Starting phenix.real_space_refine on Wed Jun 11 14:48:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n7n_0359/06_2025/6n7n_0359.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n7n_0359/06_2025/6n7n_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6n7n_0359/06_2025/6n7n_0359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n7n_0359/06_2025/6n7n_0359.map" model { file = "/net/cci-nas-00/data/ceres_data/6n7n_0359/06_2025/6n7n_0359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n7n_0359/06_2025/6n7n_0359.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.99, per 1000 atoms: 0.62 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: 3.10 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.43 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: 3.27 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2150 1.31 - 1.44: 3220 1.44 - 1.57: 7473 1.57 - 1.70: 54 1.70 - 1.83: 132 Bond restraints: 13029 Sorted by residual: bond pdb=" C6 TTP D 700 " pdb=" N1 TTP D 700 " ideal model delta sigma weight residual 1.337 1.428 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C6 TTP C 700 " pdb=" N1 TTP C 700 " ideal model delta sigma weight residual 1.337 1.427 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C6 TTP F 700 " pdb=" N1 TTP F 700 " ideal model delta sigma weight residual 1.337 1.426 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C6 TTP B 700 " pdb=" N1 TTP B 700 " ideal model delta sigma weight residual 1.337 1.425 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" C6 TTP E 700 " pdb=" N1 TTP E 700 " ideal model delta sigma weight residual 1.337 1.420 -0.083 2.00e-02 2.50e+03 1.70e+01 ... (remaining 13024 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 17194 2.64 - 5.28: 297 5.28 - 7.92: 60 7.92 - 10.56: 17 10.56 - 13.20: 6 Bond angle restraints: 17574 Sorted by residual: angle pdb=" N ILE E 442 " pdb=" CA ILE E 442 " pdb=" C ILE E 442 " ideal model delta sigma weight residual 111.81 107.50 4.31 8.60e-01 1.35e+00 2.51e+01 angle pdb=" O3' DT T 5 " pdb=" C3' DT T 5 " pdb=" C2' DT T 5 " ideal model delta sigma weight residual 111.50 118.65 -7.15 1.50e+00 4.44e-01 2.27e+01 angle pdb=" PA TTP D 700 " pdb=" O3A TTP D 700 " pdb=" PB TTP D 700 " ideal model delta sigma weight residual 120.50 133.70 -13.20 3.00e+00 1.11e-01 1.94e+01 angle pdb=" PB TTP C 700 " pdb=" O3B TTP C 700 " pdb=" PG TTP C 700 " ideal model delta sigma weight residual 120.50 132.63 -12.13 3.00e+00 1.11e-01 1.64e+01 angle pdb=" PA TTP C 700 " pdb=" O3A TTP C 700 " pdb=" PB TTP C 700 " ideal model delta sigma weight residual 120.50 132.60 -12.10 3.00e+00 1.11e-01 1.63e+01 ... (remaining 17569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.60: 7631 35.60 - 71.20: 127 71.20 - 106.80: 11 106.80 - 142.40: 5 142.40 - 178.00: 7 Dihedral angle restraints: 7781 sinusoidal: 3305 harmonic: 4476 Sorted by residual: dihedral pdb=" O2G TTP F 700 " pdb=" O3B TTP F 700 " pdb=" PG TTP F 700 " pdb=" PB TTP F 700 " ideal model delta sinusoidal sigma weight residual -180.00 -2.00 -178.00 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2G TTP D 700 " pdb=" O3B TTP D 700 " pdb=" PG TTP D 700 " pdb=" PB TTP D 700 " ideal model delta sinusoidal sigma weight residual -180.00 -2.43 -177.57 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2 TTP B 700 " pdb=" C1' TTP B 700 " pdb=" N1 TTP B 700 " pdb=" O4' TTP B 700 " ideal model delta sinusoidal sigma weight residual -58.32 114.32 -172.64 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 7778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1560 0.064 - 0.128: 377 0.128 - 0.193: 55 0.193 - 0.257: 7 0.257 - 0.321: 3 Chirality restraints: 2002 Sorted by residual: chirality pdb=" C3' DT T 5 " pdb=" C4' DT T 5 " pdb=" O3' DT T 5 " pdb=" C2' DT T 5 " both_signs ideal model delta sigma weight residual False -2.66 -2.34 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" C4' TTP B 700 " pdb=" C3' TTP B 700 " pdb=" C5' TTP B 700 " pdb=" O4' TTP B 700 " both_signs ideal model delta sigma weight residual False -2.50 -2.76 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C3' TTP F 700 " pdb=" C2' TTP F 700 " pdb=" C4' TTP F 700 " pdb=" O3' TTP F 700 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1999 not shown) Planarity restraints: 2166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 358 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.08e+00 pdb=" C ASN B 358 " -0.039 2.00e-02 2.50e+03 pdb=" O ASN B 358 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG B 359 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 342 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" C LEU C 342 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU C 342 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN C 343 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D 510 " 0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO D 511 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 511 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 511 " 0.027 5.00e-02 4.00e+02 ... (remaining 2163 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 62 2.56 - 3.15: 9191 3.15 - 3.73: 18570 3.73 - 4.32: 26525 4.32 - 4.90: 44708 Nonbonded interactions: 99056 Sorted by model distance: nonbonded pdb=" OE1 GLN D 343 " pdb="MG MG D 701 " model vdw 1.975 2.170 nonbonded pdb=" O1B TTP B 700 " pdb="MG MG B 701 " model vdw 1.985 2.170 nonbonded pdb=" NE2 GLN B 343 " pdb="MG MG B 701 " model vdw 2.041 2.250 nonbonded pdb=" O2B TTP F 700 " pdb="MG MG F 701 " model vdw 2.054 2.170 nonbonded pdb=" O1G TTP C 700 " pdb="MG MG C 701 " model vdw 2.116 2.170 ... (remaining 99051 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 264 through 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or (resid 440 and (name N or name CA or name C or name O or name CB )) o \ r resid 441 through 506 or resid 510 through 545)) selection = (chain 'B' and (resid 264 through 280 or resid 285 through 373 or resid 377 thro \ ugh 395 or resid 404 through 429 or (resid 440 and (name N or name CA or name C \ or name O or name CB )) or resid 441 through 506 or resid 510 through 545)) selection = (chain 'C' and (resid 264 through 280 or resid 285 through 373 or resid 377 thro \ ugh 395 or resid 404 through 429 or (resid 440 and (name N or name CA or name C \ or name O or name CB )) or resid 441 through 545)) selection = (chain 'D' and (resid 264 through 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or resid 440 through 506 or resid 510 through 545)) selection = (chain 'E' and (resid 264 through 429 or resid 440 through 506 or resid 510 thro \ ugh 545)) selection = (chain 'F' and (resid 264 through 506 or resid 510 through 545)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 30.310 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 13029 Z= 0.307 Angle : 0.987 13.201 17574 Z= 0.519 Chirality : 0.057 0.321 2002 Planarity : 0.004 0.048 2166 Dihedral : 14.773 177.997 4915 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.24 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (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 TRP 0.026 0.003 TRP B 541 HIS 0.008 0.002 HIS A 357 PHE 0.016 0.002 PHE D 386 TYR 0.013 0.002 TYR A 535 ARG 0.006 0.001 ARG D 359 Details of bonding type rmsd hydrogen bonds : bond 0.15778 ( 416) hydrogen bonds : angle 7.33577 ( 1188) covalent geometry : bond 0.00589 (13029) covalent geometry : angle 0.98722 (17574) *********************** 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 : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 368 LEU cc_start: 0.7895 (tt) cc_final: 0.7687 (tt) REVERT: D 504 ARG cc_start: 0.6670 (OUTLIER) cc_final: 0.6289 (ptm-80) REVERT: F 309 MET cc_start: 0.7792 (mmm) cc_final: 0.7273 (mmt) outliers start: 10 outliers final: 1 residues processed: 338 average time/residue: 0.2898 time to fit residues: 133.8838 Evaluate side-chains 177 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 175 time to evaluate : 1.512 ------------------------------------------------------------------------------- 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 134 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 66 optimal weight: 0.2980 chunk 41 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 144 optimal weight: 0.0980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 ASN B 357 HIS C 325 GLN C 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** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.163371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.146682 restraints weight = 20017.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.149324 restraints weight = 11696.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.151108 restraints weight = 7862.223| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13029 Z= 0.121 Angle : 0.584 7.117 17574 Z= 0.290 Chirality : 0.043 0.146 2002 Planarity : 0.003 0.037 2166 Dihedral : 16.134 179.777 1934 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.37 % Allowed : 9.84 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.20), residues: 1556 helix: -1.01 (0.21), residues: 514 sheet: -0.43 (0.30), residues: 322 loop : -2.30 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 381 HIS 0.007 0.001 HIS E 278 PHE 0.020 0.001 PHE B 321 TYR 0.017 0.001 TYR A 547 ARG 0.006 0.001 ARG E 517 Details of bonding type rmsd hydrogen bonds : bond 0.03172 ( 416) hydrogen bonds : angle 5.09409 ( 1188) covalent geometry : bond 0.00274 (13029) covalent geometry : angle 0.58363 (17574) *********************** 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 235 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 ARG cc_start: 0.6571 (ttp80) cc_final: 0.5302 (ttt-90) REVERT: A 542 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7520 (pp) REVERT: B 316 MET cc_start: 0.7593 (mmp) cc_final: 0.7377 (mmp) REVERT: C 438 GLU cc_start: 0.6115 (tt0) cc_final: 0.5551 (pm20) REVERT: D 441 MET cc_start: 0.7122 (mmt) cc_final: 0.6862 (mmm) REVERT: D 482 SER cc_start: 0.7439 (m) cc_final: 0.7091 (p) REVERT: E 499 ILE cc_start: 0.7055 (OUTLIER) cc_final: 0.6760 (mt) REVERT: E 503 GLU cc_start: 0.6479 (mp0) cc_final: 0.5650 (mp0) REVERT: E 517 ARG cc_start: 0.7249 (ttm-80) cc_final: 0.6978 (ttm-80) outliers start: 32 outliers final: 18 residues processed: 223 average time/residue: 0.2422 time to fit residues: 79.1195 Evaluate side-chains 183 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 1.492 ------------------------------------------------------------------------------- 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 390 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 388 ASN Chi-restraints excluded: chain C residue 514 VAL 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 E residue 482 SER Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 481 VAL Chi-restraints excluded: chain F residue 484 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 115 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 87 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 HIS ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN ** 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 = 0.4279 r_free = 0.4279 target = 0.167481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.152881 restraints weight = 19631.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.154751 restraints weight = 13004.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.156067 restraints weight = 9554.172| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13029 Z= 0.102 Angle : 0.539 7.030 17574 Z= 0.268 Chirality : 0.043 0.145 2002 Planarity : 0.002 0.025 2166 Dihedral : 15.631 178.272 1929 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.74 % Allowed : 11.70 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.21), residues: 1556 helix: -0.28 (0.23), residues: 524 sheet: -0.18 (0.31), residues: 322 loop : -2.08 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 541 HIS 0.003 0.001 HIS A 357 PHE 0.025 0.001 PHE C 321 TYR 0.014 0.001 TYR A 547 ARG 0.004 0.000 ARG E 517 Details of bonding type rmsd hydrogen bonds : bond 0.02875 ( 416) hydrogen bonds : angle 4.65864 ( 1188) covalent geometry : bond 0.00229 (13029) covalent geometry : angle 0.53879 (17574) *********************** 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 211 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 LYS cc_start: 0.4281 (ptmt) cc_final: 0.3652 (ttmt) REVERT: A 487 ARG cc_start: 0.6677 (ttp80) cc_final: 0.5490 (ttt-90) REVERT: B 316 MET cc_start: 0.7347 (mmp) cc_final: 0.7139 (mmp) REVERT: C 312 SER cc_start: 0.6871 (m) cc_final: 0.6634 (p) REVERT: C 438 GLU cc_start: 0.6001 (tt0) cc_final: 0.5714 (pm20) REVERT: D 316 MET cc_start: 0.7451 (mmm) cc_final: 0.7094 (mmt) REVERT: D 441 MET cc_start: 0.6873 (mmt) cc_final: 0.6621 (mmm) REVERT: D 482 SER cc_start: 0.7337 (m) cc_final: 0.7101 (p) REVERT: E 499 ILE cc_start: 0.6920 (OUTLIER) cc_final: 0.6580 (mt) REVERT: E 503 GLU cc_start: 0.6287 (mp0) cc_final: 0.5482 (mp0) REVERT: F 485 ASP cc_start: 0.5907 (m-30) cc_final: 0.5668 (m-30) outliers start: 37 outliers final: 19 residues processed: 196 average time/residue: 0.2322 time to fit residues: 68.4392 Evaluate side-chains 177 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 TRP Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 481 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 ASN C 465 HIS ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 HIS E 358 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.163291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.148696 restraints weight = 19846.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.150507 restraints weight = 13372.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.151759 restraints weight = 9939.029| |-----------------------------------------------------------------------------| r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13029 Z= 0.146 Angle : 0.599 9.279 17574 Z= 0.294 Chirality : 0.044 0.147 2002 Planarity : 0.003 0.028 2166 Dihedral : 15.654 173.124 1929 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.66 % Allowed : 12.88 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.21), residues: 1556 helix: -0.11 (0.23), residues: 531 sheet: -0.25 (0.30), residues: 321 loop : -1.98 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 541 HIS 0.006 0.001 HIS B 392 PHE 0.027 0.002 PHE C 321 TYR 0.013 0.001 TYR A 547 ARG 0.004 0.001 ARG E 361 Details of bonding type rmsd hydrogen bonds : bond 0.03342 ( 416) hydrogen bonds : angle 4.77086 ( 1188) covalent geometry : bond 0.00343 (13029) covalent geometry : angle 0.59938 (17574) *********************** 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 187 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 473 LYS cc_start: 0.3799 (ptmt) cc_final: 0.3008 (ttmt) REVERT: A 487 ARG cc_start: 0.6845 (ttp80) cc_final: 0.5541 (ttt-90) REVERT: C 438 GLU cc_start: 0.6063 (tt0) cc_final: 0.5626 (pm20) REVERT: D 441 MET cc_start: 0.6903 (mmt) cc_final: 0.6611 (mmm) REVERT: E 499 ILE cc_start: 0.7107 (OUTLIER) cc_final: 0.6873 (mt) REVERT: E 503 GLU cc_start: 0.6508 (mp0) cc_final: 0.5537 (mp0) outliers start: 36 outliers final: 26 residues processed: 172 average time/residue: 0.2276 time to fit residues: 59.5156 Evaluate side-chains 170 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 THR 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 514 VAL 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 267 SER Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain E residue 529 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 481 VAL Chi-restraints excluded: chain F residue 484 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 99 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 149 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 98 optimal weight: 0.1980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 506 GLN ** 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 = 0.4254 r_free = 0.4254 target = 0.165792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.151242 restraints weight = 19803.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.153129 restraints weight = 13128.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.154400 restraints weight = 9631.716| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13029 Z= 0.096 Angle : 0.520 7.602 17574 Z= 0.256 Chirality : 0.042 0.148 2002 Planarity : 0.002 0.029 2166 Dihedral : 14.919 156.808 1929 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.81 % Allowed : 12.88 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.22), residues: 1556 helix: 0.26 (0.24), residues: 527 sheet: -0.05 (0.31), residues: 311 loop : -1.78 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 329 HIS 0.003 0.001 HIS C 425 PHE 0.022 0.001 PHE C 321 TYR 0.012 0.001 TYR A 547 ARG 0.003 0.000 ARG E 517 Details of bonding type rmsd hydrogen bonds : bond 0.02702 ( 416) hydrogen bonds : angle 4.48435 ( 1188) covalent geometry : bond 0.00217 (13029) covalent geometry : angle 0.52041 (17574) *********************** 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 192 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 1.396 Fit side-chains revert: symmetry clash REVERT: A 316 MET cc_start: 0.7799 (mmt) cc_final: 0.6830 (mmp) REVERT: A 442 ILE cc_start: 0.7455 (tt) cc_final: 0.7217 (mt) REVERT: A 473 LYS cc_start: 0.3890 (ptmt) cc_final: 0.3146 (ttmt) REVERT: A 487 ARG cc_start: 0.6803 (ttp80) cc_final: 0.5463 (ttt-90) REVERT: A 542 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7018 (pp) REVERT: D 288 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6527 (mt) REVERT: E 503 GLU cc_start: 0.6280 (mp0) cc_final: 0.5500 (mp0) outliers start: 38 outliers final: 25 residues processed: 179 average time/residue: 0.2389 time to fit residues: 63.7441 Evaluate side-chains 168 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 1.566 ------------------------------------------------------------------------------- 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 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 514 VAL 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 482 SER Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 481 VAL Chi-restraints excluded: chain F residue 484 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 45 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 119 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 105 optimal weight: 0.2980 chunk 11 optimal weight: 0.7980 chunk 153 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4194 r_free = 0.4194 target = 0.160979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.147585 restraints weight = 20485.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.148562 restraints weight = 15491.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.149056 restraints weight = 12077.103| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13029 Z= 0.177 Angle : 0.630 7.367 17574 Z= 0.310 Chirality : 0.046 0.156 2002 Planarity : 0.003 0.030 2166 Dihedral : 14.909 154.323 1929 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.11 % Allowed : 13.69 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.21), residues: 1556 helix: -0.05 (0.23), residues: 533 sheet: -0.19 (0.31), residues: 312 loop : -1.91 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 329 HIS 0.007 0.001 HIS B 392 PHE 0.023 0.002 PHE C 321 TYR 0.012 0.001 TYR A 547 ARG 0.005 0.001 ARG C 522 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 416) hydrogen bonds : angle 4.84651 ( 1188) covalent geometry : bond 0.00420 (13029) covalent geometry : angle 0.62965 (17574) *********************** 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 188 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 146 time to evaluate : 1.495 Fit side-chains revert: symmetry clash REVERT: A 473 LYS cc_start: 0.3523 (ptmt) cc_final: 0.2831 (ttmt) REVERT: A 487 ARG cc_start: 0.6820 (ttp80) cc_final: 0.5515 (ttt-90) REVERT: A 542 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7078 (pp) REVERT: E 499 ILE cc_start: 0.7140 (OUTLIER) cc_final: 0.6877 (mt) outliers start: 42 outliers final: 27 residues processed: 175 average time/residue: 0.2060 time to fit residues: 55.7514 Evaluate side-chains 164 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 1.409 ------------------------------------------------------------------------------- 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 297 ASP Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 514 VAL 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 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 Chi-restraints excluded: chain F residue 484 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 158 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 20 optimal weight: 0.0970 chunk 71 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 = 0.4241 r_free = 0.4241 target = 0.165038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.150471 restraints weight = 19917.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.152355 restraints weight = 13190.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.153660 restraints weight = 9675.783| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13029 Z= 0.093 Angle : 0.514 7.009 17574 Z= 0.255 Chirality : 0.043 0.148 2002 Planarity : 0.002 0.034 2166 Dihedral : 14.416 150.471 1929 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.44 % Allowed : 14.58 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.22), residues: 1556 helix: 0.44 (0.23), residues: 533 sheet: -0.04 (0.31), residues: 315 loop : -1.82 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 329 HIS 0.003 0.001 HIS C 425 PHE 0.019 0.001 PHE C 321 TYR 0.011 0.001 TYR A 547 ARG 0.002 0.000 ARG E 517 Details of bonding type rmsd hydrogen bonds : bond 0.02689 ( 416) hydrogen bonds : angle 4.45946 ( 1188) covalent geometry : bond 0.00209 (13029) covalent geometry : angle 0.51417 (17574) *********************** 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 179 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 1.533 Fit side-chains revert: symmetry clash REVERT: A 316 MET cc_start: 0.7727 (mmt) cc_final: 0.6714 (mmp) REVERT: A 473 LYS cc_start: 0.4041 (ptmt) cc_final: 0.3350 (ttmt) REVERT: A 487 ARG cc_start: 0.6863 (ttp80) cc_final: 0.5604 (ttt-90) REVERT: A 542 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6949 (pp) REVERT: B 316 MET cc_start: 0.7126 (mmt) cc_final: 0.6802 (mmt) REVERT: D 288 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6428 (mt) REVERT: E 503 GLU cc_start: 0.6279 (mp0) cc_final: 0.5530 (mp0) outliers start: 33 outliers final: 24 residues processed: 169 average time/residue: 0.2113 time to fit residues: 55.3817 Evaluate side-chains 170 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 1.485 ------------------------------------------------------------------------------- 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 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 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 484 THR Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 516 VAL 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 63 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.158395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.144615 restraints weight = 20557.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.146089 restraints weight = 14408.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.147209 restraints weight = 11070.583| |-----------------------------------------------------------------------------| r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13029 Z= 0.235 Angle : 0.721 8.572 17574 Z= 0.355 Chirality : 0.048 0.163 2002 Planarity : 0.004 0.041 2166 Dihedral : 15.114 152.306 1929 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 3.26 % Allowed : 14.43 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.21), residues: 1556 helix: -0.21 (0.22), residues: 524 sheet: -0.43 (0.30), residues: 316 loop : -1.91 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 329 HIS 0.009 0.002 HIS B 392 PHE 0.022 0.002 PHE C 321 TYR 0.015 0.002 TYR C 394 ARG 0.006 0.001 ARG E 361 Details of bonding type rmsd hydrogen bonds : bond 0.04199 ( 416) hydrogen bonds : angle 5.13698 ( 1188) covalent geometry : bond 0.00562 (13029) covalent geometry : angle 0.72114 (17574) *********************** 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 193 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 1.519 Fit side-chains revert: symmetry clash REVERT: A 473 LYS cc_start: 0.3579 (ptmt) cc_final: 0.2960 (ttmt) REVERT: A 487 ARG cc_start: 0.6796 (ttp80) cc_final: 0.5503 (ttt-90) REVERT: A 542 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7164 (pp) REVERT: E 499 ILE cc_start: 0.7266 (OUTLIER) cc_final: 0.7051 (mt) outliers start: 44 outliers final: 32 residues processed: 181 average time/residue: 0.2248 time to fit residues: 62.0180 Evaluate side-chains 174 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 1.465 ------------------------------------------------------------------------------- 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 297 ASP Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 442 ILE 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 266 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 388 ASN 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 293 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 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 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 484 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 111 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.163561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.148994 restraints weight = 19980.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.150827 restraints weight = 13256.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.151851 restraints weight = 9761.990| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13029 Z= 0.105 Angle : 0.545 6.946 17574 Z= 0.272 Chirality : 0.043 0.152 2002 Planarity : 0.003 0.085 2166 Dihedral : 14.533 148.234 1929 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.22 % Allowed : 15.32 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.22), residues: 1556 helix: 0.27 (0.23), residues: 533 sheet: -0.21 (0.31), residues: 314 loop : -1.83 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 329 HIS 0.005 0.001 HIS C 425 PHE 0.028 0.001 PHE B 523 TYR 0.011 0.001 TYR A 547 ARG 0.003 0.000 ARG F 522 Details of bonding type rmsd hydrogen bonds : bond 0.02918 ( 416) hydrogen bonds : angle 4.58422 ( 1188) covalent geometry : bond 0.00244 (13029) covalent geometry : angle 0.54466 (17574) *********************** 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 168 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 1.530 Fit side-chains revert: symmetry clash REVERT: A 473 LYS cc_start: 0.3985 (ptmt) cc_final: 0.3272 (ttmt) REVERT: A 542 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7036 (pp) REVERT: C 370 ARG cc_start: 0.6859 (mtm180) cc_final: 0.6281 (tpm170) REVERT: E 499 ILE cc_start: 0.6969 (OUTLIER) cc_final: 0.6750 (mt) REVERT: E 503 GLU cc_start: 0.6439 (mp0) cc_final: 0.5597 (mp0) outliers start: 30 outliers final: 23 residues processed: 160 average time/residue: 0.2885 time to fit residues: 72.5111 Evaluate side-chains 158 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 279 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 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 482 SER Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain E residue 516 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 510 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 126 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 43 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN ** B 343 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.160267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.146435 restraints weight = 20184.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.147932 restraints weight = 14156.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.149043 restraints weight = 10865.866| |-----------------------------------------------------------------------------| r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13029 Z= 0.174 Angle : 0.627 7.112 17574 Z= 0.311 Chirality : 0.045 0.145 2002 Planarity : 0.004 0.075 2166 Dihedral : 14.782 149.186 1929 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.44 % Allowed : 15.40 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.21), residues: 1556 helix: 0.10 (0.23), residues: 527 sheet: -0.35 (0.31), residues: 315 loop : -1.87 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 329 HIS 0.007 0.001 HIS B 392 PHE 0.027 0.002 PHE B 523 TYR 0.011 0.001 TYR E 411 ARG 0.004 0.001 ARG E 361 Details of bonding type rmsd hydrogen bonds : bond 0.03620 ( 416) hydrogen bonds : angle 4.81385 ( 1188) covalent geometry : bond 0.00412 (13029) covalent geometry : angle 0.62736 (17574) ********************** 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 169 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 1.392 Fit side-chains revert: symmetry clash REVERT: A 473 LYS cc_start: 0.3452 (ptmt) cc_final: 0.2846 (ttmt) REVERT: A 542 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7111 (pp) REVERT: B 316 MET cc_start: 0.7444 (mmt) cc_final: 0.7151 (mmt) REVERT: C 370 ARG cc_start: 0.6793 (mtm180) cc_final: 0.6315 (tpm170) REVERT: E 499 ILE cc_start: 0.7062 (OUTLIER) cc_final: 0.6859 (mt) outliers start: 33 outliers final: 26 residues processed: 159 average time/residue: 0.2103 time to fit residues: 51.1077 Evaluate side-chains 163 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 494 GLN 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 484 THR Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 516 VAL 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 385 LEU Chi-restraints excluded: chain F residue 418 CYS 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 156 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 61 optimal weight: 0.0370 chunk 20 optimal weight: 6.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.164701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.151077 restraints weight = 19870.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.152650 restraints weight = 13687.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.153750 restraints weight = 10359.890| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13029 Z= 0.096 Angle : 0.524 6.757 17574 Z= 0.261 Chirality : 0.042 0.141 2002 Planarity : 0.003 0.069 2166 Dihedral : 14.337 149.408 1929 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.29 % Allowed : 15.47 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.22), residues: 1556 helix: 0.65 (0.24), residues: 522 sheet: -0.12 (0.31), residues: 314 loop : -1.69 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 329 HIS 0.003 0.001 HIS C 425 PHE 0.026 0.001 PHE B 523 TYR 0.011 0.001 TYR A 547 ARG 0.003 0.000 ARG F 522 Details of bonding type rmsd hydrogen bonds : bond 0.02726 ( 416) hydrogen bonds : angle 4.43447 ( 1188) covalent geometry : bond 0.00216 (13029) covalent geometry : angle 0.52355 (17574) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3921.00 seconds wall clock time: 69 minutes 12.98 seconds (4152.98 seconds total)