Starting phenix.real_space_refine on Sun Aug 9 11:35:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u30_41848/08_2026/8u30_41848_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u30_41848/08_2026/8u30_41848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u30_41848/08_2026/8u30_41848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u30_41848/08_2026/8u30_41848.map" model { file = "/net/cci-nas-00/data/ceres_data/8u30_41848/08_2026/8u30_41848_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u30_41848/08_2026/8u30_41848_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians P 12 5.49 5 S 92 5.16 5 Na 1 4.78 5 C 11324 2.51 5 N 2760 2.21 5 O 3120 1.98 5 H 17236 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34545 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 8586 Classifications: {'peptide': 527} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 512} Chain breaks: 1 Chain: "D" Number of atoms: 8586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 8586 Classifications: {'peptide': 527} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 512} Chain breaks: 1 Chain: "B" Number of atoms: 8586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 8586 Classifications: {'peptide': 527} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 512} Chain breaks: 1 Chain: "C" Number of atoms: 8586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 8586 Classifications: {'peptide': 527} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 512} Chain breaks: 1 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {' NA': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Time building chain proxies: 6.03, per 1000 atoms: 0.17 Number of scatterers: 34545 At special positions: 0 Unit cell: (122.745, 122.745, 112.725, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 92 16.00 P 12 15.00 Na 1 11.00 O 3120 8.00 N 2760 7.00 C 11324 6.00 H 17236 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 935.6 milliseconds 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3984 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 4 sheets defined 68.7% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 203 through 212 removed outlier: 3.575A pdb=" N ILE A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 223 removed outlier: 3.823A pdb=" N ASN A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 250 through 257 Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 324 through 328 removed outlier: 3.686A pdb=" N GLU A 327 " --> pdb=" O LYS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 345 through 354 removed outlier: 3.650A pdb=" N GLN A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.681A pdb=" N LEU A 365 " --> pdb=" O CYS A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.982A pdb=" N LEU A 413 " --> pdb=" O HIS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 429 Processing helix chain 'A' and resid 429 through 454 removed outlier: 3.521A pdb=" N TYR A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 500 Processing helix chain 'A' and resid 504 through 508 Processing helix chain 'A' and resid 510 through 532 Processing helix chain 'A' and resid 536 through 552 Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 559 through 599 removed outlier: 4.195A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 628 removed outlier: 3.605A pdb=" N ASN A 628 " --> pdb=" O GLY A 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 602 through 628' Processing helix chain 'A' and resid 629 through 640 removed outlier: 3.907A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 643 No H-bonds generated for 'chain 'A' and resid 641 through 643' Processing helix chain 'A' and resid 655 through 671 removed outlier: 3.543A pdb=" N PHE A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 689 Processing helix chain 'A' and resid 689 through 712 removed outlier: 3.526A pdb=" N PHE A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 212 removed outlier: 3.574A pdb=" N ILE D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 223 removed outlier: 3.823A pdb=" N ASN D 223 " --> pdb=" O LEU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 250 through 257 Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 324 through 328 removed outlier: 3.686A pdb=" N GLU D 327 " --> pdb=" O LYS D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 354 removed outlier: 3.650A pdb=" N GLN D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 366 removed outlier: 3.680A pdb=" N LEU D 365 " --> pdb=" O CYS D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 410 through 414 removed outlier: 3.982A pdb=" N LEU D 413 " --> pdb=" O HIS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 429 Processing helix chain 'D' and resid 429 through 454 removed outlier: 3.521A pdb=" N TYR D 454 " --> pdb=" O ALA D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 504 through 508 Processing helix chain 'D' and resid 510 through 532 Processing helix chain 'D' and resid 536 through 552 Processing helix chain 'D' and resid 553 through 557 Processing helix chain 'D' and resid 559 through 599 removed outlier: 4.195A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 628 removed outlier: 3.605A pdb=" N ASN D 628 " --> pdb=" O GLY D 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 602 through 628' Processing helix chain 'D' and resid 629 through 640 removed outlier: 3.908A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 643 No H-bonds generated for 'chain 'D' and resid 641 through 643' Processing helix chain 'D' and resid 655 through 671 removed outlier: 3.543A pdb=" N PHE D 659 " --> pdb=" O PHE D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 689 Processing helix chain 'D' and resid 689 through 712 removed outlier: 3.526A pdb=" N PHE D 712 " --> pdb=" O THR D 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 212 removed outlier: 3.574A pdb=" N ILE B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 223 removed outlier: 3.823A pdb=" N ASN B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'B' and resid 324 through 328 removed outlier: 3.686A pdb=" N GLU B 327 " --> pdb=" O LYS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 345 through 354 removed outlier: 3.650A pdb=" N GLN B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 366 removed outlier: 3.681A pdb=" N LEU B 365 " --> pdb=" O CYS B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 410 through 414 removed outlier: 3.982A pdb=" N LEU B 413 " --> pdb=" O HIS B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 429 Processing helix chain 'B' and resid 429 through 454 removed outlier: 3.521A pdb=" N TYR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 500 Processing helix chain 'B' and resid 504 through 508 Processing helix chain 'B' and resid 510 through 532 Processing helix chain 'B' and resid 536 through 552 Processing helix chain 'B' and resid 553 through 557 Processing helix chain 'B' and resid 559 through 599 removed outlier: 4.194A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 628 removed outlier: 3.605A pdb=" N ASN B 628 " --> pdb=" O GLY B 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 602 through 628' Processing helix chain 'B' and resid 629 through 640 removed outlier: 3.907A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 643 No H-bonds generated for 'chain 'B' and resid 641 through 643' Processing helix chain 'B' and resid 655 through 671 removed outlier: 3.544A pdb=" N PHE B 659 " --> pdb=" O PHE B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 689 Processing helix chain 'B' and resid 689 through 712 removed outlier: 3.526A pdb=" N PHE B 712 " --> pdb=" O THR B 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 212 removed outlier: 3.575A pdb=" N ILE C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 223 removed outlier: 3.823A pdb=" N ASN C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 250 through 257 Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'C' and resid 324 through 328 removed outlier: 3.686A pdb=" N GLU C 327 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.650A pdb=" N GLN C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 366 removed outlier: 3.681A pdb=" N LEU C 365 " --> pdb=" O CYS C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 410 through 414 removed outlier: 3.982A pdb=" N LEU C 413 " --> pdb=" O HIS C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 429 Processing helix chain 'C' and resid 429 through 454 removed outlier: 3.521A pdb=" N TYR C 454 " --> pdb=" O ALA C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 500 Processing helix chain 'C' and resid 504 through 508 Processing helix chain 'C' and resid 510 through 532 Processing helix chain 'C' and resid 536 through 552 Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 559 through 599 removed outlier: 4.195A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 628 removed outlier: 3.605A pdb=" N ASN C 628 " --> pdb=" O GLY C 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 602 through 628' Processing helix chain 'C' and resid 629 through 640 removed outlier: 3.907A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 643 No H-bonds generated for 'chain 'C' and resid 641 through 643' Processing helix chain 'C' and resid 655 through 671 removed outlier: 3.542A pdb=" N PHE C 659 " --> pdb=" O PHE C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 689 Processing helix chain 'C' and resid 689 through 712 removed outlier: 3.526A pdb=" N PHE C 712 " --> pdb=" O THR C 708 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 374 removed outlier: 7.141A pdb=" N LYS A 368 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASP A 383 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 368 through 374 removed outlier: 7.141A pdb=" N LYS D 368 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ASP D 383 " --> pdb=" O LYS D 368 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 368 through 374 removed outlier: 7.141A pdb=" N LYS B 368 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASP B 383 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 368 through 374 removed outlier: 7.141A pdb=" N LYS C 368 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASP C 383 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) 1032 hydrogen bonds defined for protein. 2976 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: 9.60 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17204 1.03 - 1.23: 52 1.23 - 1.42: 7577 1.42 - 1.61: 9955 1.61 - 1.81: 168 Bond restraints: 34956 Sorted by residual: bond pdb=" N GLU B 458 " pdb=" H GLU B 458 " ideal model delta sigma weight residual 0.860 0.935 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" N GLU C 458 " pdb=" H GLU C 458 " ideal model delta sigma weight residual 0.860 0.935 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" N GLU A 458 " pdb=" H GLU A 458 " ideal model delta sigma weight residual 0.860 0.935 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" N GLU D 458 " pdb=" H GLU D 458 " ideal model delta sigma weight residual 0.860 0.935 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" O52 PIO D 901 " pdb=" P5 PIO D 901 " ideal model delta sigma weight residual 1.525 1.452 0.073 2.00e-02 2.50e+03 1.32e+01 ... (remaining 34951 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.70: 62796 4.70 - 9.40: 86 9.40 - 14.11: 54 14.11 - 18.81: 0 18.81 - 23.51: 4 Bond angle restraints: 62940 Sorted by residual: angle pdb=" O11 PIO A 901 " pdb=" P1 PIO A 901 " pdb=" O12 PIO A 901 " ideal model delta sigma weight residual 121.09 97.58 23.51 3.00e+00 1.11e-01 6.14e+01 angle pdb=" O11 PIO C 901 " pdb=" P1 PIO C 901 " pdb=" O12 PIO C 901 " ideal model delta sigma weight residual 121.09 101.56 19.53 3.00e+00 1.11e-01 4.24e+01 angle pdb=" O11 PIO B 901 " pdb=" P1 PIO B 901 " pdb=" O12 PIO B 901 " ideal model delta sigma weight residual 121.09 101.57 19.52 3.00e+00 1.11e-01 4.23e+01 angle pdb=" O11 PIO D 901 " pdb=" P1 PIO D 901 " pdb=" O12 PIO D 901 " ideal model delta sigma weight residual 121.09 101.60 19.49 3.00e+00 1.11e-01 4.22e+01 angle pdb=" N VAL A 457 " pdb=" CA VAL A 457 " pdb=" C VAL A 457 " ideal model delta sigma weight residual 109.34 121.95 -12.61 2.08e+00 2.31e-01 3.67e+01 ... (remaining 62935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 14882 17.90 - 35.81: 1141 35.81 - 53.71: 305 53.71 - 71.62: 84 71.62 - 89.52: 16 Dihedral angle restraints: 16428 sinusoidal: 8688 harmonic: 7740 Sorted by residual: dihedral pdb=" CA ARG C 739 " pdb=" C ARG C 739 " pdb=" N TRP C 740 " pdb=" CA TRP C 740 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ARG A 739 " pdb=" C ARG A 739 " pdb=" N TRP A 740 " pdb=" CA TRP A 740 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ARG B 739 " pdb=" C ARG B 739 " pdb=" N TRP B 740 " pdb=" CA TRP B 740 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 16425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2452 0.063 - 0.126: 231 0.126 - 0.188: 4 0.188 - 0.251: 6 0.251 - 0.314: 7 Chirality restraints: 2700 Sorted by residual: chirality pdb=" C5 PIO C 901 " pdb=" C4 PIO C 901 " pdb=" C6 PIO C 901 " pdb=" O5 PIO C 901 " both_signs ideal model delta sigma weight residual False -2.47 -2.15 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C5 PIO B 901 " pdb=" C4 PIO B 901 " pdb=" C6 PIO B 901 " pdb=" O5 PIO B 901 " both_signs ideal model delta sigma weight residual False -2.47 -2.15 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C5 PIO D 901 " pdb=" C4 PIO D 901 " pdb=" C6 PIO D 901 " pdb=" O5 PIO D 901 " both_signs ideal model delta sigma weight residual False -2.47 -2.16 -0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 2697 not shown) Planarity restraints: 4996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 457 " 0.065 2.00e-02 2.50e+03 1.20e-01 1.43e+02 pdb=" N GLU C 458 " -0.206 2.00e-02 2.50e+03 pdb=" CA GLU C 458 " 0.056 2.00e-02 2.50e+03 pdb=" H GLU C 458 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 457 " 0.065 2.00e-02 2.50e+03 1.19e-01 1.43e+02 pdb=" N GLU B 458 " -0.206 2.00e-02 2.50e+03 pdb=" CA GLU B 458 " 0.056 2.00e-02 2.50e+03 pdb=" H GLU B 458 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 457 " -0.065 2.00e-02 2.50e+03 1.19e-01 1.43e+02 pdb=" N GLU A 458 " 0.206 2.00e-02 2.50e+03 pdb=" CA GLU A 458 " -0.056 2.00e-02 2.50e+03 pdb=" H GLU A 458 " -0.084 2.00e-02 2.50e+03 ... (remaining 4993 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 1520 2.19 - 2.79: 68011 2.79 - 3.39: 94500 3.39 - 4.00: 119757 4.00 - 4.60: 188129 Nonbonded interactions: 471917 Sorted by model distance: nonbonded pdb=" O SER A 505 " pdb=" H ASP A 509 " model vdw 1.586 2.450 nonbonded pdb=" O SER B 505 " pdb=" H ASP B 509 " model vdw 1.586 2.450 nonbonded pdb=" O SER C 505 " pdb=" H ASP C 509 " model vdw 1.586 2.450 nonbonded pdb=" O SER D 505 " pdb=" H ASP D 509 " model vdw 1.587 2.450 nonbonded pdb=" O ILE A 672 " pdb="HD21 ASN A 676 " model vdw 1.588 2.450 ... (remaining 471912 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 197 through 901) selection = chain 'B' selection = chain 'C' 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.280 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 34.180 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 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:8.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 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 : 0.005 0.073 17720 Z= 0.245 Angle : 0.908 23.511 24008 Z= 0.416 Chirality : 0.040 0.314 2700 Planarity : 0.003 0.022 2952 Dihedral : 14.481 89.522 6372 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.20), residues: 2092 helix: 2.43 (0.14), residues: 1276 sheet: -1.22 (0.86), residues: 40 loop : -1.33 (0.24), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 367 TYR 0.010 0.001 TYR C 555 PHE 0.010 0.002 PHE D 438 TRP 0.007 0.001 TRP C 749 HIS 0.003 0.001 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.24 (17720) covalent geometry : angle 0.90753 / 0.42 (24008) hydrogen bonds : bond 0.13429 / 9.02 ( 1032) hydrogen bonds : angle 4.86813 / 3.39 ( 2976) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 0.876 Fit side-chains REVERT: A 273 GLN cc_start: 0.7678 (tt0) cc_final: 0.7152 (tp40) REVERT: A 386 CYS cc_start: 0.7457 (m) cc_final: 0.7220 (m) REVERT: A 500 ARG cc_start: 0.6985 (mmt180) cc_final: 0.6595 (mtt-85) REVERT: A 691 GLN cc_start: 0.7673 (mm110) cc_final: 0.7372 (tp40) REVERT: D 273 GLN cc_start: 0.7661 (tt0) cc_final: 0.7163 (mm110) REVERT: D 386 CYS cc_start: 0.7464 (m) cc_final: 0.7228 (m) REVERT: D 500 ARG cc_start: 0.7001 (mmt180) cc_final: 0.6606 (mtt-85) REVERT: D 691 GLN cc_start: 0.7682 (mm110) cc_final: 0.7379 (tp40) REVERT: B 273 GLN cc_start: 0.7668 (tt0) cc_final: 0.7137 (tp40) REVERT: B 386 CYS cc_start: 0.7461 (m) cc_final: 0.7221 (m) REVERT: B 500 ARG cc_start: 0.6995 (mmt180) cc_final: 0.6601 (mtt-85) REVERT: B 691 GLN cc_start: 0.7687 (mm110) cc_final: 0.7380 (tp40) REVERT: C 273 GLN cc_start: 0.7667 (tt0) cc_final: 0.7140 (tp40) REVERT: C 386 CYS cc_start: 0.7459 (m) cc_final: 0.7220 (m) REVERT: C 500 ARG cc_start: 0.7000 (mmt180) cc_final: 0.6606 (mtt-85) REVERT: C 691 GLN cc_start: 0.7683 (mm110) cc_final: 0.7378 (tp40) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 1.1847 time to fit residues: 521.1025 Evaluate side-chains 255 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 ASN D 259 ASN B 259 ASN C 202 GLN C 259 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.159197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.113282 restraints weight = 55385.371| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.84 r_work: 0.2857 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17720 Z= 0.194 Angle : 0.609 10.840 24008 Z= 0.317 Chirality : 0.040 0.298 2700 Planarity : 0.004 0.043 2952 Dihedral : 7.042 58.428 2388 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.61 % Allowed : 9.68 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.19), residues: 2092 helix: 2.12 (0.14), residues: 1296 sheet: -0.79 (0.58), residues: 92 loop : -1.54 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 355 TYR 0.012 0.002 TYR D 309 PHE 0.015 0.002 PHE D 649 TRP 0.013 0.002 TRP A 740 HIS 0.004 0.001 HIS C 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (17720) covalent geometry : angle 0.60879 / 0.32 (24008) hydrogen bonds : bond 0.06804 / 4.65 ( 1032) hydrogen bonds : angle 4.12597 / 2.90 ( 2976) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 275 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 GLN cc_start: 0.7464 (tt0) cc_final: 0.6963 (tp40) REVERT: A 386 CYS cc_start: 0.8290 (m) cc_final: 0.8054 (m) REVERT: A 432 ARG cc_start: 0.7794 (mtm180) cc_final: 0.7547 (ptm160) REVERT: A 500 ARG cc_start: 0.7286 (mmt180) cc_final: 0.6567 (mtt-85) REVERT: A 691 GLN cc_start: 0.7831 (mm110) cc_final: 0.7607 (tp40) REVERT: D 273 GLN cc_start: 0.7469 (tt0) cc_final: 0.6970 (tp40) REVERT: D 386 CYS cc_start: 0.8299 (m) cc_final: 0.8066 (m) REVERT: D 432 ARG cc_start: 0.7786 (mtm180) cc_final: 0.7539 (ptm160) REVERT: D 500 ARG cc_start: 0.7295 (mmt180) cc_final: 0.6575 (mtt-85) REVERT: D 570 GLU cc_start: 0.7743 (tt0) cc_final: 0.7463 (tt0) REVERT: D 644 MET cc_start: 0.9412 (mmm) cc_final: 0.8343 (mmm) REVERT: D 691 GLN cc_start: 0.7837 (mm110) cc_final: 0.7629 (tp40) REVERT: B 273 GLN cc_start: 0.7459 (tt0) cc_final: 0.6958 (tp40) REVERT: B 386 CYS cc_start: 0.8289 (m) cc_final: 0.8059 (m) REVERT: B 432 ARG cc_start: 0.7781 (mtm180) cc_final: 0.7535 (ptm160) REVERT: B 500 ARG cc_start: 0.7284 (mmt180) cc_final: 0.6565 (mtt-85) REVERT: B 570 GLU cc_start: 0.7790 (tt0) cc_final: 0.7497 (tt0) REVERT: B 691 GLN cc_start: 0.7809 (mm110) cc_final: 0.7594 (tp40) REVERT: C 273 GLN cc_start: 0.7475 (tt0) cc_final: 0.6974 (tp40) REVERT: C 386 CYS cc_start: 0.8274 (m) cc_final: 0.8043 (m) REVERT: C 432 ARG cc_start: 0.7793 (mtm180) cc_final: 0.7545 (ptm160) REVERT: C 500 ARG cc_start: 0.7293 (mmt180) cc_final: 0.6579 (mtt-85) REVERT: C 570 GLU cc_start: 0.7760 (tt0) cc_final: 0.7474 (tt0) REVERT: C 644 MET cc_start: 0.9413 (mmm) cc_final: 0.8309 (mmm) REVERT: C 691 GLN cc_start: 0.7845 (mm110) cc_final: 0.7627 (tp40) outliers start: 30 outliers final: 8 residues processed: 281 average time/residue: 1.2758 time to fit residues: 404.6644 Evaluate side-chains 254 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 246 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 526 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 199 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.160552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.115188 restraints weight = 54874.431| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.93 r_work: 0.2862 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17720 Z= 0.149 Angle : 0.529 8.652 24008 Z= 0.278 Chirality : 0.036 0.213 2700 Planarity : 0.003 0.028 2952 Dihedral : 6.488 59.532 2388 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.29 % Allowed : 12.10 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.19), residues: 2092 helix: 2.33 (0.14), residues: 1296 sheet: -0.75 (0.56), residues: 92 loop : -1.49 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 367 TYR 0.008 0.001 TYR D 309 PHE 0.009 0.001 PHE C 649 TRP 0.008 0.001 TRP D 697 HIS 0.003 0.001 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (17720) covalent geometry : angle 0.52890 / 0.28 (24008) hydrogen bonds : bond 0.06233 / 4.27 ( 1032) hydrogen bonds : angle 3.92422 / 2.76 ( 2976) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 255 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 GLN cc_start: 0.7478 (tt0) cc_final: 0.6977 (tp40) REVERT: A 432 ARG cc_start: 0.7746 (mtm180) cc_final: 0.7454 (ptm160) REVERT: A 500 ARG cc_start: 0.7406 (mmt180) cc_final: 0.7180 (mtp85) REVERT: A 691 GLN cc_start: 0.7697 (mm110) cc_final: 0.7474 (tp40) REVERT: D 273 GLN cc_start: 0.7463 (tt0) cc_final: 0.6977 (tp40) REVERT: D 432 ARG cc_start: 0.7715 (mtm180) cc_final: 0.7419 (ptm160) REVERT: D 500 ARG cc_start: 0.7422 (mmt180) cc_final: 0.7195 (mtp85) REVERT: D 570 GLU cc_start: 0.7717 (tt0) cc_final: 0.7398 (tt0) REVERT: D 691 GLN cc_start: 0.7676 (mm110) cc_final: 0.7451 (tp40) REVERT: B 273 GLN cc_start: 0.7493 (tt0) cc_final: 0.6982 (tp40) REVERT: B 432 ARG cc_start: 0.7724 (mtm180) cc_final: 0.7427 (ptm160) REVERT: B 500 ARG cc_start: 0.7405 (mmt180) cc_final: 0.7182 (mtp85) REVERT: B 570 GLU cc_start: 0.7712 (tt0) cc_final: 0.7384 (tt0) REVERT: B 691 GLN cc_start: 0.7685 (mm110) cc_final: 0.7462 (tp40) REVERT: C 273 GLN cc_start: 0.7504 (tt0) cc_final: 0.6995 (tp40) REVERT: C 432 ARG cc_start: 0.7741 (mtm180) cc_final: 0.7445 (ptm160) REVERT: C 500 ARG cc_start: 0.7406 (mmt180) cc_final: 0.7182 (mtp85) REVERT: C 570 GLU cc_start: 0.7712 (tt0) cc_final: 0.7386 (tt0) REVERT: C 691 GLN cc_start: 0.7690 (mm110) cc_final: 0.7468 (tp40) outliers start: 24 outliers final: 20 residues processed: 263 average time/residue: 1.2591 time to fit residues: 375.3659 Evaluate side-chains 256 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 236 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 746 GLU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 746 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 92 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 156 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.159281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.113221 restraints weight = 54927.460| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.84 r_work: 0.2847 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17720 Z= 0.151 Angle : 0.530 8.700 24008 Z= 0.280 Chirality : 0.036 0.238 2700 Planarity : 0.004 0.032 2952 Dihedral : 6.364 58.460 2388 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.08 % Allowed : 13.01 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.19), residues: 2092 helix: 2.34 (0.14), residues: 1300 sheet: -0.82 (0.55), residues: 92 loop : -1.47 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 721 TYR 0.010 0.001 TYR B 309 PHE 0.011 0.001 PHE C 649 TRP 0.008 0.001 TRP C 697 HIS 0.003 0.001 HIS C 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (17720) covalent geometry : angle 0.52969 / 0.28 (24008) hydrogen bonds : bond 0.06206 / 4.25 ( 1032) hydrogen bonds : angle 3.89173 / 2.74 ( 2976) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 259 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 THR cc_start: 0.7854 (p) cc_final: 0.7463 (t) REVERT: A 273 GLN cc_start: 0.7477 (tt0) cc_final: 0.7046 (mm110) REVERT: A 432 ARG cc_start: 0.7727 (mtm180) cc_final: 0.7428 (ptm160) REVERT: A 500 ARG cc_start: 0.7453 (mmt180) cc_final: 0.7235 (mtp85) REVERT: A 691 GLN cc_start: 0.7782 (mm110) cc_final: 0.7558 (tp40) REVERT: A 748 ASN cc_start: 0.7977 (t0) cc_final: 0.7599 (t0) REVERT: D 215 THR cc_start: 0.7843 (p) cc_final: 0.7454 (t) REVERT: D 273 GLN cc_start: 0.7489 (tt0) cc_final: 0.7047 (mm110) REVERT: D 432 ARG cc_start: 0.7697 (mtm180) cc_final: 0.7397 (ptm160) REVERT: D 500 ARG cc_start: 0.7470 (mmt180) cc_final: 0.7250 (mtp85) REVERT: D 691 GLN cc_start: 0.7772 (mm110) cc_final: 0.7548 (tp40) REVERT: D 748 ASN cc_start: 0.7965 (t0) cc_final: 0.7573 (t0) REVERT: B 215 THR cc_start: 0.7843 (p) cc_final: 0.7452 (t) REVERT: B 273 GLN cc_start: 0.7493 (tt0) cc_final: 0.7051 (mm110) REVERT: B 432 ARG cc_start: 0.7713 (mtm180) cc_final: 0.7414 (ptm160) REVERT: B 500 ARG cc_start: 0.7458 (mmt180) cc_final: 0.7241 (mtp85) REVERT: B 691 GLN cc_start: 0.7770 (mm110) cc_final: 0.7546 (tp40) REVERT: B 748 ASN cc_start: 0.7948 (t0) cc_final: 0.7562 (t0) REVERT: C 215 THR cc_start: 0.7834 (p) cc_final: 0.7445 (t) REVERT: C 273 GLN cc_start: 0.7492 (tt0) cc_final: 0.7051 (mm110) REVERT: C 432 ARG cc_start: 0.7721 (mtm180) cc_final: 0.7421 (ptm160) REVERT: C 500 ARG cc_start: 0.7453 (mmt180) cc_final: 0.7238 (mtp85) REVERT: C 691 GLN cc_start: 0.7770 (mm110) cc_final: 0.7547 (tp40) REVERT: C 748 ASN cc_start: 0.7990 (t0) cc_final: 0.7589 (t0) outliers start: 20 outliers final: 20 residues processed: 263 average time/residue: 1.2218 time to fit residues: 364.6140 Evaluate side-chains 260 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 240 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 746 GLU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 746 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 125 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 21 optimal weight: 0.0470 chunk 110 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.160924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.114764 restraints weight = 55068.576| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.89 r_work: 0.2874 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 17720 Z= 0.122 Angle : 0.503 8.033 24008 Z= 0.263 Chirality : 0.035 0.221 2700 Planarity : 0.003 0.029 2952 Dihedral : 6.083 58.162 2388 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 1.29 % Allowed : 14.68 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.19), residues: 2092 helix: 2.51 (0.14), residues: 1300 sheet: -0.73 (0.55), residues: 92 loop : -1.48 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 721 TYR 0.008 0.001 TYR A 309 PHE 0.007 0.001 PHE D 742 TRP 0.008 0.001 TRP C 697 HIS 0.002 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (17720) covalent geometry : angle 0.50320 / 0.26 (24008) hydrogen bonds : bond 0.05622 / 3.86 ( 1032) hydrogen bonds : angle 3.79525 / 2.67 ( 2976) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 263 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 THR cc_start: 0.7856 (p) cc_final: 0.7468 (t) REVERT: A 237 LYS cc_start: 0.6303 (mmtt) cc_final: 0.6103 (tppp) REVERT: A 273 GLN cc_start: 0.7478 (tt0) cc_final: 0.7051 (mm110) REVERT: A 432 ARG cc_start: 0.7692 (mtm180) cc_final: 0.7394 (ptm160) REVERT: A 500 ARG cc_start: 0.7442 (mmt180) cc_final: 0.7105 (mtp85) REVERT: A 691 GLN cc_start: 0.7687 (mm110) cc_final: 0.7461 (tp40) REVERT: A 722 SER cc_start: 0.7622 (m) cc_final: 0.7018 (m) REVERT: A 743 ARG cc_start: 0.8381 (ttm110) cc_final: 0.8045 (ttm110) REVERT: A 748 ASN cc_start: 0.8000 (t0) cc_final: 0.7670 (t0) REVERT: D 215 THR cc_start: 0.7863 (p) cc_final: 0.7480 (t) REVERT: D 273 GLN cc_start: 0.7467 (tt0) cc_final: 0.7041 (mm110) REVERT: D 432 ARG cc_start: 0.7660 (mtm180) cc_final: 0.7366 (ptm160) REVERT: D 500 ARG cc_start: 0.7454 (mmt180) cc_final: 0.7118 (mtp85) REVERT: D 691 GLN cc_start: 0.7683 (mm110) cc_final: 0.7457 (tp40) REVERT: D 722 SER cc_start: 0.7630 (m) cc_final: 0.7031 (m) REVERT: D 748 ASN cc_start: 0.7997 (t0) cc_final: 0.7660 (t0) REVERT: B 215 THR cc_start: 0.7843 (p) cc_final: 0.7452 (t) REVERT: B 273 GLN cc_start: 0.7478 (tt0) cc_final: 0.7049 (mm110) REVERT: B 432 ARG cc_start: 0.7675 (mtm180) cc_final: 0.7381 (ptm160) REVERT: B 500 ARG cc_start: 0.7454 (mmt180) cc_final: 0.7119 (mtp85) REVERT: B 691 GLN cc_start: 0.7692 (mm110) cc_final: 0.7467 (tp40) REVERT: B 722 SER cc_start: 0.7623 (m) cc_final: 0.7018 (m) REVERT: B 748 ASN cc_start: 0.7993 (t0) cc_final: 0.7653 (t0) REVERT: C 215 THR cc_start: 0.7837 (p) cc_final: 0.7451 (t) REVERT: C 237 LYS cc_start: 0.6311 (mmtt) cc_final: 0.6111 (tppp) REVERT: C 273 GLN cc_start: 0.7488 (tt0) cc_final: 0.7056 (mm110) REVERT: C 432 ARG cc_start: 0.7667 (mtm180) cc_final: 0.7372 (ptm160) REVERT: C 500 ARG cc_start: 0.7450 (mmt180) cc_final: 0.7116 (mtp85) REVERT: C 691 GLN cc_start: 0.7691 (mm110) cc_final: 0.7467 (tp40) REVERT: C 722 SER cc_start: 0.7624 (m) cc_final: 0.7025 (m) REVERT: C 748 ASN cc_start: 0.8014 (t0) cc_final: 0.7683 (t0) outliers start: 24 outliers final: 20 residues processed: 267 average time/residue: 1.2349 time to fit residues: 374.9965 Evaluate side-chains 278 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 258 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 746 GLU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 746 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 101 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 177 optimal weight: 0.2980 chunk 149 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 142 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.162280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.116538 restraints weight = 54834.622| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.86 r_work: 0.2897 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 17720 Z= 0.109 Angle : 0.481 7.512 24008 Z= 0.251 Chirality : 0.034 0.202 2700 Planarity : 0.003 0.028 2952 Dihedral : 5.891 59.090 2388 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.08 % Allowed : 15.11 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.19), residues: 2092 helix: 2.79 (0.14), residues: 1280 sheet: -0.70 (0.55), residues: 92 loop : -1.36 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 557 TYR 0.008 0.001 TYR D 309 PHE 0.008 0.001 PHE D 742 TRP 0.007 0.001 TRP C 740 HIS 0.002 0.001 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (17720) covalent geometry : angle 0.48072 / 0.25 (24008) hydrogen bonds : bond 0.05111 / 3.51 ( 1032) hydrogen bonds : angle 3.71830 / 2.61 ( 2976) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 262 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 THR cc_start: 0.7822 (p) cc_final: 0.7423 (t) REVERT: A 237 LYS cc_start: 0.6272 (mmtt) cc_final: 0.6067 (tppp) REVERT: A 273 GLN cc_start: 0.7475 (tt0) cc_final: 0.7040 (mm110) REVERT: A 432 ARG cc_start: 0.7582 (mtm180) cc_final: 0.7288 (ptm160) REVERT: A 500 ARG cc_start: 0.7418 (mmt180) cc_final: 0.7123 (mtp85) REVERT: A 691 GLN cc_start: 0.7615 (mm110) cc_final: 0.7365 (tp40) REVERT: A 722 SER cc_start: 0.7651 (m) cc_final: 0.7097 (m) REVERT: A 743 ARG cc_start: 0.8344 (ttm110) cc_final: 0.8107 (ttm110) REVERT: A 748 ASN cc_start: 0.8081 (t0) cc_final: 0.7770 (t0) REVERT: D 215 THR cc_start: 0.7848 (p) cc_final: 0.7450 (t) REVERT: D 273 GLN cc_start: 0.7463 (tt0) cc_final: 0.7025 (mm110) REVERT: D 432 ARG cc_start: 0.7570 (mtm180) cc_final: 0.7272 (ptm160) REVERT: D 500 ARG cc_start: 0.7404 (mmt180) cc_final: 0.7109 (mtp85) REVERT: D 691 GLN cc_start: 0.7650 (mm110) cc_final: 0.7415 (tp40) REVERT: D 722 SER cc_start: 0.7657 (m) cc_final: 0.7102 (m) REVERT: D 743 ARG cc_start: 0.8340 (ttm110) cc_final: 0.8102 (ttm110) REVERT: D 748 ASN cc_start: 0.8052 (t0) cc_final: 0.7739 (t0) REVERT: B 215 THR cc_start: 0.7856 (p) cc_final: 0.7456 (t) REVERT: B 273 GLN cc_start: 0.7479 (tt0) cc_final: 0.7035 (mm110) REVERT: B 432 ARG cc_start: 0.7582 (mtm180) cc_final: 0.7287 (ptm160) REVERT: B 500 ARG cc_start: 0.7421 (mmt180) cc_final: 0.7127 (mtp85) REVERT: B 691 GLN cc_start: 0.7659 (mm110) cc_final: 0.7424 (tp40) REVERT: B 722 SER cc_start: 0.7646 (m) cc_final: 0.7091 (m) REVERT: B 743 ARG cc_start: 0.8347 (ttm110) cc_final: 0.8112 (ttm110) REVERT: B 748 ASN cc_start: 0.8064 (t0) cc_final: 0.7745 (t0) REVERT: C 215 THR cc_start: 0.7845 (p) cc_final: 0.7450 (t) REVERT: C 273 GLN cc_start: 0.7486 (tt0) cc_final: 0.7041 (mm110) REVERT: C 432 ARG cc_start: 0.7566 (mtm180) cc_final: 0.7268 (ptm160) REVERT: C 500 ARG cc_start: 0.7409 (mmt180) cc_final: 0.7115 (mtp85) REVERT: C 691 GLN cc_start: 0.7656 (mm110) cc_final: 0.7422 (tp40) REVERT: C 722 SER cc_start: 0.7645 (m) cc_final: 0.7089 (m) REVERT: C 743 ARG cc_start: 0.8342 (ttm110) cc_final: 0.8106 (ttm110) REVERT: C 748 ASN cc_start: 0.8084 (t0) cc_final: 0.7780 (t0) outliers start: 20 outliers final: 12 residues processed: 266 average time/residue: 1.3009 time to fit residues: 390.9047 Evaluate side-chains 265 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 253 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 526 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 84 optimal weight: 1.9990 chunk 186 optimal weight: 0.0980 chunk 51 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 102 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.160737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.114731 restraints weight = 55089.430| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.85 r_work: 0.2873 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 17720 Z= 0.122 Angle : 0.496 7.774 24008 Z= 0.260 Chirality : 0.035 0.221 2700 Planarity : 0.003 0.029 2952 Dihedral : 6.020 59.673 2388 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.08 % Allowed : 15.54 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.19), residues: 2092 helix: 2.79 (0.14), residues: 1280 sheet: -0.79 (0.55), residues: 92 loop : -1.35 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 575 TYR 0.008 0.001 TYR A 309 PHE 0.010 0.001 PHE B 742 TRP 0.006 0.001 TRP C 697 HIS 0.002 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (17720) covalent geometry : angle 0.49611 / 0.26 (24008) hydrogen bonds : bond 0.05480 / 3.76 ( 1032) hydrogen bonds : angle 3.72867 / 2.62 ( 2976) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 248 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 THR cc_start: 0.7797 (p) cc_final: 0.7415 (t) REVERT: A 237 LYS cc_start: 0.6302 (mmtt) cc_final: 0.6082 (tppp) REVERT: A 273 GLN cc_start: 0.7496 (tt0) cc_final: 0.7048 (mm110) REVERT: A 432 ARG cc_start: 0.7677 (mtm180) cc_final: 0.7378 (ptm160) REVERT: A 500 ARG cc_start: 0.7455 (mmt180) cc_final: 0.7158 (mtp85) REVERT: A 691 GLN cc_start: 0.7700 (mm110) cc_final: 0.7465 (tp40) REVERT: A 722 SER cc_start: 0.7687 (m) cc_final: 0.7109 (m) REVERT: A 743 ARG cc_start: 0.8390 (ttm110) cc_final: 0.8150 (ttm110) REVERT: D 215 THR cc_start: 0.7820 (p) cc_final: 0.7442 (t) REVERT: D 273 GLN cc_start: 0.7483 (tt0) cc_final: 0.7036 (mm110) REVERT: D 432 ARG cc_start: 0.7656 (mtm180) cc_final: 0.7357 (ptm160) REVERT: D 500 ARG cc_start: 0.7467 (mmt180) cc_final: 0.7168 (mtp85) REVERT: D 691 GLN cc_start: 0.7695 (mm110) cc_final: 0.7458 (tp40) REVERT: D 722 SER cc_start: 0.7697 (m) cc_final: 0.7125 (m) REVERT: D 743 ARG cc_start: 0.8387 (ttm110) cc_final: 0.8148 (ttm110) REVERT: B 215 THR cc_start: 0.7830 (p) cc_final: 0.7452 (t) REVERT: B 273 GLN cc_start: 0.7505 (tt0) cc_final: 0.7052 (mm110) REVERT: B 432 ARG cc_start: 0.7665 (mtm180) cc_final: 0.7366 (ptm160) REVERT: B 500 ARG cc_start: 0.7472 (mmt180) cc_final: 0.7173 (mtp85) REVERT: B 691 GLN cc_start: 0.7716 (mm110) cc_final: 0.7481 (tp40) REVERT: B 722 SER cc_start: 0.7684 (m) cc_final: 0.7104 (m) REVERT: B 743 ARG cc_start: 0.8391 (ttm110) cc_final: 0.8157 (ttm110) REVERT: C 215 THR cc_start: 0.7831 (p) cc_final: 0.7456 (t) REVERT: C 273 GLN cc_start: 0.7511 (tt0) cc_final: 0.7055 (mm110) REVERT: C 432 ARG cc_start: 0.7649 (mtm180) cc_final: 0.7347 (ptm160) REVERT: C 500 ARG cc_start: 0.7466 (mmt180) cc_final: 0.7168 (mtp85) REVERT: C 691 GLN cc_start: 0.7703 (mm110) cc_final: 0.7466 (tp40) REVERT: C 722 SER cc_start: 0.7678 (m) cc_final: 0.7100 (m) REVERT: C 743 ARG cc_start: 0.8381 (ttm110) cc_final: 0.8146 (ttm110) outliers start: 20 outliers final: 20 residues processed: 252 average time/residue: 1.2888 time to fit residues: 367.5066 Evaluate side-chains 263 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 243 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 386 CYS Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 746 GLU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 746 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 16 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 176 optimal weight: 2.9990 chunk 177 optimal weight: 0.1980 chunk 126 optimal weight: 0.0570 chunk 7 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.160189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.114227 restraints weight = 54942.327| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.84 r_work: 0.2866 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17720 Z= 0.123 Angle : 0.497 7.658 24008 Z= 0.260 Chirality : 0.034 0.217 2700 Planarity : 0.003 0.030 2952 Dihedral : 5.995 59.881 2388 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.40 % Allowed : 15.48 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.19), residues: 2092 helix: 2.77 (0.14), residues: 1284 sheet: -0.78 (0.55), residues: 92 loop : -1.37 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 474 TYR 0.008 0.001 TYR A 309 PHE 0.010 0.001 PHE B 742 TRP 0.007 0.001 TRP A 697 HIS 0.002 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (17720) covalent geometry : angle 0.49678 / 0.26 (24008) hydrogen bonds : bond 0.05473 / 3.76 ( 1032) hydrogen bonds : angle 3.72170 / 2.62 ( 2976) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 247 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 THR cc_start: 0.7810 (p) cc_final: 0.7446 (t) REVERT: A 228 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.6671 (mp10) REVERT: A 237 LYS cc_start: 0.6331 (mmtt) cc_final: 0.6119 (tppp) REVERT: A 273 GLN cc_start: 0.7509 (tt0) cc_final: 0.7054 (mm110) REVERT: A 432 ARG cc_start: 0.7695 (mtm180) cc_final: 0.7392 (ptm160) REVERT: A 500 ARG cc_start: 0.7466 (mmt180) cc_final: 0.7162 (mtp85) REVERT: A 691 GLN cc_start: 0.7721 (mm110) cc_final: 0.7474 (tp40) REVERT: A 722 SER cc_start: 0.7689 (m) cc_final: 0.7084 (m) REVERT: A 743 ARG cc_start: 0.8397 (ttm110) cc_final: 0.8051 (ttm110) REVERT: D 215 THR cc_start: 0.7842 (p) cc_final: 0.7474 (t) REVERT: D 228 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.6674 (mp10) REVERT: D 273 GLN cc_start: 0.7495 (tt0) cc_final: 0.7041 (mm110) REVERT: D 432 ARG cc_start: 0.7667 (mtm180) cc_final: 0.7363 (ptm160) REVERT: D 500 ARG cc_start: 0.7473 (mmt180) cc_final: 0.7169 (mtp85) REVERT: D 691 GLN cc_start: 0.7703 (mm110) cc_final: 0.7470 (tp40) REVERT: D 722 SER cc_start: 0.7693 (m) cc_final: 0.7096 (m) REVERT: D 743 ARG cc_start: 0.8396 (ttm110) cc_final: 0.8050 (ttm110) REVERT: B 215 THR cc_start: 0.7824 (p) cc_final: 0.7462 (t) REVERT: B 228 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.6704 (mp10) REVERT: B 273 GLN cc_start: 0.7521 (tt0) cc_final: 0.7053 (mm110) REVERT: B 432 ARG cc_start: 0.7679 (mtm180) cc_final: 0.7374 (ptm160) REVERT: B 500 ARG cc_start: 0.7478 (mmt180) cc_final: 0.7175 (mtp85) REVERT: B 691 GLN cc_start: 0.7723 (mm110) cc_final: 0.7488 (tp40) REVERT: B 722 SER cc_start: 0.7693 (m) cc_final: 0.7094 (m) REVERT: B 743 ARG cc_start: 0.8417 (ttm110) cc_final: 0.8078 (ttm110) REVERT: C 215 THR cc_start: 0.7822 (p) cc_final: 0.7458 (t) REVERT: C 228 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.6702 (mp10) REVERT: C 273 GLN cc_start: 0.7520 (tt0) cc_final: 0.7059 (mm110) REVERT: C 432 ARG cc_start: 0.7665 (mtm180) cc_final: 0.7357 (ptm160) REVERT: C 500 ARG cc_start: 0.7473 (mmt180) cc_final: 0.7170 (mtp85) REVERT: C 570 GLU cc_start: 0.7475 (tt0) cc_final: 0.7221 (tt0) REVERT: C 691 GLN cc_start: 0.7714 (mm110) cc_final: 0.7481 (tp40) REVERT: C 722 SER cc_start: 0.7683 (m) cc_final: 0.7082 (m) REVERT: C 743 ARG cc_start: 0.8384 (ttm110) cc_final: 0.8041 (ttm110) REVERT: C 748 ASN cc_start: 0.8123 (t0) cc_final: 0.7827 (t0) outliers start: 26 outliers final: 20 residues processed: 258 average time/residue: 1.3674 time to fit residues: 399.1156 Evaluate side-chains 262 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 238 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain D residue 228 GLN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 386 CYS Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 746 GLU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 746 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 149 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 199 optimal weight: 0.1980 chunk 71 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 181 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.160404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.115372 restraints weight = 54842.534| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.94 r_work: 0.2859 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17720 Z= 0.119 Angle : 0.493 7.434 24008 Z= 0.257 Chirality : 0.034 0.209 2700 Planarity : 0.003 0.029 2952 Dihedral : 5.908 59.713 2388 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.29 % Allowed : 15.81 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.19), residues: 2092 helix: 2.79 (0.14), residues: 1284 sheet: -0.73 (0.55), residues: 92 loop : -1.36 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 575 TYR 0.008 0.001 TYR A 309 PHE 0.010 0.001 PHE A 742 TRP 0.007 0.001 TRP B 697 HIS 0.002 0.001 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (17720) covalent geometry : angle 0.49263 / 0.26 (24008) hydrogen bonds : bond 0.05375 / 3.69 ( 1032) hydrogen bonds : angle 3.70755 / 2.61 ( 2976) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 THR cc_start: 0.7799 (p) cc_final: 0.7439 (t) REVERT: A 228 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.6631 (mp10) REVERT: A 273 GLN cc_start: 0.7425 (tt0) cc_final: 0.6923 (mm110) REVERT: A 432 ARG cc_start: 0.7664 (mtm180) cc_final: 0.7347 (ptm160) REVERT: A 500 ARG cc_start: 0.7466 (mmt180) cc_final: 0.7183 (mtp85) REVERT: A 691 GLN cc_start: 0.7678 (mm110) cc_final: 0.7439 (tp40) REVERT: A 722 SER cc_start: 0.7665 (m) cc_final: 0.7063 (m) REVERT: A 743 ARG cc_start: 0.8377 (ttm110) cc_final: 0.8022 (ttm110) REVERT: D 215 THR cc_start: 0.7816 (p) cc_final: 0.7456 (t) REVERT: D 228 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.6637 (mp10) REVERT: D 273 GLN cc_start: 0.7431 (tt0) cc_final: 0.6955 (mm110) REVERT: D 432 ARG cc_start: 0.7635 (mtm180) cc_final: 0.7315 (ptm160) REVERT: D 500 ARG cc_start: 0.7478 (mmt180) cc_final: 0.7190 (mtp85) REVERT: D 691 GLN cc_start: 0.7667 (mm110) cc_final: 0.7406 (tp40) REVERT: D 722 SER cc_start: 0.7672 (m) cc_final: 0.7076 (m) REVERT: D 743 ARG cc_start: 0.8378 (ttm110) cc_final: 0.8026 (ttm110) REVERT: B 215 THR cc_start: 0.7815 (p) cc_final: 0.7454 (t) REVERT: B 228 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.6693 (mp10) REVERT: B 273 GLN cc_start: 0.7435 (tt0) cc_final: 0.6929 (mm110) REVERT: B 432 ARG cc_start: 0.7640 (mtm180) cc_final: 0.7321 (ptm160) REVERT: B 500 ARG cc_start: 0.7503 (mmt180) cc_final: 0.7190 (mtp85) REVERT: B 691 GLN cc_start: 0.7665 (mm110) cc_final: 0.7403 (tp40) REVERT: B 722 SER cc_start: 0.7670 (m) cc_final: 0.7071 (m) REVERT: B 743 ARG cc_start: 0.8370 (ttm110) cc_final: 0.8021 (ttm110) REVERT: C 215 THR cc_start: 0.7817 (p) cc_final: 0.7460 (t) REVERT: C 228 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.6706 (mp10) REVERT: C 273 GLN cc_start: 0.7461 (tt0) cc_final: 0.6977 (mm110) REVERT: C 432 ARG cc_start: 0.7627 (mtm180) cc_final: 0.7312 (ptm160) REVERT: C 500 ARG cc_start: 0.7473 (mmt180) cc_final: 0.7186 (mtp85) REVERT: C 570 GLU cc_start: 0.7437 (tt0) cc_final: 0.7171 (tt0) REVERT: C 691 GLN cc_start: 0.7654 (mm110) cc_final: 0.7393 (tp40) REVERT: C 722 SER cc_start: 0.7659 (m) cc_final: 0.7058 (m) REVERT: C 743 ARG cc_start: 0.8373 (ttm110) cc_final: 0.8025 (ttm110) outliers start: 24 outliers final: 20 residues processed: 252 average time/residue: 1.3797 time to fit residues: 391.6479 Evaluate side-chains 256 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 232 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain D residue 228 GLN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 386 CYS Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 746 GLU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 746 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 196 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 260 GLN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.156414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.110951 restraints weight = 54696.328| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.95 r_work: 0.2810 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17720 Z= 0.158 Angle : 0.533 7.517 24008 Z= 0.283 Chirality : 0.036 0.235 2700 Planarity : 0.004 0.034 2952 Dihedral : 6.262 58.842 2388 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.29 % Allowed : 15.91 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.19), residues: 2092 helix: 2.57 (0.14), residues: 1284 sheet: -0.79 (0.54), residues: 92 loop : -1.40 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 212 TYR 0.009 0.001 TYR A 309 PHE 0.012 0.001 PHE D 742 TRP 0.007 0.001 TRP D 697 HIS 0.003 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (17720) covalent geometry : angle 0.53307 / 0.28 (24008) hydrogen bonds : bond 0.06303 / 4.32 ( 1032) hydrogen bonds : angle 3.81097 / 2.69 ( 2976) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 1.013 Fit side-chains REVERT: A 215 THR cc_start: 0.7803 (p) cc_final: 0.7519 (t) REVERT: A 273 GLN cc_start: 0.7562 (tt0) cc_final: 0.7036 (tp40) REVERT: A 432 ARG cc_start: 0.7819 (mtm180) cc_final: 0.7499 (ptm160) REVERT: A 500 ARG cc_start: 0.7508 (mmt180) cc_final: 0.7220 (mtp85) REVERT: A 691 GLN cc_start: 0.7784 (mm110) cc_final: 0.7567 (tp40) REVERT: A 743 ARG cc_start: 0.8437 (ttm110) cc_final: 0.8201 (ttm110) REVERT: A 748 ASN cc_start: 0.8188 (t0) cc_final: 0.7861 (t0) REVERT: D 215 THR cc_start: 0.7785 (p) cc_final: 0.7499 (t) REVERT: D 273 GLN cc_start: 0.7536 (tt0) cc_final: 0.7032 (mm110) REVERT: D 432 ARG cc_start: 0.7829 (mtm180) cc_final: 0.7506 (ptm160) REVERT: D 500 ARG cc_start: 0.7515 (mmt180) cc_final: 0.7221 (mtp85) REVERT: D 691 GLN cc_start: 0.7793 (mm110) cc_final: 0.7573 (tp40) REVERT: D 743 ARG cc_start: 0.8435 (ttm110) cc_final: 0.8197 (ttm110) REVERT: D 748 ASN cc_start: 0.8186 (t0) cc_final: 0.7863 (t0) REVERT: B 215 THR cc_start: 0.7805 (p) cc_final: 0.7518 (t) REVERT: B 273 GLN cc_start: 0.7576 (tt0) cc_final: 0.7046 (tp40) REVERT: B 432 ARG cc_start: 0.7827 (mtm180) cc_final: 0.7505 (ptm160) REVERT: B 500 ARG cc_start: 0.7503 (mmt180) cc_final: 0.7212 (mtp85) REVERT: B 691 GLN cc_start: 0.7786 (mm110) cc_final: 0.7570 (tp40) REVERT: B 743 ARG cc_start: 0.8413 (ttm110) cc_final: 0.8174 (ttm110) REVERT: B 748 ASN cc_start: 0.8186 (t0) cc_final: 0.7863 (t0) REVERT: C 215 THR cc_start: 0.7789 (p) cc_final: 0.7508 (t) REVERT: C 273 GLN cc_start: 0.7555 (tt0) cc_final: 0.7020 (tp40) REVERT: C 432 ARG cc_start: 0.7810 (mtm180) cc_final: 0.7490 (ptm160) REVERT: C 500 ARG cc_start: 0.7506 (mmt180) cc_final: 0.7216 (mtp85) REVERT: C 570 GLU cc_start: 0.7576 (tt0) cc_final: 0.7295 (tt0) REVERT: C 691 GLN cc_start: 0.7779 (mm110) cc_final: 0.7559 (tp40) REVERT: C 743 ARG cc_start: 0.8413 (ttm110) cc_final: 0.8174 (ttm110) REVERT: C 748 ASN cc_start: 0.8191 (t0) cc_final: 0.7870 (t0) outliers start: 24 outliers final: 20 residues processed: 252 average time/residue: 1.3539 time to fit residues: 385.0600 Evaluate side-chains 248 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 228 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 386 CYS Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 746 GLU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 746 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 51 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 GLN B 260 GLN ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.158680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.114712 restraints weight = 54312.015| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.87 r_work: 0.2822 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17720 Z= 0.155 Angle : 0.531 6.896 24008 Z= 0.283 Chirality : 0.036 0.219 2700 Planarity : 0.004 0.034 2952 Dihedral : 6.187 58.959 2388 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.29 % Allowed : 16.18 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.19), residues: 2092 helix: 2.44 (0.14), residues: 1304 sheet: -0.79 (0.54), residues: 92 loop : -1.56 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 721 TYR 0.008 0.001 TYR D 309 PHE 0.011 0.001 PHE A 649 TRP 0.007 0.001 TRP A 697 HIS 0.003 0.001 HIS C 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (17720) covalent geometry : angle 0.53092 / 0.28 (24008) hydrogen bonds : bond 0.06244 / 4.28 ( 1032) hydrogen bonds : angle 3.81279 / 2.69 ( 2976) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11851.36 seconds wall clock time: 201 minutes 9.04 seconds (12069.04 seconds total)