Starting phenix.real_space_refine on Wed Jul 30 23:37:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n7s_0362/07_2025/6n7s_0362.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n7s_0362/07_2025/6n7s_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_0362/07_2025/6n7s_0362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n7s_0362/07_2025/6n7s_0362.map" model { file = "/net/cci-nas-00/data/ceres_data/6n7s_0362/07_2025/6n7s_0362.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n7s_0362/07_2025/6n7s_0362.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.45, per 1000 atoms: 0.66 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: 3.15 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.47 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: 3.11 Time building geometry restraints manager: 3.72 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: 0.980 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: 0.570 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 30.710 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.300 ------------------------------------------------------------------------------- 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 : 8.33 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.031 0.004 TRP A 329 HIS 0.012 0.003 HIS D 465 PHE 0.027 0.003 PHE D 289 TYR 0.023 0.003 TYR C 535 ARG 0.013 0.001 ARG C 303 Details of bonding type rmsd hydrogen bonds : bond 0.17320 ( 299) hydrogen bonds : angle 8.97117 ( 864) covalent geometry : bond 0.00779 (12954) covalent geometry : angle 1.19794 (17457) *********************** 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 : 1.425 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: 0.7542 (mp0) REVERT: A 484 THR cc_start: 0.8992 (p) cc_final: 0.8753 (p) REVERT: A 493 ARG cc_start: 0.5022 (OUTLIER) cc_final: 0.4501 (ptt90) REVERT: A 515 LEU cc_start: 0.5832 (tt) cc_final: 0.4882 (mt) REVERT: A 533 MET cc_start: 0.6506 (mtm) cc_final: 0.5811 (mpp) REVERT: B 308 ILE cc_start: 0.8926 (mt) cc_final: 0.8501 (mp) REVERT: B 344 GLU cc_start: 0.6258 (mt-10) cc_final: 0.5328 (mp0) REVERT: B 439 ARG cc_start: 0.5884 (OUTLIER) cc_final: 0.5611 (mmp80) REVERT: B 533 MET cc_start: 0.4618 (mtm) cc_final: 0.4407 (mtp) REVERT: C 428 ILE cc_start: 0.7174 (pt) cc_final: 0.5741 (pt) REVERT: C 462 VAL cc_start: 0.7719 (t) cc_final: 0.6996 (t) REVERT: C 494 GLN cc_start: 0.7508 (mt0) cc_final: 0.7301 (mt0) REVERT: D 299 THR cc_start: 0.8128 (t) cc_final: 0.7738 (m) REVERT: D 341 MET cc_start: 0.2878 (mpm) cc_final: 0.2620 (mmp) REVERT: D 446 MET cc_start: 0.6842 (tpp) cc_final: 0.6636 (tpp) REVERT: E 444 ASN cc_start: 0.8332 (t0) cc_final: 0.8003 (t0) REVERT: E 468 ASN cc_start: 0.7076 (t0) cc_final: 0.6792 (t0) REVERT: F 335 LYS cc_start: 0.9244 (mttm) cc_final: 0.8938 (mtmt) REVERT: F 341 MET cc_start: 0.5101 (mpm) cc_final: 0.4622 (mpm) outliers start: 14 outliers final: 2 residues processed: 349 average time/residue: 0.3097 time to fit residues: 145.3390 Evaluate side-chains 185 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 181 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 48 optimal weight: 0.0980 chunk 75 optimal weight: 0.5980 chunk 92 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 HIS B 278 HIS ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 ASN ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 HIS ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.143745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.128532 restraints weight = 41551.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.130851 restraints weight = 29196.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.132488 restraints weight = 21566.547| |-----------------------------------------------------------------------------| r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5608 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12954 Z= 0.129 Angle : 0.646 10.246 17457 Z= 0.332 Chirality : 0.045 0.185 1990 Planarity : 0.004 0.068 2163 Dihedral : 13.976 143.311 1896 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.07 % Allowed : 3.19 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.18 (0.18), residues: 1555 helix: -3.37 (0.17), residues: 499 sheet: -1.79 (0.29), residues: 302 loop : -2.71 (0.19), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 381 HIS 0.007 0.001 HIS C 425 PHE 0.019 0.001 PHE B 523 TYR 0.010 0.001 TYR E 535 ARG 0.006 0.001 ARG F 359 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 299) hydrogen bonds : angle 6.39448 ( 864) covalent geometry : bond 0.00284 (12954) covalent geometry : angle 0.64597 (17457) *********************** 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 227 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 1.519 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: A 348 GLU cc_start: 0.7912 (mp0) cc_final: 0.7319 (mp0) REVERT: A 425 HIS cc_start: 0.5354 (t-170) cc_final: 0.4957 (t-170) REVERT: A 503 GLU cc_start: 0.6742 (mt-10) cc_final: 0.5454 (tm-30) REVERT: B 289 PHE cc_start: 0.7267 (m-80) cc_final: 0.7051 (m-80) REVERT: B 452 PHE cc_start: 0.5870 (t80) cc_final: 0.5494 (t80) REVERT: B 494 GLN cc_start: 0.7143 (mp-120) cc_final: 0.6881 (mm-40) REVERT: C 425 HIS cc_start: 0.7707 (t-90) cc_final: 0.7482 (t-90) REVERT: C 499 ILE cc_start: 0.7897 (mp) cc_final: 0.7241 (mp) REVERT: D 318 LYS cc_start: 0.4215 (mtmt) cc_final: 0.3292 (mttm) REVERT: D 418 CYS cc_start: 0.6336 (m) cc_final: 0.4579 (m) REVERT: E 316 MET cc_start: 0.7859 (mtp) cc_final: 0.7094 (ttp) REVERT: E 343 GLN cc_start: 0.6897 (tt0) cc_final: 0.6473 (tt0) REVERT: E 412 MET cc_start: 0.5610 (mtp) cc_final: 0.4893 (mtp) REVERT: F 335 LYS cc_start: 0.9197 (mttm) cc_final: 0.8790 (mttm) outliers start: 1 outliers final: 1 residues processed: 227 average time/residue: 0.2802 time to fit residues: 88.2435 Evaluate side-chains 171 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 143 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 145 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 122 optimal weight: 0.2980 chunk 3 optimal weight: 0.1980 chunk 103 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 380 GLN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 ASN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN D 506 GLN D 507 GLN E 425 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.138911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.123675 restraints weight = 43182.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.126094 restraints weight = 30127.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.127757 restraints weight = 22092.811| |-----------------------------------------------------------------------------| r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5779 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12954 Z= 0.132 Angle : 0.635 10.291 17457 Z= 0.318 Chirality : 0.044 0.151 1990 Planarity : 0.004 0.063 2163 Dihedral : 13.368 141.913 1896 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.07 % Allowed : 4.00 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.19), residues: 1555 helix: -2.60 (0.20), residues: 484 sheet: -1.68 (0.29), residues: 308 loop : -2.40 (0.20), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 329 HIS 0.006 0.001 HIS D 475 PHE 0.010 0.001 PHE E 523 TYR 0.009 0.001 TYR A 411 ARG 0.008 0.001 ARG C 504 Details of bonding type rmsd hydrogen bonds : bond 0.03142 ( 299) hydrogen bonds : angle 5.83760 ( 864) covalent geometry : bond 0.00291 (12954) covalent geometry : angle 0.63492 (17457) *********************** 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 209 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 1.537 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: 0.7092 (mpp-170) cc_final: 0.5962 (mtm110) REVERT: A 503 GLU cc_start: 0.6773 (mt-10) cc_final: 0.5433 (tm-30) REVERT: B 289 PHE cc_start: 0.7318 (m-80) cc_final: 0.7098 (m-80) REVERT: C 425 HIS cc_start: 0.7685 (t-90) cc_final: 0.7377 (t-90) REVERT: C 499 ILE cc_start: 0.7713 (mp) cc_final: 0.7426 (mp) REVERT: C 527 THR cc_start: 0.3835 (p) cc_final: 0.3033 (p) REVERT: D 318 LYS cc_start: 0.4997 (mtmt) cc_final: 0.3525 (mttm) REVERT: D 477 GLU cc_start: 0.5300 (pp20) cc_final: 0.4612 (tm-30) REVERT: E 316 MET cc_start: 0.8004 (mtp) cc_final: 0.7218 (ttm) REVERT: E 406 LEU cc_start: 0.8918 (pt) cc_final: 0.8434 (mp) REVERT: E 412 MET cc_start: 0.5861 (mtp) cc_final: 0.5367 (mtp) REVERT: E 441 MET cc_start: 0.5871 (tpp) cc_final: 0.5634 (tpp) REVERT: F 309 MET cc_start: 0.2917 (mmm) cc_final: 0.2656 (mmt) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.2744 time to fit residues: 80.7817 Evaluate side-chains 155 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 148 optimal weight: 0.2980 chunk 139 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 105 optimal weight: 0.0370 chunk 57 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 overall best weight: 4.0664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 475 HIS ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 HIS ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 HIS ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 HIS ** E 325 GLN ** 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 = 0.4301 r_free = 0.4301 target = 0.129398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.115489 restraints weight = 45295.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.117406 restraints weight = 32749.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.118809 restraints weight = 24780.365| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6121 moved from start: 0.6017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 12954 Z= 0.252 Angle : 0.857 9.743 17457 Z= 0.427 Chirality : 0.051 0.217 1990 Planarity : 0.006 0.102 2163 Dihedral : 14.108 138.384 1896 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 0.07 % Allowed : 3.85 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.18), residues: 1555 helix: -2.69 (0.19), residues: 513 sheet: -1.70 (0.30), residues: 292 loop : -2.60 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 329 HIS 0.009 0.002 HIS D 425 PHE 0.020 0.003 PHE A 523 TYR 0.017 0.002 TYR B 535 ARG 0.011 0.001 ARG C 504 Details of bonding type rmsd hydrogen bonds : bond 0.04360 ( 299) hydrogen bonds : angle 6.52993 ( 864) covalent geometry : bond 0.00565 (12954) covalent geometry : angle 0.85732 (17457) *********************** 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 198 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 1.501 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: B 494 GLN cc_start: 0.7489 (mp-120) cc_final: 0.7191 (mm-40) REVERT: C 425 HIS cc_start: 0.7677 (t-90) cc_final: 0.7232 (t-90) REVERT: C 467 LYS cc_start: 0.6670 (pttp) cc_final: 0.6463 (pttp) REVERT: C 494 GLN cc_start: 0.7258 (mm110) cc_final: 0.6953 (mm-40) REVERT: D 477 GLU cc_start: 0.5852 (pp20) cc_final: 0.5032 (tm-30) REVERT: D 517 ARG cc_start: 0.5852 (mmm-85) cc_final: 0.5165 (mmm-85) REVERT: E 316 MET cc_start: 0.8471 (mtp) cc_final: 0.8222 (mtp) REVERT: E 412 MET cc_start: 0.6238 (mtp) cc_final: 0.5976 (mtp) REVERT: E 441 MET cc_start: 0.5919 (tpp) cc_final: 0.5611 (tpp) REVERT: F 309 MET cc_start: 0.3842 (mmm) cc_final: 0.3161 (mmt) REVERT: F 358 ASN cc_start: 0.8562 (m110) cc_final: 0.8078 (m110) outliers start: 1 outliers final: 0 residues processed: 197 average time/residue: 0.2599 time to fit residues: 73.0701 Evaluate side-chains 155 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 9 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 45 optimal weight: 0.0070 chunk 102 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- 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 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 HIS ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 475 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.134922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.120975 restraints weight = 44485.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.122955 restraints weight = 32059.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.124274 restraints weight = 24158.541| |-----------------------------------------------------------------------------| r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5925 moved from start: 0.6234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12954 Z= 0.108 Angle : 0.601 10.406 17457 Z= 0.299 Chirality : 0.044 0.166 1990 Planarity : 0.003 0.048 2163 Dihedral : 13.381 137.905 1896 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.19), residues: 1555 helix: -2.19 (0.21), residues: 496 sheet: -1.35 (0.30), residues: 297 loop : -2.20 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A 329 HIS 0.010 0.001 HIS E 278 PHE 0.008 0.001 PHE D 289 TYR 0.008 0.001 TYR E 411 ARG 0.005 0.001 ARG A 303 Details of bonding type rmsd hydrogen bonds : bond 0.02957 ( 299) hydrogen bonds : angle 5.56844 ( 864) covalent geometry : bond 0.00241 (12954) covalent geometry : angle 0.60116 (17457) *********************** 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 206 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.488 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: B 316 MET cc_start: 0.7707 (mmp) cc_final: 0.6775 (mmt) REVERT: B 333 MET cc_start: 0.4740 (mmt) cc_final: 0.4443 (mmt) REVERT: B 370 ARG cc_start: 0.7181 (mpt180) cc_final: 0.5410 (mmm160) REVERT: B 441 MET cc_start: 0.6834 (mpp) cc_final: 0.6617 (mpp) REVERT: C 299 THR cc_start: 0.8741 (p) cc_final: 0.8458 (m) REVERT: C 425 HIS cc_start: 0.7432 (t-90) cc_final: 0.7154 (t-90) REVERT: C 428 ILE cc_start: 0.7609 (pt) cc_final: 0.6242 (pt) REVERT: C 494 GLN cc_start: 0.6849 (mm110) cc_final: 0.6604 (mm110) REVERT: D 477 GLU cc_start: 0.5835 (pp20) cc_final: 0.5053 (tm-30) REVERT: E 316 MET cc_start: 0.8091 (mtp) cc_final: 0.7257 (ttm) REVERT: E 412 MET cc_start: 0.5985 (mtp) cc_final: 0.5680 (mtp) REVERT: E 441 MET cc_start: 0.5860 (tpp) cc_final: 0.5597 (tpp) REVERT: F 473 LYS cc_start: 0.7069 (ptmm) cc_final: 0.6865 (ptmt) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2604 time to fit residues: 77.5055 Evaluate side-chains 151 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 106 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 72 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 30 optimal weight: 0.0970 chunk 117 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.136339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.122831 restraints weight = 44506.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.124726 restraints weight = 32108.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.126012 restraints weight = 24448.290| |-----------------------------------------------------------------------------| r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5888 moved from start: 0.6514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12954 Z= 0.103 Angle : 0.594 10.030 17457 Z= 0.292 Chirality : 0.044 0.182 1990 Planarity : 0.003 0.067 2163 Dihedral : 13.095 136.380 1896 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.20), residues: 1555 helix: -1.88 (0.22), residues: 494 sheet: -1.05 (0.31), residues: 280 loop : -2.02 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 329 HIS 0.004 0.001 HIS D 465 PHE 0.010 0.001 PHE E 452 TYR 0.009 0.001 TYR F 411 ARG 0.010 0.000 ARG F 413 Details of bonding type rmsd hydrogen bonds : bond 0.02715 ( 299) hydrogen bonds : angle 5.35876 ( 864) covalent geometry : bond 0.00230 (12954) covalent geometry : angle 0.59353 (17457) *********************** 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 202 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 1.462 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: B 316 MET cc_start: 0.7628 (mmp) cc_final: 0.6731 (mmt) REVERT: B 370 ARG cc_start: 0.7172 (mpt180) cc_final: 0.5436 (mmm160) REVERT: C 494 GLN cc_start: 0.7071 (mm110) cc_final: 0.6796 (mm-40) REVERT: D 477 GLU cc_start: 0.5702 (pp20) cc_final: 0.4987 (tm-30) REVERT: E 316 MET cc_start: 0.7973 (mtp) cc_final: 0.7234 (ttm) REVERT: E 341 MET cc_start: 0.5149 (mmm) cc_final: 0.4784 (mmm) REVERT: E 379 ASP cc_start: 0.7074 (m-30) cc_final: 0.6744 (m-30) REVERT: E 412 MET cc_start: 0.5885 (mtp) cc_final: 0.5558 (mtp) REVERT: E 441 MET cc_start: 0.5610 (tpp) cc_final: 0.5336 (tpp) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.2532 time to fit residues: 73.0824 Evaluate side-chains 151 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 55 optimal weight: 0.4980 chunk 56 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 146 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 126 optimal weight: 0.0770 chunk 69 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 157 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 overall best weight: 1.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS ** 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** ** F 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.133696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.120950 restraints weight = 43330.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.122673 restraints weight = 32138.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.123636 restraints weight = 24686.096| |-----------------------------------------------------------------------------| r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5970 moved from start: 0.6916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12954 Z= 0.134 Angle : 0.649 9.880 17457 Z= 0.319 Chirality : 0.045 0.180 1990 Planarity : 0.004 0.066 2163 Dihedral : 13.184 136.003 1896 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.20), residues: 1555 helix: -1.90 (0.21), residues: 489 sheet: -0.98 (0.31), residues: 282 loop : -1.99 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 329 HIS 0.008 0.001 HIS D 425 PHE 0.011 0.001 PHE A 386 TYR 0.013 0.001 TYR A 547 ARG 0.010 0.001 ARG E 276 Details of bonding type rmsd hydrogen bonds : bond 0.03045 ( 299) hydrogen bonds : angle 5.47362 ( 864) covalent geometry : bond 0.00303 (12954) covalent geometry : angle 0.64908 (17457) *********************** 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 189 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.602 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: B 335 LYS cc_start: 0.7276 (mmtt) cc_final: 0.6622 (tttt) REVERT: B 370 ARG cc_start: 0.7345 (mpt180) cc_final: 0.5517 (mmm160) REVERT: C 323 ARG cc_start: 0.7203 (ptm160) cc_final: 0.6710 (mtm180) REVERT: C 425 HIS cc_start: 0.7267 (t-90) cc_final: 0.6927 (t-90) REVERT: C 441 MET cc_start: 0.5158 (ttp) cc_final: 0.4950 (ttp) REVERT: C 494 GLN cc_start: 0.7285 (mm110) cc_final: 0.7043 (mm-40) REVERT: D 477 GLU cc_start: 0.5693 (pp20) cc_final: 0.5306 (tm-30) REVERT: E 278 HIS cc_start: 0.5828 (m90) cc_final: 0.5376 (m90) REVERT: E 316 MET cc_start: 0.8256 (mtp) cc_final: 0.7366 (ttm) REVERT: E 341 MET cc_start: 0.5134 (mmm) cc_final: 0.4560 (mmm) REVERT: E 368 LEU cc_start: 0.8186 (pp) cc_final: 0.7905 (mp) REVERT: E 412 MET cc_start: 0.6004 (mtp) cc_final: 0.5651 (mtp) REVERT: E 441 MET cc_start: 0.5601 (tpp) cc_final: 0.5365 (tpp) REVERT: F 381 TRP cc_start: 0.5653 (m-90) cc_final: 0.5328 (m-10) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.2325 time to fit residues: 64.8650 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 : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 15 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 142 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 125 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- 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 278 HIS ** 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 507 GLN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.126630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.113808 restraints weight = 46228.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.115424 restraints weight = 34591.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.116360 restraints weight = 26903.743| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6211 moved from start: 0.7809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 12954 Z= 0.250 Angle : 0.881 10.382 17457 Z= 0.434 Chirality : 0.052 0.365 1990 Planarity : 0.005 0.055 2163 Dihedral : 13.957 138.827 1896 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.19), residues: 1555 helix: -2.38 (0.20), residues: 502 sheet: -1.41 (0.32), residues: 265 loop : -2.33 (0.19), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP F 381 HIS 0.014 0.002 HIS D 425 PHE 0.019 0.003 PHE A 523 TYR 0.022 0.003 TYR D 411 ARG 0.011 0.001 ARG E 493 Details of bonding type rmsd hydrogen bonds : bond 0.04324 ( 299) hydrogen bonds : angle 6.44725 ( 864) covalent geometry : bond 0.00562 (12954) covalent geometry : angle 0.88134 (17457) *********************** 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 173 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.521 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: A 412 MET cc_start: 0.4943 (ttm) cc_final: 0.4657 (ttp) REVERT: B 370 ARG cc_start: 0.7648 (mpt180) cc_final: 0.5698 (mmm160) REVERT: B 494 GLN cc_start: 0.7546 (mp-120) cc_final: 0.7036 (mp10) REVERT: C 316 MET cc_start: 0.8104 (mmm) cc_final: 0.7688 (ttm) REVERT: C 323 ARG cc_start: 0.7082 (ptm160) cc_final: 0.6423 (ptp-110) REVERT: C 440 LYS cc_start: 0.7330 (ttpt) cc_final: 0.6919 (tmmt) REVERT: C 441 MET cc_start: 0.5427 (ttp) cc_final: 0.4738 (ttp) REVERT: C 494 GLN cc_start: 0.7299 (mm110) cc_final: 0.7054 (mm-40) REVERT: D 425 HIS cc_start: 0.6522 (t70) cc_final: 0.6268 (t70) REVERT: D 477 GLU cc_start: 0.6338 (pp20) cc_final: 0.5635 (tm-30) REVERT: E 278 HIS cc_start: 0.6244 (m90) cc_final: 0.5453 (m90) REVERT: E 316 MET cc_start: 0.8243 (mtp) cc_final: 0.8009 (mtp) REVERT: E 341 MET cc_start: 0.5492 (mmm) cc_final: 0.4857 (mmm) REVERT: E 379 ASP cc_start: 0.7176 (m-30) cc_final: 0.6712 (m-30) REVERT: E 441 MET cc_start: 0.5686 (tpp) cc_final: 0.5352 (tpp) REVERT: E 497 ASP cc_start: 0.6666 (m-30) cc_final: 0.5554 (t0) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2566 time to fit residues: 64.2862 Evaluate side-chains 133 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 42 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 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** F 325 GLN F 358 ASN ** F 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 507 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.130552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.117570 restraints weight = 44048.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.119319 restraints weight = 32416.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.120507 restraints weight = 24742.903| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6087 moved from start: 0.7904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12954 Z= 0.149 Angle : 0.690 10.044 17457 Z= 0.339 Chirality : 0.046 0.246 1990 Planarity : 0.004 0.053 2163 Dihedral : 13.563 137.732 1896 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.19), residues: 1555 helix: -2.04 (0.21), residues: 502 sheet: -1.35 (0.31), residues: 275 loop : -2.14 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 329 HIS 0.010 0.001 HIS C 425 PHE 0.012 0.002 PHE D 378 TYR 0.013 0.001 TYR D 411 ARG 0.008 0.001 ARG B 504 Details of bonding type rmsd hydrogen bonds : bond 0.03210 ( 299) hydrogen bonds : angle 5.90952 ( 864) covalent geometry : bond 0.00339 (12954) covalent geometry : angle 0.69046 (17457) *********************** 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 180 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.433 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: B 335 LYS cc_start: 0.7691 (mmtt) cc_final: 0.7353 (tttt) REVERT: B 370 ARG cc_start: 0.7626 (mpt180) cc_final: 0.5702 (mmm160) REVERT: B 494 GLN cc_start: 0.7766 (mp-120) cc_final: 0.7289 (mm-40) REVERT: C 323 ARG cc_start: 0.6927 (ptm160) cc_final: 0.6094 (ptp-170) REVERT: C 440 LYS cc_start: 0.7223 (ttpt) cc_final: 0.6817 (tmmt) REVERT: C 441 MET cc_start: 0.5743 (ttp) cc_final: 0.5083 (ttp) REVERT: C 494 GLN cc_start: 0.7315 (mm110) cc_final: 0.7092 (mm-40) REVERT: D 477 GLU cc_start: 0.6059 (pp20) cc_final: 0.5587 (tm-30) REVERT: E 278 HIS cc_start: 0.6578 (m90) cc_final: 0.5832 (m90) REVERT: E 316 MET cc_start: 0.8320 (mtp) cc_final: 0.8095 (mtp) REVERT: E 379 ASP cc_start: 0.7095 (m-30) cc_final: 0.6608 (m-30) REVERT: E 441 MET cc_start: 0.5588 (tpp) cc_final: 0.5309 (tpp) REVERT: E 497 ASP cc_start: 0.6490 (m-30) cc_final: 0.5600 (t0) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2447 time to fit residues: 65.2801 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 : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 108 optimal weight: 9.9990 chunk 137 optimal weight: 0.5980 chunk 98 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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 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** F 358 ASN ** F 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.127797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.114381 restraints weight = 45251.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.116126 restraints weight = 33099.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.117408 restraints weight = 25333.298| |-----------------------------------------------------------------------------| r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 0.8256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12954 Z= 0.201 Angle : 0.775 9.905 17457 Z= 0.383 Chirality : 0.049 0.258 1990 Planarity : 0.004 0.053 2163 Dihedral : 13.711 137.291 1896 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.19), residues: 1555 helix: -2.14 (0.20), residues: 499 sheet: -1.49 (0.32), residues: 266 loop : -2.23 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 329 HIS 0.010 0.002 HIS C 425 PHE 0.012 0.002 PHE D 289 TYR 0.015 0.002 TYR D 411 ARG 0.010 0.001 ARG B 504 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 299) hydrogen bonds : angle 6.18326 ( 864) covalent geometry : bond 0.00459 (12954) covalent geometry : angle 0.77456 (17457) ********************** 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 174 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.502 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: B 370 ARG cc_start: 0.7506 (mpt180) cc_final: 0.5650 (mmm160) REVERT: B 466 LEU cc_start: 0.6849 (mt) cc_final: 0.6518 (pp) REVERT: B 510 MET cc_start: 0.6997 (ttt) cc_final: 0.6763 (ptm) REVERT: C 323 ARG cc_start: 0.7067 (ptm160) cc_final: 0.6462 (ptp-170) REVERT: C 440 LYS cc_start: 0.7336 (ttpt) cc_final: 0.6837 (tmmt) REVERT: C 441 MET cc_start: 0.5917 (ttp) cc_final: 0.5261 (ttp) REVERT: C 494 GLN cc_start: 0.7418 (mm110) cc_final: 0.7156 (mm-40) REVERT: D 477 GLU cc_start: 0.6268 (pp20) cc_final: 0.5805 (tm-30) REVERT: E 278 HIS cc_start: 0.6516 (m90) cc_final: 0.5760 (m-70) REVERT: E 316 MET cc_start: 0.8188 (mtp) cc_final: 0.7927 (mtp) REVERT: E 341 MET cc_start: 0.4795 (mmm) cc_final: 0.4260 (mmm) REVERT: E 379 ASP cc_start: 0.7095 (m-30) cc_final: 0.6585 (m-30) REVERT: E 441 MET cc_start: 0.5561 (tpp) cc_final: 0.5173 (tpp) REVERT: E 497 ASP cc_start: 0.6615 (m-30) cc_final: 0.5734 (t0) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2434 time to fit residues: 62.4043 Evaluate side-chains 135 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 25 optimal weight: 20.0000 chunk 123 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** F 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.130309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.116625 restraints weight = 44631.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.118507 restraints weight = 32260.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.119814 restraints weight = 24424.078| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6126 moved from start: 0.8391 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= 0.162 Angle : 0.717 10.009 17457 Z= 0.353 Chirality : 0.047 0.233 1990 Planarity : 0.004 0.055 2163 Dihedral : 13.598 136.907 1896 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.19), residues: 1555 helix: -1.97 (0.21), residues: 497 sheet: -1.50 (0.31), residues: 274 loop : -2.16 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 329 HIS 0.010 0.001 HIS C 425 PHE 0.016 0.002 PHE B 523 TYR 0.011 0.001 TYR D 411 ARG 0.008 0.001 ARG E 493 Details of bonding type rmsd hydrogen bonds : bond 0.03357 ( 299) hydrogen bonds : angle 5.95084 ( 864) covalent geometry : bond 0.00371 (12954) covalent geometry : angle 0.71677 (17457) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3769.26 seconds wall clock time: 66 minutes 38.54 seconds (3998.54 seconds total)