Starting phenix.real_space_refine on Sat Jul 4 02:53:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rlt_24540/07_2026/7rlt_24540.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rlt_24540/07_2026/7rlt_24540.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rlt_24540/07_2026/7rlt_24540.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rlt_24540/07_2026/7rlt_24540.map" model { file = "/net/cci-nas-00/data/ceres_data/7rlt_24540/07_2026/7rlt_24540.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rlt_24540/07_2026/7rlt_24540.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 96 5.16 5 C 11432 2.51 5 N 3060 2.21 5 O 3404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s 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: 17996 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4478 Classifications: {'peptide': 581} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 558} Chain breaks: 1 Chain: "C" Number of atoms: 4478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4478 Classifications: {'peptide': 581} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 558} Chain breaks: 1 Chain: "B" Number of atoms: 4478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4478 Classifications: {'peptide': 581} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 558} Chain breaks: 1 Chain: "D" Number of atoms: 4478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4478 Classifications: {'peptide': 581} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 558} Chain breaks: 1 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'PNS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'PNS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Time building chain proxies: 4.17, per 1000 atoms: 0.23 Number of scatterers: 17996 At special positions: 0 Unit cell: (100.32, 106.92, 117.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 4 15.00 O 3404 8.00 N 3060 7.00 C 11432 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 784.7 milliseconds 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4264 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 20 sheets defined 49.8% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 317 through 335 removed outlier: 3.517A pdb=" N ALA A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 352 removed outlier: 3.843A pdb=" N GLY A 351 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 347 through 352' Processing helix chain 'A' and resid 353 through 368 removed outlier: 3.762A pdb=" N VAL A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 358 " --> pdb=" O SER A 354 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 366 " --> pdb=" O GLU A 362 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 381 removed outlier: 3.528A pdb=" N TYR A 379 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 397 removed outlier: 3.605A pdb=" N LYS A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 474 removed outlier: 3.605A pdb=" N LYS A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 removed outlier: 4.108A pdb=" N LYS A 479 " --> pdb=" O GLY A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 499 Processing helix chain 'A' and resid 499 through 511 Processing helix chain 'A' and resid 514 through 521 removed outlier: 3.623A pdb=" N LYS A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 537 Processing helix chain 'A' and resid 538 through 540 No H-bonds generated for 'chain 'A' and resid 538 through 540' Processing helix chain 'A' and resid 577 through 591 removed outlier: 3.509A pdb=" N LYS A 583 " --> pdb=" O MET A 579 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA A 586 " --> pdb=" O TRP A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 617 removed outlier: 4.000A pdb=" N LEU A 614 " --> pdb=" O ALA A 610 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS A 615 " --> pdb=" O GLU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 640 removed outlier: 3.967A pdb=" N GLN A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 638 " --> pdb=" O GLY A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 667 removed outlier: 3.778A pdb=" N HIS A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET A 659 " --> pdb=" O GLY A 655 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER A 665 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN A 666 " --> pdb=" O CYS A 662 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL A 667 " --> pdb=" O ALA A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 700 removed outlier: 3.812A pdb=" N GLN A 693 " --> pdb=" O ASN A 689 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 699 " --> pdb=" O GLY A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 734 removed outlier: 3.625A pdb=" N GLU A 729 " --> pdb=" O GLN A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 769 removed outlier: 3.809A pdb=" N LEU A 755 " --> pdb=" O HIS A 751 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 803 removed outlier: 3.548A pdb=" N LYS A 802 " --> pdb=" O MET A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 829 removed outlier: 3.683A pdb=" N VAL A 823 " --> pdb=" O ASP A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 853 Processing helix chain 'A' and resid 885 through 892 removed outlier: 4.224A pdb=" N LEU A 889 " --> pdb=" O GLY A 885 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN A 890 " --> pdb=" O GLU A 886 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR A 892 " --> pdb=" O ALA A 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 885 through 892' Processing helix chain 'C' and resid 317 through 335 removed outlier: 3.502A pdb=" N ALA C 326 " --> pdb=" O ALA C 322 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG C 333 " --> pdb=" O SER C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 352 removed outlier: 3.839A pdb=" N GLY C 351 " --> pdb=" O PHE C 347 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA C 352 " --> pdb=" O PHE C 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 347 through 352' Processing helix chain 'C' and resid 353 through 368 removed outlier: 3.745A pdb=" N VAL C 357 " --> pdb=" O ALA C 353 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL C 358 " --> pdb=" O SER C 354 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 366 " --> pdb=" O GLU C 362 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU C 367 " --> pdb=" O GLU C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 381 removed outlier: 4.219A pdb=" N VAL C 378 " --> pdb=" O GLU C 374 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR C 379 " --> pdb=" O ASN C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 397 removed outlier: 3.585A pdb=" N LYS C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 474 removed outlier: 3.591A pdb=" N LYS C 463 " --> pdb=" O SER C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 480 removed outlier: 4.116A pdb=" N LYS C 479 " --> pdb=" O GLY C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 499 Processing helix chain 'C' and resid 499 through 511 Processing helix chain 'C' and resid 514 through 521 removed outlier: 3.619A pdb=" N LYS C 520 " --> pdb=" O THR C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 537 Processing helix chain 'C' and resid 538 through 540 No H-bonds generated for 'chain 'C' and resid 538 through 540' Processing helix chain 'C' and resid 575 through 591 removed outlier: 3.616A pdb=" N MET C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU C 580 " --> pdb=" O PRO C 576 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA C 586 " --> pdb=" O TRP C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 617 removed outlier: 4.010A pdb=" N LEU C 614 " --> pdb=" O ALA C 610 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS C 615 " --> pdb=" O GLU C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 640 removed outlier: 3.958A pdb=" N GLN C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER C 638 " --> pdb=" O GLY C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 667 removed outlier: 3.828A pdb=" N HIS C 657 " --> pdb=" O GLU C 653 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER C 665 " --> pdb=" O SER C 661 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN C 666 " --> pdb=" O CYS C 662 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL C 667 " --> pdb=" O ALA C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 700 removed outlier: 3.795A pdb=" N GLN C 693 " --> pdb=" O ASN C 689 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 699 " --> pdb=" O GLY C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 734 removed outlier: 3.617A pdb=" N GLU C 729 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 769 removed outlier: 3.664A pdb=" N LEU C 755 " --> pdb=" O HIS C 751 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 803 removed outlier: 3.597A pdb=" N LYS C 802 " --> pdb=" O MET C 798 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 829 removed outlier: 3.688A pdb=" N VAL C 823 " --> pdb=" O ASP C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 853 Processing helix chain 'C' and resid 885 through 892 removed outlier: 4.232A pdb=" N LEU C 889 " --> pdb=" O GLY C 885 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN C 890 " --> pdb=" O GLU C 886 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU C 891 " --> pdb=" O ALA C 887 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR C 892 " --> pdb=" O ALA C 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 885 through 892' Processing helix chain 'B' and resid 317 through 335 Processing helix chain 'B' and resid 347 through 352 removed outlier: 3.837A pdb=" N GLY B 351 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 352 " --> pdb=" O PHE B 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 347 through 352' Processing helix chain 'B' and resid 353 through 368 removed outlier: 3.746A pdb=" N VAL B 357 " --> pdb=" O ALA B 353 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL B 358 " --> pdb=" O SER B 354 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU B 366 " --> pdb=" O GLU B 362 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 367 " --> pdb=" O GLU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 381 removed outlier: 4.227A pdb=" N VAL B 378 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR B 379 " --> pdb=" O ASN B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 397 removed outlier: 3.577A pdb=" N LYS B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 474 removed outlier: 3.590A pdb=" N LYS B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 480 removed outlier: 4.116A pdb=" N LYS B 479 " --> pdb=" O GLY B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 499 Processing helix chain 'B' and resid 499 through 511 Processing helix chain 'B' and resid 514 through 521 removed outlier: 3.616A pdb=" N LYS B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 537 Processing helix chain 'B' and resid 538 through 540 No H-bonds generated for 'chain 'B' and resid 538 through 540' Processing helix chain 'B' and resid 575 through 591 removed outlier: 3.587A pdb=" N MET B 579 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B 580 " --> pdb=" O PRO B 576 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B 583 " --> pdb=" O MET B 579 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA B 586 " --> pdb=" O TRP B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 617 removed outlier: 4.011A pdb=" N LEU B 614 " --> pdb=" O ALA B 610 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS B 615 " --> pdb=" O GLU B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 640 removed outlier: 3.972A pdb=" N GLN B 635 " --> pdb=" O SER B 631 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER B 638 " --> pdb=" O GLY B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 667 removed outlier: 3.843A pdb=" N HIS B 657 " --> pdb=" O GLU B 653 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER B 665 " --> pdb=" O SER B 661 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASN B 666 " --> pdb=" O CYS B 662 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 700 removed outlier: 3.798A pdb=" N GLN B 693 " --> pdb=" O ASN B 689 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 699 " --> pdb=" O GLY B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 734 removed outlier: 3.624A pdb=" N GLU B 729 " --> pdb=" O GLN B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 769 removed outlier: 3.684A pdb=" N LEU B 755 " --> pdb=" O HIS B 751 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 removed outlier: 3.578A pdb=" N LYS B 802 " --> pdb=" O MET B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 829 removed outlier: 3.701A pdb=" N VAL B 823 " --> pdb=" O ASP B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 853 Processing helix chain 'B' and resid 885 through 892 removed outlier: 4.240A pdb=" N LEU B 889 " --> pdb=" O GLY B 885 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN B 890 " --> pdb=" O GLU B 886 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU B 891 " --> pdb=" O ALA B 887 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR B 892 " --> pdb=" O ALA B 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 885 through 892' Processing helix chain 'D' and resid 317 through 335 removed outlier: 3.510A pdb=" N ALA D 326 " --> pdb=" O ALA D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 352 removed outlier: 3.838A pdb=" N GLY D 351 " --> pdb=" O PHE D 347 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA D 352 " --> pdb=" O PHE D 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 347 through 352' Processing helix chain 'D' and resid 353 through 368 removed outlier: 3.762A pdb=" N VAL D 357 " --> pdb=" O ALA D 353 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL D 358 " --> pdb=" O SER D 354 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU D 363 " --> pdb=" O ARG D 359 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU D 366 " --> pdb=" O GLU D 362 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU D 367 " --> pdb=" O GLU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 381 removed outlier: 3.534A pdb=" N TYR D 379 " --> pdb=" O ASN D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 397 removed outlier: 3.602A pdb=" N LYS D 394 " --> pdb=" O LEU D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 474 removed outlier: 3.606A pdb=" N LYS D 463 " --> pdb=" O SER D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 480 removed outlier: 4.107A pdb=" N LYS D 479 " --> pdb=" O GLY D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 499 Processing helix chain 'D' and resid 499 through 511 Processing helix chain 'D' and resid 514 through 521 removed outlier: 3.611A pdb=" N LYS D 520 " --> pdb=" O THR D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 537 Processing helix chain 'D' and resid 538 through 540 No H-bonds generated for 'chain 'D' and resid 538 through 540' Processing helix chain 'D' and resid 577 through 591 removed outlier: 3.527A pdb=" N LYS D 583 " --> pdb=" O MET D 579 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA D 586 " --> pdb=" O TRP D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 617 removed outlier: 4.002A pdb=" N LEU D 614 " --> pdb=" O ALA D 610 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS D 615 " --> pdb=" O GLU D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 640 removed outlier: 3.976A pdb=" N GLN D 635 " --> pdb=" O SER D 631 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER D 638 " --> pdb=" O GLY D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 667 removed outlier: 3.842A pdb=" N HIS D 657 " --> pdb=" O GLU D 653 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER D 665 " --> pdb=" O SER D 661 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN D 666 " --> pdb=" O CYS D 662 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL D 667 " --> pdb=" O ALA D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 700 removed outlier: 3.818A pdb=" N GLN D 693 " --> pdb=" O ASN D 689 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL D 699 " --> pdb=" O GLY D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 734 removed outlier: 3.624A pdb=" N GLU D 729 " --> pdb=" O GLN D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 751 through 768 removed outlier: 3.684A pdb=" N LEU D 755 " --> pdb=" O HIS D 751 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS D 757 " --> pdb=" O ALA D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 798 through 803 removed outlier: 3.544A pdb=" N LYS D 802 " --> pdb=" O MET D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 829 removed outlier: 3.702A pdb=" N VAL D 823 " --> pdb=" O ASP D 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 853 Processing helix chain 'D' and resid 885 through 892 removed outlier: 4.237A pdb=" N LEU D 889 " --> pdb=" O GLY D 885 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN D 890 " --> pdb=" O GLU D 886 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU D 891 " --> pdb=" O ALA D 887 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR D 892 " --> pdb=" O ALA D 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 885 through 892' Processing sheet with id=AA1, first strand: chain 'A' and resid 408 through 412 removed outlier: 3.767A pdb=" N MET A 420 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS A 411 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 425 through 426 removed outlier: 6.478A pdb=" N CYS A 567 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 645 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 647 " --> pdb=" O GLY A 568 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 438 through 442 removed outlier: 3.671A pdb=" N THR A 441 " --> pdb=" O CYS A 451 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N CYS A 451 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 557 through 563 Processing sheet with id=AA5, first strand: chain 'A' and resid 771 through 774 removed outlier: 5.889A pdb=" N LEU A 772 " --> pdb=" O THR A 792 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N THR A 792 " --> pdb=" O LEU A 772 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N CYS A 774 " --> pdb=" O VAL A 790 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR A 789 " --> pdb=" O MET A 810 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE A 812 " --> pdb=" O THR A 789 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE A 791 " --> pdb=" O ILE A 812 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N ARG A 814 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLY A 711 " --> pdb=" O ILE A 811 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N SER A 813 " --> pdb=" O GLY A 711 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU A 713 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N PHE A 815 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL A 715 " --> pdb=" O PHE A 815 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N SER A 678 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG A 712 " --> pdb=" O SER A 678 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N PHE A 839 " --> pdb=" O PRO A 679 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE A 681 " --> pdb=" O PHE A 839 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 408 through 412 removed outlier: 3.797A pdb=" N MET C 420 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS C 411 " --> pdb=" O LEU C 418 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 425 through 426 removed outlier: 6.479A pdb=" N CYS C 567 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 645 " --> pdb=" O VAL C 566 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY C 647 " --> pdb=" O GLY C 568 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 438 through 442 removed outlier: 3.665A pdb=" N THR C 441 " --> pdb=" O CYS C 451 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N CYS C 451 " --> pdb=" O THR C 441 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 557 through 563 Processing sheet with id=AB1, first strand: chain 'C' and resid 771 through 772 removed outlier: 6.649A pdb=" N THR C 789 " --> pdb=" O MET C 810 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILE C 812 " --> pdb=" O THR C 789 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N PHE C 791 " --> pdb=" O ILE C 812 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ARG C 814 " --> pdb=" O PHE C 791 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY C 711 " --> pdb=" O ILE C 811 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N SER C 813 " --> pdb=" O GLY C 711 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU C 713 " --> pdb=" O SER C 813 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N PHE C 815 " --> pdb=" O LEU C 713 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL C 715 " --> pdb=" O PHE C 815 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N SER C 678 " --> pdb=" O GLY C 711 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LEU C 713 " --> pdb=" O SER C 678 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU C 680 " --> pdb=" O LEU C 713 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N VAL C 715 " --> pdb=" O LEU C 680 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE C 682 " --> pdb=" O VAL C 715 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N PHE C 839 " --> pdb=" O PRO C 679 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE C 681 " --> pdb=" O PHE C 839 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 408 through 412 removed outlier: 3.798A pdb=" N MET B 420 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS B 411 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 425 through 426 removed outlier: 6.490A pdb=" N CYS B 567 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS B 645 " --> pdb=" O VAL B 566 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY B 647 " --> pdb=" O GLY B 568 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 646 " --> pdb=" O LYS B 669 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 438 through 442 removed outlier: 3.666A pdb=" N THR B 441 " --> pdb=" O CYS B 451 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N CYS B 451 " --> pdb=" O THR B 441 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 557 through 563 Processing sheet with id=AB6, first strand: chain 'B' and resid 771 through 774 removed outlier: 5.514A pdb=" N LEU B 772 " --> pdb=" O THR B 792 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR B 792 " --> pdb=" O LEU B 772 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N CYS B 774 " --> pdb=" O VAL B 790 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR B 789 " --> pdb=" O MET B 810 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE B 812 " --> pdb=" O THR B 789 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N PHE B 791 " --> pdb=" O ILE B 812 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ARG B 814 " --> pdb=" O PHE B 791 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY B 711 " --> pdb=" O ILE B 811 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N SER B 813 " --> pdb=" O GLY B 711 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU B 713 " --> pdb=" O SER B 813 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N PHE B 815 " --> pdb=" O LEU B 713 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL B 715 " --> pdb=" O PHE B 815 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N SER B 678 " --> pdb=" O GLY B 711 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU B 713 " --> pdb=" O SER B 678 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU B 680 " --> pdb=" O LEU B 713 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N VAL B 715 " --> pdb=" O LEU B 680 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE B 682 " --> pdb=" O VAL B 715 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N PHE B 839 " --> pdb=" O PRO B 679 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE B 681 " --> pdb=" O PHE B 839 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 408 through 412 removed outlier: 3.770A pdb=" N MET D 420 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS D 411 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 425 through 426 removed outlier: 6.483A pdb=" N CYS D 567 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS D 645 " --> pdb=" O VAL D 566 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY D 647 " --> pdb=" O GLY D 568 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 438 through 442 removed outlier: 3.671A pdb=" N THR D 441 " --> pdb=" O CYS D 451 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N CYS D 451 " --> pdb=" O THR D 441 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 557 through 563 Processing sheet with id=AC2, first strand: chain 'D' and resid 771 through 774 removed outlier: 5.560A pdb=" N LEU D 772 " --> pdb=" O THR D 792 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR D 792 " --> pdb=" O LEU D 772 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N CYS D 774 " --> pdb=" O VAL D 790 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR D 789 " --> pdb=" O MET D 810 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE D 812 " --> pdb=" O THR D 789 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE D 791 " --> pdb=" O ILE D 812 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ARG D 814 " --> pdb=" O PHE D 791 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLY D 711 " --> pdb=" O ILE D 811 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N SER D 813 " --> pdb=" O GLY D 711 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU D 713 " --> pdb=" O SER D 813 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N PHE D 815 " --> pdb=" O LEU D 713 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL D 715 " --> pdb=" O PHE D 815 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER D 678 " --> pdb=" O ALA D 710 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG D 712 " --> pdb=" O SER D 678 " (cutoff:3.500A) 738 hydrogen bonds defined for protein. 2199 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.16 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5009 1.34 - 1.46: 2859 1.46 - 1.58: 10300 1.58 - 1.70: 4 1.70 - 1.82: 148 Bond restraints: 18320 Sorted by residual: bond pdb=" O27 PNS A1002 " pdb=" P24 PNS A1002 " ideal model delta sigma weight residual 1.704 1.601 0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" O27 PNS A1001 " pdb=" P24 PNS A1001 " ideal model delta sigma weight residual 1.704 1.601 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" O27 PNS B1002 " pdb=" P24 PNS B1002 " ideal model delta sigma weight residual 1.704 1.602 0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" O27 PNS B1001 " pdb=" P24 PNS B1001 " ideal model delta sigma weight residual 1.704 1.602 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" C ARG D 781 " pdb=" N PRO D 782 " ideal model delta sigma weight residual 1.332 1.358 -0.026 1.12e-02 7.97e+03 5.35e+00 ... (remaining 18315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 19042 1.32 - 2.63: 4267 2.63 - 3.95: 1327 3.95 - 5.27: 140 5.27 - 6.58: 12 Bond angle restraints: 24788 Sorted by residual: angle pdb=" C VAL D 654 " pdb=" N GLY D 655 " pdb=" CA GLY D 655 " ideal model delta sigma weight residual 119.98 124.43 -4.45 1.11e+00 8.12e-01 1.61e+01 angle pdb=" C VAL B 633 " pdb=" N GLY B 634 " pdb=" CA GLY B 634 " ideal model delta sigma weight residual 119.98 124.42 -4.44 1.11e+00 8.12e-01 1.60e+01 angle pdb=" C VAL C 633 " pdb=" N GLY C 634 " pdb=" CA GLY C 634 " ideal model delta sigma weight residual 119.98 124.41 -4.43 1.11e+00 8.12e-01 1.59e+01 angle pdb=" C VAL B 654 " pdb=" N GLY B 655 " pdb=" CA GLY B 655 " ideal model delta sigma weight residual 120.00 124.39 -4.39 1.10e+00 8.26e-01 1.59e+01 angle pdb=" C VAL C 654 " pdb=" N GLY C 655 " pdb=" CA GLY C 655 " ideal model delta sigma weight residual 120.00 124.34 -4.34 1.10e+00 8.26e-01 1.56e+01 ... (remaining 24783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 10037 17.89 - 35.79: 734 35.79 - 53.68: 179 53.68 - 71.58: 33 71.58 - 89.47: 9 Dihedral angle restraints: 10992 sinusoidal: 4356 harmonic: 6636 Sorted by residual: dihedral pdb=" CA PRO A 871 " pdb=" C PRO A 871 " pdb=" N PHE A 872 " pdb=" CA PHE A 872 " ideal model delta harmonic sigma weight residual -180.00 -160.52 -19.48 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA PRO D 871 " pdb=" C PRO D 871 " pdb=" N PHE D 872 " pdb=" CA PHE D 872 " ideal model delta harmonic sigma weight residual -180.00 -161.25 -18.75 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA PRO C 603 " pdb=" C PRO C 603 " pdb=" N LEU C 604 " pdb=" CA LEU C 604 " ideal model delta harmonic sigma weight residual 180.00 -161.58 -18.42 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 10989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1103 0.038 - 0.075: 744 0.075 - 0.113: 757 0.113 - 0.151: 199 0.151 - 0.188: 17 Chirality restraints: 2820 Sorted by residual: chirality pdb=" CB VAL A 338 " pdb=" CA VAL A 338 " pdb=" CG1 VAL A 338 " pdb=" CG2 VAL A 338 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.88e-01 chirality pdb=" CB VAL C 338 " pdb=" CA VAL C 338 " pdb=" CG1 VAL C 338 " pdb=" CG2 VAL C 338 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CB VAL D 338 " pdb=" CA VAL D 338 " pdb=" CG1 VAL D 338 " pdb=" CG2 VAL D 338 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.67e-01 ... (remaining 2817 not shown) Planarity restraints: 3212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 781 " -0.245 9.50e-02 1.11e+02 1.10e-01 7.41e+00 pdb=" NE ARG C 781 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG C 781 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG C 781 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 781 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 531 " 0.151 9.50e-02 1.11e+02 6.76e-02 2.86e+00 pdb=" NE ARG B 531 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 531 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B 531 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 531 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 531 " 0.149 9.50e-02 1.11e+02 6.70e-02 2.80e+00 pdb=" NE ARG A 531 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 531 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 531 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 531 " 0.004 2.00e-02 2.50e+03 ... (remaining 3209 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 8176 3.00 - 3.48: 19017 3.48 - 3.95: 30329 3.95 - 4.43: 35316 4.43 - 4.90: 57869 Nonbonded interactions: 150707 Sorted by model distance: nonbonded pdb=" O MET B 525 " pdb=" OG1 THR B 529 " model vdw 2.528 3.040 nonbonded pdb=" O MET D 525 " pdb=" OG1 THR D 529 " model vdw 2.529 3.040 nonbonded pdb=" O MET C 525 " pdb=" OG1 THR C 529 " model vdw 2.537 3.040 nonbonded pdb=" O MET A 525 " pdb=" OG1 THR A 529 " model vdw 2.537 3.040 nonbonded pdb=" O ALA A 610 " pdb=" OG1 THR A 613 " model vdw 2.546 3.040 ... (remaining 150702 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = 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=0.60 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.230 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 : 0.008 0.103 18328 Z= 0.597 Angle : 1.255 6.583 24788 Z= 0.858 Chirality : 0.068 0.188 2820 Planarity : 0.006 0.110 3212 Dihedral : 13.855 89.471 6728 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 1.00 % Allowed : 10.27 % Favored : 88.73 % Rotamer: Outliers : 1.61 % Allowed : 4.11 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -4.11 (0.14), residues: 2308 helix: -1.88 (0.12), residues: 940 sheet: -3.43 (0.23), residues: 364 loop : -3.21 (0.15), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 531 TYR 0.009 0.002 TYR D 902 PHE 0.013 0.002 PHE A 872 TRP 0.009 0.002 TRP B 477 HIS 0.004 0.002 HIS B 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00832 / 0.59 (18320) covalent geometry : angle 1.25461 / 0.86 (24788) hydrogen bonds : bond 0.25931 / 17.23 ( 738) hydrogen bonds : angle 8.32666 / 5.86 ( 2199) Misc. bond : bond 0.04688 / 2.48 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 643 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.7645 (mmt) cc_final: 0.7432 (mmm) REVERT: A 363 GLU cc_start: 0.7547 (tp30) cc_final: 0.7197 (mm-30) REVERT: A 365 LYS cc_start: 0.6992 (mtpt) cc_final: 0.5770 (pttp) REVERT: A 384 PHE cc_start: 0.7761 (t80) cc_final: 0.7486 (t80) REVERT: A 410 GLU cc_start: 0.7320 (tt0) cc_final: 0.7075 (mm-30) REVERT: A 415 LYS cc_start: 0.7019 (mttt) cc_final: 0.6257 (ptpt) REVERT: A 416 LEU cc_start: 0.7977 (mt) cc_final: 0.7698 (mt) REVERT: A 422 TYR cc_start: 0.6015 (p90) cc_final: 0.5755 (p90) REVERT: A 445 THR cc_start: 0.7673 (m) cc_final: 0.7273 (t) REVERT: A 446 ASP cc_start: 0.6926 (m-30) cc_final: 0.6651 (m-30) REVERT: A 548 ASN cc_start: 0.7413 (m-40) cc_final: 0.6594 (m-40) REVERT: A 562 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7083 (mm-30) REVERT: A 602 THR cc_start: 0.9049 (p) cc_final: 0.8647 (t) REVERT: A 620 LYS cc_start: 0.7570 (mttt) cc_final: 0.7180 (ptmt) REVERT: A 690 LYS cc_start: 0.8001 (mtpt) cc_final: 0.7463 (tptp) REVERT: A 696 MET cc_start: 0.6852 (mtm) cc_final: 0.6391 (mtp) REVERT: A 702 ASN cc_start: 0.7601 (t0) cc_final: 0.7314 (t0) REVERT: A 703 LYS cc_start: 0.7735 (pttp) cc_final: 0.7238 (pttm) REVERT: A 725 GLN cc_start: 0.6624 (tm-30) cc_final: 0.6356 (tm-30) REVERT: A 744 THR cc_start: 0.8684 (m) cc_final: 0.8302 (m) REVERT: A 745 ASN cc_start: 0.7302 (m-40) cc_final: 0.7088 (m110) REVERT: A 761 TYR cc_start: 0.7576 (t80) cc_final: 0.7367 (t80) REVERT: A 763 GLN cc_start: 0.7871 (mt0) cc_final: 0.7563 (mt0) REVERT: A 784 PHE cc_start: 0.7351 (m-10) cc_final: 0.6599 (m-10) REVERT: A 804 GLU cc_start: 0.7166 (tt0) cc_final: 0.6893 (tt0) REVERT: A 824 LEU cc_start: 0.8415 (mt) cc_final: 0.7919 (mp) REVERT: A 848 TYR cc_start: 0.8343 (t80) cc_final: 0.7864 (t80) REVERT: A 852 LYS cc_start: 0.8343 (mmtt) cc_final: 0.7876 (mmtt) REVERT: A 876 LYS cc_start: 0.6792 (mtmt) cc_final: 0.6590 (mtmm) REVERT: C 332 MET cc_start: 0.7671 (mmt) cc_final: 0.7111 (tpp) REVERT: C 363 GLU cc_start: 0.7538 (tp30) cc_final: 0.7169 (mm-30) REVERT: C 365 LYS cc_start: 0.6868 (mtpt) cc_final: 0.5722 (pttp) REVERT: C 384 PHE cc_start: 0.7749 (t80) cc_final: 0.7465 (t80) REVERT: C 410 GLU cc_start: 0.7156 (tt0) cc_final: 0.6804 (mm-30) REVERT: C 414 ASN cc_start: 0.6156 (t0) cc_final: 0.5930 (t0) REVERT: C 415 LYS cc_start: 0.7040 (mttt) cc_final: 0.6243 (ptpt) REVERT: C 422 TYR cc_start: 0.5899 (p90) cc_final: 0.5640 (p90) REVERT: C 434 GLU cc_start: 0.6272 (OUTLIER) cc_final: 0.5652 (pt0) REVERT: C 445 THR cc_start: 0.7706 (m) cc_final: 0.7397 (t) REVERT: C 446 ASP cc_start: 0.6919 (m-30) cc_final: 0.6663 (m-30) REVERT: C 507 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8244 (mm-30) REVERT: C 548 ASN cc_start: 0.7379 (m-40) cc_final: 0.6715 (m-40) REVERT: C 562 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7005 (mm-30) REVERT: C 602 THR cc_start: 0.9161 (p) cc_final: 0.8734 (t) REVERT: C 620 LYS cc_start: 0.7720 (mttt) cc_final: 0.7190 (ptmt) REVERT: C 666 ASN cc_start: 0.7578 (p0) cc_final: 0.6512 (p0) REVERT: C 690 LYS cc_start: 0.7981 (mtpt) cc_final: 0.7599 (tptp) REVERT: C 696 MET cc_start: 0.6863 (mtm) cc_final: 0.6458 (mtp) REVERT: C 702 ASN cc_start: 0.7679 (t0) cc_final: 0.7305 (t0) REVERT: C 703 LYS cc_start: 0.7652 (pttp) cc_final: 0.7338 (pttm) REVERT: C 717 GLU cc_start: 0.7961 (tt0) cc_final: 0.7755 (tt0) REVERT: C 725 GLN cc_start: 0.6586 (tm-30) cc_final: 0.6304 (tm-30) REVERT: C 744 THR cc_start: 0.8674 (m) cc_final: 0.8319 (m) REVERT: C 745 ASN cc_start: 0.7456 (m-40) cc_final: 0.7237 (m110) REVERT: C 760 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7092 (tp30) REVERT: C 761 TYR cc_start: 0.7548 (t80) cc_final: 0.7324 (t80) REVERT: C 767 LYS cc_start: 0.6856 (tmtm) cc_final: 0.6471 (tptm) REVERT: C 784 PHE cc_start: 0.7597 (m-80) cc_final: 0.6906 (m-10) REVERT: C 799 TYR cc_start: 0.8022 (t80) cc_final: 0.7813 (t80) REVERT: C 803 GLU cc_start: 0.6780 (tp30) cc_final: 0.6573 (mm-30) REVERT: C 824 LEU cc_start: 0.8416 (mt) cc_final: 0.7891 (mp) REVERT: C 848 TYR cc_start: 0.8349 (t80) cc_final: 0.7745 (t80) REVERT: C 852 LYS cc_start: 0.8342 (mmtt) cc_final: 0.7851 (mmtt) REVERT: C 876 LYS cc_start: 0.6838 (mtmt) cc_final: 0.6547 (mtmm) REVERT: C 894 ARG cc_start: 0.7943 (ptt180) cc_final: 0.7684 (ptt180) REVERT: B 332 MET cc_start: 0.7646 (mmt) cc_final: 0.7098 (tpp) REVERT: B 363 GLU cc_start: 0.7180 (tp30) cc_final: 0.6824 (mm-30) REVERT: B 365 LYS cc_start: 0.6884 (mtpt) cc_final: 0.5714 (pttp) REVERT: B 384 PHE cc_start: 0.7748 (t80) cc_final: 0.7464 (t80) REVERT: B 410 GLU cc_start: 0.7161 (tt0) cc_final: 0.6824 (mm-30) REVERT: B 414 ASN cc_start: 0.6151 (t0) cc_final: 0.5932 (t0) REVERT: B 415 LYS cc_start: 0.7044 (mttt) cc_final: 0.6247 (ptpt) REVERT: B 416 LEU cc_start: 0.7986 (mt) cc_final: 0.7708 (mt) REVERT: B 422 TYR cc_start: 0.5919 (p90) cc_final: 0.5683 (p90) REVERT: B 434 GLU cc_start: 0.6274 (OUTLIER) cc_final: 0.5658 (pt0) REVERT: B 445 THR cc_start: 0.7699 (m) cc_final: 0.7361 (t) REVERT: B 446 ASP cc_start: 0.6937 (m-30) cc_final: 0.6658 (m-30) REVERT: B 494 ASP cc_start: 0.7685 (m-30) cc_final: 0.7308 (m-30) REVERT: B 528 GLN cc_start: 0.8033 (mt0) cc_final: 0.7768 (mt0) REVERT: B 562 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7063 (mm-30) REVERT: B 602 THR cc_start: 0.9165 (p) cc_final: 0.8746 (t) REVERT: B 620 LYS cc_start: 0.7718 (mttt) cc_final: 0.7184 (ptmt) REVERT: B 690 LYS cc_start: 0.7999 (mtpt) cc_final: 0.7543 (tptp) REVERT: B 702 ASN cc_start: 0.7667 (t0) cc_final: 0.7078 (t0) REVERT: B 717 GLU cc_start: 0.7966 (tt0) cc_final: 0.7759 (tt0) REVERT: B 725 GLN cc_start: 0.6594 (tm-30) cc_final: 0.6315 (tm-30) REVERT: B 744 THR cc_start: 0.8672 (m) cc_final: 0.8305 (m) REVERT: B 745 ASN cc_start: 0.7453 (m-40) cc_final: 0.7242 (m110) REVERT: B 760 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6983 (tp30) REVERT: B 761 TYR cc_start: 0.7547 (t80) cc_final: 0.7309 (t80) REVERT: B 784 PHE cc_start: 0.7605 (m-80) cc_final: 0.6980 (m-10) REVERT: B 799 TYR cc_start: 0.7947 (t80) cc_final: 0.7650 (t80) REVERT: B 803 GLU cc_start: 0.6814 (tp30) cc_final: 0.6561 (mm-30) REVERT: B 824 LEU cc_start: 0.8421 (mt) cc_final: 0.7903 (mp) REVERT: B 848 TYR cc_start: 0.8341 (t80) cc_final: 0.7750 (t80) REVERT: B 852 LYS cc_start: 0.8339 (mmtt) cc_final: 0.7847 (mmtt) REVERT: B 876 LYS cc_start: 0.6844 (mtmt) cc_final: 0.6587 (mtmm) REVERT: B 894 ARG cc_start: 0.7915 (ptt180) cc_final: 0.7675 (ptt180) REVERT: D 332 MET cc_start: 0.7633 (mmt) cc_final: 0.7079 (tpp) REVERT: D 363 GLU cc_start: 0.7274 (tp30) cc_final: 0.6967 (mm-30) REVERT: D 365 LYS cc_start: 0.7022 (mtpt) cc_final: 0.5770 (pttp) REVERT: D 384 PHE cc_start: 0.7778 (t80) cc_final: 0.7505 (t80) REVERT: D 410 GLU cc_start: 0.7133 (tt0) cc_final: 0.6785 (mm-30) REVERT: D 415 LYS cc_start: 0.7018 (mttt) cc_final: 0.6254 (ptpt) REVERT: D 416 LEU cc_start: 0.7987 (mt) cc_final: 0.7712 (mt) REVERT: D 419 GLN cc_start: 0.7328 (mt0) cc_final: 0.7053 (mt0) REVERT: D 422 TYR cc_start: 0.6117 (p90) cc_final: 0.5826 (p90) REVERT: D 445 THR cc_start: 0.7674 (m) cc_final: 0.7294 (t) REVERT: D 446 ASP cc_start: 0.6912 (m-30) cc_final: 0.6614 (m-30) REVERT: D 548 ASN cc_start: 0.7433 (m-40) cc_final: 0.6878 (m-40) REVERT: D 562 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7036 (mm-30) REVERT: D 602 THR cc_start: 0.9114 (p) cc_final: 0.8721 (t) REVERT: D 620 LYS cc_start: 0.7562 (mttt) cc_final: 0.7183 (ptmt) REVERT: D 648 PHE cc_start: 0.7195 (t80) cc_final: 0.6984 (t80) REVERT: D 690 LYS cc_start: 0.7936 (mtpt) cc_final: 0.7412 (tptp) REVERT: D 696 MET cc_start: 0.6856 (mtm) cc_final: 0.6413 (mtp) REVERT: D 702 ASN cc_start: 0.7709 (t0) cc_final: 0.7509 (t0) REVERT: D 725 GLN cc_start: 0.6614 (tm-30) cc_final: 0.6339 (tm-30) REVERT: D 744 THR cc_start: 0.8691 (m) cc_final: 0.8324 (m) REVERT: D 745 ASN cc_start: 0.7310 (m-40) cc_final: 0.7082 (m110) REVERT: D 761 TYR cc_start: 0.7556 (t80) cc_final: 0.7331 (t80) REVERT: D 763 GLN cc_start: 0.7905 (mt0) cc_final: 0.7623 (mt0) REVERT: D 784 PHE cc_start: 0.7617 (m-80) cc_final: 0.6534 (m-10) REVERT: D 804 GLU cc_start: 0.7095 (tt0) cc_final: 0.6819 (tt0) REVERT: D 824 LEU cc_start: 0.8420 (mt) cc_final: 0.8121 (mm) REVERT: D 848 TYR cc_start: 0.8346 (t80) cc_final: 0.7852 (t80) REVERT: D 852 LYS cc_start: 0.8344 (mmtt) cc_final: 0.7952 (mmtt) REVERT: D 876 LYS cc_start: 0.6736 (mtmt) cc_final: 0.6295 (mtmm) REVERT: D 883 ASP cc_start: 0.7525 (m-30) cc_final: 0.7248 (m-30) REVERT: D 894 ARG cc_start: 0.7913 (ptt180) cc_final: 0.7679 (ptt180) outliers start: 31 outliers final: 12 residues processed: 666 average time/residue: 0.1432 time to fit residues: 140.4038 Evaluate side-chains 445 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 431 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 751 HIS Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 751 HIS Chi-restraints excluded: chain B residue 434 GLU Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 751 HIS Chi-restraints excluded: chain D residue 668 LYS Chi-restraints excluded: chain D residue 688 LEU Chi-restraints excluded: chain D residue 703 LYS Chi-restraints excluded: chain D residue 751 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 457 GLN A 474 ASN A 745 ASN A 750 ASN A 844 ASN A 864 ASN A 877 GLN C 457 GLN C 474 ASN C 745 ASN C 750 ASN C 844 ASN B 457 GLN B 474 ASN B 745 ASN B 750 ASN B 844 ASN D 337 ASN D 457 GLN D 474 ASN D 745 ASN D 844 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.145329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.118845 restraints weight = 23779.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.122292 restraints weight = 13364.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.124567 restraints weight = 9276.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.125888 restraints weight = 7394.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.126966 restraints weight = 6454.968| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3384 r_free = 0.3384 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3384 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18328 Z= 0.151 Angle : 0.594 7.785 24788 Z= 0.311 Chirality : 0.040 0.182 2820 Planarity : 0.003 0.029 3212 Dihedral : 6.754 75.187 2536 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.37 % Favored : 93.54 % Rotamer: Outliers : 2.23 % Allowed : 12.37 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.93 (0.17), residues: 2308 helix: 0.44 (0.15), residues: 1008 sheet: -3.06 (0.23), residues: 408 loop : -2.36 (0.18), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 781 TYR 0.018 0.002 TYR B 408 PHE 0.017 0.002 PHE B 872 TRP 0.014 0.001 TRP C 573 HIS 0.003 0.001 HIS A 797 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (18320) covalent geometry : angle 0.59444 / 0.31 (24788) hydrogen bonds : bond 0.03770 / 2.50 ( 738) hydrogen bonds : angle 4.88775 / 3.47 ( 2199) Misc. bond : bond 0.00072 / 0.03 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 462 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 385 ARG cc_start: 0.7302 (ptm160) cc_final: 0.6330 (mpp80) REVERT: A 414 ASN cc_start: 0.6297 (t0) cc_final: 0.5983 (t0) REVERT: A 415 LYS cc_start: 0.6703 (mttt) cc_final: 0.6239 (ptpt) REVERT: A 487 ARG cc_start: 0.6676 (tpt170) cc_final: 0.6393 (tpt-90) REVERT: A 562 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7005 (mt-10) REVERT: A 607 LEU cc_start: 0.8093 (mt) cc_final: 0.7804 (mt) REVERT: A 620 LYS cc_start: 0.7590 (mttt) cc_final: 0.7203 (pptt) REVERT: A 639 ASP cc_start: 0.6744 (m-30) cc_final: 0.6517 (m-30) REVERT: A 666 ASN cc_start: 0.7081 (p0) cc_final: 0.6793 (p0) REVERT: A 690 LYS cc_start: 0.7908 (mtpt) cc_final: 0.7658 (tttm) REVERT: A 702 ASN cc_start: 0.7791 (t0) cc_final: 0.7357 (t0) REVERT: A 712 ARG cc_start: 0.8126 (mmm-85) cc_final: 0.7646 (mtm180) REVERT: A 784 PHE cc_start: 0.7465 (m-80) cc_final: 0.6929 (m-10) REVERT: A 830 THR cc_start: 0.6185 (t) cc_final: 0.5723 (t) REVERT: A 852 LYS cc_start: 0.8260 (mmtt) cc_final: 0.7995 (mmtt) REVERT: C 332 MET cc_start: 0.7758 (mmt) cc_final: 0.7557 (mmm) REVERT: C 376 GLU cc_start: 0.6196 (mm-30) cc_final: 0.5981 (tp30) REVERT: C 385 ARG cc_start: 0.7303 (ptm160) cc_final: 0.6333 (mpp80) REVERT: C 415 LYS cc_start: 0.6897 (mttt) cc_final: 0.6615 (ttmt) REVERT: C 434 GLU cc_start: 0.6183 (OUTLIER) cc_final: 0.5638 (pt0) REVERT: C 562 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6965 (mt-10) REVERT: C 607 LEU cc_start: 0.8059 (mt) cc_final: 0.7818 (mt) REVERT: C 620 LYS cc_start: 0.7638 (mttt) cc_final: 0.7262 (pptt) REVERT: C 648 PHE cc_start: 0.7559 (t80) cc_final: 0.7160 (t80) REVERT: C 664 LEU cc_start: 0.4331 (OUTLIER) cc_final: 0.3870 (pp) REVERT: C 690 LYS cc_start: 0.7878 (mtpt) cc_final: 0.7622 (tttm) REVERT: C 702 ASN cc_start: 0.7915 (t0) cc_final: 0.7420 (t0) REVERT: C 703 LYS cc_start: 0.8057 (pttp) cc_final: 0.7833 (pttm) REVERT: C 725 GLN cc_start: 0.6114 (tm-30) cc_final: 0.5661 (tm-30) REVERT: C 784 PHE cc_start: 0.7601 (m-80) cc_final: 0.6958 (m-10) REVERT: C 852 LYS cc_start: 0.8258 (mmtt) cc_final: 0.8006 (mmtt) REVERT: B 365 LYS cc_start: 0.7076 (mtpt) cc_final: 0.6318 (pttp) REVERT: B 385 ARG cc_start: 0.7301 (ptm160) cc_final: 0.6356 (mpp80) REVERT: B 415 LYS cc_start: 0.6738 (mttt) cc_final: 0.6512 (mttt) REVERT: B 434 GLU cc_start: 0.6201 (OUTLIER) cc_final: 0.5668 (pt0) REVERT: B 562 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6979 (mt-10) REVERT: B 607 LEU cc_start: 0.8152 (mt) cc_final: 0.7912 (mt) REVERT: B 620 LYS cc_start: 0.7700 (mttt) cc_final: 0.7284 (pptt) REVERT: B 690 LYS cc_start: 0.7866 (mtpt) cc_final: 0.7552 (tttm) REVERT: B 702 ASN cc_start: 0.7924 (t0) cc_final: 0.7437 (t0) REVERT: B 703 LYS cc_start: 0.8072 (pttp) cc_final: 0.7816 (pttm) REVERT: B 725 GLN cc_start: 0.6115 (tm-30) cc_final: 0.5530 (tm-30) REVERT: B 784 PHE cc_start: 0.7541 (m-10) cc_final: 0.7034 (m-10) REVERT: B 799 TYR cc_start: 0.8179 (t80) cc_final: 0.7971 (t80) REVERT: B 830 THR cc_start: 0.6291 (t) cc_final: 0.5871 (t) REVERT: B 852 LYS cc_start: 0.8244 (mmtt) cc_final: 0.7988 (mmtt) REVERT: D 385 ARG cc_start: 0.7329 (ptm160) cc_final: 0.6371 (mpp80) REVERT: D 415 LYS cc_start: 0.6735 (mttt) cc_final: 0.6264 (ptpt) REVERT: D 487 ARG cc_start: 0.6688 (tpt170) cc_final: 0.6404 (tpt-90) REVERT: D 562 GLU cc_start: 0.7340 (mt-10) cc_final: 0.7002 (mt-10) REVERT: D 607 LEU cc_start: 0.8156 (mt) cc_final: 0.7852 (mt) REVERT: D 620 LYS cc_start: 0.7596 (mttt) cc_final: 0.7218 (pptt) REVERT: D 690 LYS cc_start: 0.7888 (mtpt) cc_final: 0.7638 (tttm) REVERT: D 702 ASN cc_start: 0.7588 (t0) cc_final: 0.7266 (t0) REVERT: D 725 GLN cc_start: 0.6212 (tm-30) cc_final: 0.5733 (tm-30) REVERT: D 784 PHE cc_start: 0.7380 (m-80) cc_final: 0.6784 (m-10) REVERT: D 830 THR cc_start: 0.6141 (t) cc_final: 0.5625 (t) REVERT: D 852 LYS cc_start: 0.8261 (mmtt) cc_final: 0.8041 (mmtt) outliers start: 43 outliers final: 17 residues processed: 487 average time/residue: 0.1310 time to fit residues: 97.4928 Evaluate side-chains 375 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 355 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 751 HIS Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 751 HIS Chi-restraints excluded: chain B residue 434 GLU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 751 HIS Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 668 LYS Chi-restraints excluded: chain D residue 688 LEU Chi-restraints excluded: chain D residue 703 LYS Chi-restraints excluded: chain D residue 751 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 111 optimal weight: 1.9990 chunk 196 optimal weight: 0.0270 chunk 205 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 214 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 199 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 overall best weight: 2.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 745 ASN A 749 GLN C 745 ASN C 749 GLN B 337 ASN B 745 ASN B 749 GLN D 745 ASN D 749 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.141727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.115284 restraints weight = 23843.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.118668 restraints weight = 13507.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.120900 restraints weight = 9389.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.122296 restraints weight = 7494.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.122940 restraints weight = 6512.305| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 18328 Z= 0.168 Angle : 0.574 8.221 24788 Z= 0.299 Chirality : 0.041 0.176 2820 Planarity : 0.004 0.033 3212 Dihedral : 6.289 77.197 2528 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.33 % Favored : 93.46 % Rotamer: Outliers : 4.21 % Allowed : 16.22 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.27 (0.17), residues: 2308 helix: 0.91 (0.16), residues: 1008 sheet: -2.64 (0.26), residues: 364 loop : -2.02 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 491 TYR 0.012 0.002 TYR C 799 PHE 0.020 0.002 PHE B 384 TRP 0.013 0.001 TRP D 573 HIS 0.005 0.001 HIS C 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (18320) covalent geometry : angle 0.57430 / 0.30 (24788) hydrogen bonds : bond 0.03596 / 2.41 ( 738) hydrogen bonds : angle 4.68641 / 3.32 ( 2199) Misc. bond : bond 0.00082 / 0.04 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 387 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 365 LYS cc_start: 0.7386 (mmtp) cc_final: 0.7108 (tppt) REVERT: A 415 LYS cc_start: 0.6933 (mttt) cc_final: 0.6725 (ttmt) REVERT: A 562 GLU cc_start: 0.7357 (mt-10) cc_final: 0.7127 (mt-10) REVERT: A 607 LEU cc_start: 0.8128 (mt) cc_final: 0.7773 (mt) REVERT: A 620 LYS cc_start: 0.8001 (mttt) cc_final: 0.7516 (pptt) REVERT: A 639 ASP cc_start: 0.7011 (m-30) cc_final: 0.6701 (m-30) REVERT: A 666 ASN cc_start: 0.7027 (p0) cc_final: 0.6596 (p0) REVERT: A 690 LYS cc_start: 0.7811 (mtpt) cc_final: 0.7510 (tttm) REVERT: A 702 ASN cc_start: 0.7849 (t0) cc_final: 0.7279 (t0) REVERT: A 712 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7674 (mtm180) REVERT: A 761 TYR cc_start: 0.8073 (t80) cc_final: 0.7672 (t80) REVERT: A 784 PHE cc_start: 0.7598 (m-80) cc_final: 0.7013 (m-10) REVERT: A 806 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.7616 (m-10) REVERT: C 332 MET cc_start: 0.7873 (mmt) cc_final: 0.7501 (mmm) REVERT: C 365 LYS cc_start: 0.7107 (mmtm) cc_final: 0.6731 (tppt) REVERT: C 376 GLU cc_start: 0.6456 (mm-30) cc_final: 0.6102 (mm-30) REVERT: C 562 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7073 (mt-10) REVERT: C 607 LEU cc_start: 0.8085 (mt) cc_final: 0.7749 (mt) REVERT: C 620 LYS cc_start: 0.8109 (mttt) cc_final: 0.7601 (pptt) REVERT: C 648 PHE cc_start: 0.7513 (t80) cc_final: 0.7227 (t80) REVERT: C 690 LYS cc_start: 0.7861 (mtpt) cc_final: 0.7541 (tttm) REVERT: C 702 ASN cc_start: 0.7978 (t0) cc_final: 0.7387 (t0) REVERT: B 562 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7058 (mt-10) REVERT: B 607 LEU cc_start: 0.8104 (mt) cc_final: 0.7749 (mt) REVERT: B 620 LYS cc_start: 0.8048 (mttt) cc_final: 0.7405 (pptt) REVERT: B 690 LYS cc_start: 0.7828 (mtpt) cc_final: 0.7562 (tttm) REVERT: B 702 ASN cc_start: 0.7988 (t0) cc_final: 0.7416 (t0) REVERT: B 757 LYS cc_start: 0.8174 (ptmm) cc_final: 0.7970 (ptmm) REVERT: B 784 PHE cc_start: 0.7645 (m-10) cc_final: 0.7099 (m-10) REVERT: B 882 LYS cc_start: 0.8273 (mmtt) cc_final: 0.7810 (mmtm) REVERT: D 365 LYS cc_start: 0.7367 (mmtp) cc_final: 0.6926 (tppt) REVERT: D 415 LYS cc_start: 0.6972 (mttt) cc_final: 0.6711 (mttt) REVERT: D 562 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7089 (mt-10) REVERT: D 620 LYS cc_start: 0.7993 (mttt) cc_final: 0.7520 (pptt) REVERT: D 648 PHE cc_start: 0.7750 (t80) cc_final: 0.7448 (t80) REVERT: D 690 LYS cc_start: 0.7939 (mtpt) cc_final: 0.7564 (tttm) REVERT: D 702 ASN cc_start: 0.7808 (t0) cc_final: 0.7249 (t0) REVERT: D 761 TYR cc_start: 0.8097 (t80) cc_final: 0.7653 (t80) REVERT: D 784 PHE cc_start: 0.7740 (m-80) cc_final: 0.7113 (m-80) REVERT: D 882 LYS cc_start: 0.8210 (mmtt) cc_final: 0.7746 (mmtm) outliers start: 81 outliers final: 40 residues processed: 432 average time/residue: 0.1400 time to fit residues: 92.6390 Evaluate side-chains 376 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 334 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 751 HIS Chi-restraints excluded: chain A residue 806 PHE Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 806 PHE Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 806 PHE Chi-restraints excluded: chain B residue 810 MET Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 537 CYS Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 682 ILE Chi-restraints excluded: chain D residue 688 LEU Chi-restraints excluded: chain D residue 751 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 109 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 108 optimal weight: 0.4980 chunk 43 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 219 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 746 HIS C 746 HIS ** C 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 746 HIS ** B 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 ASN D 746 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.136357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.109831 restraints weight = 24160.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.113085 restraints weight = 13853.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.115277 restraints weight = 9740.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.116470 restraints weight = 7802.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.117533 restraints weight = 6851.072| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3320 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 18328 Z= 0.196 Angle : 0.602 13.348 24788 Z= 0.310 Chirality : 0.042 0.196 2820 Planarity : 0.004 0.042 3212 Dihedral : 5.621 46.122 2506 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.11 % Favored : 93.67 % Rotamer: Outliers : 4.73 % Allowed : 16.79 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.24 (0.17), residues: 2308 helix: 0.86 (0.16), residues: 1008 sheet: -2.48 (0.27), residues: 364 loop : -1.98 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 491 TYR 0.013 0.002 TYR B 761 PHE 0.027 0.002 PHE D 872 TRP 0.012 0.001 TRP A 573 HIS 0.003 0.001 HIS A 797 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 (18320) covalent geometry : angle 0.60248 / 0.31 (24788) hydrogen bonds : bond 0.03381 / 2.26 ( 738) hydrogen bonds : angle 4.76809 / 3.38 ( 2199) Misc. bond : bond 0.00093 / 0.04 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 339 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 365 LYS cc_start: 0.7415 (mmtp) cc_final: 0.7024 (tppt) REVERT: A 366 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7566 (mm-30) REVERT: A 385 ARG cc_start: 0.7358 (ptm160) cc_final: 0.6812 (mmm160) REVERT: A 415 LYS cc_start: 0.6804 (mttt) cc_final: 0.6408 (ptpt) REVERT: A 490 TYR cc_start: 0.7164 (t80) cc_final: 0.6693 (t80) REVERT: A 607 LEU cc_start: 0.8202 (mt) cc_final: 0.7818 (mt) REVERT: A 666 ASN cc_start: 0.7146 (p0) cc_final: 0.6694 (p0) REVERT: A 702 ASN cc_start: 0.8000 (t0) cc_final: 0.7515 (t0) REVERT: A 712 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7730 (mtm180) REVERT: A 761 TYR cc_start: 0.8019 (t80) cc_final: 0.7767 (t80) REVERT: A 806 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7578 (m-10) REVERT: C 332 MET cc_start: 0.7949 (mmt) cc_final: 0.7626 (mmm) REVERT: C 365 LYS cc_start: 0.7359 (mmtm) cc_final: 0.6945 (tppt) REVERT: C 366 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7946 (mm-30) REVERT: C 385 ARG cc_start: 0.7513 (ptm160) cc_final: 0.6784 (mmm160) REVERT: C 490 TYR cc_start: 0.7144 (t80) cc_final: 0.6703 (t80) REVERT: C 583 LYS cc_start: 0.8466 (mmmt) cc_final: 0.8252 (mmmt) REVERT: C 602 THR cc_start: 0.8970 (p) cc_final: 0.8436 (t) REVERT: C 702 ASN cc_start: 0.8031 (t0) cc_final: 0.7346 (t0) REVERT: C 768 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.5829 (tp30) REVERT: C 784 PHE cc_start: 0.7562 (m-80) cc_final: 0.7095 (m-10) REVERT: B 366 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7902 (mm-30) REVERT: B 385 ARG cc_start: 0.7262 (ptm160) cc_final: 0.6794 (mmm160) REVERT: B 490 TYR cc_start: 0.7126 (t80) cc_final: 0.6796 (t80) REVERT: B 602 THR cc_start: 0.8844 (p) cc_final: 0.8291 (t) REVERT: B 607 LEU cc_start: 0.8109 (mt) cc_final: 0.7654 (mt) REVERT: B 702 ASN cc_start: 0.8038 (t0) cc_final: 0.7368 (t0) REVERT: B 784 PHE cc_start: 0.7868 (m-10) cc_final: 0.7253 (m-10) REVERT: D 365 LYS cc_start: 0.7431 (mmtp) cc_final: 0.6978 (tppt) REVERT: D 385 ARG cc_start: 0.7327 (ptm160) cc_final: 0.6779 (mmm160) REVERT: D 415 LYS cc_start: 0.6780 (mttt) cc_final: 0.6351 (ptpt) REVERT: D 490 TYR cc_start: 0.7180 (t80) cc_final: 0.6709 (t80) REVERT: D 690 LYS cc_start: 0.7793 (mtpt) cc_final: 0.7583 (tttm) REVERT: D 697 SER cc_start: 0.7449 (OUTLIER) cc_final: 0.7084 (p) REVERT: D 702 ASN cc_start: 0.7851 (t0) cc_final: 0.7444 (t0) REVERT: D 761 TYR cc_start: 0.8068 (t80) cc_final: 0.7851 (t80) REVERT: D 806 PHE cc_start: 0.7887 (OUTLIER) cc_final: 0.7451 (m-10) outliers start: 91 outliers final: 55 residues processed: 387 average time/residue: 0.1338 time to fit residues: 80.5674 Evaluate side-chains 380 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 320 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 751 HIS Chi-restraints excluded: chain A residue 806 PHE Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain C residue 806 PHE Chi-restraints excluded: chain C residue 810 MET Chi-restraints excluded: chain C residue 836 SER Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 806 PHE Chi-restraints excluded: chain B residue 810 MET Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 537 CYS Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 682 ILE Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 806 PHE Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 820 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 149 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 192 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 221 optimal weight: 0.8980 chunk 210 optimal weight: 0.8980 chunk 217 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 chunk 204 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 HIS ** B 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.144976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.119450 restraints weight = 23656.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.122913 restraints weight = 13100.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.125252 restraints weight = 9009.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.126631 restraints weight = 7097.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.127498 restraints weight = 6144.994| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18328 Z= 0.104 Angle : 0.522 12.542 24788 Z= 0.267 Chirality : 0.039 0.155 2820 Planarity : 0.003 0.039 3212 Dihedral : 4.878 40.016 2502 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.50 % Favored : 94.28 % Rotamer: Outliers : 2.60 % Allowed : 19.54 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.18), residues: 2308 helix: 1.20 (0.16), residues: 1008 sheet: -1.96 (0.29), residues: 344 loop : -1.90 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 359 TYR 0.011 0.001 TYR C 408 PHE 0.026 0.001 PHE A 872 TRP 0.005 0.001 TRP C 582 HIS 0.003 0.001 HIS B 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (18320) covalent geometry : angle 0.52169 / 0.27 (24788) hydrogen bonds : bond 0.02710 / 1.82 ( 738) hydrogen bonds : angle 4.40510 / 3.14 ( 2199) Misc. bond : bond 0.00035 / 0.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 369 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 365 LYS cc_start: 0.7405 (mmtp) cc_final: 0.7044 (tppt) REVERT: A 366 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7512 (mm-30) REVERT: A 376 GLU cc_start: 0.6091 (tp30) cc_final: 0.5837 (tp30) REVERT: A 385 ARG cc_start: 0.7324 (ptm160) cc_final: 0.6665 (mmm160) REVERT: A 415 LYS cc_start: 0.6784 (mttt) cc_final: 0.6497 (mttt) REVERT: A 607 LEU cc_start: 0.7891 (mt) cc_final: 0.7545 (mt) REVERT: A 666 ASN cc_start: 0.7183 (p0) cc_final: 0.6772 (p0) REVERT: A 702 ASN cc_start: 0.7742 (t0) cc_final: 0.7377 (t0) REVERT: A 703 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7533 (pttm) REVERT: A 712 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7487 (mtm180) REVERT: A 761 TYR cc_start: 0.7993 (t80) cc_final: 0.7696 (t80) REVERT: A 806 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.7453 (m-10) REVERT: A 845 LYS cc_start: 0.8085 (mmmt) cc_final: 0.7750 (mmtm) REVERT: A 862 THR cc_start: 0.8860 (t) cc_final: 0.8660 (m) REVERT: C 332 MET cc_start: 0.7922 (mmt) cc_final: 0.7695 (mmm) REVERT: C 365 LYS cc_start: 0.7296 (mmtm) cc_final: 0.7041 (tptt) REVERT: C 366 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7879 (mm-30) REVERT: C 385 ARG cc_start: 0.7319 (ptm160) cc_final: 0.6843 (mmm160) REVERT: C 407 ASN cc_start: 0.7050 (m110) cc_final: 0.6847 (m-40) REVERT: C 415 LYS cc_start: 0.6741 (mttt) cc_final: 0.6520 (mttt) REVERT: C 507 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7335 (mm-30) REVERT: C 607 LEU cc_start: 0.7842 (mt) cc_final: 0.7496 (mt) REVERT: C 702 ASN cc_start: 0.7995 (t0) cc_final: 0.7361 (t0) REVERT: C 752 GLU cc_start: 0.6639 (mt-10) cc_final: 0.5947 (mt-10) REVERT: C 784 PHE cc_start: 0.7589 (m-80) cc_final: 0.6929 (m-80) REVERT: C 845 LYS cc_start: 0.8210 (mmmt) cc_final: 0.7797 (mmtm) REVERT: C 862 THR cc_start: 0.8910 (t) cc_final: 0.8690 (m) REVERT: B 332 MET cc_start: 0.7886 (mmm) cc_final: 0.7625 (mmm) REVERT: B 365 LYS cc_start: 0.7353 (mmtm) cc_final: 0.6809 (tppt) REVERT: B 366 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7875 (mm-30) REVERT: B 385 ARG cc_start: 0.7350 (ptm160) cc_final: 0.6842 (mmm160) REVERT: B 607 LEU cc_start: 0.7883 (mt) cc_final: 0.7521 (mt) REVERT: B 639 ASP cc_start: 0.6919 (m-30) cc_final: 0.6707 (m-30) REVERT: B 702 ASN cc_start: 0.7816 (t0) cc_final: 0.7249 (t0) REVERT: B 757 LYS cc_start: 0.7983 (ptmm) cc_final: 0.7767 (ptmm) REVERT: B 784 PHE cc_start: 0.7725 (m-80) cc_final: 0.7203 (m-10) REVERT: B 845 LYS cc_start: 0.8182 (mmmt) cc_final: 0.7786 (mmtm) REVERT: D 365 LYS cc_start: 0.7323 (mmtp) cc_final: 0.6984 (tptt) REVERT: D 376 GLU cc_start: 0.6117 (tp30) cc_final: 0.5874 (tp30) REVERT: D 385 ARG cc_start: 0.7400 (ptm160) cc_final: 0.6703 (mmm160) REVERT: D 415 LYS cc_start: 0.6824 (mttt) cc_final: 0.6542 (mttt) REVERT: D 702 ASN cc_start: 0.7787 (t0) cc_final: 0.7500 (t0) REVERT: D 767 LYS cc_start: 0.7422 (tmtt) cc_final: 0.7183 (ttpp) REVERT: D 803 GLU cc_start: 0.7475 (mm-30) cc_final: 0.6627 (mm-30) REVERT: D 806 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7486 (m-10) REVERT: D 845 LYS cc_start: 0.8125 (mmmt) cc_final: 0.7725 (mmtm) REVERT: D 862 THR cc_start: 0.8863 (t) cc_final: 0.8506 (m) outliers start: 50 outliers final: 28 residues processed: 392 average time/residue: 0.1360 time to fit residues: 82.4538 Evaluate side-chains 372 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 340 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 806 PHE Chi-restraints excluded: chain C residue 474 ASN Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 537 CYS Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 688 LEU Chi-restraints excluded: chain D residue 806 PHE Chi-restraints excluded: chain D residue 857 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 26 optimal weight: 1.9990 chunk 205 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 84 optimal weight: 0.9990 chunk 223 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 522 HIS ** C 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 864 ASN D 522 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.141065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.115285 restraints weight = 23888.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.118585 restraints weight = 13511.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.120823 restraints weight = 9397.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.122071 restraints weight = 7474.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.123124 restraints weight = 6542.410| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3327 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3327 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18328 Z= 0.180 Angle : 0.582 11.529 24788 Z= 0.299 Chirality : 0.041 0.186 2820 Planarity : 0.004 0.036 3212 Dihedral : 5.148 37.847 2500 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.76 % Favored : 93.02 % Rotamer: Outliers : 4.42 % Allowed : 19.49 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.18), residues: 2308 helix: 0.99 (0.16), residues: 1008 sheet: -2.11 (0.30), residues: 320 loop : -1.73 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 491 TYR 0.011 0.002 TYR B 761 PHE 0.029 0.002 PHE D 872 TRP 0.017 0.001 TRP D 582 HIS 0.003 0.001 HIS D 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (18320) covalent geometry : angle 0.58169 / 0.30 (24788) hydrogen bonds : bond 0.03213 / 2.15 ( 738) hydrogen bonds : angle 4.71182 / 3.34 ( 2199) Misc. bond : bond 0.00089 / 0.04 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 348 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 365 LYS cc_start: 0.7446 (mmtp) cc_final: 0.7096 (tppt) REVERT: A 366 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7451 (mm-30) REVERT: A 385 ARG cc_start: 0.7505 (ptm160) cc_final: 0.6865 (mmm160) REVERT: A 415 LYS cc_start: 0.6872 (mttt) cc_final: 0.6440 (ptpt) REVERT: A 490 TYR cc_start: 0.7235 (t80) cc_final: 0.6852 (t80) REVERT: A 607 LEU cc_start: 0.8030 (mt) cc_final: 0.7635 (mt) REVERT: A 666 ASN cc_start: 0.7237 (p0) cc_final: 0.6871 (p0) REVERT: A 702 ASN cc_start: 0.7861 (t0) cc_final: 0.7359 (t0) REVERT: A 703 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7655 (pttm) REVERT: A 712 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7745 (mtm180) REVERT: A 761 TYR cc_start: 0.7986 (t80) cc_final: 0.7766 (t80) REVERT: A 803 GLU cc_start: 0.7410 (mm-30) cc_final: 0.6140 (mm-30) REVERT: A 806 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.7631 (m-10) REVERT: A 845 LYS cc_start: 0.8226 (mmmt) cc_final: 0.7779 (mmtm) REVERT: C 332 MET cc_start: 0.7953 (mmt) cc_final: 0.7698 (mmm) REVERT: C 365 LYS cc_start: 0.7434 (mmtm) cc_final: 0.7113 (tppt) REVERT: C 385 ARG cc_start: 0.7346 (ptm160) cc_final: 0.6803 (mmm160) REVERT: C 407 ASN cc_start: 0.7094 (m110) cc_final: 0.6890 (m-40) REVERT: C 490 TYR cc_start: 0.7187 (t80) cc_final: 0.6814 (t80) REVERT: C 607 LEU cc_start: 0.7862 (mt) cc_final: 0.7624 (mt) REVERT: C 702 ASN cc_start: 0.7936 (t0) cc_final: 0.7314 (t0) REVERT: C 752 GLU cc_start: 0.6691 (mt-10) cc_final: 0.5845 (mt-10) REVERT: C 768 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6134 (tp30) REVERT: C 784 PHE cc_start: 0.7594 (m-80) cc_final: 0.7300 (m-80) REVERT: C 803 GLU cc_start: 0.7297 (mm-30) cc_final: 0.7070 (mt-10) REVERT: C 845 LYS cc_start: 0.8196 (mmmt) cc_final: 0.7791 (mmtm) REVERT: B 365 LYS cc_start: 0.7352 (mmtm) cc_final: 0.6910 (tppt) REVERT: B 385 ARG cc_start: 0.7312 (ptm160) cc_final: 0.6814 (mmm160) REVERT: B 490 TYR cc_start: 0.7243 (t80) cc_final: 0.6871 (t80) REVERT: B 582 TRP cc_start: 0.8681 (m-10) cc_final: 0.8381 (m-10) REVERT: B 607 LEU cc_start: 0.8024 (mt) cc_final: 0.7612 (mt) REVERT: B 702 ASN cc_start: 0.7918 (t0) cc_final: 0.7341 (t0) REVERT: B 784 PHE cc_start: 0.7883 (m-80) cc_final: 0.7263 (m-10) REVERT: B 845 LYS cc_start: 0.8187 (mmmt) cc_final: 0.7792 (mmtm) REVERT: D 365 LYS cc_start: 0.7342 (mmtp) cc_final: 0.6997 (tptt) REVERT: D 366 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7850 (mp0) REVERT: D 385 ARG cc_start: 0.7425 (ptm160) cc_final: 0.6691 (mmm160) REVERT: D 415 LYS cc_start: 0.6858 (mttt) cc_final: 0.6432 (ptpt) REVERT: D 490 TYR cc_start: 0.7258 (t80) cc_final: 0.6870 (t80) REVERT: D 702 ASN cc_start: 0.7766 (t0) cc_final: 0.7085 (t0) REVERT: D 803 GLU cc_start: 0.7409 (mm-30) cc_final: 0.6644 (mm-30) REVERT: D 845 LYS cc_start: 0.8213 (mmmt) cc_final: 0.7833 (mmtm) outliers start: 85 outliers final: 62 residues processed: 387 average time/residue: 0.1365 time to fit residues: 81.9372 Evaluate side-chains 391 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 325 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 751 HIS Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 806 PHE Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 474 ASN Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain C residue 798 MET Chi-restraints excluded: chain C residue 810 MET Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 895 ILE Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain B residue 806 PHE Chi-restraints excluded: chain B residue 810 MET Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 537 CYS Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 682 ILE Chi-restraints excluded: chain D residue 688 LEU Chi-restraints excluded: chain D residue 751 HIS Chi-restraints excluded: chain D residue 798 MET Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 857 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 170 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 220 optimal weight: 0.8980 chunk 216 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.143747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.117948 restraints weight = 23998.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.121339 restraints weight = 13492.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.123308 restraints weight = 9355.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.124955 restraints weight = 7536.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.125664 restraints weight = 6481.362| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18328 Z= 0.125 Angle : 0.541 9.374 24788 Z= 0.277 Chirality : 0.040 0.161 2820 Planarity : 0.003 0.037 3212 Dihedral : 4.821 34.679 2500 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.59 % Favored : 94.24 % Rotamer: Outliers : 3.07 % Allowed : 21.57 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.18), residues: 2308 helix: 1.14 (0.16), residues: 1016 sheet: -1.84 (0.28), residues: 360 loop : -1.73 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 554 TYR 0.010 0.001 TYR B 761 PHE 0.028 0.001 PHE D 872 TRP 0.008 0.001 TRP D 582 HIS 0.003 0.001 HIS B 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (18320) covalent geometry : angle 0.54068 / 0.28 (24788) hydrogen bonds : bond 0.02785 / 1.88 ( 738) hydrogen bonds : angle 4.49389 / 3.19 ( 2199) Misc. bond : bond 0.00059 / 0.03 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 342 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 365 LYS cc_start: 0.7416 (mmtp) cc_final: 0.7032 (tppt) REVERT: A 366 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7377 (mm-30) REVERT: A 385 ARG cc_start: 0.7509 (ptm160) cc_final: 0.6729 (mmm160) REVERT: A 415 LYS cc_start: 0.6852 (mttt) cc_final: 0.6463 (mttt) REVERT: A 607 LEU cc_start: 0.7901 (mt) cc_final: 0.7558 (mt) REVERT: A 702 ASN cc_start: 0.7869 (t0) cc_final: 0.7380 (t0) REVERT: A 703 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7577 (pttm) REVERT: A 712 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7736 (mtm180) REVERT: A 761 TYR cc_start: 0.7939 (t80) cc_final: 0.7662 (t80) REVERT: A 806 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7650 (m-10) REVERT: A 845 LYS cc_start: 0.8139 (mmmt) cc_final: 0.7764 (mmtm) REVERT: A 862 THR cc_start: 0.8836 (t) cc_final: 0.8634 (m) REVERT: C 332 MET cc_start: 0.7918 (mmt) cc_final: 0.7697 (mmm) REVERT: C 365 LYS cc_start: 0.7341 (mmtm) cc_final: 0.7083 (tppt) REVERT: C 385 ARG cc_start: 0.7404 (ptm160) cc_final: 0.6909 (mmm160) REVERT: C 407 ASN cc_start: 0.7092 (m110) cc_final: 0.6868 (m-40) REVERT: C 415 LYS cc_start: 0.6840 (mttt) cc_final: 0.6476 (mttt) REVERT: C 607 LEU cc_start: 0.7745 (mt) cc_final: 0.7522 (mt) REVERT: C 702 ASN cc_start: 0.7800 (t0) cc_final: 0.7213 (t0) REVERT: C 752 GLU cc_start: 0.6672 (mt-10) cc_final: 0.5946 (mt-10) REVERT: C 768 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6027 (tp30) REVERT: C 784 PHE cc_start: 0.7571 (m-80) cc_final: 0.7345 (m-80) REVERT: C 845 LYS cc_start: 0.8145 (mmmt) cc_final: 0.7806 (mmtm) REVERT: B 332 MET cc_start: 0.8077 (mmm) cc_final: 0.7836 (mmm) REVERT: B 365 LYS cc_start: 0.7357 (mmtm) cc_final: 0.6996 (mmtm) REVERT: B 366 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7761 (mp0) REVERT: B 385 ARG cc_start: 0.7452 (ptm160) cc_final: 0.6698 (mmm160) REVERT: B 607 LEU cc_start: 0.7899 (mt) cc_final: 0.7531 (mt) REVERT: B 702 ASN cc_start: 0.7763 (t0) cc_final: 0.7170 (t0) REVERT: B 784 PHE cc_start: 0.7787 (m-80) cc_final: 0.7232 (m-10) REVERT: B 845 LYS cc_start: 0.8157 (mmmt) cc_final: 0.7810 (mmtm) REVERT: D 365 LYS cc_start: 0.7337 (mmtp) cc_final: 0.6983 (tppt) REVERT: D 366 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7842 (mp0) REVERT: D 385 ARG cc_start: 0.7542 (ptm160) cc_final: 0.6812 (mmm160) REVERT: D 415 LYS cc_start: 0.6847 (mttt) cc_final: 0.6469 (mttt) REVERT: D 474 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.7749 (p0) REVERT: D 582 TRP cc_start: 0.8498 (m-10) cc_final: 0.8212 (m-10) REVERT: D 696 MET cc_start: 0.6080 (OUTLIER) cc_final: 0.5758 (ttm) REVERT: D 702 ASN cc_start: 0.7764 (t0) cc_final: 0.7442 (t0) REVERT: D 767 LYS cc_start: 0.7649 (tmtt) cc_final: 0.7354 (ttpp) REVERT: D 803 GLU cc_start: 0.7522 (mm-30) cc_final: 0.6980 (mm-30) REVERT: D 845 LYS cc_start: 0.8068 (mmmt) cc_final: 0.7737 (mmtm) outliers start: 59 outliers final: 45 residues processed: 372 average time/residue: 0.1336 time to fit residues: 77.6726 Evaluate side-chains 381 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 330 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 806 PHE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 474 ASN Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain C residue 798 MET Chi-restraints excluded: chain C residue 810 MET Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 474 ASN Chi-restraints excluded: chain D residue 537 CYS Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 696 MET Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 798 MET Chi-restraints excluded: chain D residue 857 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 177 optimal weight: 3.9990 chunk 218 optimal weight: 7.9990 chunk 122 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 181 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 522 HIS ** C 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.138591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.112883 restraints weight = 24229.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.116028 restraints weight = 13770.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.118199 restraints weight = 9662.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.119520 restraints weight = 7719.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.120233 restraints weight = 6711.790| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 18328 Z= 0.257 Angle : 0.655 9.804 24788 Z= 0.337 Chirality : 0.043 0.194 2820 Planarity : 0.004 0.035 3212 Dihedral : 5.589 48.040 2500 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.54 % Favored : 92.29 % Rotamer: Outliers : 4.31 % Allowed : 20.37 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.11 (0.18), residues: 2308 helix: 0.72 (0.16), residues: 1008 sheet: -2.14 (0.29), residues: 320 loop : -1.77 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 491 TYR 0.013 0.002 TYR B 761 PHE 0.032 0.002 PHE A 872 TRP 0.019 0.002 TRP B 582 HIS 0.004 0.001 HIS D 797 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.26 (18320) covalent geometry : angle 0.65534 / 0.34 (24788) hydrogen bonds : bond 0.03696 / 2.47 ( 738) hydrogen bonds : angle 4.99697 / 3.53 ( 2199) Misc. bond : bond 0.00125 / 0.06 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 345 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 365 LYS cc_start: 0.7413 (mmtp) cc_final: 0.7078 (tppt) REVERT: A 385 ARG cc_start: 0.7558 (ptm160) cc_final: 0.6742 (mmm160) REVERT: A 490 TYR cc_start: 0.7287 (t80) cc_final: 0.7053 (t80) REVERT: A 602 THR cc_start: 0.8798 (p) cc_final: 0.8517 (p) REVERT: A 702 ASN cc_start: 0.7891 (t0) cc_final: 0.7434 (t0) REVERT: A 712 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7793 (mtm180) REVERT: A 761 TYR cc_start: 0.8006 (t80) cc_final: 0.7776 (t80) REVERT: A 806 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7513 (m-10) REVERT: A 845 LYS cc_start: 0.8289 (mmmt) cc_final: 0.7930 (mmtm) REVERT: C 332 MET cc_start: 0.7981 (mmt) cc_final: 0.7526 (mmm) REVERT: C 365 LYS cc_start: 0.7433 (mmtm) cc_final: 0.7189 (tptt) REVERT: C 366 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7837 (mp0) REVERT: C 385 ARG cc_start: 0.7402 (ptm160) cc_final: 0.6734 (mmm160) REVERT: C 407 ASN cc_start: 0.7043 (m110) cc_final: 0.6790 (m-40) REVERT: C 490 TYR cc_start: 0.7223 (t80) cc_final: 0.6986 (t80) REVERT: C 602 THR cc_start: 0.8854 (p) cc_final: 0.8605 (p) REVERT: C 702 ASN cc_start: 0.7782 (t0) cc_final: 0.7172 (t0) REVERT: C 768 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.5790 (tp30) REVERT: C 784 PHE cc_start: 0.7516 (m-80) cc_final: 0.7165 (m-10) REVERT: C 806 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.7362 (m-80) REVERT: B 365 LYS cc_start: 0.7401 (mmtm) cc_final: 0.7024 (mmtm) REVERT: B 366 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7864 (mp0) REVERT: B 385 ARG cc_start: 0.7431 (ptm160) cc_final: 0.6730 (mmm160) REVERT: B 490 TYR cc_start: 0.7305 (t80) cc_final: 0.7054 (t80) REVERT: B 602 THR cc_start: 0.8810 (p) cc_final: 0.8535 (p) REVERT: B 702 ASN cc_start: 0.8036 (t0) cc_final: 0.7413 (t0) REVERT: B 784 PHE cc_start: 0.7950 (m-80) cc_final: 0.7191 (m-10) REVERT: B 803 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7279 (mt-10) REVERT: B 845 LYS cc_start: 0.8233 (mmmt) cc_final: 0.7888 (mmtm) REVERT: D 365 LYS cc_start: 0.7385 (mmtp) cc_final: 0.7065 (tppt) REVERT: D 385 ARG cc_start: 0.7492 (ptm160) cc_final: 0.6757 (mmm160) REVERT: D 490 TYR cc_start: 0.7361 (t80) cc_final: 0.6967 (t80) REVERT: D 602 THR cc_start: 0.8776 (p) cc_final: 0.8498 (p) REVERT: D 702 ASN cc_start: 0.7853 (t0) cc_final: 0.7309 (t0) REVERT: D 803 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6629 (mm-30) outliers start: 83 outliers final: 67 residues processed: 386 average time/residue: 0.1333 time to fit residues: 80.2722 Evaluate side-chains 395 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 324 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 806 PHE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain C residue 798 MET Chi-restraints excluded: chain C residue 806 PHE Chi-restraints excluded: chain C residue 810 MET Chi-restraints excluded: chain C residue 820 VAL Chi-restraints excluded: chain C residue 836 SER Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain B residue 806 PHE Chi-restraints excluded: chain B residue 810 MET Chi-restraints excluded: chain B residue 820 VAL Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 878 SER Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 460 ASP Chi-restraints excluded: chain D residue 537 CYS Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 607 LEU Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 713 LEU Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 857 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 25 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 195 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 200 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.143898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.117873 restraints weight = 23862.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.121230 restraints weight = 13495.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.123463 restraints weight = 9398.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.124825 restraints weight = 7497.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.125723 restraints weight = 6522.427| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18328 Z= 0.118 Angle : 0.561 9.604 24788 Z= 0.285 Chirality : 0.040 0.158 2820 Planarity : 0.004 0.044 3212 Dihedral : 4.844 31.777 2500 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.50 % Favored : 94.32 % Rotamer: Outliers : 2.81 % Allowed : 22.66 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.18), residues: 2308 helix: 1.04 (0.16), residues: 1016 sheet: -1.77 (0.28), residues: 360 loop : -1.78 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 531 TYR 0.009 0.001 TYR A 761 PHE 0.029 0.001 PHE A 872 TRP 0.017 0.001 TRP A 582 HIS 0.003 0.001 HIS C 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (18320) covalent geometry : angle 0.56100 / 0.29 (24788) hydrogen bonds : bond 0.02780 / 1.87 ( 738) hydrogen bonds : angle 4.52427 / 3.21 ( 2199) Misc. bond : bond 0.00055 / 0.03 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 340 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.8125 (mmm) cc_final: 0.7915 (mmm) REVERT: A 365 LYS cc_start: 0.7403 (mmtp) cc_final: 0.7068 (tppt) REVERT: A 385 ARG cc_start: 0.7550 (ptm160) cc_final: 0.6746 (mmm160) REVERT: A 415 LYS cc_start: 0.6933 (mttt) cc_final: 0.6532 (mttt) REVERT: A 702 ASN cc_start: 0.7778 (t0) cc_final: 0.7347 (t0) REVERT: A 712 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7749 (mtm180) REVERT: A 806 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.7547 (m-10) REVERT: A 845 LYS cc_start: 0.8157 (mmmt) cc_final: 0.7766 (mmtm) REVERT: A 862 THR cc_start: 0.8851 (t) cc_final: 0.8643 (m) REVERT: C 332 MET cc_start: 0.8128 (mmt) cc_final: 0.7670 (mmm) REVERT: C 365 LYS cc_start: 0.7347 (mmtm) cc_final: 0.6983 (tppt) REVERT: C 366 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7679 (mp0) REVERT: C 385 ARG cc_start: 0.7503 (ptm160) cc_final: 0.6804 (mmm160) REVERT: C 407 ASN cc_start: 0.7043 (m110) cc_final: 0.6734 (m-40) REVERT: C 415 LYS cc_start: 0.6930 (mttt) cc_final: 0.6498 (mttt) REVERT: C 607 LEU cc_start: 0.7851 (mt) cc_final: 0.7552 (mt) REVERT: C 702 ASN cc_start: 0.7877 (t0) cc_final: 0.7313 (t0) REVERT: C 768 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.5918 (tp30) REVERT: C 845 LYS cc_start: 0.8157 (mmmt) cc_final: 0.7812 (mmtm) REVERT: B 365 LYS cc_start: 0.7362 (mmtm) cc_final: 0.6987 (mmtm) REVERT: B 366 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7724 (mp0) REVERT: B 385 ARG cc_start: 0.7448 (ptm160) cc_final: 0.6737 (mmm160) REVERT: B 702 ASN cc_start: 0.7870 (t0) cc_final: 0.7363 (t0) REVERT: B 784 PHE cc_start: 0.7876 (m-80) cc_final: 0.7307 (m-10) REVERT: D 365 LYS cc_start: 0.7215 (mmtp) cc_final: 0.6994 (tppt) REVERT: D 385 ARG cc_start: 0.7483 (ptm160) cc_final: 0.6768 (mmm160) REVERT: D 415 LYS cc_start: 0.6900 (mttt) cc_final: 0.6476 (mttt) REVERT: D 602 THR cc_start: 0.8690 (p) cc_final: 0.8408 (p) REVERT: D 702 ASN cc_start: 0.7682 (t0) cc_final: 0.7339 (t0) REVERT: D 767 LYS cc_start: 0.7713 (tmtt) cc_final: 0.7399 (ttpp) REVERT: D 803 GLU cc_start: 0.7324 (mm-30) cc_final: 0.7085 (mm-30) REVERT: D 845 LYS cc_start: 0.8090 (mmmt) cc_final: 0.7757 (mmtm) REVERT: D 862 THR cc_start: 0.8948 (t) cc_final: 0.8684 (m) outliers start: 54 outliers final: 44 residues processed: 368 average time/residue: 0.1304 time to fit residues: 75.2435 Evaluate side-chains 369 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 322 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 806 PHE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 474 ASN Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain C residue 798 MET Chi-restraints excluded: chain C residue 836 SER Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 537 CYS Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 607 LEU Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain D residue 798 MET Chi-restraints excluded: chain D residue 857 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 98 optimal weight: 0.9990 chunk 141 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 0.0040 chunk 153 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 414 ASN ** C 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.145978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.120098 restraints weight = 23877.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.123516 restraints weight = 13347.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.125739 restraints weight = 9243.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.127026 restraints weight = 7388.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.128016 restraints weight = 6464.960| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18328 Z= 0.105 Angle : 0.555 10.554 24788 Z= 0.281 Chirality : 0.040 0.164 2820 Planarity : 0.003 0.037 3212 Dihedral : 4.502 28.092 2500 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.42 % Favored : 94.41 % Rotamer: Outliers : 2.34 % Allowed : 22.92 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.18), residues: 2308 helix: 1.22 (0.16), residues: 1016 sheet: -1.93 (0.29), residues: 320 loop : -1.58 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 531 TYR 0.009 0.001 TYR B 761 PHE 0.030 0.001 PHE D 872 TRP 0.014 0.001 TRP D 582 HIS 0.003 0.001 HIS C 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (18320) covalent geometry : angle 0.55523 / 0.28 (24788) hydrogen bonds : bond 0.02570 / 1.73 ( 738) hydrogen bonds : angle 4.34578 / 3.08 ( 2199) Misc. bond : bond 0.00042 / 0.02 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 363 time to evaluate : 0.703 Fit side-chains REVERT: A 362 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7319 (mm-30) REVERT: A 365 LYS cc_start: 0.7285 (mmtp) cc_final: 0.6692 (tppt) REVERT: A 366 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7658 (mp0) REVERT: A 385 ARG cc_start: 0.7493 (ptm160) cc_final: 0.6677 (mmm160) REVERT: A 415 LYS cc_start: 0.6909 (mttt) cc_final: 0.6543 (mttt) REVERT: A 702 ASN cc_start: 0.7660 (t0) cc_final: 0.7348 (t0) REVERT: A 712 ARG cc_start: 0.8225 (mmm-85) cc_final: 0.7812 (mtm180) REVERT: A 845 LYS cc_start: 0.8092 (mmmt) cc_final: 0.7747 (mmtm) REVERT: A 862 THR cc_start: 0.8866 (t) cc_final: 0.8603 (m) REVERT: C 332 MET cc_start: 0.7929 (mmt) cc_final: 0.7682 (mmm) REVERT: C 365 LYS cc_start: 0.7350 (mmtm) cc_final: 0.6983 (tppt) REVERT: C 366 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7694 (mp0) REVERT: C 385 ARG cc_start: 0.7579 (ptm160) cc_final: 0.6787 (mmm160) REVERT: C 407 ASN cc_start: 0.6969 (m110) cc_final: 0.6709 (m-40) REVERT: C 415 LYS cc_start: 0.6855 (mttt) cc_final: 0.6447 (mttt) REVERT: C 702 ASN cc_start: 0.7830 (t0) cc_final: 0.7298 (t0) REVERT: C 768 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.5761 (tp30) REVERT: C 845 LYS cc_start: 0.8065 (mmmt) cc_final: 0.7790 (mmtm) REVERT: C 862 THR cc_start: 0.8908 (t) cc_final: 0.8655 (m) REVERT: B 362 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7272 (mm-30) REVERT: B 365 LYS cc_start: 0.7386 (mmtm) cc_final: 0.6835 (mmtm) REVERT: B 385 ARG cc_start: 0.7518 (ptm160) cc_final: 0.6752 (mmm160) REVERT: B 653 GLU cc_start: 0.6489 (mp0) cc_final: 0.5830 (pt0) REVERT: B 702 ASN cc_start: 0.7832 (t0) cc_final: 0.7302 (t0) REVERT: B 784 PHE cc_start: 0.7847 (m-80) cc_final: 0.7277 (m-10) REVERT: D 385 ARG cc_start: 0.7590 (ptm160) cc_final: 0.6822 (mmm160) REVERT: D 578 MET cc_start: 0.7396 (ttm) cc_final: 0.7137 (mtm) REVERT: D 702 ASN cc_start: 0.7853 (t0) cc_final: 0.7404 (t0) REVERT: D 767 LYS cc_start: 0.7564 (tmtt) cc_final: 0.7226 (ttpp) REVERT: D 784 PHE cc_start: 0.7816 (m-80) cc_final: 0.7232 (m-10) REVERT: D 845 LYS cc_start: 0.8019 (mmmt) cc_final: 0.7742 (mmtm) REVERT: D 862 THR cc_start: 0.8965 (t) cc_final: 0.8699 (m) outliers start: 45 outliers final: 31 residues processed: 389 average time/residue: 0.1314 time to fit residues: 80.6811 Evaluate side-chains 361 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 329 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 537 CYS Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 713 LEU Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain D residue 798 MET Chi-restraints excluded: chain D residue 857 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 71 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 0.1980 chunk 117 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 chunk 190 optimal weight: 0.4980 chunk 94 optimal weight: 0.9990 chunk 211 optimal weight: 0.9990 chunk 205 optimal weight: 0.0970 chunk 101 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 ASN C 474 ASN ** C 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN ** B 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.146795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.120917 restraints weight = 23783.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.124287 restraints weight = 13323.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.126533 restraints weight = 9241.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.127800 restraints weight = 7347.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.128581 restraints weight = 6433.462| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18328 Z= 0.106 Angle : 0.571 9.733 24788 Z= 0.287 Chirality : 0.040 0.159 2820 Planarity : 0.003 0.037 3212 Dihedral : 4.404 27.700 2500 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.37 % Favored : 94.45 % Rotamer: Outliers : 2.29 % Allowed : 23.44 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.18), residues: 2308 helix: 1.19 (0.16), residues: 1016 sheet: -1.86 (0.29), residues: 320 loop : -1.54 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 554 TYR 0.010 0.001 TYR C 761 PHE 0.029 0.001 PHE A 872 TRP 0.008 0.001 TRP D 582 HIS 0.004 0.001 HIS C 754 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (18320) covalent geometry : angle 0.57082 / 0.29 (24788) hydrogen bonds : bond 0.02543 / 1.71 ( 738) hydrogen bonds : angle 4.23883 / 3.00 ( 2199) Misc. bond : bond 0.00034 / 0.02 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3032.88 seconds wall clock time: 53 minutes 33.36 seconds (3213.36 seconds total)