Starting phenix.real_space_refine on Wed Mar 4 10:27:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n7n_0359/03_2026/6n7n_0359.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n7n_0359/03_2026/6n7n_0359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6n7n_0359/03_2026/6n7n_0359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n7n_0359/03_2026/6n7n_0359.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6n7n_0359/03_2026/6n7n_0359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n7n_0359/03_2026/6n7n_0359.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 30 5.49 5 Mg 5 5.21 5 S 78 5.16 5 C 7962 2.51 5 N 2257 2.21 5 O 2522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12854 Number of models: 1 Model: "" Number of chains: 12 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: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2111 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 4, 'TRANS': 269} Chain breaks: 3 Chain: "C" Number of atoms: 2127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2127 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 4, 'TRANS': 271} 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: 1984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1984 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 252} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "T" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 300 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} 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} Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.77, per 1000 atoms: 0.22 Number of scatterers: 12854 At special positions: 0 Unit cell: (80.25, 127.33, 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 30 15.00 Mg 5 11.99 O 2522 8.00 N 2257 7.00 C 7962 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 404.2 milliseconds 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2866 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 7 sheets defined 37.1% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 273 through 280 removed outlier: 4.008A pdb=" N SER A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 removed outlier: 4.160A pdb=" N ASN A 296 " --> pdb=" O CYS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 331 removed outlier: 3.666A pdb=" N PHE A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 358 Processing helix chain 'A' and resid 361 through 364 removed outlier: 3.689A pdb=" N GLN A 364 " --> pdb=" O ARG A 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 361 through 364' Processing helix chain 'A' and resid 365 through 375 removed outlier: 3.947A pdb=" N LYS A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 375' Processing helix chain 'A' and resid 378 through 384 removed outlier: 3.831A pdb=" N ASP A 383 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.537A pdb=" N TYR A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 removed outlier: 4.104A pdb=" N VAL A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 454 Processing helix chain 'A' and resid 482 through 486 removed outlier: 3.769A pdb=" N ASP A 485 " --> pdb=" O SER A 482 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU A 486 " --> pdb=" O ILE A 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 482 through 486' Processing helix chain 'B' and resid 269 through 272 removed outlier: 3.786A pdb=" N ARG B 272 " --> pdb=" O LEU B 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 269 through 272' Processing helix chain 'B' and resid 273 through 280 removed outlier: 3.574A pdb=" N GLU B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 removed outlier: 4.319A pdb=" N ASN B 296 " --> pdb=" O CYS B 292 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 292 through 297' Processing helix chain 'B' and resid 317 through 332 Processing helix chain 'B' and resid 345 through 358 removed outlier: 3.682A pdb=" N THR B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 375 removed outlier: 3.677A pdb=" N ILE B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU B 374 " --> pdb=" O ARG B 370 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 387 removed outlier: 3.532A pdb=" N GLU B 384 " --> pdb=" O GLN B 380 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU B 385 " --> pdb=" O TRP B 381 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 414 Processing helix chain 'B' and resid 426 through 431 removed outlier: 3.966A pdb=" N VAL B 430 " --> pdb=" O ILE B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 454 Processing helix chain 'B' and resid 482 through 486 removed outlier: 3.759A pdb=" N ASP B 485 " --> pdb=" O SER B 482 " (cutoff:3.500A) removed outlier: 3.870A 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 271 through 277 removed outlier: 3.666A pdb=" N ILE C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 300 removed outlier: 4.426A pdb=" N ASN C 296 " --> pdb=" O CYS C 292 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP C 297 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS C 298 " --> pdb=" O GLY C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 331 removed outlier: 3.769A pdb=" N GLN C 328 " --> pdb=" O GLN C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 358 removed outlier: 3.697A pdb=" N THR C 349 " --> pdb=" O SER C 345 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU C 351 " --> pdb=" O GLU C 347 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 353 " --> pdb=" O THR C 349 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C 355 " --> pdb=" O GLU C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 375 removed outlier: 3.748A pdb=" N LYS C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 386 removed outlier: 4.138A pdb=" N GLN C 380 " --> pdb=" O GLY C 376 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU C 385 " --> pdb=" O TRP C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 416 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 437 through 457 removed outlier: 4.072A pdb=" N MET C 441 " --> pdb=" O ASP C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 486 removed outlier: 3.830A pdb=" N LEU C 486 " --> pdb=" O ILE C 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 277 Processing helix chain 'D' and resid 318 through 329 removed outlier: 3.648A pdb=" N GLN D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN D 325 " --> pdb=" O PHE D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 358 removed outlier: 3.696A pdb=" N THR D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 370 removed outlier: 3.660A pdb=" N LYS D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG D 370 " --> pdb=" O ASP D 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 365 through 370' Processing helix chain 'D' and resid 370 through 375 removed outlier: 3.557A pdb=" N GLU D 374 " --> pdb=" O ARG D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 386 removed outlier: 3.509A pdb=" N ASP D 383 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU D 385 " --> pdb=" O TRP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 415 Processing helix chain 'D' and resid 426 through 430 Processing helix chain 'D' and resid 440 through 457 removed outlier: 3.621A pdb=" N LEU D 445 " --> pdb=" O MET D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 478 removed outlier: 3.563A pdb=" N GLU D 477 " --> pdb=" O ALA D 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 277 Processing helix chain 'E' and resid 317 through 329 removed outlier: 3.732A pdb=" N PHE E 321 " --> pdb=" O GLY E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 358 removed outlier: 3.651A pdb=" N LEU E 353 " --> pdb=" O THR E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 372 removed outlier: 3.615A pdb=" N LYS E 369 " --> pdb=" O SER E 365 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG E 370 " --> pdb=" O ASP E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 387 removed outlier: 3.970A pdb=" N LEU E 385 " --> pdb=" O TRP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 415 Processing helix chain 'E' and resid 440 through 457 removed outlier: 3.968A pdb=" N LEU E 445 " --> pdb=" O MET E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 478 removed outlier: 3.610A pdb=" N GLU E 477 " --> pdb=" O ALA E 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 490 through 495 removed outlier: 3.512A pdb=" N GLN E 494 " --> pdb=" O GLY E 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 279 Processing helix chain 'F' and resid 317 through 329 Processing helix chain 'F' and resid 347 through 358 removed outlier: 3.632A pdb=" N LEU F 353 " --> pdb=" O THR F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 372 removed outlier: 3.975A pdb=" N ARG F 370 " --> pdb=" O ASP F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 387 removed outlier: 3.677A pdb=" N GLU F 384 " --> pdb=" O GLN F 380 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU F 385 " --> pdb=" O TRP F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 415 Processing helix chain 'F' and resid 441 through 457 removed outlier: 3.619A pdb=" N LEU F 445 " --> pdb=" O MET F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 478 removed outlier: 3.778A pdb=" N GLY F 478 " --> pdb=" O HIS F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 494 removed outlier: 3.894A pdb=" N ARG F 493 " --> pdb=" O GLY F 490 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 267 removed outlier: 3.508A pdb=" N ILE B 463 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 307 " --> pdb=" O THR B 498 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ILE B 500 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N MET B 309 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N LEU B 502 " --> pdb=" O MET B 309 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR B 311 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE B 499 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL B 514 " --> pdb=" O TYR B 532 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TYR B 532 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL B 516 " --> pdb=" O ALA B 530 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 542 through 544 removed outlier: 7.121A pdb=" N VAL A 516 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N TYR A 532 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL A 514 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE A 499 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE A 308 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLY A 338 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 266 removed outlier: 3.754A pdb=" N LEU C 393 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR C 394 " --> pdb=" O LEU C 339 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE C 308 " --> pdb=" O VAL C 462 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE C 499 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C 516 " --> pdb=" O GLY C 531 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY C 531 " --> pdb=" O VAL C 516 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE C 518 " --> pdb=" O ILE C 529 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE C 529 " --> pdb=" O ILE C 518 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 265 through 267 removed outlier: 6.748A pdb=" N GLY D 338 " --> pdb=" O ILE D 422 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE D 421 " --> pdb=" O VAL D 461 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ILE D 463 " --> pdb=" O ILE D 421 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU D 423 " --> pdb=" O ILE D 463 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ILE D 308 " --> pdb=" O VAL D 462 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N CYS D 464 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N VAL D 310 " --> pdb=" O CYS D 464 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR D 498 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE D 499 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL D 514 " --> pdb=" O TYR D 532 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TYR D 532 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL D 516 " --> pdb=" O ALA D 530 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 265 through 267 removed outlier: 3.588A pdb=" N VAL D 266 " --> pdb=" O LEU E 393 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 265 through 267 removed outlier: 3.737A pdb=" N VAL E 266 " --> pdb=" O LEU F 393 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL F 337 " --> pdb=" O HIS F 392 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N TYR F 394 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE F 421 " --> pdb=" O VAL F 461 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL F 310 " --> pdb=" O VAL F 462 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR F 498 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE F 499 " --> pdb=" O LEU F 519 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL F 514 " --> pdb=" O TYR F 532 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N TYR F 532 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL F 516 " --> pdb=" O ALA F 530 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 337 through 340 removed outlier: 6.531A pdb=" N ILE E 421 " --> pdb=" O VAL E 461 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE E 308 " --> pdb=" O VAL E 462 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N MET E 309 " --> pdb=" O ILE E 500 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N LEU E 502 " --> pdb=" O MET E 309 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR E 311 " --> pdb=" O LEU E 502 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE E 499 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL E 514 " --> pdb=" O TYR E 532 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TYR E 532 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL E 516 " --> pdb=" O ALA E 530 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2150 1.31 - 1.44: 3220 1.44 - 1.57: 7473 1.57 - 1.70: 54 1.70 - 1.83: 132 Bond restraints: 13029 Sorted by residual: bond pdb=" C6 TTP D 700 " pdb=" N1 TTP D 700 " ideal model delta sigma weight residual 1.337 1.428 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C6 TTP C 700 " pdb=" N1 TTP C 700 " ideal model delta sigma weight residual 1.337 1.427 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C6 TTP F 700 " pdb=" N1 TTP F 700 " ideal model delta sigma weight residual 1.337 1.426 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C6 TTP B 700 " pdb=" N1 TTP B 700 " ideal model delta sigma weight residual 1.337 1.425 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" C6 TTP E 700 " pdb=" N1 TTP E 700 " ideal model delta sigma weight residual 1.337 1.420 -0.083 2.00e-02 2.50e+03 1.70e+01 ... (remaining 13024 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 17194 2.64 - 5.28: 297 5.28 - 7.92: 60 7.92 - 10.56: 17 10.56 - 13.20: 6 Bond angle restraints: 17574 Sorted by residual: angle pdb=" N ILE E 442 " pdb=" CA ILE E 442 " pdb=" C ILE E 442 " ideal model delta sigma weight residual 111.81 107.50 4.31 8.60e-01 1.35e+00 2.51e+01 angle pdb=" O3' DT T 5 " pdb=" C3' DT T 5 " pdb=" C2' DT T 5 " ideal model delta sigma weight residual 111.50 118.65 -7.15 1.50e+00 4.44e-01 2.27e+01 angle pdb=" PA TTP D 700 " pdb=" O3A TTP D 700 " pdb=" PB TTP D 700 " ideal model delta sigma weight residual 120.50 133.70 -13.20 3.00e+00 1.11e-01 1.94e+01 angle pdb=" PB TTP C 700 " pdb=" O3B TTP C 700 " pdb=" PG TTP C 700 " ideal model delta sigma weight residual 120.50 132.63 -12.13 3.00e+00 1.11e-01 1.64e+01 angle pdb=" PA TTP C 700 " pdb=" O3A TTP C 700 " pdb=" PB TTP C 700 " ideal model delta sigma weight residual 120.50 132.60 -12.10 3.00e+00 1.11e-01 1.63e+01 ... (remaining 17569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.60: 7631 35.60 - 71.20: 127 71.20 - 106.80: 11 106.80 - 142.40: 5 142.40 - 178.00: 7 Dihedral angle restraints: 7781 sinusoidal: 3305 harmonic: 4476 Sorted by residual: dihedral pdb=" O2G TTP F 700 " pdb=" O3B TTP F 700 " pdb=" PG TTP F 700 " pdb=" PB TTP F 700 " ideal model delta sinusoidal sigma weight residual -180.00 -2.00 -178.00 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2G TTP D 700 " pdb=" O3B TTP D 700 " pdb=" PG TTP D 700 " pdb=" PB TTP D 700 " ideal model delta sinusoidal sigma weight residual -180.00 -2.43 -177.57 1 2.00e+01 2.50e-03 4.80e+01 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 -58.32 114.32 -172.64 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 7778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1560 0.064 - 0.128: 377 0.128 - 0.193: 55 0.193 - 0.257: 7 0.257 - 0.321: 3 Chirality restraints: 2002 Sorted by residual: chirality pdb=" C3' DT T 5 " pdb=" C4' DT T 5 " pdb=" O3' DT T 5 " pdb=" C2' DT T 5 " both_signs ideal model delta sigma weight residual False -2.66 -2.34 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" C4' TTP B 700 " pdb=" C3' TTP B 700 " pdb=" C5' TTP B 700 " pdb=" O4' TTP B 700 " both_signs ideal model delta sigma weight residual False -2.50 -2.76 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C3' TTP F 700 " pdb=" C2' TTP F 700 " pdb=" C4' TTP F 700 " pdb=" O3' TTP F 700 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1999 not shown) Planarity restraints: 2166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 358 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.08e+00 pdb=" C ASN B 358 " -0.039 2.00e-02 2.50e+03 pdb=" O ASN B 358 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG B 359 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 342 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" C LEU C 342 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU C 342 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN C 343 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D 510 " 0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO D 511 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 511 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 511 " 0.027 5.00e-02 4.00e+02 ... (remaining 2163 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 62 2.56 - 3.15: 9191 3.15 - 3.73: 18570 3.73 - 4.32: 26525 4.32 - 4.90: 44708 Nonbonded interactions: 99056 Sorted by model distance: nonbonded pdb=" OE1 GLN D 343 " pdb="MG MG D 701 " model vdw 1.975 2.170 nonbonded pdb=" O1B TTP B 700 " pdb="MG MG B 701 " model vdw 1.985 2.170 nonbonded pdb=" NE2 GLN B 343 " pdb="MG MG B 701 " model vdw 2.041 2.250 nonbonded pdb=" O2B TTP F 700 " pdb="MG MG F 701 " model vdw 2.054 2.170 nonbonded pdb=" O1G TTP C 700 " pdb="MG MG C 701 " model vdw 2.116 2.170 ... (remaining 99051 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 440 and (name N or name CA or name C or name O or name CB )) o \ r resid 441 through 506 or resid 510 through 545)) selection = (chain 'B' and (resid 264 through 280 or resid 285 through 373 or resid 377 thro \ ugh 395 or resid 404 through 429 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 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 440 through 506 or resid 510 through 545)) selection = (chain 'E' and (resid 264 through 429 or resid 440 through 506 or resid 510 thro \ ugh 545)) selection = (chain 'F' and (resid 264 through 506 or resid 510 through 545)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.360 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 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 : 0.006 0.091 13029 Z= 0.307 Angle : 0.987 13.201 17574 Z= 0.519 Chirality : 0.057 0.321 2002 Planarity : 0.004 0.048 2166 Dihedral : 14.773 177.997 4915 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.74 % Allowed : 3.48 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.49 (0.18), residues: 1556 helix: -2.73 (0.17), residues: 521 sheet: -0.65 (0.30), residues: 318 loop : -2.75 (0.19), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 359 TYR 0.013 0.002 TYR A 535 PHE 0.016 0.002 PHE D 386 TRP 0.026 0.003 TRP B 541 HIS 0.008 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00589 (13029) covalent geometry : angle 0.98722 (17574) hydrogen bonds : bond 0.15778 ( 416) hydrogen bonds : angle 7.33577 ( 1188) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 329 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 368 LEU cc_start: 0.7895 (tt) cc_final: 0.7688 (tt) REVERT: D 504 ARG cc_start: 0.6670 (OUTLIER) cc_final: 0.6289 (ptm-80) REVERT: F 309 MET cc_start: 0.7792 (mmm) cc_final: 0.7275 (mmt) outliers start: 10 outliers final: 1 residues processed: 338 average time/residue: 0.1343 time to fit residues: 62.2019 Evaluate side-chains 177 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 175 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 504 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.0070 chunk 149 optimal weight: 0.9990 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 ASN B 357 HIS C 325 GLN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 ASN D 358 ASN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 HIS E 358 ASN E 425 HIS E 507 GLN F 325 GLN ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 ASN ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.167584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.151060 restraints weight = 19602.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.153783 restraints weight = 11185.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.155665 restraints weight = 7387.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.156906 restraints weight = 5417.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.157692 restraints weight = 4319.358| |-----------------------------------------------------------------------------| r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13029 Z= 0.094 Angle : 0.544 6.704 17574 Z= 0.271 Chirality : 0.042 0.144 2002 Planarity : 0.003 0.036 2166 Dihedral : 15.997 177.092 1934 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.70 % Allowed : 10.07 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.20), residues: 1556 helix: -0.92 (0.22), residues: 513 sheet: -0.29 (0.30), residues: 321 loop : -2.23 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 517 TYR 0.017 0.001 TYR A 547 PHE 0.022 0.001 PHE B 321 TRP 0.007 0.001 TRP C 381 HIS 0.006 0.001 HIS E 278 Details of bonding type rmsd covalent geometry : bond 0.00200 (13029) covalent geometry : angle 0.54416 (17574) hydrogen bonds : bond 0.02794 ( 416) hydrogen bonds : angle 4.99125 ( 1188) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 215 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 ASP cc_start: 0.3777 (t0) cc_final: 0.3557 (t0) REVERT: A 487 ARG cc_start: 0.6616 (ttp80) cc_final: 0.5322 (ttt-90) REVERT: A 542 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7385 (pp) REVERT: B 344 GLU cc_start: 0.5673 (mp0) cc_final: 0.5206 (mp0) REVERT: C 438 GLU cc_start: 0.6057 (tt0) cc_final: 0.5612 (pm20) REVERT: D 441 MET cc_start: 0.6807 (mmt) cc_final: 0.6563 (mmm) REVERT: D 482 SER cc_start: 0.7386 (m) cc_final: 0.7024 (p) REVERT: E 343 GLN cc_start: 0.6222 (tt0) cc_final: 0.5835 (tp-100) outliers start: 23 outliers final: 12 residues processed: 227 average time/residue: 0.1050 time to fit residues: 35.2405 Evaluate side-chains 175 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain F residue 481 VAL Chi-restraints excluded: chain F residue 533 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 62 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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** A 475 HIS ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 GLN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.163869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.149251 restraints weight = 20085.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.151126 restraints weight = 13355.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.152395 restraints weight = 9827.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.153324 restraints weight = 7851.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.153953 restraints weight = 6638.195| |-----------------------------------------------------------------------------| r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13029 Z= 0.154 Angle : 0.625 8.063 17574 Z= 0.307 Chirality : 0.045 0.153 2002 Planarity : 0.003 0.030 2166 Dihedral : 15.886 178.551 1929 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.03 % Allowed : 12.14 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.21), residues: 1556 helix: -0.44 (0.22), residues: 533 sheet: -0.34 (0.30), residues: 323 loop : -2.13 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 517 TYR 0.015 0.001 TYR A 547 PHE 0.023 0.002 PHE C 321 TRP 0.011 0.002 TRP A 329 HIS 0.007 0.001 HIS B 392 Details of bonding type rmsd covalent geometry : bond 0.00359 (13029) covalent geometry : angle 0.62548 (17574) hydrogen bonds : bond 0.03538 ( 416) hydrogen bonds : angle 4.80369 ( 1188) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 473 LYS cc_start: 0.3541 (ptmt) cc_final: 0.2825 (ttmt) REVERT: A 487 ARG cc_start: 0.6706 (ttp80) cc_final: 0.5520 (ttt-90) REVERT: A 542 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7450 (pp) REVERT: C 438 GLU cc_start: 0.6008 (tt0) cc_final: 0.5720 (pm20) REVERT: D 288 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6678 (mt) REVERT: D 441 MET cc_start: 0.6951 (mmt) cc_final: 0.6686 (mmm) REVERT: D 482 SER cc_start: 0.7303 (m) cc_final: 0.7053 (p) REVERT: E 343 GLN cc_start: 0.6276 (tt0) cc_final: 0.5951 (tp-100) REVERT: E 499 ILE cc_start: 0.7034 (OUTLIER) cc_final: 0.6703 (mt) REVERT: E 503 GLU cc_start: 0.6490 (mp0) cc_final: 0.5422 (mp0) outliers start: 41 outliers final: 26 residues processed: 192 average time/residue: 0.1012 time to fit residues: 29.2118 Evaluate side-chains 172 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 481 VAL Chi-restraints excluded: chain F residue 484 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 68 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 HIS B 444 ASN C 465 HIS ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.160325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.145712 restraints weight = 20373.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.147515 restraints weight = 13616.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.148786 restraints weight = 10097.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.149554 restraints weight = 8078.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.150267 restraints weight = 6913.605| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13029 Z= 0.188 Angle : 0.665 7.938 17574 Z= 0.329 Chirality : 0.046 0.151 2002 Planarity : 0.004 0.035 2166 Dihedral : 15.968 177.236 1929 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.85 % Allowed : 11.70 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.21), residues: 1556 helix: -0.38 (0.22), residues: 528 sheet: -0.44 (0.30), residues: 313 loop : -2.05 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 517 TYR 0.014 0.002 TYR A 547 PHE 0.021 0.002 PHE C 321 TRP 0.013 0.002 TRP A 329 HIS 0.009 0.001 HIS B 392 Details of bonding type rmsd covalent geometry : bond 0.00450 (13029) covalent geometry : angle 0.66471 (17574) hydrogen bonds : bond 0.03819 ( 416) hydrogen bonds : angle 4.96746 ( 1188) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 146 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 473 LYS cc_start: 0.3084 (ptmt) cc_final: 0.2220 (ttmt) REVERT: A 487 ARG cc_start: 0.7013 (ttp80) cc_final: 0.5675 (ttt-90) REVERT: A 542 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7487 (pp) REVERT: D 441 MET cc_start: 0.6889 (mmt) cc_final: 0.6566 (mmm) REVERT: E 343 GLN cc_start: 0.6033 (tt0) cc_final: 0.5741 (tp-100) REVERT: E 499 ILE cc_start: 0.7106 (OUTLIER) cc_final: 0.6848 (mt) REVERT: E 503 GLU cc_start: 0.6608 (mp0) cc_final: 0.5367 (mp0) REVERT: E 517 ARG cc_start: 0.7313 (ttm-80) cc_final: 0.7108 (ttm-80) outliers start: 52 outliers final: 30 residues processed: 184 average time/residue: 0.0962 time to fit residues: 26.8242 Evaluate side-chains 170 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 481 VAL Chi-restraints excluded: chain F residue 484 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 111 optimal weight: 0.0980 chunk 60 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 114 optimal weight: 0.6980 chunk 151 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 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 = 0.4246 r_free = 0.4246 target = 0.165136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.150499 restraints weight = 20071.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.152425 restraints weight = 13283.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.153730 restraints weight = 9736.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.154675 restraints weight = 7772.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.155246 restraints weight = 6525.191| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13029 Z= 0.098 Angle : 0.528 7.874 17574 Z= 0.262 Chirality : 0.042 0.147 2002 Planarity : 0.002 0.020 2166 Dihedral : 15.091 176.400 1929 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.74 % Allowed : 13.99 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.21), residues: 1556 helix: 0.16 (0.23), residues: 531 sheet: -0.21 (0.30), residues: 314 loop : -1.90 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 517 TYR 0.012 0.001 TYR A 547 PHE 0.017 0.001 PHE C 321 TRP 0.007 0.001 TRP A 329 HIS 0.003 0.001 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00222 (13029) covalent geometry : angle 0.52796 (17574) hydrogen bonds : bond 0.02765 ( 416) hydrogen bonds : angle 4.47371 ( 1188) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 460 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7234 (tp) REVERT: A 473 LYS cc_start: 0.3768 (ptmt) cc_final: 0.3076 (ttmt) REVERT: A 487 ARG cc_start: 0.6820 (ttp80) cc_final: 0.5506 (ttt-90) REVERT: A 542 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7331 (pp) REVERT: B 316 MET cc_start: 0.7168 (mmt) cc_final: 0.6836 (mmt) REVERT: D 288 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6455 (mt) REVERT: D 441 MET cc_start: 0.6743 (mmt) cc_final: 0.6410 (mmm) REVERT: E 499 ILE cc_start: 0.7072 (OUTLIER) cc_final: 0.6779 (mt) REVERT: E 503 GLU cc_start: 0.6385 (mp0) cc_final: 0.5542 (mp0) REVERT: E 517 ARG cc_start: 0.7218 (ttm-80) cc_final: 0.6869 (ttm110) outliers start: 37 outliers final: 22 residues processed: 175 average time/residue: 0.0963 time to fit residues: 25.8211 Evaluate side-chains 169 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 481 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 75 optimal weight: 0.1980 chunk 52 optimal weight: 10.0000 chunk 154 optimal weight: 6.9990 chunk 1 optimal weight: 0.0020 chunk 127 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 0.0020 chunk 155 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 148 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 overall best weight: 0.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 HIS ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 ASN F 325 GLN ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.169659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.155234 restraints weight = 19536.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.157214 restraints weight = 12885.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.158563 restraints weight = 9368.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.159466 restraints weight = 7396.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.159950 restraints weight = 6234.366| |-----------------------------------------------------------------------------| r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13029 Z= 0.078 Angle : 0.482 7.671 17574 Z= 0.239 Chirality : 0.041 0.143 2002 Planarity : 0.002 0.024 2166 Dihedral : 14.368 171.063 1929 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.00 % Allowed : 15.25 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.22), residues: 1556 helix: 0.70 (0.24), residues: 532 sheet: 0.18 (0.31), residues: 325 loop : -1.71 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 504 TYR 0.011 0.001 TYR A 547 PHE 0.028 0.001 PHE C 321 TRP 0.005 0.001 TRP A 329 HIS 0.003 0.000 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00165 (13029) covalent geometry : angle 0.48234 (17574) hydrogen bonds : bond 0.02306 ( 416) hydrogen bonds : angle 4.09901 ( 1188) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7714 (mmt) cc_final: 0.6836 (mmp) REVERT: A 473 LYS cc_start: 0.4060 (ptmt) cc_final: 0.3093 (ttmt) REVERT: A 542 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7152 (pp) REVERT: B 316 MET cc_start: 0.6897 (mmt) cc_final: 0.6561 (mmt) REVERT: C 370 ARG cc_start: 0.6645 (mtm180) cc_final: 0.6241 (tpm170) REVERT: D 288 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6286 (mt) REVERT: E 503 GLU cc_start: 0.6205 (mp0) cc_final: 0.5612 (mp0) outliers start: 27 outliers final: 15 residues processed: 172 average time/residue: 0.0997 time to fit residues: 25.7483 Evaluate side-chains 160 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 481 VAL Chi-restraints excluded: chain F residue 510 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 116 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 104 optimal weight: 0.0030 chunk 136 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.165353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.150844 restraints weight = 19859.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.152767 restraints weight = 13121.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.154115 restraints weight = 9627.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.155029 restraints weight = 7603.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.155649 restraints weight = 6397.896| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13029 Z= 0.108 Angle : 0.531 9.984 17574 Z= 0.262 Chirality : 0.042 0.139 2002 Planarity : 0.002 0.029 2166 Dihedral : 14.453 165.571 1929 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.00 % Allowed : 15.47 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.22), residues: 1556 helix: 0.70 (0.24), residues: 533 sheet: 0.22 (0.31), residues: 310 loop : -1.67 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 517 TYR 0.010 0.001 TYR A 547 PHE 0.023 0.001 PHE C 321 TRP 0.012 0.001 TRP A 329 HIS 0.003 0.001 HIS B 392 Details of bonding type rmsd covalent geometry : bond 0.00252 (13029) covalent geometry : angle 0.53119 (17574) hydrogen bonds : bond 0.02820 ( 416) hydrogen bonds : angle 4.23661 ( 1188) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 316 MET cc_start: 0.7737 (mmt) cc_final: 0.7404 (mmp) REVERT: A 473 LYS cc_start: 0.3908 (ptmt) cc_final: 0.2954 (ttmt) REVERT: A 542 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7221 (pp) REVERT: C 370 ARG cc_start: 0.6674 (mtm180) cc_final: 0.6222 (tpm170) REVERT: D 288 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.6265 (mt) REVERT: E 499 ILE cc_start: 0.6893 (OUTLIER) cc_final: 0.6587 (mt) REVERT: E 503 GLU cc_start: 0.6260 (mp0) cc_final: 0.5548 (mp0) REVERT: E 517 ARG cc_start: 0.7240 (ttm-80) cc_final: 0.6695 (ttm170) outliers start: 27 outliers final: 20 residues processed: 161 average time/residue: 0.0982 time to fit residues: 24.1098 Evaluate side-chains 163 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain E residue 529 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 481 VAL Chi-restraints excluded: chain F residue 510 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 22 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 64 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 136 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 HIS ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 HIS ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.166512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.153336 restraints weight = 19784.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.154023 restraints weight = 15564.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.154995 restraints weight = 12042.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.155625 restraints weight = 9913.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.155736 restraints weight = 8882.738| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13029 Z= 0.095 Angle : 0.508 8.295 17574 Z= 0.252 Chirality : 0.042 0.137 2002 Planarity : 0.002 0.039 2166 Dihedral : 14.171 152.163 1929 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.07 % Allowed : 15.40 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.22), residues: 1556 helix: 0.73 (0.23), residues: 544 sheet: 0.29 (0.32), residues: 310 loop : -1.69 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 517 TYR 0.010 0.001 TYR A 547 PHE 0.021 0.001 PHE C 321 TRP 0.012 0.001 TRP A 329 HIS 0.003 0.001 HIS A 465 Details of bonding type rmsd covalent geometry : bond 0.00218 (13029) covalent geometry : angle 0.50803 (17574) hydrogen bonds : bond 0.02648 ( 416) hydrogen bonds : angle 4.20289 ( 1188) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 316 MET cc_start: 0.7748 (mmt) cc_final: 0.7400 (mmp) REVERT: A 473 LYS cc_start: 0.4029 (ptmt) cc_final: 0.2994 (ttmt) REVERT: A 542 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7202 (pp) REVERT: B 316 MET cc_start: 0.6992 (mmt) cc_final: 0.6674 (mmt) REVERT: C 370 ARG cc_start: 0.6665 (mtm180) cc_final: 0.6201 (tpm170) REVERT: D 288 LEU cc_start: 0.6625 (OUTLIER) cc_final: 0.6253 (mt) REVERT: E 499 ILE cc_start: 0.6885 (OUTLIER) cc_final: 0.6504 (mt) REVERT: E 503 GLU cc_start: 0.6193 (mp0) cc_final: 0.5569 (mp0) REVERT: E 517 ARG cc_start: 0.7216 (ttm-80) cc_final: 0.6680 (ttm170) outliers start: 28 outliers final: 22 residues processed: 162 average time/residue: 0.0921 time to fit residues: 23.0635 Evaluate side-chains 163 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain E residue 529 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 481 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 4 optimal weight: 10.0000 chunk 121 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 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 = 0.4252 r_free = 0.4252 target = 0.165645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.152348 restraints weight = 19953.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.153409 restraints weight = 15212.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.154097 restraints weight = 11767.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.154712 restraints weight = 9974.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.154821 restraints weight = 8776.503| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13029 Z= 0.100 Angle : 0.521 7.931 17574 Z= 0.257 Chirality : 0.042 0.138 2002 Planarity : 0.002 0.044 2166 Dihedral : 14.061 147.512 1929 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.00 % Allowed : 15.32 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.22), residues: 1556 helix: 0.81 (0.24), residues: 536 sheet: 0.28 (0.32), residues: 310 loop : -1.65 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 517 TYR 0.010 0.001 TYR A 547 PHE 0.021 0.001 PHE C 321 TRP 0.013 0.001 TRP A 329 HIS 0.003 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00231 (13029) covalent geometry : angle 0.52091 (17574) hydrogen bonds : bond 0.02744 ( 416) hydrogen bonds : angle 4.18542 ( 1188) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 316 MET cc_start: 0.7761 (mmt) cc_final: 0.7401 (mmp) REVERT: A 473 LYS cc_start: 0.3873 (ptmt) cc_final: 0.2890 (ttmt) REVERT: A 542 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7209 (pp) REVERT: B 316 MET cc_start: 0.7035 (mmt) cc_final: 0.6722 (mmt) REVERT: C 370 ARG cc_start: 0.6695 (mtm180) cc_final: 0.6217 (tpm170) REVERT: E 499 ILE cc_start: 0.6880 (OUTLIER) cc_final: 0.6519 (mt) REVERT: E 503 GLU cc_start: 0.6163 (mp0) cc_final: 0.5515 (mp0) REVERT: E 517 ARG cc_start: 0.7261 (ttm-80) cc_final: 0.6699 (ttm170) outliers start: 27 outliers final: 21 residues processed: 162 average time/residue: 0.0999 time to fit residues: 24.7873 Evaluate side-chains 160 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain E residue 529 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 481 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 57 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 151 optimal weight: 0.0570 chunk 55 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 133 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 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 = 0.4263 r_free = 0.4263 target = 0.166628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.152113 restraints weight = 19983.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.154065 restraints weight = 13123.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.155412 restraints weight = 9554.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.156283 restraints weight = 7550.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.156913 restraints weight = 6364.275| |-----------------------------------------------------------------------------| r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13029 Z= 0.090 Angle : 0.500 7.534 17574 Z= 0.248 Chirality : 0.042 0.136 2002 Planarity : 0.002 0.047 2166 Dihedral : 13.950 145.835 1929 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.78 % Allowed : 15.69 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.22), residues: 1556 helix: 0.99 (0.24), residues: 524 sheet: 0.27 (0.31), residues: 326 loop : -1.50 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 517 TYR 0.010 0.001 TYR A 547 PHE 0.021 0.001 PHE C 321 TRP 0.011 0.001 TRP A 329 HIS 0.003 0.001 HIS B 392 Details of bonding type rmsd covalent geometry : bond 0.00205 (13029) covalent geometry : angle 0.50012 (17574) hydrogen bonds : bond 0.02580 ( 416) hydrogen bonds : angle 4.11180 ( 1188) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 316 MET cc_start: 0.7671 (mmt) cc_final: 0.7311 (mmp) REVERT: A 473 LYS cc_start: 0.3966 (ptmt) cc_final: 0.3054 (ttmt) REVERT: A 542 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7117 (pp) REVERT: B 316 MET cc_start: 0.7087 (mmt) cc_final: 0.6758 (mmt) REVERT: C 370 ARG cc_start: 0.6602 (mtm180) cc_final: 0.6206 (tpm170) REVERT: E 499 ILE cc_start: 0.6879 (OUTLIER) cc_final: 0.6515 (mt) REVERT: E 503 GLU cc_start: 0.6285 (mp0) cc_final: 0.5582 (mp0) outliers start: 24 outliers final: 21 residues processed: 156 average time/residue: 0.0947 time to fit residues: 22.8369 Evaluate side-chains 164 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain E residue 529 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 481 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 46 optimal weight: 0.0980 chunk 94 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 84 optimal weight: 0.0050 chunk 85 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 overall best weight: 1.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** 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 = 0.4218 r_free = 0.4218 target = 0.162874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.149328 restraints weight = 20134.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.150280 restraints weight = 15328.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.150838 restraints weight = 12545.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.151731 restraints weight = 10570.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.151742 restraints weight = 9056.048| |-----------------------------------------------------------------------------| r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13029 Z= 0.135 Angle : 0.566 8.021 17574 Z= 0.280 Chirality : 0.043 0.142 2002 Planarity : 0.003 0.048 2166 Dihedral : 14.232 147.558 1929 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.00 % Allowed : 15.62 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.22), residues: 1556 helix: 0.78 (0.24), residues: 521 sheet: 0.18 (0.31), residues: 316 loop : -1.58 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 517 TYR 0.010 0.001 TYR A 547 PHE 0.022 0.002 PHE C 321 TRP 0.014 0.001 TRP A 329 HIS 0.005 0.001 HIS B 392 Details of bonding type rmsd covalent geometry : bond 0.00318 (13029) covalent geometry : angle 0.56647 (17574) hydrogen bonds : bond 0.03168 ( 416) hydrogen bonds : angle 4.37657 ( 1188) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1907.00 seconds wall clock time: 33 minutes 43.13 seconds (2023.13 seconds total)