Starting phenix.real_space_refine on Mon Jul 6 10:18:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u30_41848/07_2026/8u30_41848_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u30_41848/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8u30_41848/07_2026/8u30_41848_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u30_41848/07_2026/8u30_41848_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u30_41848/07_2026/8u30_41848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u30_41848/07_2026/8u30_41848.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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, 47 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 6.42, per 1000 atoms: 0.19 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: 3.24 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.67 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: 8.26 Time building geometry restraints manager: 4.65 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.240 Extract box with map and model: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 34.990 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 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:7.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.540 ------------------------------------------------------------------------------- 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 : 0.990 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: 1.1693 time to fit residues: 512.8363 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 : 0.975 ------------------------------------------------------------------------------- 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... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.160863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.115767 restraints weight = 55344.900| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.89 r_work: 0.2866 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17720 Z= 0.189 Angle : 0.592 10.963 24008 Z= 0.309 Chirality : 0.038 0.232 2700 Planarity : 0.004 0.034 2952 Dihedral : 7.083 59.844 2388 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % 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: 1.30 (0.19), residues: 2092 helix: 2.21 (0.14), residues: 1296 sheet: -0.77 (0.58), residues: 92 loop : -1.57 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 355 TYR 0.011 0.002 TYR B 554 PHE 0.014 0.001 PHE C 649 TRP 0.011 0.002 TRP C 740 HIS 0.003 0.001 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (17720) covalent geometry : angle 0.59161 / 0.31 (24008) hydrogen bonds : bond 0.06834 / 4.67 ( 1032) hydrogen bonds : angle 4.13148 / 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 289 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 259 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 GLN cc_start: 0.7438 (tt0) cc_final: 0.6939 (tp40) REVERT: A 386 CYS cc_start: 0.8291 (m) cc_final: 0.8077 (m) REVERT: A 432 ARG cc_start: 0.7724 (mtm180) cc_final: 0.7508 (ptm160) REVERT: A 500 ARG cc_start: 0.7240 (mmt180) cc_final: 0.6863 (mtp85) REVERT: A 691 GLN cc_start: 0.7817 (mm110) cc_final: 0.7585 (tp40) REVERT: D 273 GLN cc_start: 0.7436 (tt0) cc_final: 0.6943 (tp40) REVERT: D 386 CYS cc_start: 0.8273 (m) cc_final: 0.8055 (m) REVERT: D 432 ARG cc_start: 0.7715 (mtm180) cc_final: 0.7497 (ptm160) REVERT: D 500 ARG cc_start: 0.7245 (mmt180) cc_final: 0.6871 (mtp85) REVERT: D 570 GLU cc_start: 0.7811 (tt0) cc_final: 0.7540 (tt0) REVERT: D 644 MET cc_start: 0.9357 (mmm) cc_final: 0.8945 (mmm) REVERT: D 691 GLN cc_start: 0.7801 (mm110) cc_final: 0.7572 (tp40) REVERT: B 273 GLN cc_start: 0.7428 (tt0) cc_final: 0.6923 (tp40) REVERT: B 386 CYS cc_start: 0.8275 (m) cc_final: 0.8061 (m) REVERT: B 432 ARG cc_start: 0.7721 (mtm180) cc_final: 0.7507 (ptm160) REVERT: B 500 ARG cc_start: 0.7240 (mmt180) cc_final: 0.6865 (mtp85) REVERT: B 570 GLU cc_start: 0.7808 (tt0) cc_final: 0.7528 (tt0) REVERT: B 691 GLN cc_start: 0.7808 (mm110) cc_final: 0.7575 (tp40) REVERT: C 273 GLN cc_start: 0.7449 (tt0) cc_final: 0.6948 (tp40) REVERT: C 386 CYS cc_start: 0.8263 (m) cc_final: 0.8046 (m) REVERT: C 432 ARG cc_start: 0.7727 (mtm180) cc_final: 0.7510 (ptm160) REVERT: C 500 ARG cc_start: 0.7233 (mmt180) cc_final: 0.6861 (mtp85) REVERT: C 570 GLU cc_start: 0.7808 (tt0) cc_final: 0.7529 (tt0) REVERT: C 644 MET cc_start: 0.9355 (mmm) cc_final: 0.8964 (mmm) REVERT: C 691 GLN cc_start: 0.7804 (mm110) cc_final: 0.7573 (tp40) outliers start: 30 outliers final: 8 residues processed: 265 average time/residue: 1.3093 time to fit residues: 390.9534 Evaluate side-chains 241 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 233 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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: 1.9990 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: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 ASN D 259 ASN B 259 ASN C 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.159756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.114283 restraints weight = 54958.384| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.94 r_work: 0.2853 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17720 Z= 0.168 Angle : 0.547 8.708 24008 Z= 0.289 Chirality : 0.037 0.233 2700 Planarity : 0.004 0.031 2952 Dihedral : 6.616 57.893 2388 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.29 % Allowed : 11.29 % Favored : 87.42 % 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: 1.30 (0.19), residues: 2092 helix: 2.19 (0.14), residues: 1296 sheet: -0.87 (0.54), residues: 92 loop : -1.53 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 721 TYR 0.010 0.001 TYR D 472 PHE 0.016 0.001 PHE B 304 TRP 0.008 0.001 TRP B 697 HIS 0.004 0.001 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (17720) covalent geometry : angle 0.54666 / 0.29 (24008) hydrogen bonds : bond 0.06534 / 4.47 ( 1032) hydrogen bonds : angle 3.96133 / 2.79 ( 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 303 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 279 time to evaluate : 0.961 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: 0.7456 (tt0) cc_final: 0.6968 (tp40) REVERT: A 432 ARG cc_start: 0.7770 (mtm180) cc_final: 0.7477 (ptm160) REVERT: A 500 ARG cc_start: 0.7376 (mmt180) cc_final: 0.7147 (mtp85) REVERT: A 691 GLN cc_start: 0.7770 (mm110) cc_final: 0.7546 (tp40) REVERT: A 748 ASN cc_start: 0.7899 (t0) cc_final: 0.7522 (t0) REVERT: D 273 GLN cc_start: 0.7463 (tt0) cc_final: 0.7029 (mm110) REVERT: D 432 ARG cc_start: 0.7749 (mtm180) cc_final: 0.7453 (ptm160) REVERT: D 500 ARG cc_start: 0.7403 (mmt180) cc_final: 0.7175 (mtp85) REVERT: D 570 GLU cc_start: 0.7755 (tt0) cc_final: 0.7454 (tt0) REVERT: D 691 GLN cc_start: 0.7792 (mm110) cc_final: 0.7570 (tp40) REVERT: D 748 ASN cc_start: 0.7880 (t0) cc_final: 0.7496 (t0) REVERT: B 273 GLN cc_start: 0.7454 (tt0) cc_final: 0.7030 (mm110) REVERT: B 432 ARG cc_start: 0.7761 (mtm180) cc_final: 0.7465 (ptm160) REVERT: B 500 ARG cc_start: 0.7376 (mmt180) cc_final: 0.7151 (mtp85) REVERT: B 691 GLN cc_start: 0.7809 (mm110) cc_final: 0.7584 (tp40) REVERT: B 748 ASN cc_start: 0.7889 (t0) cc_final: 0.7511 (t0) REVERT: C 273 GLN cc_start: 0.7468 (tt0) cc_final: 0.7044 (mm110) REVERT: C 432 ARG cc_start: 0.7768 (mtm180) cc_final: 0.7473 (ptm160) REVERT: C 500 ARG cc_start: 0.7383 (mmt180) cc_final: 0.7158 (mtp85) REVERT: C 570 GLU cc_start: 0.7752 (tt0) cc_final: 0.7432 (tt0) REVERT: C 691 GLN cc_start: 0.7795 (mm110) cc_final: 0.7573 (tp40) REVERT: C 748 ASN cc_start: 0.7897 (t0) cc_final: 0.7517 (t0) outliers start: 24 outliers final: 15 residues processed: 287 average time/residue: 1.1543 time to fit residues: 376.2754 Evaluate side-chains 263 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 248 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain C residue 574 LEU 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: 6.9990 chunk 37 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.158297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.113233 restraints weight = 55156.671| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.94 r_work: 0.2822 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17720 Z= 0.169 Angle : 0.550 8.946 24008 Z= 0.291 Chirality : 0.037 0.253 2700 Planarity : 0.004 0.033 2952 Dihedral : 6.566 58.079 2388 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.61 % Allowed : 13.17 % Favored : 85.22 % 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: 1.29 (0.19), residues: 2092 helix: 2.16 (0.14), residues: 1300 sheet: -0.84 (0.54), residues: 92 loop : -1.51 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 721 TYR 0.009 0.001 TYR B 309 PHE 0.011 0.001 PHE C 649 TRP 0.008 0.001 TRP B 697 HIS 0.003 0.001 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (17720) covalent geometry : angle 0.55044 / 0.29 (24008) hydrogen bonds : bond 0.06609 / 4.52 ( 1032) hydrogen bonds : angle 3.94563 / 2.78 ( 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 290 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 260 time to evaluate : 0.877 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: 0.7917 (p) cc_final: 0.7578 (m) REVERT: A 273 GLN cc_start: 0.7491 (tt0) cc_final: 0.7073 (mm110) REVERT: A 432 ARG cc_start: 0.7783 (mtm180) cc_final: 0.7488 (ptm160) REVERT: A 500 ARG cc_start: 0.7475 (mmt180) cc_final: 0.7247 (mtp85) REVERT: A 691 GLN cc_start: 0.7818 (mm110) cc_final: 0.7597 (tp40) REVERT: A 748 ASN cc_start: 0.8005 (t0) cc_final: 0.7600 (t0) REVERT: D 215 THR cc_start: 0.7923 (p) cc_final: 0.7585 (m) REVERT: D 273 GLN cc_start: 0.7492 (tt0) cc_final: 0.7070 (mm110) REVERT: D 432 ARG cc_start: 0.7770 (mtm180) cc_final: 0.7474 (ptm160) REVERT: D 500 ARG cc_start: 0.7490 (mmt180) cc_final: 0.7260 (mtp85) REVERT: D 691 GLN cc_start: 0.7802 (mm110) cc_final: 0.7581 (tp40) REVERT: D 748 ASN cc_start: 0.7986 (t0) cc_final: 0.7584 (t0) REVERT: B 215 THR cc_start: 0.7941 (p) cc_final: 0.7595 (m) REVERT: B 237 LYS cc_start: 0.6379 (mmtt) cc_final: 0.6176 (tppp) REVERT: B 273 GLN cc_start: 0.7492 (tt0) cc_final: 0.7070 (mm110) REVERT: B 432 ARG cc_start: 0.7781 (mtm180) cc_final: 0.7487 (ptm160) REVERT: B 500 ARG cc_start: 0.7473 (mmt180) cc_final: 0.7246 (mtp85) REVERT: B 691 GLN cc_start: 0.7799 (mm110) cc_final: 0.7579 (tp40) REVERT: B 748 ASN cc_start: 0.7974 (t0) cc_final: 0.7577 (t0) REVERT: C 215 THR cc_start: 0.7932 (p) cc_final: 0.7575 (m) REVERT: C 237 LYS cc_start: 0.6372 (mmtt) cc_final: 0.6171 (tppp) REVERT: C 273 GLN cc_start: 0.7501 (tt0) cc_final: 0.7078 (mm110) REVERT: C 432 ARG cc_start: 0.7783 (mtm180) cc_final: 0.7484 (ptm160) REVERT: C 500 ARG cc_start: 0.7469 (mmt180) cc_final: 0.7242 (mtp85) REVERT: C 691 GLN cc_start: 0.7810 (mm110) cc_final: 0.7590 (tp40) REVERT: C 748 ASN cc_start: 0.8005 (t0) cc_final: 0.7609 (t0) outliers start: 30 outliers final: 23 residues processed: 272 average time/residue: 1.1728 time to fit residues: 361.8344 Evaluate side-chains 264 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 241 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 660 ILE 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 660 ILE 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 660 ILE 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 514 ILE Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 660 ILE 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: 0.4980 chunk 121 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 27 optimal weight: 0.0570 chunk 52 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 chunk 174 optimal weight: 0.5980 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.161455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.115697 restraints weight = 55095.659| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.86 r_work: 0.2886 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 17720 Z= 0.115 Angle : 0.496 7.945 24008 Z= 0.259 Chirality : 0.034 0.215 2700 Planarity : 0.003 0.029 2952 Dihedral : 6.024 57.893 2388 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.40 % Allowed : 14.19 % Favored : 84.41 % 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: 2.53 (0.14), residues: 1292 sheet: -0.67 (0.55), residues: 92 loop : -1.47 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 721 TYR 0.007 0.001 TYR D 309 PHE 0.006 0.001 PHE B 304 TRP 0.008 0.001 TRP B 697 HIS 0.002 0.001 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (17720) covalent geometry : angle 0.49557 / 0.26 (24008) hydrogen bonds : bond 0.05387 / 3.70 ( 1032) hydrogen bonds : angle 3.80131 / 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 284 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 258 time to evaluate : 0.956 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: 0.7881 (p) cc_final: 0.7522 (t) REVERT: A 237 LYS cc_start: 0.6277 (mmtt) cc_final: 0.6062 (tppp) REVERT: A 273 GLN cc_start: 0.7466 (tt0) cc_final: 0.7053 (mm110) REVERT: A 432 ARG cc_start: 0.7650 (mtm180) cc_final: 0.7353 (ptm160) REVERT: A 500 ARG cc_start: 0.7449 (mmt180) cc_final: 0.7145 (mtp85) REVERT: A 691 GLN cc_start: 0.7648 (mm110) cc_final: 0.7407 (tp40) REVERT: A 722 SER cc_start: 0.7674 (m) cc_final: 0.7122 (m) REVERT: A 743 ARG cc_start: 0.8363 (ttm110) cc_final: 0.8026 (ttm110) REVERT: A 748 ASN cc_start: 0.8016 (t0) cc_final: 0.7694 (t0) REVERT: D 215 THR cc_start: 0.7920 (p) cc_final: 0.7574 (m) REVERT: D 273 GLN cc_start: 0.7452 (tt0) cc_final: 0.7041 (mm110) REVERT: D 432 ARG cc_start: 0.7620 (mtm180) cc_final: 0.7319 (ptm160) REVERT: D 500 ARG cc_start: 0.7459 (mmt180) cc_final: 0.7158 (mtp85) REVERT: D 691 GLN cc_start: 0.7640 (mm110) cc_final: 0.7395 (tp40) REVERT: D 722 SER cc_start: 0.7646 (m) cc_final: 0.7091 (m) REVERT: D 743 ARG cc_start: 0.8355 (ttm110) cc_final: 0.8017 (ttm110) REVERT: D 748 ASN cc_start: 0.7997 (t0) cc_final: 0.7672 (t0) REVERT: B 215 THR cc_start: 0.7900 (p) cc_final: 0.7539 (t) REVERT: B 237 LYS cc_start: 0.6262 (mmtt) cc_final: 0.6047 (tppp) REVERT: B 273 GLN cc_start: 0.7465 (tt0) cc_final: 0.7039 (mm110) REVERT: B 432 ARG cc_start: 0.7640 (mtm180) cc_final: 0.7343 (ptm160) REVERT: B 500 ARG cc_start: 0.7462 (mmt180) cc_final: 0.7161 (mtp85) REVERT: B 691 GLN cc_start: 0.7648 (mm110) cc_final: 0.7404 (tp40) REVERT: B 722 SER cc_start: 0.7665 (m) cc_final: 0.7112 (m) REVERT: B 743 ARG cc_start: 0.8370 (ttm110) cc_final: 0.8039 (ttm110) REVERT: B 748 ASN cc_start: 0.7997 (t0) cc_final: 0.7673 (t0) REVERT: C 215 THR cc_start: 0.7889 (p) cc_final: 0.7532 (t) REVERT: C 237 LYS cc_start: 0.6276 (mmtt) cc_final: 0.6060 (tppp) REVERT: C 273 GLN cc_start: 0.7472 (tt0) cc_final: 0.7052 (mm110) REVERT: C 432 ARG cc_start: 0.7631 (mtm180) cc_final: 0.7333 (ptm160) REVERT: C 500 ARG cc_start: 0.7459 (mmt180) cc_final: 0.7158 (mtp85) REVERT: C 691 GLN cc_start: 0.7640 (mm110) cc_final: 0.7395 (tp40) REVERT: C 722 SER cc_start: 0.7635 (m) cc_final: 0.7080 (m) REVERT: C 743 ARG cc_start: 0.8356 (ttm110) cc_final: 0.8022 (ttm110) REVERT: C 748 ASN cc_start: 0.8012 (t0) cc_final: 0.7694 (t0) outliers start: 26 outliers final: 17 residues processed: 266 average time/residue: 1.2492 time to fit residues: 374.5878 Evaluate side-chains 265 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 248 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 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 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 746 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 101 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 191 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.160099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.114148 restraints weight = 55049.426| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.87 r_work: 0.2864 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3579 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= 0.131 Angle : 0.508 8.011 24008 Z= 0.267 Chirality : 0.035 0.231 2700 Planarity : 0.003 0.032 2952 Dihedral : 6.100 57.344 2388 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.10 % Allowed : 13.82 % Favored : 84.09 % 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: 1.66 (0.19), residues: 2092 helix: 2.50 (0.14), residues: 1300 sheet: -0.74 (0.54), residues: 92 loop : -1.47 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 721 TYR 0.008 0.001 TYR C 309 PHE 0.010 0.001 PHE A 742 TRP 0.006 0.001 TRP A 697 HIS 0.002 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (17720) covalent geometry : angle 0.50808 / 0.27 (24008) hydrogen bonds : bond 0.05742 / 3.94 ( 1032) hydrogen bonds : angle 3.78321 / 2.66 ( 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 292 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 253 time to evaluate : 0.735 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: 0.7910 (p) cc_final: 0.7578 (m) REVERT: A 228 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.6640 (mp10) REVERT: A 237 LYS cc_start: 0.6282 (mmtt) cc_final: 0.6064 (tppp) REVERT: A 273 GLN cc_start: 0.7474 (tt0) cc_final: 0.7044 (mm110) REVERT: A 432 ARG cc_start: 0.7670 (mtm180) cc_final: 0.7369 (ptm160) REVERT: A 500 ARG cc_start: 0.7465 (mmt180) cc_final: 0.7154 (mtp85) REVERT: A 691 GLN cc_start: 0.7679 (mm110) cc_final: 0.7447 (tp40) REVERT: A 722 SER cc_start: 0.7721 (m) cc_final: 0.7088 (m) REVERT: A 743 ARG cc_start: 0.8405 (ttm110) cc_final: 0.8160 (ttm110) REVERT: A 748 ASN cc_start: 0.8024 (t0) cc_final: 0.7695 (t0) REVERT: D 215 THR cc_start: 0.7923 (p) cc_final: 0.7592 (m) REVERT: D 228 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.6644 (mp10) REVERT: D 273 GLN cc_start: 0.7471 (tt0) cc_final: 0.7036 (mm110) REVERT: D 432 ARG cc_start: 0.7641 (mtm180) cc_final: 0.7338 (ptm160) REVERT: D 500 ARG cc_start: 0.7475 (mmt180) cc_final: 0.7163 (mtp85) REVERT: D 691 GLN cc_start: 0.7706 (mm110) cc_final: 0.7470 (tp40) REVERT: D 722 SER cc_start: 0.7726 (m) cc_final: 0.7099 (m) REVERT: D 743 ARG cc_start: 0.8391 (ttm110) cc_final: 0.8142 (ttm110) REVERT: D 748 ASN cc_start: 0.8000 (t0) cc_final: 0.7668 (t0) REVERT: B 215 THR cc_start: 0.7911 (p) cc_final: 0.7570 (m) REVERT: B 228 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.6627 (mp10) REVERT: B 237 LYS cc_start: 0.6299 (mmtt) cc_final: 0.6085 (tppp) REVERT: B 273 GLN cc_start: 0.7481 (tt0) cc_final: 0.7042 (mm110) REVERT: B 432 ARG cc_start: 0.7654 (mtm180) cc_final: 0.7358 (ptm160) REVERT: B 500 ARG cc_start: 0.7475 (mmt180) cc_final: 0.7166 (mtp85) REVERT: B 691 GLN cc_start: 0.7726 (mm110) cc_final: 0.7493 (tp40) REVERT: B 722 SER cc_start: 0.7713 (m) cc_final: 0.7080 (m) REVERT: B 743 ARG cc_start: 0.8396 (ttm110) cc_final: 0.8152 (ttm110) REVERT: B 748 ASN cc_start: 0.8004 (t0) cc_final: 0.7675 (t0) REVERT: C 215 THR cc_start: 0.7910 (p) cc_final: 0.7561 (t) REVERT: C 228 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.6655 (mp10) REVERT: C 237 LYS cc_start: 0.6311 (mmtt) cc_final: 0.6098 (tppp) REVERT: C 273 GLN cc_start: 0.7490 (tt0) cc_final: 0.7049 (mm110) REVERT: C 432 ARG cc_start: 0.7638 (mtm180) cc_final: 0.7340 (ptm160) REVERT: C 500 ARG cc_start: 0.7473 (mmt180) cc_final: 0.7165 (mtp85) REVERT: C 691 GLN cc_start: 0.7719 (mm110) cc_final: 0.7486 (tp40) REVERT: C 722 SER cc_start: 0.7707 (m) cc_final: 0.7076 (m) REVERT: C 743 ARG cc_start: 0.8376 (ttm110) cc_final: 0.8127 (ttm110) REVERT: C 748 ASN cc_start: 0.8045 (t0) cc_final: 0.7728 (t0) outliers start: 39 outliers final: 25 residues processed: 269 average time/residue: 1.2536 time to fit residues: 380.5196 Evaluate side-chains 276 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 247 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU 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 574 LEU Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain D residue 216 LEU 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 216 LEU 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 216 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 84 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 107 optimal weight: 0.0870 chunk 143 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 overall best weight: 1.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.159112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.112660 restraints weight = 55294.720| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.92 r_work: 0.2847 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17720 Z= 0.145 Angle : 0.519 8.161 24008 Z= 0.274 Chirality : 0.036 0.245 2700 Planarity : 0.004 0.034 2952 Dihedral : 6.236 57.005 2388 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 1.77 % Allowed : 14.25 % Favored : 83.98 % 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: 1.58 (0.19), residues: 2092 helix: 2.44 (0.14), residues: 1300 sheet: -0.78 (0.54), residues: 92 loop : -1.50 (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 0.010 0.001 PHE B 742 TRP 0.007 0.001 TRP A 697 HIS 0.002 0.001 HIS D 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (17720) covalent geometry : angle 0.51905 / 0.27 (24008) hydrogen bonds : bond 0.06085 / 4.17 ( 1032) hydrogen bonds : angle 3.81355 / 2.69 ( 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: 33 poor density : 235 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 THR cc_start: 0.7863 (p) cc_final: 0.7542 (t) REVERT: A 228 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.6606 (mp10) REVERT: A 237 LYS cc_start: 0.6269 (mmtt) cc_final: 0.6034 (tppp) REVERT: A 273 GLN cc_start: 0.7455 (tt0) cc_final: 0.7004 (mm110) REVERT: A 432 ARG cc_start: 0.7680 (mtm180) cc_final: 0.7362 (ptm160) REVERT: A 500 ARG cc_start: 0.7471 (mmt180) cc_final: 0.7145 (mtp85) REVERT: A 691 GLN cc_start: 0.7664 (mm110) cc_final: 0.7428 (tp40) REVERT: A 743 ARG cc_start: 0.8356 (ttm110) cc_final: 0.8091 (ttm110) REVERT: A 748 ASN cc_start: 0.8086 (t0) cc_final: 0.7736 (t0) REVERT: D 215 THR cc_start: 0.7864 (p) cc_final: 0.7577 (m) REVERT: D 228 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.6601 (mp10) REVERT: D 273 GLN cc_start: 0.7468 (tt0) cc_final: 0.7011 (mm110) REVERT: D 432 ARG cc_start: 0.7648 (mtm180) cc_final: 0.7328 (ptm160) REVERT: D 500 ARG cc_start: 0.7486 (mmt180) cc_final: 0.7159 (mtp85) REVERT: D 691 GLN cc_start: 0.7708 (mm110) cc_final: 0.7471 (tp40) REVERT: D 743 ARG cc_start: 0.8347 (ttm110) cc_final: 0.8081 (ttm110) REVERT: D 748 ASN cc_start: 0.8063 (t0) cc_final: 0.7706 (t0) REVERT: B 215 THR cc_start: 0.7872 (p) cc_final: 0.7575 (m) REVERT: B 228 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.6590 (mp10) REVERT: B 237 LYS cc_start: 0.6254 (mmtt) cc_final: 0.6024 (tppp) REVERT: B 273 GLN cc_start: 0.7487 (tt0) cc_final: 0.7024 (mm110) REVERT: B 432 ARG cc_start: 0.7658 (mtm180) cc_final: 0.7337 (ptm160) REVERT: B 500 ARG cc_start: 0.7499 (mmt180) cc_final: 0.7181 (mtp85) REVERT: B 691 GLN cc_start: 0.7711 (mm110) cc_final: 0.7475 (tp40) REVERT: B 743 ARG cc_start: 0.8344 (ttm110) cc_final: 0.8081 (ttm110) REVERT: B 748 ASN cc_start: 0.8061 (t0) cc_final: 0.7715 (t0) REVERT: C 215 THR cc_start: 0.7840 (p) cc_final: 0.7507 (t) REVERT: C 228 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.6604 (mp10) REVERT: C 237 LYS cc_start: 0.6253 (mmtt) cc_final: 0.6024 (tppp) REVERT: C 273 GLN cc_start: 0.7472 (tt0) cc_final: 0.7007 (mm110) REVERT: C 432 ARG cc_start: 0.7644 (mtm180) cc_final: 0.7322 (ptm160) REVERT: C 500 ARG cc_start: 0.7495 (mmt180) cc_final: 0.7176 (mtp85) REVERT: C 691 GLN cc_start: 0.7696 (mm110) cc_final: 0.7459 (tp40) REVERT: C 743 ARG cc_start: 0.8337 (ttm110) cc_final: 0.8072 (ttm110) REVERT: C 748 ASN cc_start: 0.8085 (t0) cc_final: 0.7742 (t0) outliers start: 33 outliers final: 25 residues processed: 254 average time/residue: 1.2825 time to fit residues: 368.3714 Evaluate side-chains 263 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 234 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU 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 574 LEU Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain D residue 216 LEU 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 216 LEU 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 216 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 16 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 176 optimal weight: 0.5980 chunk 177 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.159057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.114048 restraints weight = 55093.915| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.93 r_work: 0.2838 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17720 Z= 0.135 Angle : 0.513 7.895 24008 Z= 0.269 Chirality : 0.035 0.232 2700 Planarity : 0.003 0.033 2952 Dihedral : 6.135 56.836 2388 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.61 % Allowed : 14.35 % 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: 1.59 (0.19), residues: 2092 helix: 2.47 (0.14), residues: 1304 sheet: -0.72 (0.55), residues: 92 loop : -1.57 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 474 TYR 0.008 0.001 TYR B 309 PHE 0.009 0.001 PHE A 649 TRP 0.007 0.001 TRP D 697 HIS 0.002 0.001 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (17720) covalent geometry : angle 0.51307 / 0.27 (24008) hydrogen bonds : bond 0.05880 / 4.04 ( 1032) hydrogen bonds : angle 3.78675 / 2.67 ( 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 265 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 235 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 THR cc_start: 0.7852 (p) cc_final: 0.7530 (t) REVERT: A 228 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.6646 (mp10) REVERT: A 237 LYS cc_start: 0.6322 (mmtt) cc_final: 0.6088 (tppp) REVERT: A 273 GLN cc_start: 0.7490 (tt0) cc_final: 0.7033 (mm110) REVERT: A 432 ARG cc_start: 0.7700 (mtm180) cc_final: 0.7378 (ptm160) REVERT: A 500 ARG cc_start: 0.7494 (mmt180) cc_final: 0.7165 (mtp85) REVERT: A 691 GLN cc_start: 0.7734 (mm110) cc_final: 0.7508 (tp40) REVERT: A 743 ARG cc_start: 0.8365 (ttm110) cc_final: 0.8111 (ttm110) REVERT: A 748 ASN cc_start: 0.8130 (t0) cc_final: 0.7798 (t0) REVERT: D 215 THR cc_start: 0.7840 (p) cc_final: 0.7510 (t) REVERT: D 228 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.6649 (mp10) REVERT: D 273 GLN cc_start: 0.7482 (tt0) cc_final: 0.7021 (mm110) REVERT: D 432 ARG cc_start: 0.7673 (mtm180) cc_final: 0.7346 (ptm160) REVERT: D 500 ARG cc_start: 0.7494 (mmt180) cc_final: 0.7165 (mtp85) REVERT: D 691 GLN cc_start: 0.7730 (mm110) cc_final: 0.7500 (tp40) REVERT: D 743 ARG cc_start: 0.8360 (ttm110) cc_final: 0.8104 (ttm110) REVERT: D 748 ASN cc_start: 0.8110 (t0) cc_final: 0.7775 (t0) REVERT: B 215 THR cc_start: 0.7839 (p) cc_final: 0.7508 (t) REVERT: B 228 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.6628 (mp10) REVERT: B 237 LYS cc_start: 0.6320 (mmtt) cc_final: 0.6088 (tppp) REVERT: B 273 GLN cc_start: 0.7502 (tt0) cc_final: 0.7038 (mm110) REVERT: B 432 ARG cc_start: 0.7702 (mtm180) cc_final: 0.7377 (ptm160) REVERT: B 500 ARG cc_start: 0.7503 (mmt180) cc_final: 0.7185 (mtp85) REVERT: B 691 GLN cc_start: 0.7747 (mm110) cc_final: 0.7505 (tp40) REVERT: B 743 ARG cc_start: 0.8353 (ttm110) cc_final: 0.8103 (ttm110) REVERT: B 748 ASN cc_start: 0.8110 (t0) cc_final: 0.7783 (t0) REVERT: C 215 THR cc_start: 0.7885 (p) cc_final: 0.7567 (t) REVERT: C 228 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.6649 (mp10) REVERT: C 237 LYS cc_start: 0.6328 (mmtt) cc_final: 0.6096 (tppp) REVERT: C 273 GLN cc_start: 0.7500 (tt0) cc_final: 0.7034 (mm110) REVERT: C 432 ARG cc_start: 0.7691 (mtm180) cc_final: 0.7366 (ptm160) REVERT: C 500 ARG cc_start: 0.7452 (mmt180) cc_final: 0.7156 (mtp85) REVERT: C 691 GLN cc_start: 0.7734 (mm110) cc_final: 0.7506 (tp40) REVERT: C 743 ARG cc_start: 0.8350 (ttm110) cc_final: 0.8093 (ttm110) REVERT: C 748 ASN cc_start: 0.8137 (t0) cc_final: 0.7807 (t0) outliers start: 30 outliers final: 25 residues processed: 252 average time/residue: 1.2302 time to fit residues: 351.0863 Evaluate side-chains 262 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 233 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU 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 574 LEU Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain D residue 216 LEU 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 216 LEU 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 216 LEU 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: 2.9990 chunk 144 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 199 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 181 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.158710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.113728 restraints weight = 54928.430| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.90 r_work: 0.2835 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17720 Z= 0.140 Angle : 0.514 7.722 24008 Z= 0.271 Chirality : 0.035 0.231 2700 Planarity : 0.003 0.034 2952 Dihedral : 6.134 56.615 2388 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 1.77 % Allowed : 14.09 % Favored : 84.14 % 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: 1.58 (0.19), residues: 2092 helix: 2.45 (0.14), residues: 1304 sheet: -0.73 (0.55), residues: 92 loop : -1.57 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 721 TYR 0.008 0.001 TYR D 309 PHE 0.010 0.001 PHE A 649 TRP 0.007 0.001 TRP D 697 HIS 0.002 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (17720) covalent geometry : angle 0.51434 / 0.27 (24008) hydrogen bonds : bond 0.05972 / 4.10 ( 1032) hydrogen bonds : angle 3.79092 / 2.67 ( 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 269 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 236 time to evaluate : 0.938 Fit side-chains REVERT: A 215 THR cc_start: 0.7821 (p) cc_final: 0.7520 (t) REVERT: A 228 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.6628 (mp10) REVERT: A 237 LYS cc_start: 0.6234 (mmtt) cc_final: 0.5973 (tppp) REVERT: A 273 GLN cc_start: 0.7483 (tt0) cc_final: 0.7018 (mm110) REVERT: A 432 ARG cc_start: 0.7663 (mtm180) cc_final: 0.7328 (ptm160) REVERT: A 500 ARG cc_start: 0.7461 (mmt180) cc_final: 0.7145 (mtp85) REVERT: A 660 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8725 (mm) REVERT: A 691 GLN cc_start: 0.7714 (mm110) cc_final: 0.7482 (tp40) REVERT: A 743 ARG cc_start: 0.8353 (ttm110) cc_final: 0.8090 (ttm110) REVERT: A 748 ASN cc_start: 0.8138 (t0) cc_final: 0.7805 (t0) REVERT: D 215 THR cc_start: 0.7854 (p) cc_final: 0.7553 (t) REVERT: D 228 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.6629 (mp10) REVERT: D 273 GLN cc_start: 0.7474 (tt0) cc_final: 0.7004 (mm110) REVERT: D 432 ARG cc_start: 0.7629 (mtm180) cc_final: 0.7291 (ptm160) REVERT: D 500 ARG cc_start: 0.7462 (mmt180) cc_final: 0.7146 (mtp85) REVERT: D 660 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8719 (mm) REVERT: D 691 GLN cc_start: 0.7710 (mm110) cc_final: 0.7475 (tp40) REVERT: D 743 ARG cc_start: 0.8350 (ttm110) cc_final: 0.8086 (ttm110) REVERT: D 748 ASN cc_start: 0.8122 (t0) cc_final: 0.7793 (t0) REVERT: B 215 THR cc_start: 0.7838 (p) cc_final: 0.7529 (t) REVERT: B 228 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.6602 (mp10) REVERT: B 237 LYS cc_start: 0.6227 (mmtt) cc_final: 0.5972 (tppp) REVERT: B 273 GLN cc_start: 0.7495 (tt0) cc_final: 0.7020 (mm110) REVERT: B 432 ARG cc_start: 0.7632 (mtm180) cc_final: 0.7299 (ptm160) REVERT: B 500 ARG cc_start: 0.7468 (mmt180) cc_final: 0.7158 (mtp85) REVERT: B 660 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8723 (mm) REVERT: B 691 GLN cc_start: 0.7719 (mm110) cc_final: 0.7485 (tp40) REVERT: B 743 ARG cc_start: 0.8343 (ttm110) cc_final: 0.8083 (ttm110) REVERT: B 748 ASN cc_start: 0.8123 (t0) cc_final: 0.7797 (t0) REVERT: C 215 THR cc_start: 0.7830 (p) cc_final: 0.7528 (t) REVERT: C 228 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.6625 (mp10) REVERT: C 237 LYS cc_start: 0.6237 (mmtt) cc_final: 0.5982 (tppp) REVERT: C 273 GLN cc_start: 0.7490 (tt0) cc_final: 0.7017 (mm110) REVERT: C 432 ARG cc_start: 0.7626 (mtm180) cc_final: 0.7292 (ptm160) REVERT: C 500 ARG cc_start: 0.7454 (mmt180) cc_final: 0.7147 (mtp85) REVERT: C 660 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8731 (mm) REVERT: C 691 GLN cc_start: 0.7707 (mm110) cc_final: 0.7474 (tp40) REVERT: C 743 ARG cc_start: 0.8338 (ttm110) cc_final: 0.8074 (ttm110) REVERT: C 748 ASN cc_start: 0.8145 (t0) cc_final: 0.7823 (t0) outliers start: 33 outliers final: 25 residues processed: 256 average time/residue: 1.1732 time to fit residues: 340.0250 Evaluate side-chains 256 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 223 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU 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 574 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain D residue 216 LEU 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 660 ILE Chi-restraints excluded: chain D residue 746 GLU Chi-restraints excluded: chain B residue 216 LEU 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 660 ILE Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 216 LEU 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 660 ILE 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: 0.6980 chunk 201 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 177 optimal weight: 0.3980 chunk 70 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.156226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.111187 restraints weight = 54584.270| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.92 r_work: 0.2800 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17720 Z= 0.168 Angle : 0.548 7.715 24008 Z= 0.292 Chirality : 0.037 0.244 2700 Planarity : 0.004 0.036 2952 Dihedral : 6.376 56.526 2388 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.88 % Allowed : 14.52 % Favored : 83.60 % 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: 1.43 (0.19), residues: 2092 helix: 2.32 (0.14), residues: 1304 sheet: -0.75 (0.54), residues: 92 loop : -1.59 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 721 TYR 0.009 0.001 TYR B 309 PHE 0.012 0.001 PHE C 649 TRP 0.007 0.001 TRP C 697 HIS 0.003 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (17720) covalent geometry : angle 0.54751 / 0.29 (24008) hydrogen bonds : bond 0.06541 / 4.48 ( 1032) hydrogen bonds : angle 3.85606 / 2.72 ( 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 254 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 219 time to evaluate : 0.898 Fit side-chains REVERT: A 215 THR cc_start: 0.7786 (p) cc_final: 0.7503 (t) REVERT: A 273 GLN cc_start: 0.7545 (tt0) cc_final: 0.7045 (mm110) REVERT: A 432 ARG cc_start: 0.7767 (mtm180) cc_final: 0.7435 (ptm160) REVERT: A 500 ARG cc_start: 0.7510 (mmt180) cc_final: 0.7193 (mtp85) REVERT: A 691 GLN cc_start: 0.7785 (mm110) cc_final: 0.7569 (tp40) REVERT: A 748 ASN cc_start: 0.8122 (t0) cc_final: 0.7781 (t0) REVERT: D 215 THR cc_start: 0.7787 (p) cc_final: 0.7508 (t) REVERT: D 273 GLN cc_start: 0.7541 (tt0) cc_final: 0.7041 (mm110) REVERT: D 432 ARG cc_start: 0.7772 (mtm180) cc_final: 0.7438 (ptm160) REVERT: D 500 ARG cc_start: 0.7503 (mmt180) cc_final: 0.7184 (mtp85) REVERT: D 691 GLN cc_start: 0.7786 (mm110) cc_final: 0.7570 (tp40) REVERT: D 748 ASN cc_start: 0.8111 (t0) cc_final: 0.7773 (t0) REVERT: B 215 THR cc_start: 0.7785 (p) cc_final: 0.7501 (t) REVERT: B 273 GLN cc_start: 0.7552 (tt0) cc_final: 0.7051 (mm110) REVERT: B 432 ARG cc_start: 0.7787 (mtm180) cc_final: 0.7458 (ptm160) REVERT: B 500 ARG cc_start: 0.7527 (mmt180) cc_final: 0.7215 (mtp85) REVERT: B 691 GLN cc_start: 0.7775 (mm110) cc_final: 0.7563 (tp40) REVERT: B 748 ASN cc_start: 0.8118 (t0) cc_final: 0.7781 (t0) REVERT: C 215 THR cc_start: 0.7764 (p) cc_final: 0.7488 (t) REVERT: C 273 GLN cc_start: 0.7544 (tt0) cc_final: 0.7041 (mm110) REVERT: C 432 ARG cc_start: 0.7755 (mtm180) cc_final: 0.7420 (ptm160) REVERT: C 500 ARG cc_start: 0.7525 (mmt180) cc_final: 0.7211 (mtp85) REVERT: C 691 GLN cc_start: 0.7778 (mm110) cc_final: 0.7562 (tp40) REVERT: C 748 ASN cc_start: 0.8102 (t0) cc_final: 0.7771 (t0) outliers start: 35 outliers final: 29 residues processed: 241 average time/residue: 1.2379 time to fit residues: 337.0256 Evaluate side-chains 239 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 210 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU 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 574 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain D residue 216 LEU 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 660 ILE Chi-restraints excluded: chain D residue 746 GLU Chi-restraints excluded: chain B residue 216 LEU 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 660 ILE Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 216 LEU 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 660 ILE 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: 1.9990 chunk 70 optimal weight: 2.9990 chunk 149 optimal weight: 0.0030 chunk 122 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.157719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.113058 restraints weight = 54314.725| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.91 r_work: 0.2827 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17720 Z= 0.135 Angle : 0.519 6.855 24008 Z= 0.278 Chirality : 0.035 0.208 2700 Planarity : 0.003 0.033 2952 Dihedral : 6.068 56.677 2388 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.51 % Allowed : 15.32 % Favored : 83.17 % 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: 1.57 (0.19), residues: 2092 helix: 2.45 (0.14), residues: 1304 sheet: -0.68 (0.55), residues: 92 loop : -1.58 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 721 TYR 0.008 0.001 TYR C 309 PHE 0.009 0.001 PHE B 742 TRP 0.008 0.001 TRP D 697 HIS 0.002 0.001 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (17720) covalent geometry : angle 0.51945 / 0.28 (24008) hydrogen bonds : bond 0.05889 / 4.04 ( 1032) hydrogen bonds : angle 3.78628 / 2.67 ( 2976) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11169.97 seconds wall clock time: 189 minutes 23.86 seconds (11363.86 seconds total)