Starting phenix.real_space_refine on Thu Aug 6 17:05:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i0k_35042/08_2026/8i0k_35042.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i0k_35042/08_2026/8i0k_35042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8i0k_35042/08_2026/8i0k_35042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i0k_35042/08_2026/8i0k_35042.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i0k_35042/08_2026/8i0k_35042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i0k_35042/08_2026/8i0k_35042.map" } resolution = 2.86 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= -0.003 sd= 0.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 4 5.49 5 Mg 2 5.21 5 S 100 5.16 5 C 10485 2.51 5 N 2902 2.21 5 O 3043 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16537 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 875, 6999 Classifications: {'peptide': 875} Link IDs: {'PTRANS': 47, 'TRANS': 827} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 6999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 875, 6999 Classifications: {'peptide': 875} Link IDs: {'PTRANS': 47, 'TRANS': 827} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2484 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 10, 'TRANS': 291} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Unusual residues: {' CA': 1, ' MG': 1, '8EL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.15, per 1000 atoms: 0.19 Number of scatterers: 16537 At special positions: 0 Unit cell: (111.15, 133.38, 124.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 S 100 16.00 P 4 15.00 Mg 2 11.99 O 3043 8.00 N 2902 7.00 C 10485 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 558.7 milliseconds 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3872 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 16 sheets defined 50.1% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 125 through 141 removed outlier: 4.151A pdb=" N ALA A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 145 removed outlier: 3.758A pdb=" N ALA A 145 " --> pdb=" O HIS A 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 145' Processing helix chain 'A' and resid 168 through 176 Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.545A pdb=" N LEU A 182 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP A 183 " --> pdb=" O SER A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 removed outlier: 4.018A pdb=" N GLN A 216 " --> pdb=" O MET A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 240 removed outlier: 3.526A pdb=" N CYS A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR A 240 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 272 removed outlier: 3.933A pdb=" N GLU A 265 " --> pdb=" O SER A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 300 Processing helix chain 'A' and resid 313 through 321 Processing helix chain 'A' and resid 325 through 333 removed outlier: 3.817A pdb=" N PHE A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 380 through 395 Processing helix chain 'A' and resid 411 through 415 removed outlier: 3.566A pdb=" N ALA A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 411 through 415' Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 451 through 455 Processing helix chain 'A' and resid 463 through 468 removed outlier: 3.650A pdb=" N VAL A 468 " --> pdb=" O ALA A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 498 removed outlier: 3.887A pdb=" N TYR A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 495 " --> pdb=" O ALA A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 522 removed outlier: 3.828A pdb=" N PHE A 521 " --> pdb=" O GLU A 518 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 522 " --> pdb=" O PRO A 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 518 through 522' Processing helix chain 'A' and resid 523 through 531 removed outlier: 3.592A pdb=" N TYR A 527 " --> pdb=" O GLN A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 548 removed outlier: 3.573A pdb=" N LYS A 539 " --> pdb=" O PRO A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 575 removed outlier: 3.698A pdb=" N ILE A 559 " --> pdb=" O TYR A 555 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 623 removed outlier: 3.631A pdb=" N LEU A 614 " --> pdb=" O THR A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 648 removed outlier: 3.584A pdb=" N ASN A 648 " --> pdb=" O GLU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 667 removed outlier: 3.689A pdb=" N GLU A 657 " --> pdb=" O TRP A 653 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR A 658 " --> pdb=" O ALA A 654 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER A 663 " --> pdb=" O MET A 659 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 706 removed outlier: 4.125A pdb=" N LEU A 706 " --> pdb=" O MET A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 734 removed outlier: 3.807A pdb=" N GLY A 727 " --> pdb=" O TYR A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 753 removed outlier: 3.793A pdb=" N HIS A 751 " --> pdb=" O GLY A 748 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASN A 752 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 753 " --> pdb=" O PHE A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 761 Processing helix chain 'A' and resid 764 through 769 Processing helix chain 'A' and resid 787 through 791 Processing helix chain 'A' and resid 794 through 800 removed outlier: 3.904A pdb=" N PHE A 798 " --> pdb=" O ARG A 794 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 800 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 824 Processing helix chain 'A' and resid 834 through 848 removed outlier: 3.795A pdb=" N LEU A 842 " --> pdb=" O PHE A 838 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG A 843 " --> pdb=" O PHE A 839 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A 846 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 864 removed outlier: 3.866A pdb=" N LEU A 863 " --> pdb=" O LYS A 860 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG A 864 " --> pdb=" O SER A 861 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 860 through 864' Processing helix chain 'A' and resid 873 through 875 No H-bonds generated for 'chain 'A' and resid 873 through 875' Processing helix chain 'A' and resid 894 through 898 Processing helix chain 'A' and resid 907 through 919 removed outlier: 4.049A pdb=" N ASP A 911 " --> pdb=" O LYS A 907 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 914 " --> pdb=" O TYR A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 948 removed outlier: 3.701A pdb=" N LEU A 941 " --> pdb=" O PRO A 937 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR A 948 " --> pdb=" O GLU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 977 removed outlier: 4.085A pdb=" N ARG A 972 " --> pdb=" O TYR A 968 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 977 " --> pdb=" O LEU A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1014 removed outlier: 3.529A pdb=" N HIS A1002 " --> pdb=" O ASN A 998 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A1014 " --> pdb=" O LEU A1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 141 removed outlier: 4.150A pdb=" N ALA B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR B 137 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 145 removed outlier: 3.759A pdb=" N ALA B 145 " --> pdb=" O HIS B 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 142 through 145' Processing helix chain 'B' and resid 168 through 176 Processing helix chain 'B' and resid 178 through 182 removed outlier: 3.545A pdb=" N LEU B 182 " --> pdb=" O GLU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 215 Processing helix chain 'B' and resid 227 through 240 removed outlier: 3.869A pdb=" N THR B 240 " --> pdb=" O GLN B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 272 removed outlier: 3.932A pdb=" N GLU B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 300 Processing helix chain 'B' and resid 313 through 321 Processing helix chain 'B' and resid 325 through 333 removed outlier: 3.765A pdb=" N PHE B 333 " --> pdb=" O ILE B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 395 Processing helix chain 'B' and resid 411 through 415 removed outlier: 3.566A pdb=" N ALA B 415 " --> pdb=" O ASP B 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 411 through 415' Processing helix chain 'B' and resid 418 through 427 Processing helix chain 'B' and resid 451 through 455 Processing helix chain 'B' and resid 463 through 468 removed outlier: 3.651A pdb=" N VAL B 468 " --> pdb=" O ALA B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 498 removed outlier: 3.888A pdb=" N TYR B 485 " --> pdb=" O GLU B 481 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 495 " --> pdb=" O ALA B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 522 removed outlier: 3.795A pdb=" N PHE B 521 " --> pdb=" O GLU B 518 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR B 522 " --> pdb=" O PRO B 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 518 through 522' Processing helix chain 'B' and resid 523 through 531 removed outlier: 3.851A pdb=" N TYR B 527 " --> pdb=" O GLN B 523 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS B 528 " --> pdb=" O PRO B 524 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN B 529 " --> pdb=" O LEU B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 548 removed outlier: 3.572A pdb=" N LYS B 539 " --> pdb=" O PRO B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 575 removed outlier: 3.523A pdb=" N ILE B 559 " --> pdb=" O TYR B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 622 removed outlier: 3.633A pdb=" N LEU B 614 " --> pdb=" O THR B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 648 removed outlier: 3.583A pdb=" N ASN B 648 " --> pdb=" O GLU B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 667 removed outlier: 3.690A pdb=" N GLU B 657 " --> pdb=" O TRP B 653 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR B 658 " --> pdb=" O ALA B 654 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER B 663 " --> pdb=" O MET B 659 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU B 667 " --> pdb=" O SER B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 706 removed outlier: 4.069A pdb=" N LEU B 706 " --> pdb=" O MET B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 734 removed outlier: 3.807A pdb=" N GLY B 727 " --> pdb=" O TYR B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 753 removed outlier: 3.792A pdb=" N HIS B 751 " --> pdb=" O GLY B 748 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASN B 752 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR B 753 " --> pdb=" O PHE B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 761 Processing helix chain 'B' and resid 764 through 769 Processing helix chain 'B' and resid 787 through 791 removed outlier: 4.037A pdb=" N SER B 791 " --> pdb=" O PRO B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 801 removed outlier: 3.904A pdb=" N PHE B 798 " --> pdb=" O ARG B 794 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN B 800 " --> pdb=" O GLU B 796 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET B 801 " --> pdb=" O ARG B 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.705A pdb=" N ASP B 824 " --> pdb=" O ASN B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 848 removed outlier: 3.795A pdb=" N LEU B 842 " --> pdb=" O PHE B 838 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 843 " --> pdb=" O PHE B 839 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE B 846 " --> pdb=" O LEU B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 864 removed outlier: 3.864A pdb=" N LEU B 863 " --> pdb=" O LYS B 860 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 864 " --> pdb=" O SER B 861 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 860 through 864' Processing helix chain 'B' and resid 873 through 875 No H-bonds generated for 'chain 'B' and resid 873 through 875' Processing helix chain 'B' and resid 889 through 894 removed outlier: 3.995A pdb=" N GLN B 893 " --> pdb=" O GLY B 889 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN B 894 " --> pdb=" O PRO B 890 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 889 through 894' Processing helix chain 'B' and resid 907 through 919 removed outlier: 4.043A pdb=" N ASP B 911 " --> pdb=" O LYS B 907 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG B 914 " --> pdb=" O TYR B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 948 Processing helix chain 'B' and resid 968 through 977 removed outlier: 4.085A pdb=" N ARG B 972 " --> pdb=" O TYR B 968 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 977 " --> pdb=" O LEU B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1014 removed outlier: 3.604A pdb=" N HIS B1002 " --> pdb=" O ASN B 998 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU B1003 " --> pdb=" O LYS B 999 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B1004 " --> pdb=" O LYS B1000 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE B1014 " --> pdb=" O LEU B1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 227 removed outlier: 5.714A pdb=" N LYS C 199 " --> pdb=" O ASP C 195 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N SER C 200 " --> pdb=" O ASN C 196 " (cutoff:3.500A) Proline residue: C 210 - end of helix Processing helix chain 'C' and resid 238 through 256 Processing helix chain 'C' and resid 259 through 264 removed outlier: 3.795A pdb=" N LYS C 264 " --> pdb=" O LYS C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 298 removed outlier: 3.580A pdb=" N LYS C 295 " --> pdb=" O HIS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 321 removed outlier: 3.549A pdb=" N ARG C 309 " --> pdb=" O ASP C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 354 Processing helix chain 'C' and resid 393 through 404 removed outlier: 3.965A pdb=" N THR C 403 " --> pdb=" O TRP C 399 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS C 404 " --> pdb=" O PHE C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 434 removed outlier: 3.525A pdb=" N ALA C 408 " --> pdb=" O LYS C 404 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU C 416 " --> pdb=" O MET C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 457 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 187 Processing sheet with id=AA2, first strand: chain 'A' and resid 218 through 221 removed outlier: 6.519A pdb=" N PHE A 473 " --> pdb=" O ASP A 504 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL A 506 " --> pdb=" O PHE A 473 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL A 475 " --> pdb=" O VAL A 506 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N VAL A 438 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SER A 405 " --> pdb=" O VAL A 438 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N VAL A 440 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 407 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N VAL A 442 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N HIS A 409 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR A 304 " --> pdb=" O MET A 404 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE A 406 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE A 306 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N LEU A 408 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLY A 308 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 8.896A pdb=" N GLY A 410 " --> pdb=" O GLY A 308 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 650 through 651 Processing sheet with id=AA4, first strand: chain 'A' and resid 713 through 717 removed outlier: 3.777A pdb=" N GLY A 675 " --> pdb=" O CYS A 716 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N VAL A 776 " --> pdb=" O ALA A 739 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL A 741 " --> pdb=" O VAL A 776 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LEU A 778 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TRP A 743 " --> pdb=" O LEU A 778 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU A 777 " --> pdb=" O ILE A 856 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR A 858 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU A 779 " --> pdb=" O THR A 858 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL A 828 " --> pdb=" O ILE A 855 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N PHE A 857 " --> pdb=" O VAL A 828 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N VAL A 830 " --> pdb=" O PHE A 857 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 690 through 691 Processing sheet with id=AA6, first strand: chain 'A' and resid 884 through 885 removed outlier: 3.602A pdb=" N ARG A 929 " --> pdb=" O ILE A 885 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU A 901 " --> pdb=" O ALA A 954 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N CYS A 956 " --> pdb=" O LEU A 901 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N PHE A 903 " --> pdb=" O CYS A 956 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N GLU A 958 " --> pdb=" O PHE A 903 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU A 953 " --> pdb=" O TRP A 984 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ALA A 986 " --> pdb=" O LEU A 953 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N TRP A 955 " --> pdb=" O ALA A 986 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ARG A 988 " --> pdb=" O TRP A 955 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N GLN A 957 " --> pdb=" O ARG A 988 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AA8, first strand: chain 'B' and resid 218 through 221 removed outlier: 6.519A pdb=" N PHE B 473 " --> pdb=" O ASP B 504 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL B 506 " --> pdb=" O PHE B 473 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL B 475 " --> pdb=" O VAL B 506 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N VAL B 438 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N SER B 405 " --> pdb=" O VAL B 438 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N VAL B 440 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU B 407 " --> pdb=" O VAL B 440 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL B 442 " --> pdb=" O LEU B 407 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N HIS B 409 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR B 304 " --> pdb=" O MET B 404 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE B 406 " --> pdb=" O TYR B 304 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE B 306 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N LEU B 408 " --> pdb=" O ILE B 306 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLY B 308 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N GLY B 410 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AB1, first strand: chain 'B' and resid 713 through 717 removed outlier: 3.779A pdb=" N GLY B 675 " --> pdb=" O CYS B 716 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N VAL B 776 " --> pdb=" O ALA B 739 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL B 741 " --> pdb=" O VAL B 776 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LEU B 778 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP B 743 " --> pdb=" O LEU B 778 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU B 777 " --> pdb=" O ILE B 856 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR B 858 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU B 779 " --> pdb=" O THR B 858 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 690 through 691 Processing sheet with id=AB3, first strand: chain 'B' and resid 884 through 885 removed outlier: 3.601A pdb=" N ARG B 929 " --> pdb=" O ILE B 885 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU B 901 " --> pdb=" O ALA B 954 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N CYS B 956 " --> pdb=" O LEU B 901 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N PHE B 903 " --> pdb=" O CYS B 956 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N GLU B 958 " --> pdb=" O PHE B 903 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU B 953 " --> pdb=" O TRP B 984 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA B 986 " --> pdb=" O LEU B 953 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N TRP B 955 " --> pdb=" O ALA B 986 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ARG B 988 " --> pdb=" O TRP B 955 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N GLN B 957 " --> pdb=" O ARG B 988 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 231 through 233 Processing sheet with id=AB5, first strand: chain 'C' and resid 325 through 326 removed outlier: 7.151A pdb=" N GLN C 325 " --> pdb=" O MET C 369 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 379 through 380 Processing sheet with id=AB7, first strand: chain 'C' and resid 437 through 440 removed outlier: 6.335A pdb=" N LYS C 437 " --> pdb=" O LEU C 469 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N ILE C 471 " --> pdb=" O LYS C 437 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N TYR C 439 " --> pdb=" O ILE C 471 " (cutoff:3.500A) 683 hydrogen bonds defined for protein. 1905 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: 2.73 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2746 1.31 - 1.44: 4497 1.44 - 1.56: 9518 1.56 - 1.69: 6 1.69 - 1.81: 156 Bond restraints: 16923 Sorted by residual: bond pdb=" C2 8EL B1102 " pdb=" N3 8EL B1102 " ideal model delta sigma weight residual 1.462 1.326 0.136 2.00e-02 2.50e+03 4.59e+01 bond pdb=" C2 8EL B1102 " pdb=" S1 8EL B1102 " ideal model delta sigma weight residual 1.819 1.709 0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" N PRO A 935 " pdb=" CA PRO A 935 " ideal model delta sigma weight residual 1.469 1.409 0.060 1.28e-02 6.10e+03 2.20e+01 bond pdb=" O3A 8EL B1102 " pdb=" PB 8EL B1102 " ideal model delta sigma weight residual 1.700 1.612 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C PRO A 935 " pdb=" O PRO A 935 " ideal model delta sigma weight residual 1.235 1.183 0.052 1.30e-02 5.92e+03 1.58e+01 ... (remaining 16918 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.55: 22797 4.55 - 9.10: 126 9.10 - 13.65: 3 13.65 - 18.20: 0 18.20 - 22.75: 1 Bond angle restraints: 22927 Sorted by residual: angle pdb=" N PRO A 935 " pdb=" CA PRO A 935 " pdb=" C PRO A 935 " ideal model delta sigma weight residual 112.47 89.72 22.75 2.06e+00 2.36e-01 1.22e+02 angle pdb=" N PRO B 764 " pdb=" CA PRO B 764 " pdb=" CB PRO B 764 " ideal model delta sigma weight residual 103.25 96.67 6.58 1.05e+00 9.07e-01 3.93e+01 angle pdb=" O ASP A 824 " pdb=" C ASP A 824 " pdb=" N CYS A 825 " ideal model delta sigma weight residual 122.68 129.70 -7.02 1.38e+00 5.25e-01 2.59e+01 angle pdb=" C ASP A 818 " pdb=" CA ASP A 818 " pdb=" CB ASP A 818 " ideal model delta sigma weight residual 110.79 102.45 8.34 1.68e+00 3.54e-01 2.46e+01 angle pdb=" O3A TPP A1102 " pdb=" PB TPP A1102 " pdb=" O3B TPP A1102 " ideal model delta sigma weight residual 104.26 110.71 -6.45 1.33e+00 5.64e-01 2.35e+01 ... (remaining 22922 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 9301 17.93 - 35.86: 734 35.86 - 53.78: 132 53.78 - 71.71: 52 71.71 - 89.64: 7 Dihedral angle restraints: 10226 sinusoidal: 4243 harmonic: 5983 Sorted by residual: dihedral pdb=" N PRO A 935 " pdb=" C PRO A 935 " pdb=" CA PRO A 935 " pdb=" CB PRO A 935 " ideal model delta harmonic sigma weight residual 115.10 102.68 12.42 0 2.50e+00 1.60e-01 2.47e+01 dihedral pdb=" CA ARG C 455 " pdb=" C ARG C 455 " pdb=" N LEU C 456 " pdb=" CA LEU C 456 " ideal model delta harmonic sigma weight residual 180.00 156.97 23.03 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA ASP B 967 " pdb=" C ASP B 967 " pdb=" N TYR B 968 " pdb=" CA TYR B 968 " ideal model delta harmonic sigma weight residual 180.00 158.49 21.51 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 10223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2041 0.093 - 0.186: 402 0.186 - 0.279: 50 0.279 - 0.372: 6 0.372 - 0.465: 1 Chirality restraints: 2500 Sorted by residual: chirality pdb=" CA ILE A 152 " pdb=" N ILE A 152 " pdb=" C ILE A 152 " pdb=" CB ILE A 152 " both_signs ideal model delta sigma weight residual False 2.43 2.90 -0.46 2.00e-01 2.50e+01 5.40e+00 chirality pdb=" CA ILE B 152 " pdb=" N ILE B 152 " pdb=" C ILE B 152 " pdb=" CB ILE B 152 " both_signs ideal model delta sigma weight residual False 2.43 2.80 -0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA ILE B 322 " pdb=" N ILE B 322 " pdb=" C ILE B 322 " pdb=" CB ILE B 322 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 2497 not shown) Planarity restraints: 2977 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 934 " 0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C SER A 934 " -0.066 2.00e-02 2.50e+03 pdb=" O SER A 934 " 0.024 2.00e-02 2.50e+03 pdb=" N PRO A 935 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 282 " -0.018 2.00e-02 2.50e+03 3.80e-02 1.45e+01 pdb=" C VAL C 282 " 0.066 2.00e-02 2.50e+03 pdb=" O VAL C 282 " -0.025 2.00e-02 2.50e+03 pdb=" N MET C 283 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 942 " -0.019 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C LEU B 942 " 0.063 2.00e-02 2.50e+03 pdb=" O LEU B 942 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS B 943 " -0.021 2.00e-02 2.50e+03 ... (remaining 2974 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 69 2.54 - 3.13: 12547 3.13 - 3.72: 24167 3.72 - 4.31: 35721 4.31 - 4.90: 60023 Nonbonded interactions: 132527 Sorted by model distance: nonbonded pdb=" OD1 ASN A 444 " pdb="MG MG A1101 " model vdw 1.954 2.170 nonbonded pdb=" OD1 ASN B 444 " pdb="MG MG B1101 " model vdw 1.955 2.170 nonbonded pdb="MG MG A1101 " pdb=" O3B TPP A1102 " model vdw 1.969 2.170 nonbonded pdb=" OG SER A 457 " pdb=" O HIS B 425 " model vdw 2.079 3.040 nonbonded pdb=" O ALA A 815 " pdb=" N PHE A 817 " model vdw 2.103 3.120 ... (remaining 132522 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 123 through 1101) selection = (chain 'B' and resid 123 through 1101) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.730 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 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 : 0.009 0.136 16923 Z= 0.574 Angle : 1.113 22.745 22927 Z= 0.759 Chirality : 0.072 0.465 2500 Planarity : 0.006 0.090 2977 Dihedral : 13.900 89.641 6354 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.48 % Favored : 94.22 % Rotamer: Outliers : 0.66 % Allowed : 4.13 % Favored : 95.20 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % 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: -0.62 (0.18), residues: 2042 helix: 0.59 (0.18), residues: 845 sheet: -0.04 (0.34), residues: 219 loop : -1.40 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 135 TYR 0.021 0.002 TYR B 354 PHE 0.026 0.002 PHE A 817 TRP 0.030 0.002 TRP B 827 HIS 0.010 0.002 HIS B 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00906 / 0.57 (16923) covalent geometry : angle 1.11303 / 0.76 (22927) hydrogen bonds : bond 0.21480 / 14.35 ( 683) hydrogen bonds : angle 6.71999 / 4.77 ( 1905) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 373 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 VAL cc_start: 0.7246 (OUTLIER) cc_final: 0.7011 (t) REVERT: A 563 ASP cc_start: 0.7333 (m-30) cc_final: 0.7022 (m-30) REVERT: A 920 ASP cc_start: 0.7370 (t70) cc_final: 0.7168 (t0) REVERT: B 327 GLU cc_start: 0.6662 (mt-10) cc_final: 0.6310 (mp0) REVERT: B 401 LYS cc_start: 0.8642 (tppp) cc_final: 0.7948 (tttm) REVERT: B 454 MET cc_start: 0.7834 (mpp) cc_final: 0.7537 (mmt) outliers start: 12 outliers final: 3 residues processed: 383 average time/residue: 0.6141 time to fit residues: 258.1706 Evaluate side-chains 227 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 223 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 816 ASN Chi-restraints excluded: chain B residue 818 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 GLN A 514 ASN A 670 HIS ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 ASN A 998 ASN A1007 GLN B 328 GLN B 332 GLN B 373 ASN B 710 GLN B 831 ASN C 291 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.178746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.121487 restraints weight = 19742.926| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.28 r_work: 0.3215 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16923 Z= 0.123 Angle : 0.596 9.835 22927 Z= 0.310 Chirality : 0.044 0.203 2500 Planarity : 0.005 0.066 2977 Dihedral : 6.113 75.064 2282 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.62 % Favored : 96.33 % Rotamer: Outliers : 2.32 % Allowed : 13.29 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.13 (0.19), residues: 2042 helix: 1.33 (0.18), residues: 873 sheet: -0.09 (0.32), residues: 254 loop : -1.09 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 135 TYR 0.016 0.001 TYR B 354 PHE 0.009 0.001 PHE A 839 TRP 0.014 0.001 TRP B 827 HIS 0.003 0.001 HIS B 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (16923) covalent geometry : angle 0.59631 / 0.31 (22927) hydrogen bonds : bond 0.04816 / 3.31 ( 683) hydrogen bonds : angle 4.61944 / 3.30 ( 1905) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 262 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 ARG cc_start: 0.8361 (ttm170) cc_final: 0.8002 (mtt-85) REVERT: A 266 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6819 (mp0) REVERT: A 567 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7673 (mp0) REVERT: A 817 PHE cc_start: 0.5977 (t80) cc_final: 0.5725 (t80) REVERT: A 825 CYS cc_start: 0.7393 (OUTLIER) cc_final: 0.7031 (p) REVERT: A 920 ASP cc_start: 0.8159 (t70) cc_final: 0.7878 (OUTLIER) REVERT: A 1007 GLN cc_start: 0.8446 (tp40) cc_final: 0.8206 (tp-100) REVERT: B 328 GLN cc_start: 0.7773 (mp10) cc_final: 0.7340 (mp-120) REVERT: B 454 MET cc_start: 0.8516 (mpp) cc_final: 0.7944 (mmt) REVERT: B 534 LYS cc_start: 0.8181 (mtpp) cc_final: 0.7950 (mtpt) REVERT: B 557 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.6781 (pt0) REVERT: B 558 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7323 (mm-30) REVERT: B 561 LYS cc_start: 0.7856 (ttmm) cc_final: 0.7393 (tttt) REVERT: B 563 ASP cc_start: 0.8191 (m-30) cc_final: 0.7764 (t70) REVERT: B 829 VAL cc_start: 0.8917 (m) cc_final: 0.8663 (t) REVERT: B 901 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8109 (tt) REVERT: C 369 MET cc_start: 0.2640 (ttm) cc_final: 0.2320 (tmt) outliers start: 42 outliers final: 14 residues processed: 282 average time/residue: 0.5748 time to fit residues: 178.6455 Evaluate side-chains 229 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 211 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 816 ASN Chi-restraints excluded: chain A residue 825 CYS Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 818 ASP Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain C residue 252 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 142 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 99 optimal weight: 0.0770 chunk 184 optimal weight: 20.0000 chunk 141 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 chunk 178 optimal weight: 30.0000 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 GLN A 311 HIS A 476 ASN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 HIS B 332 GLN B 376 HIS B 632 HIS B 676 GLN B 760 GLN ** B 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 HIS C 333 GLN C 385 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.170713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112256 restraints weight = 19857.556| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.27 r_work: 0.3030 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16923 Z= 0.155 Angle : 0.600 15.443 22927 Z= 0.307 Chirality : 0.046 0.201 2500 Planarity : 0.005 0.052 2977 Dihedral : 5.851 85.348 2279 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.92 % Allowed : 14.61 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.32 (0.19), residues: 2042 helix: 1.51 (0.18), residues: 880 sheet: -0.06 (0.32), residues: 260 loop : -1.01 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 277 TYR 0.018 0.002 TYR B 527 PHE 0.011 0.001 PHE B1019 TRP 0.013 0.001 TRP B 827 HIS 0.005 0.001 HIS A 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (16923) covalent geometry : angle 0.59957 / 0.31 (22927) hydrogen bonds : bond 0.04831 / 3.30 ( 683) hydrogen bonds : angle 4.45041 / 3.18 ( 1905) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 231 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 204 ARG cc_start: 0.8394 (ttm170) cc_final: 0.8071 (mtt-85) REVERT: A 266 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: A 572 ARG cc_start: 0.7372 (mmt180) cc_final: 0.6997 (tpp-160) REVERT: A 915 GLU cc_start: 0.8235 (tp30) cc_final: 0.7702 (tp30) REVERT: A 920 ASP cc_start: 0.8263 (t70) cc_final: 0.7988 (t0) REVERT: B 154 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7435 (p0) REVERT: B 269 GLN cc_start: 0.7860 (tp40) cc_final: 0.7638 (tt0) REVERT: B 328 GLN cc_start: 0.7861 (mp10) cc_final: 0.7581 (mp10) REVERT: B 332 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7577 (mm-40) REVERT: B 454 MET cc_start: 0.8716 (mpp) cc_final: 0.8072 (mmt) REVERT: B 499 LYS cc_start: 0.8801 (mtpt) cc_final: 0.8523 (mtpt) REVERT: B 531 ARG cc_start: 0.8605 (mpt-90) cc_final: 0.8402 (mpt-90) REVERT: B 557 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7215 (pt0) REVERT: B 558 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7283 (mm-30) REVERT: B 561 LYS cc_start: 0.7810 (ttmm) cc_final: 0.7345 (tttt) REVERT: B 563 ASP cc_start: 0.8098 (m-30) cc_final: 0.7677 (t70) REVERT: B 901 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8740 (tt) REVERT: B 958 GLU cc_start: 0.8118 (tp30) cc_final: 0.7737 (tt0) REVERT: B 999 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8016 (tmtt) REVERT: C 369 MET cc_start: 0.2462 (ttm) cc_final: 0.2227 (tmt) outliers start: 53 outliers final: 19 residues processed: 262 average time/residue: 0.5885 time to fit residues: 169.9145 Evaluate side-chains 226 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 676 GLN Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 783 MET Chi-restraints excluded: chain B residue 818 ASP Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 999 LYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 252 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 95 optimal weight: 2.9990 chunk 2 optimal weight: 0.2980 chunk 186 optimal weight: 9.9990 chunk 11 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 152 optimal weight: 0.0020 chunk 119 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 GLN A 355 HIS A 538 GLN A 760 GLN B 547 GLN B 670 HIS B 676 GLN B 760 GLN B 865 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.173459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.115407 restraints weight = 19619.587| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.28 r_work: 0.3046 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16923 Z= 0.101 Angle : 0.522 13.124 22927 Z= 0.266 Chirality : 0.042 0.201 2500 Planarity : 0.004 0.045 2977 Dihedral : 5.488 74.171 2277 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.82 % Allowed : 17.03 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.58 (0.19), residues: 2042 helix: 1.76 (0.18), residues: 875 sheet: 0.02 (0.32), residues: 273 loop : -0.89 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 864 TYR 0.018 0.001 TYR A 354 PHE 0.010 0.001 PHE A 839 TRP 0.008 0.001 TRP B 827 HIS 0.003 0.001 HIS B 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (16923) covalent geometry : angle 0.52221 / 0.27 (22927) hydrogen bonds : bond 0.03524 / 2.40 ( 683) hydrogen bonds : angle 4.17826 / 2.99 ( 1905) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 HIS cc_start: 0.6706 (m90) cc_final: 0.6499 (m-70) REVERT: A 266 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6793 (mp0) REVERT: A 356 ARG cc_start: 0.7605 (mtp180) cc_final: 0.7177 (mtm110) REVERT: A 563 ASP cc_start: 0.7785 (t0) cc_final: 0.7222 (t0) REVERT: A 567 GLU cc_start: 0.8161 (mp0) cc_final: 0.7895 (mp0) REVERT: A 572 ARG cc_start: 0.7272 (mmt180) cc_final: 0.6917 (tpp-160) REVERT: A 915 GLU cc_start: 0.8182 (tp30) cc_final: 0.7720 (tp30) REVERT: A 920 ASP cc_start: 0.8210 (t70) cc_final: 0.7965 (t0) REVERT: A 1017 ASP cc_start: 0.7917 (m-30) cc_final: 0.7136 (m-30) REVERT: B 266 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7138 (mm-30) REVERT: B 275 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.6999 (mp0) REVERT: B 281 GLU cc_start: 0.8339 (mp0) cc_final: 0.7954 (mp0) REVERT: B 328 GLN cc_start: 0.7829 (mp10) cc_final: 0.7449 (mp10) REVERT: B 499 LYS cc_start: 0.8777 (mtpt) cc_final: 0.8540 (mtpt) REVERT: B 557 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7436 (pt0) REVERT: B 558 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7276 (mm-30) REVERT: B 561 LYS cc_start: 0.7783 (ttmm) cc_final: 0.7311 (tttt) REVERT: B 563 ASP cc_start: 0.8112 (m-30) cc_final: 0.7679 (t70) REVERT: B 917 LYS cc_start: 0.8681 (ptmm) cc_final: 0.8429 (tttm) REVERT: B 958 GLU cc_start: 0.8020 (tp30) cc_final: 0.7693 (tt0) REVERT: B 999 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8026 (tmtt) REVERT: C 222 LEU cc_start: 0.3246 (OUTLIER) cc_final: 0.3011 (mt) REVERT: C 369 MET cc_start: 0.2423 (ttm) cc_final: 0.2180 (tmt) outliers start: 33 outliers final: 11 residues processed: 255 average time/residue: 0.5995 time to fit residues: 168.3314 Evaluate side-chains 226 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 210 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 999 LYS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 418 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 197 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 132 optimal weight: 0.2980 chunk 54 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 195 optimal weight: 0.9990 chunk 153 optimal weight: 7.9990 chunk 174 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 GLN A 355 HIS A 476 ASN A 538 GLN A 760 GLN B 245 GLN B 269 GLN B 332 GLN B 773 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.172723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114746 restraints weight = 19559.435| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.25 r_work: 0.3040 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16923 Z= 0.104 Angle : 0.523 13.734 22927 Z= 0.264 Chirality : 0.042 0.175 2500 Planarity : 0.004 0.042 2977 Dihedral : 5.288 75.738 2275 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.26 % Allowed : 18.08 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.68 (0.19), residues: 2042 helix: 1.83 (0.18), residues: 880 sheet: -0.02 (0.33), residues: 252 loop : -0.79 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 531 TYR 0.017 0.001 TYR A 354 PHE 0.009 0.001 PHE A 839 TRP 0.007 0.001 TRP A 493 HIS 0.003 0.001 HIS A 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (16923) covalent geometry : angle 0.52330 / 0.26 (22927) hydrogen bonds : bond 0.03454 / 2.35 ( 683) hydrogen bonds : angle 4.09966 / 2.93 ( 1905) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 223 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 HIS cc_start: 0.6795 (m90) cc_final: 0.6528 (m-70) REVERT: A 266 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6887 (mp0) REVERT: A 356 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7127 (mtm110) REVERT: A 399 GLU cc_start: 0.8164 (pm20) cc_final: 0.7343 (tp30) REVERT: A 453 ARG cc_start: 0.8250 (tpt90) cc_final: 0.8040 (tpt90) REVERT: A 915 GLU cc_start: 0.8109 (tp30) cc_final: 0.7526 (tp30) REVERT: A 920 ASP cc_start: 0.8240 (t70) cc_final: 0.8018 (t0) REVERT: A 1017 ASP cc_start: 0.7927 (m-30) cc_final: 0.7094 (m-30) REVERT: B 164 ASP cc_start: 0.8520 (m-30) cc_final: 0.8253 (t0) REVERT: B 266 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7215 (mm-30) REVERT: B 281 GLU cc_start: 0.8352 (mp0) cc_final: 0.7998 (mp0) REVERT: B 328 GLN cc_start: 0.7862 (mp10) cc_final: 0.7479 (mp10) REVERT: B 399 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7647 (pt0) REVERT: B 499 LYS cc_start: 0.8794 (mtpt) cc_final: 0.8549 (mtpt) REVERT: B 516 MET cc_start: 0.7789 (mmm) cc_final: 0.7583 (mmm) REVERT: B 531 ARG cc_start: 0.8585 (mpt-90) cc_final: 0.8380 (mpt-90) REVERT: B 557 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7631 (pp20) REVERT: B 558 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7502 (mt-10) REVERT: B 561 LYS cc_start: 0.7798 (ttmm) cc_final: 0.7302 (tttt) REVERT: B 563 ASP cc_start: 0.8090 (m-30) cc_final: 0.7662 (t70) REVERT: B 659 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.7890 (mpp) REVERT: B 786 MET cc_start: 0.8419 (ttm) cc_final: 0.7931 (tpp) REVERT: B 958 GLU cc_start: 0.8026 (tp30) cc_final: 0.7731 (tt0) REVERT: B 999 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8058 (tmtt) REVERT: C 369 MET cc_start: 0.2456 (ttm) cc_final: 0.2190 (tmt) outliers start: 41 outliers final: 18 residues processed: 245 average time/residue: 0.5964 time to fit residues: 160.4423 Evaluate side-chains 231 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 783 MET Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 999 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 176 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 GLN A 476 ASN A 538 GLN A 772 GLN B 332 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.168830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.110771 restraints weight = 19665.617| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.23 r_work: 0.2996 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16923 Z= 0.156 Angle : 0.568 12.678 22927 Z= 0.288 Chirality : 0.045 0.156 2500 Planarity : 0.004 0.047 2977 Dihedral : 5.546 79.022 2275 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.54 % Allowed : 19.02 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.55 (0.19), residues: 2042 helix: 1.70 (0.18), residues: 887 sheet: -0.11 (0.32), residues: 268 loop : -0.85 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 572 TYR 0.018 0.002 TYR B 527 PHE 0.010 0.001 PHE A 414 TRP 0.011 0.001 TRP A 493 HIS 0.005 0.001 HIS B 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (16923) covalent geometry : angle 0.56806 / 0.29 (22927) hydrogen bonds : bond 0.04238 / 2.89 ( 683) hydrogen bonds : angle 4.22452 / 3.02 ( 1905) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 127 HIS cc_start: 0.6702 (m90) cc_final: 0.6408 (m-70) REVERT: A 188 LEU cc_start: 0.7710 (mp) cc_final: 0.7380 (mt) REVERT: A 266 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6902 (mp0) REVERT: A 557 GLU cc_start: 0.8787 (pp20) cc_final: 0.8569 (pp20) REVERT: A 1017 ASP cc_start: 0.7980 (m-30) cc_final: 0.7147 (m-30) REVERT: B 266 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7222 (mm-30) REVERT: B 281 GLU cc_start: 0.8448 (mp0) cc_final: 0.8050 (mp0) REVERT: B 328 GLN cc_start: 0.7860 (mp10) cc_final: 0.7476 (mp10) REVERT: B 499 LYS cc_start: 0.8844 (mtpt) cc_final: 0.8586 (mtpt) REVERT: B 531 ARG cc_start: 0.8575 (mpt-90) cc_final: 0.8346 (mpt-90) REVERT: B 557 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7688 (pp20) REVERT: B 558 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7487 (mt-10) REVERT: B 559 ILE cc_start: 0.8294 (mt) cc_final: 0.8055 (mp) REVERT: B 561 LYS cc_start: 0.7871 (ttmm) cc_final: 0.7381 (tttt) REVERT: B 659 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.7820 (mpp) REVERT: B 744 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.7922 (tm-30) REVERT: B 958 GLU cc_start: 0.8038 (tp30) cc_final: 0.7717 (tt0) REVERT: B 999 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8051 (tmtt) REVERT: B 1000 LYS cc_start: 0.8620 (tptp) cc_final: 0.7853 (tttm) REVERT: C 369 MET cc_start: 0.2393 (ttm) cc_final: 0.2134 (tmt) outliers start: 46 outliers final: 22 residues processed: 230 average time/residue: 0.6574 time to fit residues: 165.8118 Evaluate side-chains 219 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 999 LYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 252 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 201 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 47 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 92 optimal weight: 0.5980 chunk 72 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 GLN A 355 HIS A 772 GLN B 245 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.169985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.111649 restraints weight = 19592.296| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.26 r_work: 0.3009 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16923 Z= 0.125 Angle : 0.538 12.442 22927 Z= 0.272 Chirality : 0.043 0.150 2500 Planarity : 0.004 0.046 2977 Dihedral : 5.451 77.864 2275 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.32 % Allowed : 19.68 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.58 (0.19), residues: 2042 helix: 1.76 (0.18), residues: 893 sheet: -0.09 (0.32), residues: 267 loop : -0.91 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 572 TYR 0.018 0.001 TYR A 354 PHE 0.009 0.001 PHE A 839 TRP 0.008 0.001 TRP B 653 HIS 0.004 0.001 HIS B 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 (16923) covalent geometry : angle 0.53795 / 0.27 (22927) hydrogen bonds : bond 0.03667 / 2.51 ( 683) hydrogen bonds : angle 4.13761 / 2.96 ( 1905) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 213 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: A 127 HIS cc_start: 0.6750 (m90) cc_final: 0.6426 (m-70) REVERT: A 188 LEU cc_start: 0.7670 (mp) cc_final: 0.7372 (mt) REVERT: A 266 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6960 (mp0) REVERT: A 356 ARG cc_start: 0.7580 (mtp180) cc_final: 0.7155 (mtm110) REVERT: A 399 GLU cc_start: 0.8012 (pm20) cc_final: 0.7548 (tp30) REVERT: A 554 GLU cc_start: 0.6712 (tm-30) cc_final: 0.6507 (tm-30) REVERT: A 557 GLU cc_start: 0.8777 (pp20) cc_final: 0.8494 (pp20) REVERT: A 558 GLU cc_start: 0.8057 (pt0) cc_final: 0.7807 (pt0) REVERT: A 563 ASP cc_start: 0.8165 (t0) cc_final: 0.7502 (m-30) REVERT: A 915 GLU cc_start: 0.8130 (tp30) cc_final: 0.7588 (tp30) REVERT: A 1017 ASP cc_start: 0.7948 (m-30) cc_final: 0.7101 (m-30) REVERT: B 164 ASP cc_start: 0.8561 (m-30) cc_final: 0.8343 (t0) REVERT: B 266 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7209 (mm-30) REVERT: B 281 GLU cc_start: 0.8416 (mp0) cc_final: 0.8009 (mp0) REVERT: B 328 GLN cc_start: 0.7909 (mp10) cc_final: 0.7467 (mp-120) REVERT: B 399 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7688 (pt0) REVERT: B 428 ASP cc_start: 0.8944 (t0) cc_final: 0.8694 (t0) REVERT: B 499 LYS cc_start: 0.8819 (mtpt) cc_final: 0.8569 (mtpt) REVERT: B 531 ARG cc_start: 0.8576 (mpt-90) cc_final: 0.8333 (mpt-90) REVERT: B 557 GLU cc_start: 0.8208 (pt0) cc_final: 0.7697 (pp20) REVERT: B 558 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7545 (mt-10) REVERT: B 561 LYS cc_start: 0.7829 (ttmm) cc_final: 0.7338 (ttpt) REVERT: B 659 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.7841 (mpp) REVERT: B 744 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: B 786 MET cc_start: 0.8458 (ttm) cc_final: 0.7950 (tpp) REVERT: B 958 GLU cc_start: 0.8045 (tp30) cc_final: 0.7759 (tt0) REVERT: B 999 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8074 (tmtt) REVERT: B 1000 LYS cc_start: 0.8616 (tptp) cc_final: 0.7833 (tttm) REVERT: C 370 ILE cc_start: 0.2949 (OUTLIER) cc_final: 0.2522 (mm) outliers start: 42 outliers final: 20 residues processed: 243 average time/residue: 0.6179 time to fit residues: 165.1993 Evaluate side-chains 225 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 999 LYS Chi-restraints excluded: chain C residue 370 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 70 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 GLN A 355 HIS A 476 ASN A 760 GLN A 772 GLN B 332 GLN C 333 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.170243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.112202 restraints weight = 19763.680| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.25 r_work: 0.3009 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16923 Z= 0.101 Angle : 0.525 11.465 22927 Z= 0.265 Chirality : 0.042 0.153 2500 Planarity : 0.004 0.045 2977 Dihedral : 5.349 74.654 2275 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.04 % Allowed : 19.85 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.69 (0.19), residues: 2042 helix: 1.87 (0.18), residues: 892 sheet: -0.06 (0.33), residues: 251 loop : -0.84 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 572 TYR 0.019 0.001 TYR B 354 PHE 0.011 0.001 PHE B 903 TRP 0.007 0.001 TRP B 653 HIS 0.003 0.001 HIS A 688 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (16923) covalent geometry : angle 0.52493 / 0.26 (22927) hydrogen bonds : bond 0.03251 / 2.22 ( 683) hydrogen bonds : angle 4.04344 / 2.89 ( 1905) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 215 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: A 127 HIS cc_start: 0.6752 (m90) cc_final: 0.6416 (m-70) REVERT: A 188 LEU cc_start: 0.7615 (mp) cc_final: 0.7313 (mt) REVERT: A 266 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: A 356 ARG cc_start: 0.7507 (mtp180) cc_final: 0.7081 (mtm110) REVERT: A 554 GLU cc_start: 0.6708 (tm-30) cc_final: 0.6432 (tm-30) REVERT: A 557 GLU cc_start: 0.8754 (pp20) cc_final: 0.8452 (pp20) REVERT: A 563 ASP cc_start: 0.8111 (t0) cc_final: 0.7458 (m-30) REVERT: A 915 GLU cc_start: 0.8117 (tp30) cc_final: 0.7639 (tp30) REVERT: A 1017 ASP cc_start: 0.7935 (m-30) cc_final: 0.7050 (m-30) REVERT: B 164 ASP cc_start: 0.8561 (m-30) cc_final: 0.8348 (t0) REVERT: B 266 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7168 (mm-30) REVERT: B 281 GLU cc_start: 0.8365 (mp0) cc_final: 0.7963 (mp0) REVERT: B 328 GLN cc_start: 0.7856 (mp10) cc_final: 0.7472 (mp-120) REVERT: B 399 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7664 (pt0) REVERT: B 428 ASP cc_start: 0.8906 (t0) cc_final: 0.8691 (t0) REVERT: B 499 LYS cc_start: 0.8820 (mtpt) cc_final: 0.8576 (mtpt) REVERT: B 531 ARG cc_start: 0.8580 (mpt-90) cc_final: 0.8346 (mpt-90) REVERT: B 554 GLU cc_start: 0.7810 (tt0) cc_final: 0.7272 (mt-10) REVERT: B 557 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7693 (pp20) REVERT: B 558 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7569 (mt-10) REVERT: B 559 ILE cc_start: 0.8220 (mt) cc_final: 0.8011 (mp) REVERT: B 561 LYS cc_start: 0.7750 (ttmm) cc_final: 0.7289 (ttpt) REVERT: B 744 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.7914 (tm-30) REVERT: B 786 MET cc_start: 0.8468 (ttm) cc_final: 0.7951 (tpp) REVERT: B 958 GLU cc_start: 0.8002 (tp30) cc_final: 0.7702 (tt0) REVERT: B 999 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8099 (tmtt) REVERT: B 1000 LYS cc_start: 0.8590 (tptp) cc_final: 0.7799 (tttm) outliers start: 37 outliers final: 18 residues processed: 239 average time/residue: 0.6476 time to fit residues: 170.2470 Evaluate side-chains 227 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 204 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 999 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 139 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 157 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 141 optimal weight: 8.9990 chunk 97 optimal weight: 0.5980 chunk 133 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 GLN A 476 ASN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 GLN B 131 GLN B 245 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.166981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.109107 restraints weight = 19616.976| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.22 r_work: 0.2967 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16923 Z= 0.173 Angle : 0.595 12.561 22927 Z= 0.301 Chirality : 0.045 0.155 2500 Planarity : 0.004 0.045 2977 Dihedral : 5.693 79.306 2275 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.09 % Allowed : 19.90 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.19), residues: 2042 helix: 1.66 (0.18), residues: 899 sheet: -0.16 (0.32), residues: 267 loop : -0.91 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 357 TYR 0.018 0.002 TYR B 527 PHE 0.011 0.001 PHE A 414 TRP 0.013 0.001 TRP A 493 HIS 0.007 0.001 HIS A 688 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.17 (16923) covalent geometry : angle 0.59469 / 0.30 (22927) hydrogen bonds : bond 0.04480 / 3.06 ( 683) hydrogen bonds : angle 4.24810 / 3.04 ( 1905) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 127 HIS cc_start: 0.6762 (m90) cc_final: 0.6422 (m-70) REVERT: A 188 LEU cc_start: 0.7646 (mp) cc_final: 0.7421 (mt) REVERT: A 266 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: A 554 GLU cc_start: 0.6658 (tm-30) cc_final: 0.6403 (tm-30) REVERT: A 557 GLU cc_start: 0.8737 (pp20) cc_final: 0.8391 (pp20) REVERT: A 558 GLU cc_start: 0.8114 (pt0) cc_final: 0.7794 (pt0) REVERT: A 563 ASP cc_start: 0.8148 (t0) cc_final: 0.7462 (m-30) REVERT: A 1017 ASP cc_start: 0.8011 (m-30) cc_final: 0.7168 (m-30) REVERT: B 266 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7247 (mm-30) REVERT: B 328 GLN cc_start: 0.7958 (mp10) cc_final: 0.7597 (mp10) REVERT: B 399 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7706 (pt0) REVERT: B 499 LYS cc_start: 0.8860 (mtpt) cc_final: 0.8595 (mtpt) REVERT: B 554 GLU cc_start: 0.7885 (tt0) cc_final: 0.7337 (mt-10) REVERT: B 557 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7746 (pp20) REVERT: B 558 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7654 (mt-10) REVERT: B 559 ILE cc_start: 0.8280 (mt) cc_final: 0.8078 (mp) REVERT: B 561 LYS cc_start: 0.7833 (ttmm) cc_final: 0.7341 (ttpt) REVERT: B 744 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.7889 (tm-30) REVERT: B 867 GLU cc_start: 0.8543 (pt0) cc_final: 0.8241 (pt0) REVERT: B 916 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7989 (ttp-170) REVERT: B 958 GLU cc_start: 0.8080 (tp30) cc_final: 0.7774 (tt0) REVERT: B 999 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8109 (tmtt) REVERT: B 1000 LYS cc_start: 0.8634 (tptp) cc_final: 0.7843 (tttm) outliers start: 38 outliers final: 23 residues processed: 227 average time/residue: 0.6216 time to fit residues: 154.6174 Evaluate side-chains 223 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 783 MET Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 916 ARG Chi-restraints excluded: chain B residue 999 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 44 optimal weight: 5.9990 chunk 32 optimal weight: 0.0470 chunk 71 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 198 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 GLN A 355 HIS A 632 HIS B 131 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.163465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.104956 restraints weight = 19665.870| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.24 r_work: 0.2938 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 16923 Z= 0.225 Angle : 0.640 12.441 22927 Z= 0.326 Chirality : 0.047 0.161 2500 Planarity : 0.005 0.046 2977 Dihedral : 6.030 88.759 2275 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.09 % Allowed : 20.29 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.34 (0.19), residues: 2042 helix: 1.60 (0.18), residues: 878 sheet: -0.22 (0.32), residues: 259 loop : -1.01 (0.19), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 572 TYR 0.018 0.002 TYR B 527 PHE 0.013 0.002 PHE A 414 TRP 0.014 0.002 TRP A 493 HIS 0.009 0.001 HIS A 688 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.23 (16923) covalent geometry : angle 0.64029 / 0.33 (22927) hydrogen bonds : bond 0.05045 / 3.44 ( 683) hydrogen bonds : angle 4.38474 / 3.15 ( 1905) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 127 HIS cc_start: 0.6740 (m90) cc_final: 0.6395 (m-70) REVERT: A 188 LEU cc_start: 0.7621 (mp) cc_final: 0.7411 (mt) REVERT: A 266 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6916 (mp0) REVERT: A 563 ASP cc_start: 0.8125 (t0) cc_final: 0.7435 (m-30) REVERT: A 1017 ASP cc_start: 0.8036 (m-30) cc_final: 0.7237 (m-30) REVERT: B 266 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7249 (mm-30) REVERT: B 328 GLN cc_start: 0.7981 (mp10) cc_final: 0.7580 (mp-120) REVERT: B 399 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7752 (pt0) REVERT: B 499 LYS cc_start: 0.8867 (mtpt) cc_final: 0.8646 (mtpt) REVERT: B 557 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7733 (pp20) REVERT: B 558 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7673 (mt-10) REVERT: B 559 ILE cc_start: 0.8291 (mt) cc_final: 0.8082 (mp) REVERT: B 561 LYS cc_start: 0.7784 (ttmm) cc_final: 0.7279 (tttt) REVERT: B 867 GLU cc_start: 0.8506 (pt0) cc_final: 0.8262 (pt0) REVERT: B 916 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.8029 (ttp-170) REVERT: B 958 GLU cc_start: 0.8109 (tp30) cc_final: 0.7775 (tt0) REVERT: B 999 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8290 (tmtt) REVERT: B 1000 LYS cc_start: 0.8647 (tptp) cc_final: 0.7842 (tttm) outliers start: 38 outliers final: 23 residues processed: 225 average time/residue: 0.6057 time to fit residues: 149.9727 Evaluate side-chains 215 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 783 MET Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 916 ARG Chi-restraints excluded: chain B residue 999 LYS Chi-restraints excluded: chain C residue 477 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 52 optimal weight: 0.9990 chunk 190 optimal weight: 30.0000 chunk 92 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.165804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.107522 restraints weight = 19544.899| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.24 r_work: 0.3011 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16923 Z= 0.138 Angle : 0.576 12.038 22927 Z= 0.292 Chirality : 0.044 0.179 2500 Planarity : 0.004 0.046 2977 Dihedral : 5.782 87.452 2275 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.98 % Allowed : 20.95 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.51 (0.19), residues: 2042 helix: 1.72 (0.18), residues: 883 sheet: -0.17 (0.32), residues: 259 loop : -0.91 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 572 TYR 0.017 0.001 TYR A 354 PHE 0.010 0.001 PHE A 839 TRP 0.009 0.001 TRP B 769 HIS 0.004 0.001 HIS A 688 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (16923) covalent geometry : angle 0.57574 / 0.29 (22927) hydrogen bonds : bond 0.03915 / 2.68 ( 683) hydrogen bonds : angle 4.21236 / 3.03 ( 1905) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6148.09 seconds wall clock time: 105 minutes 9.90 seconds (6309.90 seconds total)