Starting phenix.real_space_refine on Sat Sep 12 01:43:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6n7n_0359/09_2026/6n7n_0359.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n7n_0359/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6n7n_0359/09_2026/6n7n_0359.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6n7n_0359/09_2026/6n7n_0359.cif" model { file = "/net/cci-nas-00/data/ceres_data/6n7n_0359/09_2026/6n7n_0359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n7n_0359/09_2026/6n7n_0359.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6n7n_0359/09_2026/6n7n_0359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n7n_0359/09_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-2.2.1-6174/lib/python3.11/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: 2.41, per 1000 atoms: 0.19 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: 0.95 Conformation dependent library (CDL) restraints added in 528.9 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: 0.32 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: 1.40 Time building geometry restraints manager: 1.28 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: 17192 2.64 - 5.28: 299 5.28 - 7.92: 59 7.92 - 10.56: 18 10.56 - 13.20: 6 Bond angle restraints: 17574 Sorted by residual: angle pdb=" O5' DT T 10 " pdb=" C5' DT T 10 " pdb=" C4' DT T 10 " ideal model delta sigma weight residual 109.40 113.42 -4.02 8.00e-01 1.56e+00 2.52e+01 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=" 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=" N3 DT T 8 " pdb=" C4 DT T 8 " pdb=" O4 DT T 8 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT T 11 " pdb=" C4 DT T 11 " pdb=" O4 DT T 11 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+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 - 0.078: 1688 0.078 - 0.157: 290 0.157 - 0.235: 15 0.235 - 0.313: 8 0.313 - 0.391: 1 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 -2.73 -2.34 -0.39 2.00e-01 2.50e+01 3.83e+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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.750 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 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= 0.318 Angle : 0.990 13.201 17574 Z= 0.538 Chirality : 0.058 0.391 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/Z covalent geometry : bond 0.00589 / 0.32 (13029) covalent geometry : angle 0.99027 / 0.54 (17574) hydrogen bonds : bond 0.15778 / 10.85 ( 416) hydrogen bonds : angle 7.33577 / 5.10 ( 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 : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 368 LEU cc_start: 0.7895 (tt) cc_final: 0.7690 (tt) REVERT: D 504 ARG cc_start: 0.6670 (OUTLIER) cc_final: 0.6288 (ptm-80) REVERT: F 309 MET cc_start: 0.7792 (mmm) cc_final: 0.7273 (mmt) outliers start: 10 outliers final: 1 residues processed: 338 average time/residue: 0.1313 time to fit residues: 61.3981 Evaluate side-chains 176 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 174 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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... ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 ASN B 357 HIS C 325 GLN C 380 GLN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 ASN C 475 HIS 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.170209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.155771 restraints weight = 19073.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.157765 restraints weight = 12262.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.159160 restraints weight = 8756.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.160059 restraints weight = 6816.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.160743 restraints weight = 5675.371| |-----------------------------------------------------------------------------| r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13029 Z= 0.100 Angle : 0.569 6.758 17574 Z= 0.285 Chirality : 0.043 0.157 2002 Planarity : 0.003 0.036 2166 Dihedral : 16.427 174.508 1934 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.85 % Allowed : 9.92 % 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: -2.22 (0.20), residues: 1556 helix: -1.13 (0.21), residues: 524 sheet: -0.29 (0.30), residues: 320 loop : -2.29 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 517 TYR 0.018 0.001 TYR A 547 PHE 0.018 0.001 PHE B 321 TRP 0.007 0.001 TRP C 329 HIS 0.010 0.001 HIS E 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 (13029) covalent geometry : angle 0.56890 / 0.29 (17574) hydrogen bonds : bond 0.03146 / 2.11 ( 416) hydrogen bonds : angle 5.19701 / 3.67 ( 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 223 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 LYS cc_start: 0.3747 (ptmt) cc_final: 0.3074 (ttmt) REVERT: A 487 ARG cc_start: 0.6612 (ttp80) cc_final: 0.5376 (ttt-90) REVERT: A 542 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7517 (pp) REVERT: B 344 GLU cc_start: 0.5738 (mp0) cc_final: 0.5420 (mp0) REVERT: C 438 GLU cc_start: 0.5980 (tt0) cc_final: 0.5694 (pm20) REVERT: D 482 SER cc_start: 0.7281 (m) cc_final: 0.6997 (p) REVERT: E 364 GLN cc_start: 0.6923 (tm-30) cc_final: 0.6642 (tt0) outliers start: 25 outliers final: 16 residues processed: 215 average time/residue: 0.0995 time to fit residues: 32.1353 Evaluate side-chains 176 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 367 SER Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain E residue 507 GLN Chi-restraints excluded: chain E residue 545 SER Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 385 LEU 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: 1.9990 chunk 101 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.164064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.149173 restraints weight = 20006.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.151078 restraints weight = 13364.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.152334 restraints weight = 9852.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.153127 restraints weight = 7883.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.153849 restraints weight = 6739.377| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13029 Z= 0.167 Angle : 0.650 7.314 17574 Z= 0.320 Chirality : 0.046 0.177 2002 Planarity : 0.004 0.035 2166 Dihedral : 16.294 179.603 1929 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.03 % Allowed : 11.32 % Favored : 85.64 % 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: -1.81 (0.21), residues: 1556 helix: -0.51 (0.22), residues: 511 sheet: -0.29 (0.31), residues: 320 loop : -2.14 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 361 TYR 0.014 0.002 TYR A 547 PHE 0.029 0.002 PHE C 321 TRP 0.012 0.002 TRP A 329 HIS 0.006 0.001 HIS B 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (13029) covalent geometry : angle 0.65041 / 0.32 (17574) hydrogen bonds : bond 0.03645 / 2.46 ( 416) hydrogen bonds : angle 4.98310 / 3.48 ( 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 205 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 164 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 ARG cc_start: 0.6640 (ttp80) cc_final: 0.5481 (ttt-90) REVERT: A 542 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7553 (pp) REVERT: D 369 LYS cc_start: 0.8218 (mtpt) cc_final: 0.8013 (mttt) REVERT: D 441 MET cc_start: 0.6931 (mmt) cc_final: 0.6657 (mmm) REVERT: E 499 ILE cc_start: 0.7050 (OUTLIER) cc_final: 0.6731 (mt) REVERT: E 503 GLU cc_start: 0.6522 (mp0) cc_final: 0.5428 (mp0) REVERT: F 485 ASP cc_start: 0.6200 (m-30) cc_final: 0.5972 (m-30) outliers start: 41 outliers final: 26 residues processed: 188 average time/residue: 0.1074 time to fit residues: 30.6556 Evaluate side-chains 175 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 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 390 THR Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 456 THR 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 373 ILE 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 288 LEU Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 483 ILE 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 379 ASP Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 458 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: 0.9990 chunk 58 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 50 optimal weight: 0.0040 chunk 15 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 380 GLN ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 HIS ** 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 = 0.4273 r_free = 0.4273 target = 0.167493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.152621 restraints weight = 19701.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.154541 restraints weight = 13040.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.155833 restraints weight = 9552.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.156802 restraints weight = 7570.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.157363 restraints weight = 6388.450| |-----------------------------------------------------------------------------| r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.2957 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= 0.096 Angle : 0.532 6.819 17574 Z= 0.265 Chirality : 0.043 0.144 2002 Planarity : 0.002 0.033 2166 Dihedral : 15.762 177.590 1929 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.37 % Allowed : 12.44 % Favored : 85.20 % 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: -1.34 (0.21), residues: 1556 helix: 0.05 (0.23), residues: 515 sheet: -0.13 (0.31), residues: 321 loop : -1.97 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 493 TYR 0.013 0.001 TYR A 547 PHE 0.019 0.001 PHE C 321 TRP 0.006 0.001 TRP A 329 HIS 0.003 0.001 HIS C 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (13029) covalent geometry : angle 0.53208 / 0.27 (17574) hydrogen bonds : bond 0.02738 / 1.82 ( 416) hydrogen bonds : angle 4.65288 / 3.27 ( 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 201 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 ASN cc_start: 0.7550 (m-40) cc_final: 0.7052 (m110) REVERT: A 446 MET cc_start: 0.7554 (mtp) cc_final: 0.7203 (mtp) REVERT: A 473 LYS cc_start: 0.4020 (ptmt) cc_final: 0.3349 (ttmt) REVERT: A 487 ARG cc_start: 0.6615 (ttp80) cc_final: 0.5469 (ttt-90) REVERT: A 542 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7295 (pp) REVERT: C 438 GLU cc_start: 0.5840 (tt0) cc_final: 0.5520 (pm20) REVERT: D 288 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6590 (mt) REVERT: D 441 MET cc_start: 0.6813 (mmt) cc_final: 0.6568 (mmm) REVERT: D 482 SER cc_start: 0.7355 (m) cc_final: 0.7085 (p) REVERT: F 485 ASP cc_start: 0.6107 (m-30) cc_final: 0.5901 (m-30) outliers start: 32 outliers final: 18 residues processed: 189 average time/residue: 0.1050 time to fit residues: 30.4112 Evaluate side-chains 171 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 GLN 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 481 VAL 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 279 LEU 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 F residue 322 VAL Chi-restraints excluded: chain F residue 458 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 111 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 82 optimal weight: 0.0070 chunk 78 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 chunk 36 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 151 optimal weight: 0.0040 chunk 20 optimal weight: 4.9990 overall best weight: 0.4010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** E 358 ASN E 425 HIS E 475 HIS ** 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 = 0.4283 r_free = 0.4283 target = 0.168423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.153722 restraints weight = 19824.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.155673 restraints weight = 13023.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.157039 restraints weight = 9507.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.157850 restraints weight = 7507.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.158599 restraints weight = 6369.371| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13029 Z= 0.087 Angle : 0.514 6.837 17574 Z= 0.256 Chirality : 0.042 0.144 2002 Planarity : 0.002 0.023 2166 Dihedral : 15.436 173.711 1929 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.44 % Allowed : 13.18 % Favored : 84.38 % 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: -1.05 (0.22), residues: 1556 helix: 0.29 (0.24), residues: 521 sheet: 0.03 (0.31), residues: 321 loop : -1.80 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 517 TYR 0.011 0.001 TYR A 547 PHE 0.026 0.001 PHE C 321 TRP 0.007 0.001 TRP A 329 HIS 0.005 0.000 HIS C 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.09 (13029) covalent geometry : angle 0.51418 / 0.26 (17574) hydrogen bonds : bond 0.02542 / 1.67 ( 416) hydrogen bonds : angle 4.47918 / 3.16 ( 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 188 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 LYS cc_start: 0.3794 (ptmt) cc_final: 0.3144 (ttmt) REVERT: A 487 ARG cc_start: 0.6742 (ttp80) cc_final: 0.5580 (ttt-90) REVERT: A 542 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7237 (pp) REVERT: C 446 MET cc_start: 0.7345 (ttt) cc_final: 0.7117 (tpp) REVERT: D 288 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6472 (mt) REVERT: D 441 MET cc_start: 0.6788 (mmt) cc_final: 0.6486 (mmm) REVERT: D 482 SER cc_start: 0.7269 (m) cc_final: 0.7046 (p) REVERT: F 485 ASP cc_start: 0.5941 (m-30) cc_final: 0.5716 (m-30) outliers start: 33 outliers final: 22 residues processed: 177 average time/residue: 0.1033 time to fit residues: 28.2354 Evaluate side-chains 168 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 309 MET Chi-restraints excluded: chain B residue 311 THR 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 447 THR Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 481 VAL Chi-restraints excluded: chain F residue 533 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 75 optimal weight: 0.2980 chunk 52 optimal weight: 9.9990 chunk 154 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 127 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 148 optimal weight: 0.2980 chunk 48 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 HIS ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 HIS ** 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 = 0.4263 r_free = 0.4263 target = 0.166784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.152267 restraints weight = 19723.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.154094 restraints weight = 13039.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.155396 restraints weight = 9593.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.156334 restraints weight = 7623.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.156897 restraints weight = 6418.808| |-----------------------------------------------------------------------------| r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.3356 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= 0.103 Angle : 0.531 7.548 17574 Z= 0.263 Chirality : 0.043 0.189 2002 Planarity : 0.002 0.023 2166 Dihedral : 15.159 167.324 1929 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.96 % Allowed : 13.10 % Favored : 83.94 % 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: -0.92 (0.22), residues: 1556 helix: 0.44 (0.24), residues: 530 sheet: 0.09 (0.31), residues: 329 loop : -1.80 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 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/Z covalent geometry : bond 0.00231 / 0.10 (13029) covalent geometry : angle 0.53124 / 0.26 (17574) hydrogen bonds : bond 0.02777 / 1.82 ( 416) hydrogen bonds : angle 4.41553 / 3.11 ( 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 191 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 487 ARG cc_start: 0.6763 (ttp80) cc_final: 0.5579 (ttt-90) REVERT: A 542 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7175 (pp) REVERT: D 288 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6418 (mt) REVERT: D 441 MET cc_start: 0.6856 (mmt) cc_final: 0.6537 (mmm) REVERT: E 499 ILE cc_start: 0.7078 (OUTLIER) cc_final: 0.6737 (mt) REVERT: F 485 ASP cc_start: 0.6194 (m-30) cc_final: 0.5985 (m-30) outliers start: 40 outliers final: 30 residues processed: 175 average time/residue: 0.1009 time to fit residues: 27.5416 Evaluate side-chains 178 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 309 MET Chi-restraints excluded: chain B residue 311 THR 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 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 279 LEU 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 483 ILE 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 428 ILE Chi-restraints excluded: chain E residue 477 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 116 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 156 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 136 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 475 HIS ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 ASN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 HIS ** 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 = 0.4228 r_free = 0.4228 target = 0.164143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.149497 restraints weight = 19917.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.151365 restraints weight = 13174.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.152703 restraints weight = 9707.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.153614 restraints weight = 7668.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.154137 restraints weight = 6469.709| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13029 Z= 0.139 Angle : 0.584 7.238 17574 Z= 0.288 Chirality : 0.044 0.202 2002 Planarity : 0.003 0.033 2166 Dihedral : 15.099 160.923 1929 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.03 % Allowed : 13.47 % Favored : 83.49 % 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: -1.06 (0.22), residues: 1556 helix: 0.30 (0.23), residues: 529 sheet: -0.06 (0.30), residues: 329 loop : -1.82 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 361 TYR 0.010 0.001 TYR A 547 PHE 0.023 0.002 PHE C 321 TRP 0.016 0.002 TRP A 329 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (13029) covalent geometry : angle 0.58387 / 0.29 (17574) hydrogen bonds : bond 0.03168 / 2.10 ( 416) hydrogen bonds : angle 4.58764 / 3.22 ( 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 187 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 473 LYS cc_start: 0.3818 (ptmt) cc_final: 0.3258 (ttmt) REVERT: A 487 ARG cc_start: 0.6745 (ttp80) cc_final: 0.5525 (ttt-90) REVERT: A 542 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7264 (pp) REVERT: C 463 ILE cc_start: 0.5985 (mm) cc_final: 0.5766 (mm) REVERT: D 288 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6449 (mt) REVERT: D 441 MET cc_start: 0.6858 (mmt) cc_final: 0.6564 (mmm) REVERT: E 499 ILE cc_start: 0.7069 (OUTLIER) cc_final: 0.6774 (mt) outliers start: 41 outliers final: 29 residues processed: 173 average time/residue: 0.1021 time to fit residues: 27.4050 Evaluate side-chains 174 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 309 MET Chi-restraints excluded: chain B residue 311 THR 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 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 447 THR 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 267 SER Chi-restraints excluded: chain E residue 477 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 22 optimal weight: 9.9990 chunk 31 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 75 optimal weight: 0.0570 chunk 73 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 136 optimal weight: 9.9990 overall best weight: 1.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** E 425 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.164129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.149607 restraints weight = 19912.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.151439 restraints weight = 13248.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.152727 restraints weight = 9768.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.153502 restraints weight = 7789.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.154207 restraints weight = 6635.499| |-----------------------------------------------------------------------------| r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13029 Z= 0.130 Angle : 0.567 7.572 17574 Z= 0.280 Chirality : 0.044 0.147 2002 Planarity : 0.003 0.036 2166 Dihedral : 14.877 155.106 1929 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.89 % Allowed : 13.62 % Favored : 83.49 % 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: -1.01 (0.22), residues: 1556 helix: 0.38 (0.23), residues: 529 sheet: -0.07 (0.31), residues: 321 loop : -1.79 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 517 TYR 0.010 0.001 TYR A 547 PHE 0.021 0.001 PHE C 321 TRP 0.014 0.001 TRP A 329 HIS 0.005 0.001 HIS B 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (13029) covalent geometry : angle 0.56708 / 0.28 (17574) hydrogen bonds : bond 0.03094 / 2.03 ( 416) hydrogen bonds : angle 4.58021 / 3.21 ( 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 179 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 140 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 473 LYS cc_start: 0.3585 (ptmt) cc_final: 0.3018 (ttmt) REVERT: A 487 ARG cc_start: 0.6890 (ttp80) cc_final: 0.5545 (ttt-90) REVERT: A 542 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7240 (pp) REVERT: B 316 MET cc_start: 0.7243 (mmt) cc_final: 0.6855 (mmt) REVERT: C 463 ILE cc_start: 0.5987 (mm) cc_final: 0.5749 (mm) REVERT: D 288 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6447 (mt) REVERT: D 441 MET cc_start: 0.6870 (mmt) cc_final: 0.6567 (mmm) REVERT: E 499 ILE cc_start: 0.7011 (OUTLIER) cc_final: 0.6739 (mt) outliers start: 39 outliers final: 28 residues processed: 166 average time/residue: 0.1019 time to fit residues: 26.1569 Evaluate side-chains 170 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 311 THR 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 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 447 THR 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 267 SER Chi-restraints excluded: chain E residue 477 GLU 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: 7.9990 chunk 121 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4209 r_free = 0.4209 target = 0.162551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.148013 restraints weight = 20177.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.149810 restraints weight = 13332.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.151098 restraints weight = 9801.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.151889 restraints weight = 7800.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.152589 restraints weight = 6630.318| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13029 Z= 0.144 Angle : 0.591 7.156 17574 Z= 0.291 Chirality : 0.045 0.156 2002 Planarity : 0.003 0.041 2166 Dihedral : 14.687 153.246 1929 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.59 % Allowed : 13.99 % Favored : 83.42 % 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: -1.02 (0.22), residues: 1556 helix: 0.38 (0.23), residues: 518 sheet: -0.16 (0.31), residues: 316 loop : -1.71 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 361 TYR 0.010 0.001 TYR A 547 PHE 0.022 0.002 PHE C 321 TRP 0.018 0.001 TRP A 329 HIS 0.005 0.001 HIS B 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (13029) covalent geometry : angle 0.59096 / 0.29 (17574) hydrogen bonds : bond 0.03327 / 2.19 ( 416) hydrogen bonds : angle 4.65890 / 3.24 ( 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 180 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 473 LYS cc_start: 0.3526 (ptmt) cc_final: 0.3027 (ttmt) REVERT: A 487 ARG cc_start: 0.6783 (ttp80) cc_final: 0.5479 (ttt-90) REVERT: A 542 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7296 (pp) REVERT: C 463 ILE cc_start: 0.5831 (mm) cc_final: 0.5592 (mm) REVERT: D 288 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6424 (mt) REVERT: D 441 MET cc_start: 0.6910 (mmt) cc_final: 0.6561 (mmm) REVERT: E 499 ILE cc_start: 0.7082 (OUTLIER) cc_final: 0.6846 (mt) outliers start: 35 outliers final: 27 residues processed: 171 average time/residue: 0.1036 time to fit residues: 27.3182 Evaluate side-chains 172 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 311 THR 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 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 267 SER Chi-restraints excluded: chain E residue 477 GLU 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: 5.9990 chunk 39 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 133 optimal weight: 0.0020 chunk 53 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.165287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.150938 restraints weight = 20174.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.152450 restraints weight = 13745.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.153732 restraints weight = 9869.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.153897 restraints weight = 8435.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.154247 restraints weight = 7925.253| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13029 Z= 0.096 Angle : 0.527 9.818 17574 Z= 0.261 Chirality : 0.043 0.189 2002 Planarity : 0.002 0.043 2166 Dihedral : 14.425 151.633 1929 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.22 % Allowed : 14.51 % 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: -0.72 (0.22), residues: 1556 helix: 0.70 (0.24), residues: 519 sheet: 0.12 (0.31), residues: 322 loop : -1.68 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 517 TYR 0.009 0.001 TYR A 547 PHE 0.019 0.001 PHE C 321 TRP 0.013 0.001 TRP A 329 HIS 0.002 0.001 HIS B 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (13029) covalent geometry : angle 0.52734 / 0.26 (17574) hydrogen bonds : bond 0.02750 / 1.80 ( 416) hydrogen bonds : angle 4.43534 / 3.10 ( 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 176 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7905 (mmt) cc_final: 0.6959 (mmp) REVERT: A 473 LYS cc_start: 0.3734 (ptmt) cc_final: 0.3194 (ttmt) REVERT: A 487 ARG cc_start: 0.6671 (ttp80) cc_final: 0.5377 (ttt-90) REVERT: A 542 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7193 (pp) REVERT: B 316 MET cc_start: 0.7166 (mmt) cc_final: 0.6828 (mmt) REVERT: D 288 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6355 (mt) REVERT: E 499 ILE cc_start: 0.6994 (OUTLIER) cc_final: 0.6739 (mt) outliers start: 30 outliers final: 23 residues processed: 166 average time/residue: 0.1028 time to fit residues: 26.4165 Evaluate side-chains 168 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 311 THR 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 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 267 SER Chi-restraints excluded: chain E residue 477 GLU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 46 optimal weight: 0.0970 chunk 94 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.163544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.148999 restraints weight = 20249.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.150833 restraints weight = 13397.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.152144 restraints weight = 9859.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.152916 restraints weight = 7811.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.153640 restraints weight = 6657.405| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13029 Z= 0.136 Angle : 0.571 9.514 17574 Z= 0.282 Chirality : 0.044 0.173 2002 Planarity : 0.003 0.045 2166 Dihedral : 14.542 151.335 1929 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.22 % Allowed : 14.66 % Favored : 83.12 % 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: -0.84 (0.22), residues: 1556 helix: 0.54 (0.23), residues: 518 sheet: 0.07 (0.31), residues: 320 loop : -1.70 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 361 TYR 0.009 0.001 TYR A 547 PHE 0.020 0.001 PHE C 321 TRP 0.015 0.001 TRP A 329 HIS 0.015 0.001 HIS F 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (13029) covalent geometry : angle 0.57107 / 0.28 (17574) hydrogen bonds : bond 0.03181 / 2.08 ( 416) hydrogen bonds : angle 4.52521 / 3.15 ( 1188) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2148.07 seconds wall clock time: 38 minutes 14.34 seconds (2294.34 seconds total)