removed outlier: 4.432A pdb=" N ILE E 372 " --> pdb=" O LEU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 387 removed outlier: 3.552A pdb=" N GLU E 384 " --> pdb=" O GLN E 380 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU E 385 " --> pdb=" O TRP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 415 removed outlier: 4.276A pdb=" N MET E 412 " --> pdb=" O LYS E 408 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG E 413 " --> pdb=" O LEU E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 444 Processing helix chain 'E' and resid 445 through 457 removed outlier: 3.915A pdb=" N GLY E 451 " --> pdb=" O THR E 447 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR E 456 " --> pdb=" O PHE E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 478 removed outlier: 4.224A pdb=" N GLU E 477 " --> pdb=" O ALA E 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 272 removed outlier: 3.702A pdb=" N SER F 270 " --> pdb=" O SER F 267 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU F 271 " --> pdb=" O ALA F 268 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG F 272 " --> pdb=" O LEU F 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 267 through 272' Processing helix chain 'F' and resid 273 through 279 Processing helix chain 'F' and resid 317 through 323 removed outlier: 3.820A pdb=" N ARG F 323 " --> pdb=" O SER F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 329 removed outlier: 3.615A pdb=" N LEU F 327 " --> pdb=" O ARG F 323 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN F 328 " --> pdb=" O GLN F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 350 Processing helix chain 'F' and resid 351 through 358 Processing helix chain 'F' and resid 366 through 373 removed outlier: 4.021A pdb=" N ARG F 370 " --> pdb=" O ASP F 366 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE F 373 " --> pdb=" O LYS F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 384 Processing helix chain 'F' and resid 405 through 410 Processing helix chain 'F' and resid 410 through 415 removed outlier: 3.961A pdb=" N SER F 414 " --> pdb=" O ALA F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 457 removed outlier: 3.923A pdb=" N LEU F 449 " --> pdb=" O LEU F 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 493 removed outlier: 3.703A pdb=" N LEU F 492 " --> pdb=" O SER F 489 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 267 removed outlier: 3.936A pdb=" N VAL A 266 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE B 421 " --> pdb=" O VAL B 461 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ILE B 463 " --> pdb=" O ILE B 421 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU B 423 " --> pdb=" O ILE B 463 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 310 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR B 498 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE B 499 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL B 514 " --> pdb=" O TYR B 532 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TYR B 532 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL B 516 " --> pdb=" O ALA B 530 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 420 through 423 removed outlier: 4.297A pdb=" N ILE A 308 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE A 499 " --> pdb=" O LEU A 519 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 337 through 338 removed outlier: 6.631A pdb=" N VAL A 337 " --> pdb=" O HIS A 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 391 through 394 removed outlier: 3.542A pdb=" N ILE C 308 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL C 307 " --> pdb=" O THR C 498 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE C 500 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N MET C 309 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LEU C 502 " --> pdb=" O MET C 309 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N THR C 311 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY C 531 " --> pdb=" O VAL C 516 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE C 518 " --> pdb=" O ILE C 529 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ILE C 529 " --> pdb=" O ILE C 518 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 422 through 423 removed outlier: 3.579A pdb=" N ILE D 463 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILE D 308 " --> pdb=" O VAL D 462 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR D 498 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE D 499 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG D 517 " --> pdb=" O ALA D 501 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 422 through 423 removed outlier: 3.579A pdb=" N ILE D 463 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILE D 308 " --> pdb=" O VAL D 462 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR D 498 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE D 499 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG D 517 " --> pdb=" O ALA D 501 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL D 514 " --> pdb=" O TYR D 532 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR D 532 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL D 516 " --> pdb=" O ALA D 530 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 266 through 267 Processing sheet with id=AA8, first strand: chain 'E' and resid 307 through 309 removed outlier: 3.762A pdb=" N ILE E 422 " --> pdb=" O GLY E 338 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 498 through 503 removed outlier: 6.082A pdb=" N ILE E 499 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL E 514 " --> pdb=" O TYR E 532 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR E 532 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL E 516 " --> pdb=" O ALA E 530 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 308 through 311 removed outlier: 3.552A pdb=" N VAL F 514 " --> pdb=" O MET F 533 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL F 516 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLY F 531 " --> pdb=" O VAL F 516 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE F 518 " --> pdb=" O ILE F 529 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ILE F 529 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR F 532 " --> pdb=" O SER F 545 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 336 through 340 removed outlier: 6.650A pdb=" N LYS F 336 " --> pdb=" O ASP F 419 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ILE F 421 " --> pdb=" O LYS F 336 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY F 338 " --> pdb=" O ILE F 421 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU F 423 " --> pdb=" O GLY F 338 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA F 340 " --> pdb=" O LEU F 423 " (cutoff:3.500A) 305 hydrogen bonds defined for protein. 864 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: 1.75 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2145 1.31 - 1.43: 3175 1.43 - 1.56: 7456 1.56 - 1.69: 46 1.69 - 1.82: 132 Bond restraints: 12954 Sorted by residual: bond pdb=" C6 TTP E 700 " pdb=" N1 TTP E 700 " ideal model delta sigma weight residual 1.337 1.427 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C6 TTP B 700 " pdb=" N1 TTP B 700 " ideal model delta sigma weight residual 1.337 1.427 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C6 TTP D 700 " pdb=" N1 TTP D 700 " ideal model delta sigma weight residual 1.337 1.425 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C2 TTP B 700 " pdb=" N1 TTP B 700 " ideal model delta sigma weight residual 1.410 1.488 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C2 TTP E 700 " pdb=" N1 TTP E 700 " ideal model delta sigma weight residual 1.410 1.487 -0.077 2.00e-02 2.50e+03 1.50e+01 ... (remaining 12949 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 16632 2.43 - 4.87: 681 4.87 - 7.30: 102 7.30 - 9.74: 30 9.74 - 12.17: 12 Bond angle restraints: 17457 Sorted by residual: angle pdb=" N LEU B 356 " pdb=" CA LEU B 356 " pdb=" C LEU B 356 " ideal model delta sigma weight residual 111.02 100.94 10.08 1.52e+00 4.33e-01 4.40e+01 angle pdb=" N PHE B 289 " pdb=" CA PHE B 289 " pdb=" C PHE B 289 " ideal model delta sigma weight residual 109.60 118.52 -8.92 1.53e+00 4.27e-01 3.40e+01 angle pdb=" N HIS C 357 " pdb=" CA HIS C 357 " pdb=" C HIS C 357 " ideal model delta sigma weight residual 111.28 117.55 -6.27 1.09e+00 8.42e-01 3.31e+01 angle pdb=" N ILE F 275 " pdb=" CA ILE F 275 " pdb=" C ILE F 275 " ideal model delta sigma weight residual 111.00 105.42 5.58 1.09e+00 8.42e-01 2.62e+01 angle pdb=" N TYR B 411 " pdb=" CA TYR B 411 " pdb=" C TYR B 411 " ideal model delta sigma weight residual 111.82 117.59 -5.77 1.16e+00 7.43e-01 2.47e+01 ... (remaining 17452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 7594 35.33 - 70.67: 132 70.67 - 106.00: 14 106.00 - 141.33: 5 141.33 - 176.66: 3 Dihedral angle restraints: 7748 sinusoidal: 3275 harmonic: 4473 Sorted by residual: dihedral pdb=" C2 TTP B 700 " pdb=" C1' TTP B 700 " pdb=" N1 TTP B 700 " pdb=" O4' TTP B 700 " ideal model delta sinusoidal sigma weight residual -58.32 118.35 -176.66 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2 TTP E 700 " pdb=" C1' TTP E 700 " pdb=" N1 TTP E 700 " pdb=" O4' TTP E 700 " ideal model delta sinusoidal sigma weight residual 301.68 134.74 166.94 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C2 TTP D 700 " pdb=" C1' TTP D 700 " pdb=" N1 TTP D 700 " pdb=" O4' TTP D 700 " ideal model delta sinusoidal sigma weight residual 301.68 150.44 151.24 1 2.00e+01 2.50e-03 4.50e+01 ... (remaining 7745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1333 0.059 - 0.117: 519 0.117 - 0.176: 106 0.176 - 0.234: 23 0.234 - 0.293: 9 Chirality restraints: 1990 Sorted by residual: chirality pdb=" CA ASP B 352 " pdb=" N ASP B 352 " pdb=" C ASP B 352 " pdb=" CB ASP B 352 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA HIS B 357 " pdb=" N HIS B 357 " pdb=" C HIS B 357 " pdb=" CB HIS B 357 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C3' TTP C 700 " pdb=" C2' TTP C 700 " pdb=" C4' TTP C 700 " pdb=" O3' TTP C 700 " both_signs ideal model delta sigma weight residual False -2.51 -2.78 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 1987 not shown) Planarity restraints: 2163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU F 515 " -0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C LEU F 515 " 0.061 2.00e-02 2.50e+03 pdb=" O LEU F 515 " -0.023 2.00e-02 2.50e+03 pdb=" N VAL F 516 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 347 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.31e+00 pdb=" C GLU E 347 " 0.050 2.00e-02 2.50e+03 pdb=" O GLU E 347 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU E 348 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 322 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.89e+00 pdb=" C VAL C 322 " -0.045 2.00e-02 2.50e+03 pdb=" O VAL C 322 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG C 323 " 0.015 2.00e-02 2.50e+03 ... (remaining 2160 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 26 2.43 - 3.05: 7203 3.05 - 3.66: 18279 3.66 - 4.28: 27769 4.28 - 4.90: 45276 Nonbonded interactions: 98553 Sorted by model distance: nonbonded pdb=" OE1 GLN C 343 " pdb="MG MG C 701 " model vdw 1.812 2.170 nonbonded pdb=" OE1 GLN E 343 " pdb="MG MG E 701 " model vdw 1.922 2.170 nonbonded pdb=" O1B TTP E 700 " pdb="MG MG E 701 " model vdw 1.987 2.170 nonbonded pdb=" O2G TTP D 700 " pdb="MG MG D 701 " model vdw 2.000 2.170 nonbonded pdb=" O1G TTP C 700 " pdb="MG MG C 701 " model vdw 2.121 2.170 ... (remaining 98548 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 264 through 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or resid 439 or (resid 440 and (name N or name CA or name C or name O or \ name CB )) or resid 441 through 506 or resid 510 through 545)) selection = (chain 'B' and (resid 264 through 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or resid 439 or (resid 440 and (name N or name CA or name C or name O or \ name CB )) or resid 441 through 506 or resid 510 through 545)) selection = (chain 'C' and (resid 264 through 280 or resid 285 through 373 or resid 377 thro \ ugh 395 or resid 404 through 429 or resid 439 or (resid 440 and (name N or name \ CA or name C or name O or name CB )) or resid 441 through 545)) selection = (chain 'D' and (resid 264 through 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or resid 439 through 506 or resid 510 through 545)) selection = (chain 'E' and (resid 264 through 506 or resid 510 through 545)) selection = (chain 'F' and (resid 264 through 506 or resid 510 through 545)) } 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: 1.170 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.360 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5427 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 : 0.008 0.090 12954 Z= 0.371 Angle : 1.198 12.171 17457 Z= 0.636 Chirality : 0.066 0.293 1990 Planarity : 0.005 0.054 2163 Dihedral : 14.865 176.665 4884 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.54 % Favored : 87.46 % Rotamer: Outliers : 1.04 % Allowed : 4.37 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.07 (0.16), residues: 1555 helix: -4.29 (0.12), residues: 485 sheet: -2.12 (0.30), residues: 276 loop : -3.22 (0.17), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 303 TYR 0.023 0.003 TYR C 535 PHE 0.027 0.003 PHE D 289 TRP 0.031 0.004 TRP A 329 HIS 0.012 0.003 HIS D 465 Details of bonding type rmsd covalent geometry : bond 0.00779 (12954) covalent geometry : angle 1.19794 (17457) hydrogen bonds : bond 0.17320 ( 299) hydrogen bonds : angle 8.97117 ( 864) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 338 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 GLU cc_start: 0.7967 (mp0) cc_final: 0.7541 (mp0) REVERT: A 484 THR cc_start: 0.8992 (p) cc_final: 0.8758 (p) REVERT: A 493 ARG cc_start: 0.5022 (OUTLIER) cc_final: 0.4473 (ptt90) REVERT: A 515 LEU cc_start: 0.5832 (tt) cc_final: 0.4886 (mt) REVERT: A 533 MET cc_start: 0.6506 (mtm) cc_final: 0.5815 (mpp) REVERT: B 308 ILE cc_start: 0.8926 (mt) cc_final: 0.8503 (mp) REVERT: B 344 GLU cc_start: 0.6258 (mt-10) cc_final: 0.5325 (mp0) REVERT: B 439 ARG cc_start: 0.5884 (OUTLIER) cc_final: 0.5609 (mmp80) REVERT: B 533 MET cc_start: 0.4619 (mtm) cc_final: 0.4401 (mtp) REVERT: C 428 ILE cc_start: 0.7174 (pt) cc_final: 0.5748 (pt) REVERT: C 462 VAL cc_start: 0.7719 (t) cc_final: 0.7004 (t) REVERT: D 299 THR cc_start: 0.8128 (t) cc_final: 0.7739 (m) REVERT: D 341 MET cc_start: 0.2878 (mpm) cc_final: 0.2647 (mmp) REVERT: D 446 MET cc_start: 0.6842 (tpp) cc_final: 0.6630 (tpp) REVERT: E 444 ASN cc_start: 0.8332 (t0) cc_final: 0.7998 (t0) REVERT: E 468 ASN cc_start: 0.7076 (t0) cc_final: 0.6793 (t0) REVERT: F 335 LYS cc_start: 0.9244 (mttm) cc_final: 0.8937 (mtmt) REVERT: F 341 MET cc_start: 0.5101 (mpm) cc_final: 0.4629 (mpm) outliers start: 14 outliers final: 2 residues processed: 349 average time/residue: 0.1409 time to fit residues: 66.6002 Evaluate side-chains 186 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 182 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 9.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 475 HIS ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 HIS ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 ASN ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 HIS D 358 ASN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 HIS E 475 HIS F 465 HIS F 475 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.144212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.129176 restraints weight = 41340.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.131422 restraints weight = 28996.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.133085 restraints weight = 21419.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.134225 restraints weight = 16636.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.135195 restraints weight = 13511.152| |-----------------------------------------------------------------------------| r_work (final): 0.4363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5547 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12954 Z= 0.126 Angle : 0.644 10.867 17457 Z= 0.330 Chirality : 0.045 0.184 1990 Planarity : 0.004 0.064 2163 Dihedral : 13.930 143.044 1896 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.07 % Allowed : 3.48 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.14 (0.18), residues: 1555 helix: -3.32 (0.17), residues: 503 sheet: -1.78 (0.29), residues: 302 loop : -2.68 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 493 TYR 0.009 0.001 TYR E 535 PHE 0.021 0.001 PHE B 523 TRP 0.017 0.001 TRP E 381 HIS 0.008 0.001 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00285 (12954) covalent geometry : angle 0.64385 (17457) hydrogen bonds : bond 0.03271 ( 299) hydrogen bonds : angle 6.32935 ( 864) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 231 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 GLU cc_start: 0.7905 (mp0) cc_final: 0.7301 (mp0) REVERT: A 503 GLU cc_start: 0.6551 (mt-10) cc_final: 0.5441 (tm-30) REVERT: B 289 PHE cc_start: 0.7250 (m-80) cc_final: 0.7046 (m-80) REVERT: B 452 PHE cc_start: 0.5887 (t80) cc_final: 0.5668 (t80) REVERT: B 494 GLN cc_start: 0.7104 (mp-120) cc_final: 0.6901 (mm-40) REVERT: C 425 HIS cc_start: 0.7650 (t-90) cc_final: 0.7436 (t-90) REVERT: C 435 GLU cc_start: 0.3857 (mm-30) cc_final: 0.3249 (mt-10) REVERT: C 499 ILE cc_start: 0.7916 (mp) cc_final: 0.7274 (mp) REVERT: D 318 LYS cc_start: 0.4308 (mtmt) cc_final: 0.3249 (mttm) REVERT: D 418 CYS cc_start: 0.6414 (m) cc_final: 0.4791 (m) REVERT: E 316 MET cc_start: 0.7748 (mtp) cc_final: 0.7066 (ttp) REVERT: E 343 GLN cc_start: 0.6897 (tt0) cc_final: 0.6470 (mt0) REVERT: E 412 MET cc_start: 0.5624 (mtp) cc_final: 0.4940 (mtp) REVERT: E 444 ASN cc_start: 0.8172 (t0) cc_final: 0.7971 (t0) REVERT: F 335 LYS cc_start: 0.9232 (mttm) cc_final: 0.8958 (mttm) outliers start: 1 outliers final: 1 residues processed: 232 average time/residue: 0.1245 time to fit residues: 40.4703 Evaluate side-chains 172 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 111 optimal weight: 20.0000 chunk 141 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 151 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 GLN C 392 HIS ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 HIS ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 GLN F 358 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.132103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.117306 restraints weight = 45164.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.119522 restraints weight = 31816.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.121012 restraints weight = 23664.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.122162 restraints weight = 18664.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.122808 restraints weight = 15302.335| |-----------------------------------------------------------------------------| r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5977 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12954 Z= 0.249 Angle : 0.814 11.315 17457 Z= 0.410 Chirality : 0.049 0.192 1990 Planarity : 0.005 0.058 2163 Dihedral : 14.194 137.056 1896 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.84 (0.18), residues: 1555 helix: -2.87 (0.19), residues: 488 sheet: -1.79 (0.30), residues: 289 loop : -2.61 (0.19), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 522 TYR 0.018 0.002 TYR A 411 PHE 0.017 0.002 PHE E 452 TRP 0.020 0.002 TRP A 329 HIS 0.008 0.002 HIS D 465 Details of bonding type rmsd covalent geometry : bond 0.00526 (12954) covalent geometry : angle 0.81412 (17457) hydrogen bonds : bond 0.04041 ( 299) hydrogen bonds : angle 6.56460 ( 864) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 ARG cc_start: 0.7219 (mpp-170) cc_final: 0.6536 (mtm110) REVERT: A 503 GLU cc_start: 0.6507 (mt-10) cc_final: 0.5461 (tm-30) REVERT: B 494 GLN cc_start: 0.7438 (mp-120) cc_final: 0.7061 (mm-40) REVERT: C 425 HIS cc_start: 0.7770 (t-90) cc_final: 0.7447 (t-90) REVERT: C 441 MET cc_start: 0.5128 (ttt) cc_final: 0.3841 (ttp) REVERT: D 316 MET cc_start: 0.7788 (ttm) cc_final: 0.7519 (ttt) REVERT: D 477 GLU cc_start: 0.5565 (pp20) cc_final: 0.4891 (tm-30) REVERT: E 271 LEU cc_start: 0.7892 (tp) cc_final: 0.7665 (mt) REVERT: E 412 MET cc_start: 0.6161 (mtp) cc_final: 0.5852 (mtp) REVERT: E 441 MET cc_start: 0.5770 (tpp) cc_final: 0.5396 (tpp) REVERT: F 309 MET cc_start: 0.3252 (mmm) cc_final: 0.2834 (mmt) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1240 time to fit residues: 34.7010 Evaluate side-chains 146 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 89 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 118 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.132353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.119105 restraints weight = 43807.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.120863 restraints weight = 31918.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.121949 restraints weight = 24382.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.123012 restraints weight = 19741.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.123625 restraints weight = 16576.817| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5990 moved from start: 0.6037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12954 Z= 0.183 Angle : 0.713 10.073 17457 Z= 0.357 Chirality : 0.047 0.191 1990 Planarity : 0.004 0.045 2163 Dihedral : 13.796 139.247 1896 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.48 (0.19), residues: 1555 helix: -2.52 (0.20), residues: 501 sheet: -1.65 (0.29), residues: 298 loop : -2.38 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 504 TYR 0.013 0.002 TYR D 411 PHE 0.020 0.002 PHE E 386 TRP 0.034 0.002 TRP A 329 HIS 0.006 0.001 HIS D 475 Details of bonding type rmsd covalent geometry : bond 0.00412 (12954) covalent geometry : angle 0.71292 (17457) hydrogen bonds : bond 0.03515 ( 299) hydrogen bonds : angle 6.15527 ( 864) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 MET cc_start: 0.6800 (mpp) cc_final: 0.5955 (mpp) REVERT: B 335 LYS cc_start: 0.7403 (mptt) cc_final: 0.7041 (tttt) REVERT: B 370 ARG cc_start: 0.6767 (mmt180) cc_final: 0.5043 (mmm160) REVERT: C 425 HIS cc_start: 0.7677 (t-90) cc_final: 0.7363 (t-90) REVERT: C 428 ILE cc_start: 0.7661 (pt) cc_final: 0.6316 (pt) REVERT: C 435 GLU cc_start: 0.5148 (mt-10) cc_final: 0.4605 (mt-10) REVERT: C 441 MET cc_start: 0.4775 (ttt) cc_final: 0.3734 (ttp) REVERT: D 316 MET cc_start: 0.7943 (ttm) cc_final: 0.7676 (ttt) REVERT: D 477 GLU cc_start: 0.5798 (pp20) cc_final: 0.5176 (tm-30) REVERT: E 408 LYS cc_start: 0.4464 (mmtt) cc_final: 0.3257 (tttt) REVERT: E 412 MET cc_start: 0.6350 (mtp) cc_final: 0.6043 (mtp) REVERT: E 441 MET cc_start: 0.5602 (tpp) cc_final: 0.5325 (tpp) REVERT: E 517 ARG cc_start: 0.6377 (ttp-170) cc_final: 0.6033 (ttt180) REVERT: F 309 MET cc_start: 0.3683 (mmm) cc_final: 0.2890 (mmt) REVERT: F 473 LYS cc_start: 0.7234 (ptmm) cc_final: 0.6848 (ptmm) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1188 time to fit residues: 34.2901 Evaluate side-chains 147 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 69 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 HIS ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.130829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.117317 restraints weight = 45688.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.119099 restraints weight = 33474.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.120321 restraints weight = 25579.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.121088 restraints weight = 20586.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.121939 restraints weight = 17443.805| |-----------------------------------------------------------------------------| r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6034 moved from start: 0.6608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12954 Z= 0.169 Angle : 0.691 10.704 17457 Z= 0.343 Chirality : 0.047 0.174 1990 Planarity : 0.004 0.058 2163 Dihedral : 13.646 136.197 1896 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.29 (0.19), residues: 1555 helix: -2.26 (0.21), residues: 509 sheet: -1.53 (0.30), residues: 301 loop : -2.34 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 493 TYR 0.014 0.002 TYR D 411 PHE 0.010 0.001 PHE D 289 TRP 0.041 0.002 TRP A 329 HIS 0.009 0.001 HIS D 425 Details of bonding type rmsd covalent geometry : bond 0.00384 (12954) covalent geometry : angle 0.69145 (17457) hydrogen bonds : bond 0.03343 ( 299) hydrogen bonds : angle 6.04871 ( 864) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 TRP cc_start: 0.7641 (m-90) cc_final: 0.7424 (m-90) REVERT: B 311 THR cc_start: 0.8145 (t) cc_final: 0.7575 (m) REVERT: B 370 ARG cc_start: 0.6955 (mmt180) cc_final: 0.5277 (mmm160) REVERT: B 494 GLN cc_start: 0.7628 (mp-120) cc_final: 0.7326 (mm-40) REVERT: C 425 HIS cc_start: 0.7604 (t-90) cc_final: 0.7250 (t-90) REVERT: C 428 ILE cc_start: 0.7622 (pt) cc_final: 0.6379 (pt) REVERT: C 440 LYS cc_start: 0.7809 (tmmt) cc_final: 0.7529 (tmmt) REVERT: C 467 LYS cc_start: 0.7582 (pttp) cc_final: 0.7238 (pttp) REVERT: D 316 MET cc_start: 0.7958 (ttm) cc_final: 0.7692 (ttt) REVERT: D 477 GLU cc_start: 0.5788 (pp20) cc_final: 0.5128 (tm-30) REVERT: E 408 LYS cc_start: 0.4371 (mmtt) cc_final: 0.3200 (tttt) REVERT: E 412 MET cc_start: 0.6359 (mtp) cc_final: 0.6068 (mtp) REVERT: E 441 MET cc_start: 0.5563 (tpp) cc_final: 0.5209 (tpp) REVERT: E 497 ASP cc_start: 0.6505 (m-30) cc_final: 0.5430 (t0) REVERT: F 309 MET cc_start: 0.3904 (mmm) cc_final: 0.3369 (mmt) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1110 time to fit residues: 30.4517 Evaluate side-chains 145 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 71 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 88 optimal weight: 0.0970 chunk 96 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 105 optimal weight: 7.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 HIS ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 506 GLN F 358 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.130751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.117693 restraints weight = 44047.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.119497 restraints weight = 32321.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.120741 restraints weight = 24442.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.121557 restraints weight = 19570.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.122353 restraints weight = 16445.221| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6038 moved from start: 0.7100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12954 Z= 0.161 Angle : 0.685 11.858 17457 Z= 0.339 Chirality : 0.046 0.171 1990 Planarity : 0.004 0.044 2163 Dihedral : 13.552 135.940 1896 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.19), residues: 1555 helix: -2.08 (0.21), residues: 491 sheet: -1.51 (0.30), residues: 297 loop : -2.26 (0.20), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 413 TYR 0.013 0.002 TYR D 411 PHE 0.013 0.002 PHE E 386 TRP 0.032 0.002 TRP A 329 HIS 0.006 0.001 HIS D 425 Details of bonding type rmsd covalent geometry : bond 0.00362 (12954) covalent geometry : angle 0.68513 (17457) hydrogen bonds : bond 0.03235 ( 299) hydrogen bonds : angle 5.97438 ( 864) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 311 THR cc_start: 0.8037 (t) cc_final: 0.7384 (m) REVERT: B 335 LYS cc_start: 0.7520 (mptt) cc_final: 0.7100 (tttt) REVERT: B 370 ARG cc_start: 0.7053 (mmt180) cc_final: 0.5442 (mmm160) REVERT: B 494 GLN cc_start: 0.7901 (mp-120) cc_final: 0.7569 (mm-40) REVERT: B 498 THR cc_start: 0.7368 (p) cc_final: 0.7128 (p) REVERT: C 441 MET cc_start: 0.5644 (ttt) cc_final: 0.5229 (ttp) REVERT: D 341 MET cc_start: 0.3753 (mmm) cc_final: 0.3416 (mmm) REVERT: D 477 GLU cc_start: 0.6070 (pp20) cc_final: 0.5427 (tm-30) REVERT: E 278 HIS cc_start: 0.6543 (m90) cc_final: 0.6026 (m90) REVERT: E 412 MET cc_start: 0.6315 (mtp) cc_final: 0.6015 (mtp) REVERT: E 441 MET cc_start: 0.5484 (tpp) cc_final: 0.5126 (tpp) REVERT: E 497 ASP cc_start: 0.6434 (m-30) cc_final: 0.5471 (t0) REVERT: F 309 MET cc_start: 0.4143 (mmm) cc_final: 0.3936 (tpp) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1127 time to fit residues: 30.4902 Evaluate side-chains 139 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 41 optimal weight: 7.9990 chunk 117 optimal weight: 0.0070 chunk 99 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.132458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.119371 restraints weight = 43538.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.121117 restraints weight = 31883.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.122412 restraints weight = 24297.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.123367 restraints weight = 19400.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.124137 restraints weight = 16113.651| |-----------------------------------------------------------------------------| r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5973 moved from start: 0.7322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12954 Z= 0.124 Angle : 0.645 12.245 17457 Z= 0.316 Chirality : 0.045 0.182 1990 Planarity : 0.003 0.044 2163 Dihedral : 13.368 136.947 1896 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.20), residues: 1555 helix: -1.97 (0.21), residues: 501 sheet: -1.30 (0.31), residues: 282 loop : -2.14 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 493 TYR 0.010 0.001 TYR F 532 PHE 0.018 0.001 PHE B 378 TRP 0.051 0.002 TRP A 329 HIS 0.003 0.001 HIS D 425 Details of bonding type rmsd covalent geometry : bond 0.00283 (12954) covalent geometry : angle 0.64506 (17457) hydrogen bonds : bond 0.02927 ( 299) hydrogen bonds : angle 5.72156 ( 864) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 ASN cc_start: 0.5746 (m-40) cc_final: 0.4573 (p0) REVERT: B 311 THR cc_start: 0.8280 (t) cc_final: 0.7597 (m) REVERT: B 364 GLN cc_start: 0.6933 (tm-30) cc_final: 0.6672 (tm-30) REVERT: B 370 ARG cc_start: 0.7034 (mmt180) cc_final: 0.5365 (mmm160) REVERT: B 494 GLN cc_start: 0.7966 (mp-120) cc_final: 0.7534 (mp10) REVERT: B 498 THR cc_start: 0.7241 (p) cc_final: 0.6801 (p) REVERT: B 510 MET cc_start: 0.6787 (ttt) cc_final: 0.6520 (ptm) REVERT: C 323 ARG cc_start: 0.7069 (ptm160) cc_final: 0.5721 (ptp-110) REVERT: C 425 HIS cc_start: 0.7554 (t-90) cc_final: 0.7141 (t-90) REVERT: C 441 MET cc_start: 0.5657 (ttt) cc_final: 0.5177 (ttp) REVERT: D 288 LEU cc_start: 0.8578 (mt) cc_final: 0.8336 (mp) REVERT: D 477 GLU cc_start: 0.5947 (pp20) cc_final: 0.5422 (tm-30) REVERT: E 278 HIS cc_start: 0.6739 (m90) cc_final: 0.5907 (m90) REVERT: E 412 MET cc_start: 0.6081 (mtp) cc_final: 0.5782 (mtp) REVERT: E 441 MET cc_start: 0.5314 (tpp) cc_final: 0.5011 (tpp) REVERT: E 497 ASP cc_start: 0.6434 (m-30) cc_final: 0.5412 (t0) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.0945 time to fit residues: 27.4482 Evaluate side-chains 144 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 65 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 132 optimal weight: 0.0170 chunk 47 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 10 optimal weight: 0.0000 chunk 37 optimal weight: 0.5980 overall best weight: 1.3226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 GLN F 358 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.133409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.119938 restraints weight = 43397.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.121779 restraints weight = 31612.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.123115 restraints weight = 23965.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.124116 restraints weight = 19108.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.124674 restraints weight = 15812.766| |-----------------------------------------------------------------------------| r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5958 moved from start: 0.7472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12954 Z= 0.113 Angle : 0.631 11.282 17457 Z= 0.307 Chirality : 0.045 0.200 1990 Planarity : 0.003 0.049 2163 Dihedral : 13.244 136.839 1896 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.20), residues: 1555 helix: -1.81 (0.21), residues: 510 sheet: -1.16 (0.31), residues: 283 loop : -1.98 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 517 TYR 0.008 0.001 TYR D 411 PHE 0.009 0.001 PHE B 289 TRP 0.067 0.002 TRP A 329 HIS 0.003 0.001 HIS D 425 Details of bonding type rmsd covalent geometry : bond 0.00257 (12954) covalent geometry : angle 0.63106 (17457) hydrogen bonds : bond 0.02799 ( 299) hydrogen bonds : angle 5.59735 ( 864) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 ASN cc_start: 0.5693 (m-40) cc_final: 0.4553 (p0) REVERT: B 311 THR cc_start: 0.8138 (t) cc_final: 0.7580 (m) REVERT: B 364 GLN cc_start: 0.7065 (tm-30) cc_final: 0.6777 (tm-30) REVERT: B 370 ARG cc_start: 0.7048 (mmt180) cc_final: 0.5904 (mmp-170) REVERT: B 412 MET cc_start: 0.5490 (mmt) cc_final: 0.5205 (mmt) REVERT: B 494 GLN cc_start: 0.8051 (mp-120) cc_final: 0.7526 (mm-40) REVERT: B 510 MET cc_start: 0.6948 (ttt) cc_final: 0.6607 (ptm) REVERT: C 323 ARG cc_start: 0.7033 (ptm160) cc_final: 0.6799 (mtm180) REVERT: C 412 MET cc_start: 0.7513 (tpp) cc_final: 0.7198 (ttm) REVERT: C 425 HIS cc_start: 0.7330 (t-90) cc_final: 0.6965 (t-90) REVERT: C 441 MET cc_start: 0.5876 (ttt) cc_final: 0.5474 (ttp) REVERT: D 275 ILE cc_start: 0.7232 (mt) cc_final: 0.6944 (mt) REVERT: D 477 GLU cc_start: 0.5895 (pp20) cc_final: 0.5366 (tm-30) REVERT: E 278 HIS cc_start: 0.6434 (m90) cc_final: 0.5867 (m90) REVERT: E 406 LEU cc_start: 0.8829 (pt) cc_final: 0.8619 (mp) REVERT: E 412 MET cc_start: 0.5959 (mtp) cc_final: 0.5669 (mtp) REVERT: E 441 MET cc_start: 0.5336 (tpp) cc_final: 0.5067 (tpp) REVERT: E 497 ASP cc_start: 0.6332 (m-30) cc_final: 0.5366 (t0) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1068 time to fit residues: 28.5255 Evaluate side-chains 142 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 113 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 156 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 42 optimal weight: 0.0270 chunk 24 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 GLN F 358 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.133914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.121066 restraints weight = 43469.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.122762 restraints weight = 32026.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.123988 restraints weight = 24678.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.124689 restraints weight = 19762.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.125493 restraints weight = 16857.811| |-----------------------------------------------------------------------------| r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5926 moved from start: 0.7622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12954 Z= 0.109 Angle : 0.625 10.572 17457 Z= 0.305 Chirality : 0.044 0.237 1990 Planarity : 0.004 0.089 2163 Dihedral : 13.167 136.489 1896 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.20), residues: 1555 helix: -1.64 (0.22), residues: 514 sheet: -1.02 (0.32), residues: 282 loop : -1.98 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 517 TYR 0.007 0.001 TYR A 532 PHE 0.009 0.001 PHE B 289 TRP 0.063 0.002 TRP A 329 HIS 0.003 0.001 HIS D 425 Details of bonding type rmsd covalent geometry : bond 0.00249 (12954) covalent geometry : angle 0.62502 (17457) hydrogen bonds : bond 0.02832 ( 299) hydrogen bonds : angle 5.50349 ( 864) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 HIS cc_start: 0.5874 (t-170) cc_final: 0.5359 (t-170) REVERT: A 505 ASN cc_start: 0.5629 (m-40) cc_final: 0.5208 (m-40) REVERT: B 311 THR cc_start: 0.8093 (t) cc_final: 0.7592 (m) REVERT: B 364 GLN cc_start: 0.6953 (tm-30) cc_final: 0.6734 (tm-30) REVERT: B 370 ARG cc_start: 0.6835 (mmt180) cc_final: 0.5771 (mmp-170) REVERT: B 412 MET cc_start: 0.5471 (mmt) cc_final: 0.5201 (mmt) REVERT: B 494 GLN cc_start: 0.7846 (mp-120) cc_final: 0.7629 (mm-40) REVERT: B 510 MET cc_start: 0.6841 (ttt) cc_final: 0.6552 (ptm) REVERT: C 323 ARG cc_start: 0.6893 (ptm160) cc_final: 0.6299 (ptp-170) REVERT: C 441 MET cc_start: 0.5809 (ttt) cc_final: 0.5424 (ttp) REVERT: D 477 GLU cc_start: 0.5895 (pp20) cc_final: 0.5361 (tm-30) REVERT: E 278 HIS cc_start: 0.6530 (m90) cc_final: 0.5936 (m90) REVERT: E 412 MET cc_start: 0.6073 (mtp) cc_final: 0.5860 (ttm) REVERT: E 441 MET cc_start: 0.5273 (tpp) cc_final: 0.4954 (tpp) REVERT: E 468 ASN cc_start: 0.7649 (t0) cc_final: 0.7447 (t0) REVERT: E 497 ASP cc_start: 0.6300 (m-30) cc_final: 0.5305 (t0) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1019 time to fit residues: 27.5157 Evaluate side-chains 138 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 14 optimal weight: 5.9990 chunk 61 optimal weight: 0.0270 chunk 6 optimal weight: 0.2980 chunk 27 optimal weight: 20.0000 chunk 152 optimal weight: 10.0000 chunk 153 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.6442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 GLN ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 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 = 0.4316 r_free = 0.4316 target = 0.130371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.117346 restraints weight = 45202.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.119097 restraints weight = 33075.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.120281 restraints weight = 25315.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.121033 restraints weight = 20361.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.121831 restraints weight = 17327.995| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.7950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12954 Z= 0.168 Angle : 0.717 10.030 17457 Z= 0.351 Chirality : 0.048 0.346 1990 Planarity : 0.004 0.078 2163 Dihedral : 13.424 137.481 1896 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.20), residues: 1555 helix: -1.70 (0.22), residues: 492 sheet: -1.23 (0.31), residues: 277 loop : -2.02 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 493 TYR 0.011 0.002 TYR A 411 PHE 0.011 0.002 PHE E 382 TRP 0.060 0.002 TRP A 329 HIS 0.012 0.001 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00384 (12954) covalent geometry : angle 0.71653 (17457) hydrogen bonds : bond 0.03403 ( 299) hydrogen bonds : angle 5.82872 ( 864) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 HIS cc_start: 0.6052 (t-170) cc_final: 0.5588 (t-170) REVERT: B 316 MET cc_start: 0.8146 (mmp) cc_final: 0.7163 (mmt) REVERT: B 364 GLN cc_start: 0.7112 (tm-30) cc_final: 0.6779 (tm-30) REVERT: B 370 ARG cc_start: 0.7020 (mmt180) cc_final: 0.5943 (mmp-170) REVERT: C 323 ARG cc_start: 0.6938 (ptm160) cc_final: 0.5591 (ptp-110) REVERT: C 441 MET cc_start: 0.6024 (ttt) cc_final: 0.5585 (ttp) REVERT: D 425 HIS cc_start: 0.6832 (t70) cc_final: 0.6303 (t-90) REVERT: D 477 GLU cc_start: 0.5925 (pp20) cc_final: 0.5383 (tm-30) REVERT: D 517 ARG cc_start: 0.5708 (tpm170) cc_final: 0.5236 (ttt90) REVERT: E 278 HIS cc_start: 0.6356 (m90) cc_final: 0.5710 (m90) REVERT: E 412 MET cc_start: 0.6171 (mtp) cc_final: 0.5957 (ttm) REVERT: E 441 MET cc_start: 0.5371 (tpp) cc_final: 0.5045 (tpp) REVERT: E 497 ASP cc_start: 0.6399 (m-30) cc_final: 0.5371 (t0) REVERT: E 506 GLN cc_start: 0.6229 (tt0) cc_final: 0.5321 (tp-100) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.1000 time to fit residues: 27.0695 Evaluate side-chains 143 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 44 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 137 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 HIS ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 GLN ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.124477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.111385 restraints weight = 46753.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.112876 restraints weight = 33999.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.114204 restraints weight = 26340.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.114989 restraints weight = 21198.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.115742 restraints weight = 17894.873| |-----------------------------------------------------------------------------| r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6264 moved from start: 0.8742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 12954 Z= 0.293 Angle : 0.956 10.308 17457 Z= 0.475 Chirality : 0.055 0.393 1990 Planarity : 0.006 0.065 2163 Dihedral : 14.370 139.749 1896 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 24.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.53 (0.19), residues: 1555 helix: -2.43 (0.19), residues: 494 sheet: -1.64 (0.32), residues: 251 loop : -2.52 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 493 TYR 0.022 0.003 TYR E 411 PHE 0.023 0.003 PHE D 386 TRP 0.058 0.003 TRP A 329 HIS 0.009 0.002 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00666 (12954) covalent geometry : angle 0.95590 (17457) hydrogen bonds : bond 0.04611 ( 299) hydrogen bonds : angle 6.91112 ( 864) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1740.41 seconds wall clock time: 31 minutes 8.97 seconds (1868.97 seconds total)