Starting phenix.real_space_refine on Mon Jan 20 05:20:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wy4_37915/01_2025/8wy4_37915.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wy4_37915/01_2025/8wy4_37915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wy4_37915/01_2025/8wy4_37915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wy4_37915/01_2025/8wy4_37915.map" model { file = "/net/cci-nas-00/data/ceres_data/8wy4_37915/01_2025/8wy4_37915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wy4_37915/01_2025/8wy4_37915.cif" } resolution = 2.81 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= 0.031 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 48 5.16 5 C 9504 2.51 5 N 2448 2.21 5 O 2852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 14864 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3685 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 8, 'TRANS': 442} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, D Time building chain proxies: 8.85, per 1000 atoms: 0.60 Number of scatterers: 14864 At special positions: 0 Unit cell: (115.08, 190.68, 68.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 12 15.00 O 2852 8.00 N 2448 7.00 C 9504 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.56 Conformation dependent library (CDL) restraints added in 2.0 seconds 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3416 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 16 sheets defined 42.8% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 31 through 47 removed outlier: 3.960A pdb=" N LEU A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 83 through 91 removed outlier: 3.860A pdb=" N LYS A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.612A pdb=" N LEU A 324 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR A 326 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 removed outlier: 3.784A pdb=" N SER A 368 " --> pdb=" O LYS A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 395 removed outlier: 3.558A pdb=" N LYS A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 413 through 423 removed outlier: 3.630A pdb=" N THR A 419 " --> pdb=" O HIS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 457 removed outlier: 4.019A pdb=" N CYS A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 493 Processing helix chain 'A' and resid 493 through 503 removed outlier: 3.671A pdb=" N GLU A 503 " --> pdb=" O GLU A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 528 removed outlier: 3.592A pdb=" N SER A 518 " --> pdb=" O ASN A 514 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLU A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N SER A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE A 528 " --> pdb=" O MET A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 540 removed outlier: 3.662A pdb=" N TYR A 536 " --> pdb=" O ASP A 532 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER A 540 " --> pdb=" O TYR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 551 removed outlier: 3.632A pdb=" N ASN A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN A 551 " --> pdb=" O GLU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 562 removed outlier: 3.564A pdb=" N CYS A 557 " --> pdb=" O SER A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 574 Processing helix chain 'B' and resid 31 through 47 removed outlier: 3.960A pdb=" N LEU B 39 " --> pdb=" O LYS B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 83 through 91 removed outlier: 3.861A pdb=" N LYS B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 308 Processing helix chain 'B' and resid 321 through 326 removed outlier: 3.612A pdb=" N LEU B 324 " --> pdb=" O SER B 321 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR B 326 " --> pdb=" O GLU B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 370 removed outlier: 3.784A pdb=" N SER B 368 " --> pdb=" O LYS B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 395 removed outlier: 3.558A pdb=" N LYS B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 413 through 423 removed outlier: 3.630A pdb=" N THR B 419 " --> pdb=" O HIS B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 457 removed outlier: 4.019A pdb=" N CYS B 453 " --> pdb=" O GLY B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 493 Processing helix chain 'B' and resid 493 through 503 removed outlier: 3.671A pdb=" N GLU B 503 " --> pdb=" O GLU B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 528 removed outlier: 3.592A pdb=" N SER B 518 " --> pdb=" O ASN B 514 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA B 519 " --> pdb=" O ASP B 515 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLU B 522 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N SER B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE B 528 " --> pdb=" O MET B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 540 removed outlier: 3.662A pdb=" N TYR B 536 " --> pdb=" O ASP B 532 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER B 540 " --> pdb=" O TYR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 551 removed outlier: 3.632A pdb=" N ASN B 544 " --> pdb=" O SER B 540 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN B 551 " --> pdb=" O GLU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 562 removed outlier: 3.564A pdb=" N CYS B 557 " --> pdb=" O SER B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 574 Processing helix chain 'D' and resid 31 through 47 removed outlier: 3.960A pdb=" N LEU D 39 " --> pdb=" O LYS D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 83 through 91 removed outlier: 3.859A pdb=" N LYS D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 308 Processing helix chain 'D' and resid 321 through 326 removed outlier: 3.612A pdb=" N LEU D 324 " --> pdb=" O SER D 321 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR D 326 " --> pdb=" O GLU D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 370 removed outlier: 3.784A pdb=" N SER D 368 " --> pdb=" O LYS D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 395 removed outlier: 3.558A pdb=" N LYS D 384 " --> pdb=" O GLY D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 402 Processing helix chain 'D' and resid 413 through 423 removed outlier: 3.629A pdb=" N THR D 419 " --> pdb=" O HIS D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 457 removed outlier: 4.020A pdb=" N CYS D 453 " --> pdb=" O GLY D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 493 Processing helix chain 'D' and resid 493 through 503 removed outlier: 3.671A pdb=" N GLU D 503 " --> pdb=" O GLU D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 528 removed outlier: 3.592A pdb=" N SER D 518 " --> pdb=" O ASN D 514 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA D 519 " --> pdb=" O ASP D 515 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLU D 522 " --> pdb=" O SER D 518 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N SER D 523 " --> pdb=" O ALA D 519 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE D 528 " --> pdb=" O MET D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 540 removed outlier: 3.662A pdb=" N TYR D 536 " --> pdb=" O ASP D 532 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER D 540 " --> pdb=" O TYR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 551 removed outlier: 3.632A pdb=" N ASN D 544 " --> pdb=" O SER D 540 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN D 551 " --> pdb=" O GLU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 562 removed outlier: 3.564A pdb=" N CYS D 557 " --> pdb=" O SER D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 574 Processing helix chain 'C' and resid 31 through 47 removed outlier: 3.959A pdb=" N LEU C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 Processing helix chain 'C' and resid 83 through 91 removed outlier: 3.860A pdb=" N LYS C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 308 Processing helix chain 'C' and resid 321 through 326 removed outlier: 3.612A pdb=" N LEU C 324 " --> pdb=" O SER C 321 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR C 326 " --> pdb=" O GLU C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 370 removed outlier: 3.784A pdb=" N SER C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 395 removed outlier: 3.558A pdb=" N LYS C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 402 Processing helix chain 'C' and resid 413 through 423 removed outlier: 3.630A pdb=" N THR C 419 " --> pdb=" O HIS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 457 removed outlier: 4.019A pdb=" N CYS C 453 " --> pdb=" O GLY C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 493 Processing helix chain 'C' and resid 493 through 503 removed outlier: 3.671A pdb=" N GLU C 503 " --> pdb=" O GLU C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 528 removed outlier: 3.592A pdb=" N SER C 518 " --> pdb=" O ASN C 514 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA C 519 " --> pdb=" O ASP C 515 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLU C 522 " --> pdb=" O SER C 518 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N SER C 523 " --> pdb=" O ALA C 519 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE C 528 " --> pdb=" O MET C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 540 removed outlier: 3.662A pdb=" N TYR C 536 " --> pdb=" O ASP C 532 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER C 540 " --> pdb=" O TYR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 551 removed outlier: 3.633A pdb=" N ASN C 544 " --> pdb=" O SER C 540 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN C 551 " --> pdb=" O GLU C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 562 removed outlier: 3.565A pdb=" N CYS C 557 " --> pdb=" O SER C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 574 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20 removed outlier: 3.533A pdb=" N ILE A 8 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN A 5 " --> pdb=" O THR A 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY A 127 " --> pdb=" O TYR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 154 removed outlier: 6.726A pdb=" N VAL A 283 " --> pdb=" O TYR A 314 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N PHE A 316 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR A 285 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N SER A 318 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE A 287 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL A 26 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL A 336 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE A 28 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 403 through 407 removed outlier: 6.723A pdb=" N ARG A 374 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU A 406 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU A 376 " --> pdb=" O LEU A 406 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 437 Processing sheet with id=AA5, first strand: chain 'B' and resid 17 through 20 removed outlier: 3.533A pdb=" N ILE B 8 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN B 5 " --> pdb=" O THR B 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY B 127 " --> pdb=" O TYR B 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 154 removed outlier: 6.727A pdb=" N VAL B 283 " --> pdb=" O TYR B 314 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N PHE B 316 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR B 285 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N SER B 318 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE B 287 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL B 26 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL B 336 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE B 28 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 403 through 407 removed outlier: 6.724A pdb=" N ARG B 374 " --> pdb=" O PHE B 404 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU B 406 " --> pdb=" O ARG B 374 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU B 376 " --> pdb=" O LEU B 406 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 435 through 437 Processing sheet with id=AA9, first strand: chain 'D' and resid 17 through 20 removed outlier: 3.532A pdb=" N ILE D 8 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN D 5 " --> pdb=" O THR D 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY D 127 " --> pdb=" O TYR D 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 149 through 154 removed outlier: 6.726A pdb=" N VAL D 283 " --> pdb=" O TYR D 314 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N PHE D 316 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR D 285 " --> pdb=" O PHE D 316 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N SER D 318 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE D 287 " --> pdb=" O SER D 318 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL D 26 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL D 336 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE D 28 " --> pdb=" O VAL D 336 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 403 through 407 removed outlier: 6.723A pdb=" N ARG D 374 " --> pdb=" O PHE D 404 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU D 406 " --> pdb=" O ARG D 374 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU D 376 " --> pdb=" O LEU D 406 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 435 through 437 Processing sheet with id=AB4, first strand: chain 'C' and resid 17 through 20 removed outlier: 3.534A pdb=" N ILE C 8 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN C 5 " --> pdb=" O THR C 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY C 127 " --> pdb=" O TYR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 149 through 154 removed outlier: 4.299A pdb=" N TYR C 314 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL C 26 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL C 336 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE C 28 " --> pdb=" O VAL C 336 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 403 through 407 removed outlier: 6.723A pdb=" N ARG C 374 " --> pdb=" O PHE C 404 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU C 406 " --> pdb=" O ARG C 374 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU C 376 " --> pdb=" O LEU C 406 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 435 through 437 600 hydrogen bonds defined for protein. 1716 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: 4.81 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4400 1.34 - 1.46: 2405 1.46 - 1.57: 8223 1.57 - 1.69: 20 1.69 - 1.81: 76 Bond restraints: 15124 Sorted by residual: bond pdb=" N GLU B 503 " pdb=" CA GLU B 503 " ideal model delta sigma weight residual 1.457 1.486 -0.029 6.40e-03 2.44e+04 2.06e+01 bond pdb=" N GLU A 503 " pdb=" CA GLU A 503 " ideal model delta sigma weight residual 1.457 1.486 -0.029 6.40e-03 2.44e+04 2.06e+01 bond pdb=" N GLU C 503 " pdb=" CA GLU C 503 " ideal model delta sigma weight residual 1.457 1.486 -0.029 6.40e-03 2.44e+04 2.06e+01 bond pdb=" N GLU D 503 " pdb=" CA GLU D 503 " ideal model delta sigma weight residual 1.457 1.485 -0.028 6.40e-03 2.44e+04 1.94e+01 bond pdb=" N VAL A 497 " pdb=" CA VAL A 497 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.19e-02 7.06e+03 8.75e+00 ... (remaining 15119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 19535 2.41 - 4.82: 665 4.82 - 7.23: 124 7.23 - 9.64: 12 9.64 - 12.06: 8 Bond angle restraints: 20344 Sorted by residual: angle pdb=" C LYS A 116 " pdb=" N GLU A 117 " pdb=" CA GLU A 117 " ideal model delta sigma weight residual 121.54 130.91 -9.37 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C LYS D 116 " pdb=" N GLU D 117 " pdb=" CA GLU D 117 " ideal model delta sigma weight residual 121.54 130.87 -9.33 1.91e+00 2.74e-01 2.39e+01 angle pdb=" C LYS B 116 " pdb=" N GLU B 117 " pdb=" CA GLU B 117 " ideal model delta sigma weight residual 121.54 130.87 -9.33 1.91e+00 2.74e-01 2.39e+01 angle pdb=" C LYS C 116 " pdb=" N GLU C 117 " pdb=" CA GLU C 117 " ideal model delta sigma weight residual 121.54 130.85 -9.31 1.91e+00 2.74e-01 2.38e+01 angle pdb=" N ASP B 22 " pdb=" CA ASP B 22 " pdb=" C ASP B 22 " ideal model delta sigma weight residual 108.45 102.61 5.84 1.26e+00 6.30e-01 2.15e+01 ... (remaining 20339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 8132 17.18 - 34.36: 900 34.36 - 51.55: 200 51.55 - 68.73: 36 68.73 - 85.91: 20 Dihedral angle restraints: 9288 sinusoidal: 3992 harmonic: 5296 Sorted by residual: dihedral pdb=" CA ASP B 76 " pdb=" C ASP B 76 " pdb=" N LEU B 77 " pdb=" CA LEU B 77 " ideal model delta harmonic sigma weight residual -180.00 -153.37 -26.63 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA ASP C 76 " pdb=" C ASP C 76 " pdb=" N LEU C 77 " pdb=" CA LEU C 77 " ideal model delta harmonic sigma weight residual 180.00 -153.39 -26.61 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA ASP D 76 " pdb=" C ASP D 76 " pdb=" N LEU D 77 " pdb=" CA LEU D 77 " ideal model delta harmonic sigma weight residual -180.00 -153.41 -26.59 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 9285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1641 0.057 - 0.114: 416 0.114 - 0.171: 168 0.171 - 0.228: 23 0.228 - 0.285: 8 Chirality restraints: 2256 Sorted by residual: chirality pdb=" CB ILE C 6 " pdb=" CA ILE C 6 " pdb=" CG1 ILE C 6 " pdb=" CG2 ILE C 6 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB ILE D 6 " pdb=" CA ILE D 6 " pdb=" CG1 ILE D 6 " pdb=" CG2 ILE D 6 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB ILE B 6 " pdb=" CA ILE B 6 " pdb=" CG1 ILE B 6 " pdb=" CG2 ILE B 6 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 2253 not shown) Planarity restraints: 2564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 9 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.47e+00 pdb=" C LYS B 9 " 0.037 2.00e-02 2.50e+03 pdb=" O LYS B 9 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN B 10 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 9 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C LYS C 9 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS C 9 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN C 10 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 9 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.28e+00 pdb=" C LYS A 9 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS A 9 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN A 10 " 0.012 2.00e-02 2.50e+03 ... (remaining 2561 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 4842 2.87 - 3.38: 12020 3.38 - 3.89: 24467 3.89 - 4.39: 27338 4.39 - 4.90: 47837 Nonbonded interactions: 116504 Sorted by model distance: nonbonded pdb=" OG SER D 4 " pdb=" OD2 ASP D 76 " model vdw 2.368 3.040 nonbonded pdb=" OG SER B 4 " pdb=" OD2 ASP B 76 " model vdw 2.369 3.040 nonbonded pdb=" OG SER C 4 " pdb=" OD2 ASP C 76 " model vdw 2.369 3.040 nonbonded pdb=" OG SER A 4 " pdb=" OD2 ASP A 76 " model vdw 2.370 3.040 nonbonded pdb=" OG1 THR A 339 " pdb=" O LYS A 341 " model vdw 2.378 3.040 ... (remaining 116499 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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 individual isotropic 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: 3.220 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: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.650 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:12.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 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 0.056 15124 Z= 0.389 Angle : 1.057 12.055 20344 Z= 0.595 Chirality : 0.061 0.285 2256 Planarity : 0.006 0.045 2564 Dihedral : 15.320 85.911 5872 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.16), residues: 1788 helix: -3.71 (0.09), residues: 732 sheet: 0.05 (0.27), residues: 392 loop : -1.83 (0.20), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.006 TRP D 126 HIS 0.006 0.002 HIS A 415 PHE 0.031 0.002 PHE A 315 TYR 0.022 0.002 TYR A 326 ARG 0.016 0.001 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 1.668 Fit side-chains REVERT: A 141 ASN cc_start: 0.6872 (m-40) cc_final: 0.6356 (m-40) REVERT: A 422 ASP cc_start: 0.7603 (m-30) cc_final: 0.7394 (t0) REVERT: A 474 LYS cc_start: 0.7773 (mttt) cc_final: 0.7516 (mttt) REVERT: B 141 ASN cc_start: 0.6822 (m-40) cc_final: 0.6322 (m-40) REVERT: B 422 ASP cc_start: 0.7606 (m-30) cc_final: 0.7400 (t0) REVERT: D 141 ASN cc_start: 0.6873 (m-40) cc_final: 0.6357 (m-40) REVERT: D 422 ASP cc_start: 0.7605 (m-30) cc_final: 0.7395 (t0) REVERT: D 474 LYS cc_start: 0.7753 (mttt) cc_final: 0.7523 (mttt) REVERT: C 141 ASN cc_start: 0.6874 (m-40) cc_final: 0.6357 (m-40) REVERT: C 422 ASP cc_start: 0.7604 (m-30) cc_final: 0.7387 (t0) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 1.3528 time to fit residues: 399.7345 Evaluate side-chains 167 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.7980 chunk 136 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 0.0060 chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 0.0970 chunk 141 optimal weight: 0.0870 chunk 54 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 overall best weight: 0.3372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.233092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.203836 restraints weight = 16948.508| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 1.74 r_work: 0.4126 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4019 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15124 Z= 0.159 Angle : 0.574 8.467 20344 Z= 0.312 Chirality : 0.045 0.170 2256 Planarity : 0.003 0.022 2564 Dihedral : 8.599 50.416 2076 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.27 % Allowed : 8.39 % Favored : 90.34 % 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: -1.52 (0.18), residues: 1788 helix: -1.18 (0.16), residues: 700 sheet: 0.09 (0.28), residues: 408 loop : -1.32 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 126 HIS 0.004 0.001 HIS D 415 PHE 0.009 0.001 PHE A 316 TYR 0.013 0.001 TYR C 314 ARG 0.005 0.000 ARG D 332 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 1.661 Fit side-chains REVERT: A 141 ASN cc_start: 0.6894 (m-40) cc_final: 0.6459 (m-40) REVERT: A 474 LYS cc_start: 0.7705 (mttt) cc_final: 0.7342 (mtmt) REVERT: B 141 ASN cc_start: 0.6898 (m-40) cc_final: 0.6468 (m-40) REVERT: D 141 ASN cc_start: 0.6869 (m-40) cc_final: 0.6448 (m-40) REVERT: D 474 LYS cc_start: 0.7690 (mttt) cc_final: 0.7317 (mtmt) REVERT: C 141 ASN cc_start: 0.6885 (m-40) cc_final: 0.6443 (m-40) outliers start: 21 outliers final: 5 residues processed: 187 average time/residue: 1.3384 time to fit residues: 276.2821 Evaluate side-chains 165 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 160 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain C residue 455 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 179 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 176 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 136 optimal weight: 0.2980 chunk 145 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS B 415 HIS D 415 HIS C 415 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.226036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.194903 restraints weight = 16935.426| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 1.73 r_work: 0.4041 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3932 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15124 Z= 0.275 Angle : 0.672 9.990 20344 Z= 0.353 Chirality : 0.047 0.161 2256 Planarity : 0.004 0.056 2564 Dihedral : 7.987 52.207 2076 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.36 % Allowed : 10.75 % Favored : 86.90 % 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: -0.81 (0.19), residues: 1788 helix: -0.02 (0.19), residues: 688 sheet: 0.01 (0.27), residues: 404 loop : -1.29 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 126 HIS 0.007 0.001 HIS A 415 PHE 0.015 0.002 PHE C 371 TYR 0.023 0.002 TYR C 314 ARG 0.009 0.001 ARG C 332 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 186 time to evaluate : 1.841 Fit side-chains REVERT: A 139 ARG cc_start: 0.6577 (mmm160) cc_final: 0.6083 (mmm160) REVERT: A 141 ASN cc_start: 0.7159 (m-40) cc_final: 0.6871 (m-40) REVERT: A 392 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7296 (p0) REVERT: A 474 LYS cc_start: 0.7554 (mttt) cc_final: 0.7050 (mttt) REVERT: A 509 GLU cc_start: 0.7336 (tt0) cc_final: 0.7131 (tt0) REVERT: B 139 ARG cc_start: 0.6583 (mmm160) cc_final: 0.6092 (mmm160) REVERT: B 141 ASN cc_start: 0.7159 (m-40) cc_final: 0.6863 (m-40) REVERT: B 414 ASN cc_start: 0.7112 (p0) cc_final: 0.6897 (t160) REVERT: B 509 GLU cc_start: 0.7302 (tt0) cc_final: 0.7095 (tt0) REVERT: D 139 ARG cc_start: 0.6599 (mmm160) cc_final: 0.6109 (mmm160) REVERT: D 141 ASN cc_start: 0.7147 (m-40) cc_final: 0.6867 (m-40) REVERT: D 414 ASN cc_start: 0.7087 (p0) cc_final: 0.6882 (t160) REVERT: D 474 LYS cc_start: 0.7584 (mttt) cc_final: 0.7083 (mttt) REVERT: D 509 GLU cc_start: 0.7329 (tt0) cc_final: 0.7120 (tt0) REVERT: C 139 ARG cc_start: 0.6573 (mmm160) cc_final: 0.6080 (mmm160) REVERT: C 141 ASN cc_start: 0.7155 (m-40) cc_final: 0.6877 (m-40) REVERT: C 392 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7304 (p0) REVERT: C 414 ASN cc_start: 0.7072 (p0) cc_final: 0.6863 (t160) REVERT: C 509 GLU cc_start: 0.7357 (tt0) cc_final: 0.7145 (tt0) outliers start: 39 outliers final: 11 residues processed: 212 average time/residue: 1.3459 time to fit residues: 313.1364 Evaluate side-chains 172 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 74 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 170 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 130 optimal weight: 0.4980 chunk 96 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.222584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.192011 restraints weight = 17190.634| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 1.67 r_work: 0.4022 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3914 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15124 Z= 0.271 Angle : 0.652 10.185 20344 Z= 0.343 Chirality : 0.047 0.159 2256 Planarity : 0.004 0.059 2564 Dihedral : 7.683 52.935 2076 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.32 % Allowed : 14.37 % 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: -0.44 (0.20), residues: 1788 helix: 0.60 (0.20), residues: 680 sheet: -0.05 (0.27), residues: 396 loop : -1.24 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 126 HIS 0.004 0.001 HIS D 415 PHE 0.014 0.002 PHE C 315 TYR 0.020 0.002 TYR C 314 ARG 0.008 0.001 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 171 time to evaluate : 1.734 Fit side-chains REVERT: A 59 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7583 (p0) REVERT: A 141 ASN cc_start: 0.7168 (m-40) cc_final: 0.6938 (m-40) REVERT: A 392 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7315 (p0) REVERT: A 474 LYS cc_start: 0.7440 (mttt) cc_final: 0.7064 (mttt) REVERT: A 509 GLU cc_start: 0.7377 (tt0) cc_final: 0.7173 (tt0) REVERT: B 141 ASN cc_start: 0.7226 (m-40) cc_final: 0.6982 (m-40) REVERT: B 392 ASP cc_start: 0.7610 (p0) cc_final: 0.7317 (p0) REVERT: B 509 GLU cc_start: 0.7338 (tt0) cc_final: 0.7133 (tt0) REVERT: D 392 ASP cc_start: 0.7611 (p0) cc_final: 0.7322 (p0) REVERT: D 474 LYS cc_start: 0.7422 (mttt) cc_final: 0.7046 (mttt) REVERT: D 509 GLU cc_start: 0.7349 (tt0) cc_final: 0.7147 (tt0) REVERT: C 59 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7326 (p0) REVERT: C 392 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7305 (p0) REVERT: C 509 GLU cc_start: 0.7357 (tt0) cc_final: 0.7155 (tt0) outliers start: 55 outliers final: 23 residues processed: 211 average time/residue: 1.3508 time to fit residues: 312.9096 Evaluate side-chains 191 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 523 SER Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 80 optimal weight: 4.9990 chunk 130 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 4 optimal weight: 0.2980 chunk 157 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN A 455 ASN B 414 ASN B 455 ASN D 414 ASN D 455 ASN C 414 ASN C 455 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.222147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.191513 restraints weight = 17337.763| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 1.67 r_work: 0.4023 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3916 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15124 Z= 0.267 Angle : 0.649 10.373 20344 Z= 0.339 Chirality : 0.047 0.161 2256 Planarity : 0.004 0.061 2564 Dihedral : 7.612 54.999 2076 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.17 % Allowed : 14.79 % Favored : 81.04 % 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: -0.22 (0.20), residues: 1788 helix: 0.92 (0.20), residues: 680 sheet: -0.10 (0.27), residues: 396 loop : -1.17 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 126 HIS 0.004 0.001 HIS C 415 PHE 0.013 0.002 PHE A 315 TYR 0.019 0.002 TYR C 314 ARG 0.007 0.001 ARG D 332 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 174 time to evaluate : 1.709 Fit side-chains REVERT: A 59 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7560 (p0) REVERT: A 373 GLU cc_start: 0.6583 (mm-30) cc_final: 0.6066 (pt0) REVERT: A 392 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7420 (p0) REVERT: A 474 LYS cc_start: 0.7225 (mttt) cc_final: 0.6876 (mttt) REVERT: A 509 GLU cc_start: 0.7366 (tt0) cc_final: 0.7130 (tt0) REVERT: B 373 GLU cc_start: 0.6658 (mm-30) cc_final: 0.6153 (pt0) REVERT: B 392 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7383 (p0) REVERT: B 509 GLU cc_start: 0.7328 (tt0) cc_final: 0.7094 (tt0) REVERT: D 373 GLU cc_start: 0.6639 (mm-30) cc_final: 0.6152 (pt0) REVERT: D 392 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7433 (p0) REVERT: D 474 LYS cc_start: 0.7257 (mttt) cc_final: 0.6907 (mttt) REVERT: D 509 GLU cc_start: 0.7346 (tt0) cc_final: 0.7115 (tt0) REVERT: C 59 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7357 (p0) REVERT: C 373 GLU cc_start: 0.6568 (mm-30) cc_final: 0.6060 (pt0) REVERT: C 392 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7420 (p0) REVERT: C 509 GLU cc_start: 0.7343 (tt0) cc_final: 0.7060 (tt0) outliers start: 69 outliers final: 28 residues processed: 215 average time/residue: 1.3864 time to fit residues: 327.5445 Evaluate side-chains 201 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 523 SER Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 60 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 121 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 174 optimal weight: 7.9990 chunk 163 optimal weight: 0.0170 chunk 39 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 ASN D 414 ASN C 414 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.221293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.190689 restraints weight = 17264.721| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 1.67 r_work: 0.4017 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3913 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15124 Z= 0.266 Angle : 0.652 10.457 20344 Z= 0.341 Chirality : 0.047 0.159 2256 Planarity : 0.004 0.067 2564 Dihedral : 7.561 57.188 2076 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.05 % Allowed : 15.22 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.20), residues: 1788 helix: 1.15 (0.20), residues: 680 sheet: -0.17 (0.27), residues: 396 loop : -1.05 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 126 HIS 0.004 0.001 HIS A 415 PHE 0.014 0.002 PHE C 315 TYR 0.019 0.002 TYR C 314 ARG 0.007 0.001 ARG C 332 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 169 time to evaluate : 1.782 Fit side-chains REVERT: A 285 TYR cc_start: 0.7959 (m-80) cc_final: 0.7469 (m-80) REVERT: A 373 GLU cc_start: 0.6495 (mm-30) cc_final: 0.6030 (pt0) REVERT: A 392 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7442 (p0) REVERT: A 474 LYS cc_start: 0.7199 (mttt) cc_final: 0.6883 (mmpt) REVERT: A 509 GLU cc_start: 0.7408 (tt0) cc_final: 0.7102 (tt0) REVERT: B 285 TYR cc_start: 0.7948 (m-80) cc_final: 0.7453 (m-80) REVERT: B 373 GLU cc_start: 0.6617 (mm-30) cc_final: 0.6146 (pt0) REVERT: B 392 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7440 (p0) REVERT: B 478 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7388 (tttp) REVERT: B 509 GLU cc_start: 0.7394 (tt0) cc_final: 0.7173 (tt0) REVERT: D 285 TYR cc_start: 0.7950 (m-80) cc_final: 0.7450 (m-80) REVERT: D 373 GLU cc_start: 0.6642 (mm-30) cc_final: 0.6149 (pt0) REVERT: D 392 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7470 (p0) REVERT: D 474 LYS cc_start: 0.7173 (mttt) cc_final: 0.6823 (mttt) REVERT: D 509 GLU cc_start: 0.7384 (tt0) cc_final: 0.7163 (tt0) REVERT: C 59 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7392 (p0) REVERT: C 373 GLU cc_start: 0.6555 (mm-30) cc_final: 0.6071 (pt0) REVERT: C 392 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7447 (p0) REVERT: C 478 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7377 (tttp) REVERT: C 509 GLU cc_start: 0.7378 (tt0) cc_final: 0.7158 (tt0) outliers start: 67 outliers final: 30 residues processed: 216 average time/residue: 1.2912 time to fit residues: 307.7424 Evaluate side-chains 201 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 523 SER Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 101 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 60 optimal weight: 0.0970 chunk 59 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.223326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.192856 restraints weight = 17226.228| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 1.66 r_work: 0.4040 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3932 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15124 Z= 0.185 Angle : 0.602 11.023 20344 Z= 0.312 Chirality : 0.045 0.149 2256 Planarity : 0.003 0.048 2564 Dihedral : 7.383 57.684 2076 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.32 % Allowed : 16.43 % Favored : 80.25 % 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: 0.18 (0.20), residues: 1788 helix: 1.44 (0.20), residues: 680 sheet: -0.12 (0.27), residues: 396 loop : -1.00 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 126 HIS 0.004 0.001 HIS B 415 PHE 0.013 0.001 PHE C 315 TYR 0.014 0.001 TYR C 314 ARG 0.006 0.001 ARG C 481 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 168 time to evaluate : 1.628 Fit side-chains REVERT: A 285 TYR cc_start: 0.7954 (m-80) cc_final: 0.7447 (m-80) REVERT: A 317 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8571 (tp) REVERT: A 373 GLU cc_start: 0.6485 (mm-30) cc_final: 0.6007 (pt0) REVERT: A 392 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7436 (p0) REVERT: A 474 LYS cc_start: 0.7105 (mttt) cc_final: 0.6815 (mmpt) REVERT: A 509 GLU cc_start: 0.7396 (tt0) cc_final: 0.7101 (tt0) REVERT: B 285 TYR cc_start: 0.7935 (m-80) cc_final: 0.7426 (m-80) REVERT: B 317 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8568 (tp) REVERT: B 373 GLU cc_start: 0.6585 (mm-30) cc_final: 0.6124 (pt0) REVERT: B 392 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7431 (p0) REVERT: B 509 GLU cc_start: 0.7358 (tt0) cc_final: 0.7146 (tt0) REVERT: D 285 TYR cc_start: 0.7951 (m-80) cc_final: 0.7437 (m-80) REVERT: D 317 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8568 (tp) REVERT: D 373 GLU cc_start: 0.6604 (mm-30) cc_final: 0.6170 (pt0) REVERT: D 392 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7443 (p0) REVERT: D 474 LYS cc_start: 0.7099 (mttt) cc_final: 0.6801 (mmpt) REVERT: D 509 GLU cc_start: 0.7400 (tt0) cc_final: 0.7190 (tt0) REVERT: C 59 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.7312 (p0) REVERT: C 373 GLU cc_start: 0.6525 (mm-30) cc_final: 0.6025 (pt0) REVERT: C 392 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7427 (p0) REVERT: C 509 GLU cc_start: 0.7353 (tt0) cc_final: 0.7137 (tt0) outliers start: 55 outliers final: 23 residues processed: 204 average time/residue: 1.2922 time to fit residues: 291.3076 Evaluate side-chains 194 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 523 SER Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 141 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 85 optimal weight: 0.2980 chunk 114 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.220929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.190212 restraints weight = 17224.141| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 1.67 r_work: 0.4012 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3907 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15124 Z= 0.280 Angle : 0.662 11.135 20344 Z= 0.342 Chirality : 0.047 0.159 2256 Planarity : 0.004 0.071 2564 Dihedral : 7.509 59.068 2076 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.68 % Allowed : 16.73 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.20), residues: 1788 helix: 1.37 (0.20), residues: 680 sheet: -0.20 (0.26), residues: 396 loop : -0.96 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 126 HIS 0.004 0.001 HIS B 415 PHE 0.014 0.002 PHE C 315 TYR 0.020 0.002 TYR C 314 ARG 0.007 0.001 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 175 time to evaluate : 1.634 Fit side-chains REVERT: A 152 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.7986 (mp) REVERT: A 285 TYR cc_start: 0.7971 (m-80) cc_final: 0.7471 (m-80) REVERT: A 317 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8574 (tp) REVERT: A 373 GLU cc_start: 0.6586 (mm-30) cc_final: 0.6143 (pt0) REVERT: A 392 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7467 (p0) REVERT: A 474 LYS cc_start: 0.7098 (mttt) cc_final: 0.6801 (mmpt) REVERT: A 509 GLU cc_start: 0.7460 (tt0) cc_final: 0.7173 (tt0) REVERT: B 152 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.7987 (mp) REVERT: B 285 TYR cc_start: 0.7958 (m-80) cc_final: 0.7455 (m-80) REVERT: B 317 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8575 (tp) REVERT: B 373 GLU cc_start: 0.6679 (mm-30) cc_final: 0.6231 (pt0) REVERT: B 392 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7497 (p0) REVERT: B 474 LYS cc_start: 0.6732 (mtmt) cc_final: 0.6461 (mmpt) REVERT: B 478 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7313 (tttp) REVERT: B 509 GLU cc_start: 0.7414 (tt0) cc_final: 0.7164 (tt0) REVERT: D 152 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.7971 (mp) REVERT: D 285 TYR cc_start: 0.7956 (m-80) cc_final: 0.7447 (m-80) REVERT: D 317 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8572 (tp) REVERT: D 373 GLU cc_start: 0.6675 (mm-30) cc_final: 0.6204 (pt0) REVERT: D 392 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7499 (p0) REVERT: D 474 LYS cc_start: 0.7072 (mttt) cc_final: 0.6771 (mmpt) REVERT: D 509 GLU cc_start: 0.7444 (tt0) cc_final: 0.7196 (tt0) REVERT: C 59 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7402 (p0) REVERT: C 373 GLU cc_start: 0.6568 (mm-30) cc_final: 0.6129 (mm-30) REVERT: C 392 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7451 (p0) REVERT: C 474 LYS cc_start: 0.6708 (mtmt) cc_final: 0.6457 (mmpt) REVERT: C 478 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7301 (tttp) REVERT: C 509 GLU cc_start: 0.7324 (tt0) cc_final: 0.7076 (tt0) outliers start: 61 outliers final: 25 residues processed: 212 average time/residue: 1.2490 time to fit residues: 294.1821 Evaluate side-chains 210 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 523 SER Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 117 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN B 330 ASN D 330 ASN C 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.222718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.192187 restraints weight = 17154.452| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 1.66 r_work: 0.4032 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3925 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15124 Z= 0.197 Angle : 0.612 11.546 20344 Z= 0.316 Chirality : 0.045 0.150 2256 Planarity : 0.003 0.051 2564 Dihedral : 7.392 59.601 2076 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.96 % Allowed : 17.93 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.27 (0.21), residues: 1788 helix: 1.54 (0.20), residues: 680 sheet: -0.17 (0.27), residues: 396 loop : -0.90 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 126 HIS 0.004 0.001 HIS D 415 PHE 0.013 0.001 PHE D 315 TYR 0.015 0.001 TYR C 314 ARG 0.008 0.001 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 170 time to evaluate : 1.684 Fit side-chains REVERT: A 285 TYR cc_start: 0.7951 (m-80) cc_final: 0.7437 (m-80) REVERT: A 317 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8576 (tp) REVERT: A 373 GLU cc_start: 0.6544 (mm-30) cc_final: 0.6104 (pt0) REVERT: A 392 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7336 (p0) REVERT: A 474 LYS cc_start: 0.7053 (mttt) cc_final: 0.6754 (mmpt) REVERT: A 509 GLU cc_start: 0.7389 (tt0) cc_final: 0.7113 (tt0) REVERT: B 285 TYR cc_start: 0.7943 (m-80) cc_final: 0.7426 (m-80) REVERT: B 317 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8573 (tp) REVERT: B 373 GLU cc_start: 0.6604 (mm-30) cc_final: 0.6174 (pt0) REVERT: B 392 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7412 (p0) REVERT: B 459 ARG cc_start: 0.7674 (mtm-85) cc_final: 0.7424 (mtm-85) REVERT: B 474 LYS cc_start: 0.6703 (mtmt) cc_final: 0.6453 (mmpt) REVERT: B 509 GLU cc_start: 0.7343 (tt0) cc_final: 0.7099 (tt0) REVERT: D 285 TYR cc_start: 0.7955 (m-80) cc_final: 0.7434 (m-80) REVERT: D 317 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8574 (tp) REVERT: D 373 GLU cc_start: 0.6602 (mm-30) cc_final: 0.6172 (pt0) REVERT: D 392 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7424 (p0) REVERT: D 474 LYS cc_start: 0.7028 (mttt) cc_final: 0.6728 (mmpt) REVERT: D 509 GLU cc_start: 0.7357 (tt0) cc_final: 0.7117 (tt0) REVERT: C 59 ASP cc_start: 0.7618 (OUTLIER) cc_final: 0.7335 (p0) REVERT: C 373 GLU cc_start: 0.6596 (mm-30) cc_final: 0.6133 (pt0) REVERT: C 392 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7338 (p0) REVERT: C 509 GLU cc_start: 0.7343 (tt0) cc_final: 0.7100 (tt0) outliers start: 49 outliers final: 24 residues processed: 200 average time/residue: 1.2527 time to fit residues: 277.2928 Evaluate side-chains 197 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 523 SER Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 70 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 52 optimal weight: 0.0270 chunk 175 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.222325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.191796 restraints weight = 17255.208| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 1.66 r_work: 0.4024 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3917 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15124 Z= 0.225 Angle : 0.628 11.456 20344 Z= 0.323 Chirality : 0.046 0.154 2256 Planarity : 0.004 0.057 2564 Dihedral : 7.414 59.160 2076 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.17 % Allowed : 18.78 % Favored : 79.05 % 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: 0.30 (0.20), residues: 1788 helix: 1.54 (0.20), residues: 680 sheet: 0.10 (0.26), residues: 380 loop : -1.02 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 126 HIS 0.004 0.001 HIS A 415 PHE 0.013 0.002 PHE D 315 TYR 0.017 0.001 TYR C 314 ARG 0.007 0.001 ARG A 481 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 1.648 Fit side-chains REVERT: A 285 TYR cc_start: 0.7973 (m-80) cc_final: 0.7481 (m-80) REVERT: A 317 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8584 (tp) REVERT: A 373 GLU cc_start: 0.6599 (mm-30) cc_final: 0.6132 (pt0) REVERT: A 392 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7344 (p0) REVERT: A 474 LYS cc_start: 0.6980 (mttt) cc_final: 0.6693 (mmpt) REVERT: B 110 GLU cc_start: 0.7427 (mp0) cc_final: 0.7195 (mp0) REVERT: B 285 TYR cc_start: 0.7957 (m-80) cc_final: 0.7480 (m-80) REVERT: B 317 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8584 (tp) REVERT: B 373 GLU cc_start: 0.6614 (mm-30) cc_final: 0.6197 (pt0) REVERT: B 392 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7407 (p0) REVERT: B 474 LYS cc_start: 0.6676 (mtmt) cc_final: 0.6381 (mmpt) REVERT: B 509 GLU cc_start: 0.7368 (tt0) cc_final: 0.7116 (tt0) REVERT: D 285 TYR cc_start: 0.7970 (m-80) cc_final: 0.7491 (m-80) REVERT: D 317 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8587 (tp) REVERT: D 373 GLU cc_start: 0.6617 (mm-30) cc_final: 0.6182 (pt0) REVERT: D 392 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7415 (p0) REVERT: D 474 LYS cc_start: 0.6972 (mttt) cc_final: 0.6685 (mmpt) REVERT: D 509 GLU cc_start: 0.7379 (tt0) cc_final: 0.7130 (tt0) REVERT: C 59 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7389 (p0) REVERT: C 373 GLU cc_start: 0.6629 (mm-30) cc_final: 0.6165 (pt0) REVERT: C 392 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7342 (p0) REVERT: C 474 LYS cc_start: 0.6692 (mttt) cc_final: 0.6451 (mmpt) REVERT: C 509 GLU cc_start: 0.7352 (tt0) cc_final: 0.7095 (tt0) outliers start: 36 outliers final: 26 residues processed: 185 average time/residue: 1.3451 time to fit residues: 273.9109 Evaluate side-chains 200 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 523 SER Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 131 optimal weight: 3.9990 chunk 98 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 0.0870 chunk 80 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.220970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.190203 restraints weight = 17219.848| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 1.67 r_work: 0.4009 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3902 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15124 Z= 0.286 Angle : 0.671 11.671 20344 Z= 0.344 Chirality : 0.047 0.159 2256 Planarity : 0.004 0.070 2564 Dihedral : 7.512 59.814 2076 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.72 % Allowed : 18.54 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.20), residues: 1788 helix: 1.43 (0.20), residues: 680 sheet: 0.02 (0.26), residues: 380 loop : -1.04 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 126 HIS 0.004 0.001 HIS A 415 PHE 0.014 0.002 PHE C 315 TYR 0.020 0.002 TYR C 314 ARG 0.007 0.001 ARG C 332 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10416.91 seconds wall clock time: 186 minutes 9.04 seconds (11169.04 seconds total)