Starting phenix.real_space_refine on Sat Jul 4 12:40:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y0j_33547/07_2026/7y0j_33547.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y0j_33547/07_2026/7y0j_33547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y0j_33547/07_2026/7y0j_33547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y0j_33547/07_2026/7y0j_33547.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y0j_33547/07_2026/7y0j_33547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y0j_33547/07_2026/7y0j_33547.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7y0j_33547/07_2026/7y0j_33547.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y0j_33547/07_2026/7y0j_33547.cif" } resolution = 3.62 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= 0.002 sd= 0.041 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: 4 Type Number sf(0) Gaussians S 103 5.16 5 C 13053 2.51 5 N 3503 2.21 5 O 4058 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20717 Number of models: 1 Model: "" Number of chains: 23 Chain: "M" Number of atoms: 2161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2161 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 6, 'TRANS': 247} Chain breaks: 4 Chain: "A" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1798 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 18, 'TRANS': 213} Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1769 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 18, 'TRANS': 209} Chain: "C" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1779 Classifications: {'peptide': 230} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 18, 'TRANS': 211} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 18, 'TRANS': 205} Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 18, 'TRANS': 205} Chain: "F" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1723 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 18, 'TRANS': 202} Chain breaks: 1 Chain: "G" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1742 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 18, 'TRANS': 205} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1730 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 18, 'TRANS': 203} Chain breaks: 1 Chain: "K" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1737 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 18, 'TRANS': 204} Chain breaks: 1 Chain: "L" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1773 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 209} Chain breaks: 1 Chain: "J" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 851 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain breaks: 1 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.86, per 1000 atoms: 0.23 Number of scatterers: 20717 At special positions: 0 Unit cell: (107.1, 172.55, 198.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 103 16.00 O 4058 8.00 N 3503 7.00 C 13053 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS M1600 " - pdb=" SG CYS M1613 " distance=2.03 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 536 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 536 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 426 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 536 " distance=2.03 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 426 " distance=2.03 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 536 " distance=2.03 Simple disulfide: pdb=" SG CYS E 474 " - pdb=" SG CYS E 536 " distance=2.03 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 426 " distance=2.03 Simple disulfide: pdb=" SG CYS F 474 " - pdb=" SG CYS F 536 " distance=2.03 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 426 " distance=2.03 Simple disulfide: pdb=" SG CYS G 474 " - pdb=" SG CYS G 536 " distance=2.03 Simple disulfide: pdb=" SG CYS H 367 " - pdb=" SG CYS H 426 " distance=2.03 Simple disulfide: pdb=" SG CYS H 474 " - pdb=" SG CYS H 536 " distance=2.04 Simple disulfide: pdb=" SG CYS K 367 " - pdb=" SG CYS K 426 " distance=2.03 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 536 " distance=2.03 Simple disulfide: pdb=" SG CYS L 367 " - pdb=" SG CYS L 426 " distance=2.03 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 536 " distance=2.03 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=2.03 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 133 " distance=2.03 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 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 601 " - " ASN A 563 " " NAG B 601 " - " ASN B 563 " " NAG C 601 " - " ASN C 563 " " NAG D 601 " - " ASN D 563 " " NAG E 601 " - " ASN E 563 " " NAG F 601 " - " ASN F 563 " " NAG G 601 " - " ASN G 563 " " NAG H 601 " - " ASN H 563 " " NAG I 1 " - " ASN J 48 " " NAG K 601 " - " ASN K 563 " " NAG L 601 " - " ASN L 563 " Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 702.6 milliseconds 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5038 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 56 sheets defined 19.7% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'M' and resid 1623 through 1628 Processing helix chain 'M' and resid 1636 through 1660 removed outlier: 3.607A pdb=" N LYS M1642 " --> pdb=" O ASP M1638 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU M1643 " --> pdb=" O ASP M1639 " (cutoff:3.500A) Processing helix chain 'M' and resid 1672 through 1690 Processing helix chain 'M' and resid 1697 through 1717 removed outlier: 3.860A pdb=" N LYS M1702 " --> pdb=" O ARG M1698 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE M1703 " --> pdb=" O GLU M1699 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN M1704 " --> pdb=" O GLN M1700 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL M1708 " --> pdb=" O GLN M1704 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS M1709 " --> pdb=" O GLU M1705 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE M1710 " --> pdb=" O ARG M1706 " (cutoff:3.500A) Processing helix chain 'M' and resid 1719 through 1724 Processing helix chain 'M' and resid 1732 through 1743 Processing helix chain 'M' and resid 1743 through 1752 removed outlier: 3.787A pdb=" N ILE M1747 " --> pdb=" O HIS M1743 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TRP M1748 " --> pdb=" O ARG M1744 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN M1749 " --> pdb=" O LYS M1745 " (cutoff:3.500A) Processing helix chain 'M' and resid 1791 through 1795 Processing helix chain 'M' and resid 1796 through 1817 removed outlier: 3.900A pdb=" N TYR M1817 " --> pdb=" O GLN M1813 " (cutoff:3.500A) Processing helix chain 'M' and resid 1846 through 1860 removed outlier: 4.344A pdb=" N GLU M1851 " --> pdb=" O LYS M1847 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU M1852 " --> pdb=" O THR M1848 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR M1853 " --> pdb=" O LYS M1849 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TRP M1860 " --> pdb=" O PHE M1856 " (cutoff:3.500A) Processing helix chain 'M' and resid 1862 through 1869 removed outlier: 3.532A pdb=" N ASN M1866 " --> pdb=" O SER M1862 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU M1867 " --> pdb=" O GLN M1863 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU M1868 " --> pdb=" O TYR M1864 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS M1869 " --> pdb=" O ILE M1865 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 1862 through 1869' Processing helix chain 'M' and resid 1902 through 1914 removed outlier: 4.488A pdb=" N GLN M1906 " --> pdb=" O GLU M1902 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE M1907 " --> pdb=" O ASN M1903 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU M1914 " --> pdb=" O ASN M1910 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 360 removed outlier: 3.506A pdb=" N PHE A 358 " --> pdb=" O PHE A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 460 through 466 removed outlier: 3.700A pdb=" N LEU A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 531 removed outlier: 3.536A pdb=" N GLY A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'B' and resid 353 through 361 Processing helix chain 'B' and resid 414 through 421 removed outlier: 3.761A pdb=" N TRP B 418 " --> pdb=" O CYS B 414 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 467 removed outlier: 3.538A pdb=" N ARG B 467 " --> pdb=" O GLN B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 530 Processing helix chain 'B' and resid 553 through 557 removed outlier: 4.032A pdb=" N GLY B 557 " --> pdb=" O LYS B 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 460 through 466 removed outlier: 3.808A pdb=" N LEU C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN C 465 " --> pdb=" O ARG C 461 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU C 466 " --> pdb=" O GLU C 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 460 through 466' Processing helix chain 'C' and resid 524 through 530 Processing helix chain 'C' and resid 567 through 572 Processing helix chain 'D' and resid 353 through 360 removed outlier: 3.737A pdb=" N THR D 360 " --> pdb=" O SER D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 removed outlier: 3.612A pdb=" N ASN D 419 " --> pdb=" O GLU D 415 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY D 421 " --> pdb=" O ASP D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 466 Processing helix chain 'D' and resid 496 through 500 removed outlier: 3.694A pdb=" N TYR D 500 " --> pdb=" O PRO D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 530 Processing helix chain 'E' and resid 353 through 361 removed outlier: 3.939A pdb=" N LEU E 359 " --> pdb=" O ALA E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 removed outlier: 4.013A pdb=" N GLY E 421 " --> pdb=" O ASP E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 467 removed outlier: 3.795A pdb=" N LEU E 466 " --> pdb=" O GLU E 462 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG E 467 " --> pdb=" O GLN E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 529 Processing helix chain 'E' and resid 553 through 557 removed outlier: 3.570A pdb=" N THR E 556 " --> pdb=" O ASP E 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 360 Processing helix chain 'F' and resid 414 through 421 removed outlier: 3.521A pdb=" N TRP F 418 " --> pdb=" O CYS F 414 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY F 421 " --> pdb=" O ASP F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 467 removed outlier: 3.641A pdb=" N ARG F 467 " --> pdb=" O GLN F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 530 Processing helix chain 'G' and resid 353 through 361 Processing helix chain 'G' and resid 414 through 421 Processing helix chain 'G' and resid 460 through 467 removed outlier: 3.796A pdb=" N LEU G 464 " --> pdb=" O ALA G 460 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN G 465 " --> pdb=" O ARG G 461 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU G 466 " --> pdb=" O GLU G 462 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG G 467 " --> pdb=" O GLN G 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 460 through 467' Processing helix chain 'G' and resid 525 through 530 Processing helix chain 'G' and resid 553 through 558 removed outlier: 3.912A pdb=" N GLY G 557 " --> pdb=" O ASP G 553 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS G 558 " --> pdb=" O LYS G 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 553 through 558' Processing helix chain 'H' and resid 353 through 361 Processing helix chain 'H' and resid 414 through 421 removed outlier: 3.708A pdb=" N GLY H 421 " --> pdb=" O ASP H 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 460 through 467 removed outlier: 3.604A pdb=" N LEU H 464 " --> pdb=" O ALA H 460 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU H 466 " --> pdb=" O GLU H 462 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG H 467 " --> pdb=" O GLN H 463 " (cutoff:3.500A) Processing helix chain 'H' and resid 524 through 531 removed outlier: 3.629A pdb=" N ASN H 529 " --> pdb=" O GLU H 525 " (cutoff:3.500A) Processing helix chain 'K' and resid 353 through 361 removed outlier: 3.768A pdb=" N LEU K 359 " --> pdb=" O ALA K 355 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 421 Processing helix chain 'K' and resid 462 through 467 removed outlier: 4.167A pdb=" N LEU K 466 " --> pdb=" O GLU K 462 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG K 467 " --> pdb=" O GLN K 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 462 through 467' Processing helix chain 'K' and resid 524 through 531 removed outlier: 3.762A pdb=" N TRP K 528 " --> pdb=" O SER K 524 " (cutoff:3.500A) Processing helix chain 'K' and resid 553 through 557 removed outlier: 3.654A pdb=" N GLY K 557 " --> pdb=" O LYS K 554 " (cutoff:3.500A) Processing helix chain 'L' and resid 353 through 361 Processing helix chain 'L' and resid 414 through 421 removed outlier: 3.728A pdb=" N TRP L 418 " --> pdb=" O CYS L 414 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY L 421 " --> pdb=" O ASP L 417 " (cutoff:3.500A) Processing helix chain 'L' and resid 460 through 466 removed outlier: 3.647A pdb=" N LEU L 466 " --> pdb=" O GLU L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 524 through 530 Processing helix chain 'J' and resid 63 through 69 removed outlier: 3.540A pdb=" N LEU J 67 " --> pdb=" O HIS J 63 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 346 through 350 removed outlier: 3.703A pdb=" N THR A 366 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 381 through 383 Processing sheet with id=AA3, first strand: chain 'A' and resid 453 through 457 removed outlier: 3.542A pdb=" N THR A 477 " --> pdb=" O ASP A 453 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR A 473 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 519 " --> pdb=" O CYS A 474 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 501 " --> pdb=" O ILE A 520 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 453 through 457 removed outlier: 3.542A pdb=" N THR A 477 " --> pdb=" O ASP A 453 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR A 473 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 476 " --> pdb=" O ALA A 517 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 493 through 494 removed outlier: 3.690A pdb=" N GLN A 487 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET A 489 " --> pdb=" O THR A 535 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 552 " --> pdb=" O TYR A 534 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 346 through 348 Processing sheet with id=AA7, first strand: chain 'B' and resid 364 through 366 Processing sheet with id=AA8, first strand: chain 'B' and resid 379 through 384 removed outlier: 3.527A pdb=" N ILE B 441 " --> pdb=" O PHE B 424 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 455 through 457 removed outlier: 3.623A pdb=" N TYR B 455 " --> pdb=" O LEU B 475 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 473 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B 519 " --> pdb=" O CYS B 474 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 485 through 489 removed outlier: 3.570A pdb=" N TYR B 534 " --> pdb=" O VAL B 552 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 506 through 507 Processing sheet with id=AB3, first strand: chain 'C' and resid 346 through 350 removed outlier: 3.759A pdb=" N ARG C 346 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR C 366 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR C 363 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N PHE C 405 " --> pdb=" O ASP C 371 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 379 through 383 Processing sheet with id=AB5, first strand: chain 'C' and resid 455 through 457 removed outlier: 3.731A pdb=" N THR C 473 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 520 " --> pdb=" O VAL C 501 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 477 through 479 Processing sheet with id=AB7, first strand: chain 'C' and resid 493 through 494 removed outlier: 4.174A pdb=" N TYR C 534 " --> pdb=" O VAL C 552 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 552 " --> pdb=" O TYR C 534 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 565 through 566 removed outlier: 7.064A pdb=" N LEU C 566 " --> pdb=" O VAL D 567 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 346 through 349 removed outlier: 3.996A pdb=" N ARG D 346 " --> pdb=" O THR D 370 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 379 through 383 removed outlier: 3.503A pdb=" N THR D 379 " --> pdb=" O THR D 429 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR D 429 " --> pdb=" O THR D 379 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER D 381 " --> pdb=" O THR D 427 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE D 424 " --> pdb=" O ILE D 441 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS D 426 " --> pdb=" O GLN D 439 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN D 439 " --> pdb=" O CYS D 426 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 455 through 457 removed outlier: 3.749A pdb=" N THR D 473 " --> pdb=" O LEU D 457 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 477 through 479 removed outlier: 5.609A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 493 through 494 removed outlier: 3.536A pdb=" N GLN D 490 " --> pdb=" O GLN D 493 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR D 534 " --> pdb=" O VAL D 552 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL D 552 " --> pdb=" O TYR D 534 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 346 through 348 removed outlier: 3.534A pdb=" N PHE E 348 " --> pdb=" O LEU E 368 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 363 through 366 removed outlier: 4.347A pdb=" N THR E 363 " --> pdb=" O ILE E 413 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU E 365 " --> pdb=" O ALA E 411 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA E 411 " --> pdb=" O LEU E 365 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 390 through 391 removed outlier: 3.644A pdb=" N LYS E 391 " --> pdb=" O TRP E 382 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TRP E 382 " --> pdb=" O LYS E 391 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER E 381 " --> pdb=" O THR E 427 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR E 425 " --> pdb=" O THR E 383 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 455 through 457 removed outlier: 3.591A pdb=" N LEU E 457 " --> pdb=" O THR E 473 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR E 473 " --> pdb=" O LEU E 457 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY E 478 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 493 through 494 Processing sheet with id=AD1, first strand: chain 'E' and resid 493 through 494 removed outlier: 4.287A pdb=" N TYR E 534 " --> pdb=" O VAL E 552 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL E 552 " --> pdb=" O TYR E 534 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 346 through 350 removed outlier: 4.312A pdb=" N THR F 366 " --> pdb=" O ILE F 350 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR F 363 " --> pdb=" O ILE F 413 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE F 413 " --> pdb=" O THR F 363 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU F 365 " --> pdb=" O ALA F 411 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA F 411 " --> pdb=" O LEU F 365 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 389 through 390 removed outlier: 4.717A pdb=" N TRP F 382 " --> pdb=" O VAL F 390 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE F 441 " --> pdb=" O PHE F 424 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 455 through 457 removed outlier: 3.632A pdb=" N TYR F 455 " --> pdb=" O LEU F 475 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU F 475 " --> pdb=" O TYR F 455 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR F 473 " --> pdb=" O LEU F 457 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 493 through 494 removed outlier: 3.555A pdb=" N GLN F 487 " --> pdb=" O VAL F 537 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG F 550 " --> pdb=" O CYS F 536 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 506 through 507 Processing sheet with id=AD7, first strand: chain 'F' and resid 565 through 567 removed outlier: 6.068A pdb=" N SER F 565 " --> pdb=" O LEU G 566 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN H 563 " --> pdb=" O VAL K 564 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LEU K 566 " --> pdb=" O ASN H 563 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N SER H 565 " --> pdb=" O LEU K 566 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN K 563 " --> pdb=" O VAL L 564 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N LEU L 566 " --> pdb=" O ASN K 563 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N SER K 565 " --> pdb=" O LEU L 566 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N MET L 568 " --> pdb=" O SER K 565 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL K 567 " --> pdb=" O MET L 568 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE J 39 " --> pdb=" O SER L 565 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 347 through 350 removed outlier: 4.089A pdb=" N THR G 366 " --> pdb=" O ILE G 350 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR G 363 " --> pdb=" O ILE G 413 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU G 365 " --> pdb=" O ALA G 411 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA G 411 " --> pdb=" O LEU G 365 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS G 367 " --> pdb=" O GLY G 409 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY G 409 " --> pdb=" O CYS G 367 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 379 through 383 removed outlier: 4.110A pdb=" N THR G 379 " --> pdb=" O THR G 429 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR G 429 " --> pdb=" O THR G 379 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR G 427 " --> pdb=" O SER G 381 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE G 424 " --> pdb=" O ILE G 441 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE G 441 " --> pdb=" O PHE G 424 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 455 through 457 removed outlier: 5.279A pdb=" N TYR G 515 " --> pdb=" O GLY G 478 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 485 through 489 removed outlier: 3.514A pdb=" N PHE G 485 " --> pdb=" O ALA G 539 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR G 548 " --> pdb=" O VAL G 538 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 346 through 348 Processing sheet with id=AE4, first strand: chain 'H' and resid 363 through 364 removed outlier: 4.315A pdb=" N THR H 363 " --> pdb=" O ILE H 413 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE H 413 " --> pdb=" O THR H 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'H' and resid 380 through 383 removed outlier: 3.511A pdb=" N CYS H 426 " --> pdb=" O GLN H 439 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN H 439 " --> pdb=" O CYS H 426 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU H 437 " --> pdb=" O VAL H 428 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.970A pdb=" N THR H 477 " --> pdb=" O ASP H 453 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR H 473 " --> pdb=" O LEU H 457 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N CYS H 474 " --> pdb=" O SER H 519 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER H 519 " --> pdb=" O CYS H 474 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL H 501 " --> pdb=" O ILE H 520 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 493 through 494 removed outlier: 3.603A pdb=" N CYS H 536 " --> pdb=" O ARG H 550 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG H 550 " --> pdb=" O CYS H 536 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL H 538 " --> pdb=" O THR H 548 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 506 through 507 Processing sheet with id=AE9, first strand: chain 'K' and resid 347 through 350 removed outlier: 4.260A pdb=" N THR K 366 " --> pdb=" O ILE K 350 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 389 through 390 removed outlier: 3.589A pdb=" N TRP K 382 " --> pdb=" O VAL K 390 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN K 439 " --> pdb=" O CYS K 426 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 455 through 457 removed outlier: 3.625A pdb=" N THR K 473 " --> pdb=" O LEU K 457 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 477 through 479 removed outlier: 6.243A pdb=" N TYR K 515 " --> pdb=" O GLY K 478 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 493 through 494 Processing sheet with id=AF5, first strand: chain 'L' and resid 346 through 350 removed outlier: 3.996A pdb=" N ARG L 346 " --> pdb=" O THR L 370 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR L 370 " --> pdb=" O ARG L 346 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE L 350 " --> pdb=" O THR L 366 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR L 366 " --> pdb=" O ILE L 350 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU L 368 " --> pdb=" O GLY L 409 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N GLY L 409 " --> pdb=" O LEU L 368 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR L 370 " --> pdb=" O ALA L 407 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ALA L 407 " --> pdb=" O THR L 370 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU L 372 " --> pdb=" O PHE L 405 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 379 through 383 removed outlier: 3.961A pdb=" N THR L 379 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR L 429 " --> pdb=" O THR L 379 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 453 through 457 removed outlier: 3.655A pdb=" N TYR L 455 " --> pdb=" O LEU L 475 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR L 473 " --> pdb=" O LEU L 457 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS L 474 " --> pdb=" O SER L 519 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER L 519 " --> pdb=" O CYS L 474 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 453 through 457 removed outlier: 3.655A pdb=" N TYR L 455 " --> pdb=" O LEU L 475 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR L 473 " --> pdb=" O LEU L 457 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N TYR L 515 " --> pdb=" O GLY L 478 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 493 through 494 removed outlier: 3.643A pdb=" N ARG L 550 " --> pdb=" O CYS L 536 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL L 538 " --> pdb=" O THR L 548 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR L 548 " --> pdb=" O VAL L 538 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 20 through 22 removed outlier: 4.009A pdb=" N ILE J 22 " --> pdb=" O ILE J 32 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE J 32 " --> pdb=" O ILE J 22 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 110 through 116 removed outlier: 4.006A pdb=" N ALA J 111 " --> pdb=" O THR J 126 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL J 113 " --> pdb=" O VAL J 124 " (cutoff:3.500A) 590 hydrogen bonds defined for protein. 1485 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.55 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6608 1.34 - 1.46: 4549 1.46 - 1.58: 9929 1.58 - 1.70: 0 1.70 - 1.83: 138 Bond restraints: 21224 Sorted by residual: bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.22e+00 bond pdb=" CB ARG M1932 " pdb=" CG ARG M1932 " ideal model delta sigma weight residual 1.520 1.577 -0.057 3.00e-02 1.11e+03 3.61e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.55e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.92e+00 bond pdb=" C1 NAG F 601 " pdb=" O5 NAG F 601 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.84e+00 ... (remaining 21219 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 28126 1.82 - 3.64: 752 3.64 - 5.46: 86 5.46 - 7.28: 29 7.28 - 9.10: 7 Bond angle restraints: 29000 Sorted by residual: angle pdb=" N GLU M1804 " pdb=" CA GLU M1804 " pdb=" CB GLU M1804 " ideal model delta sigma weight residual 110.12 117.42 -7.30 1.47e+00 4.63e-01 2.47e+01 angle pdb=" CA PRO G 512 " pdb=" N PRO G 512 " pdb=" CD PRO G 512 " ideal model delta sigma weight residual 112.00 105.56 6.44 1.40e+00 5.10e-01 2.11e+01 angle pdb=" CA ARG M1932 " pdb=" CB ARG M1932 " pdb=" CG ARG M1932 " ideal model delta sigma weight residual 114.10 123.20 -9.10 2.00e+00 2.50e-01 2.07e+01 angle pdb=" CB ARG M1932 " pdb=" CG ARG M1932 " pdb=" CD ARG M1932 " ideal model delta sigma weight residual 111.30 120.40 -9.10 2.30e+00 1.89e-01 1.57e+01 angle pdb=" CA ASN K 402 " pdb=" CB ASN K 402 " pdb=" CG ASN K 402 " ideal model delta sigma weight residual 112.60 116.32 -3.72 1.00e+00 1.00e+00 1.38e+01 ... (remaining 28995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 11569 17.96 - 35.91: 996 35.91 - 53.87: 181 53.87 - 71.83: 36 71.83 - 89.78: 15 Dihedral angle restraints: 12797 sinusoidal: 5081 harmonic: 7716 Sorted by residual: dihedral pdb=" CB CYS C 474 " pdb=" SG CYS C 474 " pdb=" SG CYS C 536 " pdb=" CB CYS C 536 " ideal model delta sinusoidal sigma weight residual 93.00 169.99 -76.99 1 1.00e+01 1.00e-02 7.44e+01 dihedral pdb=" CB CYS G 367 " pdb=" SG CYS G 367 " pdb=" SG CYS G 426 " pdb=" CB CYS G 426 " ideal model delta sinusoidal sigma weight residual 93.00 162.40 -69.40 1 1.00e+01 1.00e-02 6.22e+01 dihedral pdb=" CB CYS D 474 " pdb=" SG CYS D 474 " pdb=" SG CYS D 536 " pdb=" CB CYS D 536 " ideal model delta sinusoidal sigma weight residual 93.00 160.45 -67.45 1 1.00e+01 1.00e-02 5.92e+01 ... (remaining 12794 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3100 0.088 - 0.175: 295 0.175 - 0.263: 10 0.263 - 0.350: 0 0.350 - 0.438: 2 Chirality restraints: 3407 Sorted by residual: chirality pdb=" C1 NAG G 601 " pdb=" ND2 ASN G 563 " pdb=" C2 NAG G 601 " pdb=" O5 NAG G 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" C1 NAG H 601 " pdb=" ND2 ASN H 563 " pdb=" C2 NAG H 601 " pdb=" O5 NAG H 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" C1 NAG K 601 " pdb=" ND2 ASN K 563 " pdb=" C2 NAG K 601 " pdb=" O5 NAG K 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 3404 not shown) Planarity restraints: 3704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA G 511 " -0.093 5.00e-02 4.00e+02 1.38e-01 3.04e+01 pdb=" N PRO G 512 " 0.238 5.00e-02 4.00e+02 pdb=" CA PRO G 512 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO G 512 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 488 " 0.020 2.00e-02 2.50e+03 2.14e-02 1.15e+01 pdb=" CG TRP E 488 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP E 488 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP E 488 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 488 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 488 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 488 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 488 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 488 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP E 488 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN L 563 " 0.029 2.00e-02 2.50e+03 2.62e-02 8.56e+00 pdb=" CG ASN L 563 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN L 563 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN L 563 " -0.024 2.00e-02 2.50e+03 pdb=" C1 NAG L 601 " 0.028 2.00e-02 2.50e+03 ... (remaining 3701 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 979 2.72 - 3.27: 20527 3.27 - 3.81: 32123 3.81 - 4.36: 37347 4.36 - 4.90: 63914 Nonbonded interactions: 154890 Sorted by model distance: nonbonded pdb=" OG SER E 524 " pdb=" OE1 GLU E 527 " model vdw 2.181 3.040 nonbonded pdb=" O THR L 533 " pdb=" OG1 THR L 551 " model vdw 2.187 3.040 nonbonded pdb=" O ARG M1800 " pdb=" OG1 THR M1803 " model vdw 2.202 3.040 nonbonded pdb=" OG SER G 524 " pdb=" OE1 GLU G 527 " model vdw 2.218 3.040 nonbonded pdb=" O ASN K 402 " pdb=" ND2 ASN K 402 " model vdw 2.220 3.120 ... (remaining 154885 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 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'B' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'C' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 568 o \ r resid 601)) selection = (chain 'D' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 601)) selection = (chain 'E' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 601)) selection = (chain 'F' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 601)) selection = (chain 'G' and (resid 345 through 444 or resid 449 through 512 or (resid 513 and \ (name N or name CA or name C )) or resid 514 through 601)) selection = (chain 'H' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 601)) selection = (chain 'K' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'L' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 512 or (resid 513 and (name N \ or name CA or name C )) or resid 514 through 568 or resid 601)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.200 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: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.430 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 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 : 0.003 0.077 21258 Z= 0.150 Angle : 0.709 12.840 29080 Z= 0.364 Chirality : 0.048 0.438 3407 Planarity : 0.006 0.138 3693 Dihedral : 13.991 89.784 7693 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.13 % Allowed : 0.38 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % 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: -0.97 (0.16), residues: 2574 helix: -0.37 (0.26), residues: 366 sheet: -0.13 (0.19), residues: 778 loop : -0.98 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 423 TYR 0.028 0.001 TYR G 375 PHE 0.028 0.001 PHE G 405 TRP 0.057 0.002 TRP E 488 HIS 0.006 0.001 HIS C 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (21224) covalent geometry : angle 0.68692 / 0.36 (29000) SS BOND : bond 0.00247 / 0.15 ( 22) SS BOND : angle 0.81088 / 0.54 ( 44) hydrogen bonds : bond 0.28727 / 19.10 ( 574) hydrogen bonds : angle 9.78765 / 6.90 ( 1485) link_BETA1-4 : bond 0.01388 / 0.73 ( 1) link_BETA1-4 : angle 2.03007 / 1.25 ( 3) link_NAG-ASN : bond 0.00773 / 0.42 ( 11) link_NAG-ASN : angle 5.16883 / 3.49 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 364 time to evaluate : 0.602 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 1677 MET cc_start: 0.8241 (ttt) cc_final: 0.7435 (tmm) REVERT: M 1860 TRP cc_start: 0.4556 (m-10) cc_final: 0.4053 (m-10) REVERT: C 364 LYS cc_start: 0.7390 (mttp) cc_final: 0.7178 (mtpp) REVERT: D 417 ASP cc_start: 0.7758 (t70) cc_final: 0.7501 (t70) REVERT: F 493 GLN cc_start: 0.7981 (pp30) cc_final: 0.7757 (pp30) REVERT: F 560 THR cc_start: 0.8170 (p) cc_final: 0.7956 (t) REVERT: H 489 MET cc_start: 0.8129 (tpp) cc_final: 0.7597 (mmt) REVERT: H 554 LYS cc_start: 0.8419 (tmmt) cc_final: 0.8155 (tmtt) REVERT: K 483 ASP cc_start: 0.7073 (t0) cc_final: 0.6647 (t0) REVERT: L 493 GLN cc_start: 0.8756 (mp10) cc_final: 0.8421 (mp10) REVERT: L 499 LYS cc_start: 0.7734 (mmmt) cc_final: 0.7380 (mttt) REVERT: L 553 ASP cc_start: 0.6852 (t70) cc_final: 0.6397 (t70) outliers start: 3 outliers final: 1 residues processed: 365 average time/residue: 0.1434 time to fit residues: 80.5904 Evaluate side-chains 274 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 273 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 402 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 0.0170 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 overall best weight: 1.4422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M1610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1657 GLN A 487 GLN B 419 ASN D 439 GLN ** E 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 518 HIS ** F 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 393 HIS G 529 ASN H 385 GLN ** K 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 518 HIS L 419 ASN J 29 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.184357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.121392 restraints weight = 27936.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.118885 restraints weight = 19671.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.119541 restraints weight = 17618.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.120625 restraints weight = 17196.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.120671 restraints weight = 15134.648| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21258 Z= 0.173 Angle : 0.668 11.698 29080 Z= 0.348 Chirality : 0.047 0.381 3407 Planarity : 0.005 0.056 3693 Dihedral : 4.912 33.942 2812 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.02 % Allowed : 9.35 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % 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: -0.97 (0.16), residues: 2574 helix: -0.35 (0.24), residues: 406 sheet: -0.11 (0.18), residues: 820 loop : -1.03 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 467 TYR 0.019 0.002 TYR A 500 PHE 0.020 0.002 PHE L 348 TRP 0.049 0.002 TRP E 488 HIS 0.010 0.001 HIS M1808 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (21224) covalent geometry : angle 0.64915 / 0.34 (29000) SS BOND : bond 0.00383 / 0.25 ( 22) SS BOND : angle 0.94063 / 0.63 ( 44) hydrogen bonds : bond 0.05474 / 3.64 ( 574) hydrogen bonds : angle 7.15775 / 5.07 ( 1485) link_BETA1-4 : bond 0.01110 / 0.58 ( 1) link_BETA1-4 : angle 1.88503 / 1.30 ( 3) link_NAG-ASN : bond 0.00496 / 0.28 ( 11) link_NAG-ASN : angle 4.63247 / 3.09 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 313 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: M 1792 TYR cc_start: 0.8338 (m-80) cc_final: 0.7957 (m-80) REVERT: D 417 ASP cc_start: 0.8221 (t70) cc_final: 0.7957 (t70) REVERT: H 489 MET cc_start: 0.8152 (tpp) cc_final: 0.7554 (mmt) REVERT: H 490 GLN cc_start: 0.7208 (tp40) cc_final: 0.6780 (tm-30) REVERT: H 545 ASN cc_start: 0.7163 (t0) cc_final: 0.6959 (t0) REVERT: K 463 GLN cc_start: 0.8605 (tp40) cc_final: 0.8253 (mm-40) REVERT: K 464 LEU cc_start: 0.8906 (mt) cc_final: 0.8685 (mt) REVERT: K 483 ASP cc_start: 0.7268 (t0) cc_final: 0.6727 (t0) REVERT: K 518 HIS cc_start: 0.7588 (OUTLIER) cc_final: 0.7348 (t-170) REVERT: L 493 GLN cc_start: 0.8659 (mp10) cc_final: 0.8348 (mp10) REVERT: L 499 LYS cc_start: 0.7796 (mmmt) cc_final: 0.7386 (mttt) outliers start: 24 outliers final: 14 residues processed: 321 average time/residue: 0.1293 time to fit residues: 64.3584 Evaluate side-chains 291 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 276 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1921 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 526 GLU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain G residue 393 HIS Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain G residue 541 GLU Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 555 SER Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain J residue 29 ASN Chi-restraints excluded: chain J residue 49 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 210 optimal weight: 6.9990 chunk 195 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 59 optimal weight: 0.0970 chunk 121 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M1610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1657 GLN A 487 GLN B 419 ASN ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 487 GLN H 385 GLN H 463 GLN ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.181910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.115969 restraints weight = 27839.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.114519 restraints weight = 20899.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.115293 restraints weight = 16961.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.115992 restraints weight = 16481.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.116325 restraints weight = 14733.212| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 21258 Z= 0.208 Angle : 0.675 12.725 29080 Z= 0.349 Chirality : 0.048 0.408 3407 Planarity : 0.005 0.055 3693 Dihedral : 5.017 25.299 2810 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.91 % Allowed : 12.87 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.16), residues: 2574 helix: -0.37 (0.23), residues: 406 sheet: -0.18 (0.18), residues: 795 loop : -1.10 (0.16), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 467 TYR 0.024 0.002 TYR C 375 PHE 0.035 0.002 PHE L 354 TRP 0.043 0.002 TRP E 488 HIS 0.011 0.001 HIS K 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 (21224) covalent geometry : angle 0.65449 / 0.35 (29000) SS BOND : bond 0.00451 / 0.31 ( 22) SS BOND : angle 0.97227 / 0.63 ( 44) hydrogen bonds : bond 0.05019 / 3.34 ( 574) hydrogen bonds : angle 6.70380 / 4.76 ( 1485) link_BETA1-4 : bond 0.00573 / 0.30 ( 1) link_BETA1-4 : angle 1.73414 / 1.08 ( 3) link_NAG-ASN : bond 0.00558 / 0.32 ( 11) link_NAG-ASN : angle 4.84109 / 3.14 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 290 time to evaluate : 0.808 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: M 1608 TYR cc_start: 0.5153 (t80) cc_final: 0.4869 (t80) REVERT: A 521 LEU cc_start: 0.7954 (tp) cc_final: 0.7666 (tt) REVERT: D 417 ASP cc_start: 0.8227 (t70) cc_final: 0.8005 (t70) REVERT: E 490 GLN cc_start: 0.6944 (pp30) cc_final: 0.6737 (pp30) REVERT: F 493 GLN cc_start: 0.7763 (pp30) cc_final: 0.7495 (pp30) REVERT: H 463 GLN cc_start: 0.8760 (tt0) cc_final: 0.8533 (tt0) REVERT: H 490 GLN cc_start: 0.7249 (tp40) cc_final: 0.6863 (tm-30) REVERT: K 463 GLN cc_start: 0.8752 (tp40) cc_final: 0.8289 (mm-40) REVERT: K 483 ASP cc_start: 0.7375 (t0) cc_final: 0.6779 (t0) REVERT: L 489 MET cc_start: 0.6554 (tpp) cc_final: 0.6289 (tpp) REVERT: L 499 LYS cc_start: 0.7841 (mmmt) cc_final: 0.7459 (mttt) outliers start: 45 outliers final: 31 residues processed: 316 average time/residue: 0.1338 time to fit residues: 65.7003 Evaluate side-chains 305 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 274 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1921 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 526 GLU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 535 THR Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 393 HIS Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 555 SER Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 533 THR Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain J residue 29 ASN Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 101 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 232 optimal weight: 5.9990 chunk 186 optimal weight: 30.0000 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 chunk 204 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M1610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1657 GLN E 529 ASN ** F 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 487 GLN ** F 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 393 HIS ** H 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 518 HIS ** L 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.180579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.114756 restraints weight = 27854.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.113145 restraints weight = 20599.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.114060 restraints weight = 17910.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.114841 restraints weight = 17077.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.115151 restraints weight = 14826.184| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 21258 Z= 0.218 Angle : 0.680 12.430 29080 Z= 0.351 Chirality : 0.049 0.417 3407 Planarity : 0.005 0.055 3693 Dihedral : 5.091 26.648 2810 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.29 % Allowed : 14.87 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.16), residues: 2574 helix: -0.32 (0.24), residues: 401 sheet: -0.33 (0.18), residues: 812 loop : -1.11 (0.16), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 451 TYR 0.021 0.002 TYR C 375 PHE 0.023 0.002 PHE L 354 TRP 0.049 0.002 TRP E 488 HIS 0.006 0.001 HIS F 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.22 (21224) covalent geometry : angle 0.66011 / 0.35 (29000) SS BOND : bond 0.00572 / 0.37 ( 22) SS BOND : angle 0.96447 / 0.62 ( 44) hydrogen bonds : bond 0.04618 / 3.07 ( 574) hydrogen bonds : angle 6.50309 / 4.62 ( 1485) link_BETA1-4 : bond 0.00997 / 0.52 ( 1) link_BETA1-4 : angle 1.93163 / 1.27 ( 3) link_NAG-ASN : bond 0.00545 / 0.31 ( 11) link_NAG-ASN : angle 4.77122 / 3.05 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 286 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: M 1608 TYR cc_start: 0.5108 (t80) cc_final: 0.4677 (t80) REVERT: M 1610 ASN cc_start: 0.7506 (m-40) cc_final: 0.6726 (m-40) REVERT: A 424 PHE cc_start: 0.7335 (m-80) cc_final: 0.7034 (m-80) REVERT: B 378 VAL cc_start: 0.6288 (OUTLIER) cc_final: 0.5728 (p) REVERT: C 423 ARG cc_start: 0.8163 (ttm110) cc_final: 0.7748 (tmm160) REVERT: E 490 GLN cc_start: 0.7038 (pp30) cc_final: 0.6793 (pp30) REVERT: G 391 LYS cc_start: 0.6824 (tptp) cc_final: 0.6448 (tptp) REVERT: G 489 MET cc_start: 0.7284 (mmt) cc_final: 0.6676 (mmp) REVERT: H 471 THR cc_start: 0.8413 (p) cc_final: 0.8209 (p) REVERT: H 490 GLN cc_start: 0.7226 (tp40) cc_final: 0.6875 (tm-30) REVERT: K 463 GLN cc_start: 0.8785 (tp40) cc_final: 0.8493 (mm-40) REVERT: K 483 ASP cc_start: 0.7498 (t0) cc_final: 0.6928 (t0) REVERT: K 506 MET cc_start: 0.7693 (tpp) cc_final: 0.7358 (tpp) REVERT: L 489 MET cc_start: 0.6840 (tpp) cc_final: 0.6557 (tpp) REVERT: L 499 LYS cc_start: 0.7791 (mmmt) cc_final: 0.7408 (mttt) outliers start: 54 outliers final: 40 residues processed: 322 average time/residue: 0.1385 time to fit residues: 68.3388 Evaluate side-chains 307 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 266 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1613 CYS Chi-restraints excluded: chain M residue 1911 VAL Chi-restraints excluded: chain M residue 1921 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 518 HIS Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 526 GLU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 535 THR Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 393 HIS Chi-restraints excluded: chain G residue 419 ASN Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain K residue 454 VAL Chi-restraints excluded: chain K residue 555 SER Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain J residue 29 ASN Chi-restraints excluded: chain J residue 101 TYR Chi-restraints excluded: chain J residue 123 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 239 optimal weight: 0.0030 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 224 optimal weight: 0.9980 chunk 226 optimal weight: 8.9990 chunk 187 optimal weight: 5.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M1610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1657 GLN B 419 ASN ** F 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 487 GLN ** H 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 393 HIS ** K 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 493 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.182181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.115515 restraints weight = 27704.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.114490 restraints weight = 20986.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.115429 restraints weight = 16741.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.115943 restraints weight = 15807.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.116315 restraints weight = 14990.187| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21258 Z= 0.162 Angle : 0.644 14.709 29080 Z= 0.329 Chirality : 0.047 0.399 3407 Planarity : 0.005 0.054 3693 Dihedral : 4.925 25.506 2810 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.72 % Allowed : 15.97 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.16), residues: 2574 helix: -0.28 (0.24), residues: 408 sheet: -0.25 (0.18), residues: 804 loop : -1.04 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 384 TYR 0.020 0.001 TYR C 375 PHE 0.024 0.002 PHE B 405 TRP 0.053 0.002 TRP E 488 HIS 0.006 0.001 HIS F 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (21224) covalent geometry : angle 0.62637 / 0.32 (29000) SS BOND : bond 0.00351 / 0.23 ( 22) SS BOND : angle 0.84855 / 0.54 ( 44) hydrogen bonds : bond 0.04157 / 2.77 ( 574) hydrogen bonds : angle 6.20217 / 4.39 ( 1485) link_BETA1-4 : bond 0.01069 / 0.56 ( 1) link_BETA1-4 : angle 1.87467 / 1.35 ( 3) link_NAG-ASN : bond 0.00443 / 0.23 ( 11) link_NAG-ASN : angle 4.40601 / 2.81 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 289 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 378 VAL cc_start: 0.6445 (OUTLIER) cc_final: 0.5892 (p) REVERT: C 423 ARG cc_start: 0.8150 (ttm110) cc_final: 0.7727 (tmm160) REVERT: C 477 THR cc_start: 0.8645 (t) cc_final: 0.8396 (m) REVERT: E 490 GLN cc_start: 0.7033 (pp30) cc_final: 0.6810 (pp30) REVERT: F 493 GLN cc_start: 0.7825 (pp30) cc_final: 0.7151 (pp30) REVERT: G 391 LYS cc_start: 0.6716 (tptp) cc_final: 0.6496 (tptp) REVERT: H 490 GLN cc_start: 0.7209 (tp40) cc_final: 0.6922 (tm-30) REVERT: K 463 GLN cc_start: 0.8831 (tp40) cc_final: 0.8606 (mm-40) REVERT: K 483 ASP cc_start: 0.7496 (t0) cc_final: 0.6905 (t0) REVERT: K 506 MET cc_start: 0.7685 (tpp) cc_final: 0.7348 (tpp) REVERT: L 489 MET cc_start: 0.6903 (tpp) cc_final: 0.6313 (mmm) REVERT: L 499 LYS cc_start: 0.7814 (mmmt) cc_final: 0.7439 (mttt) REVERT: L 521 LEU cc_start: 0.7686 (tp) cc_final: 0.7398 (tp) outliers start: 64 outliers final: 41 residues processed: 333 average time/residue: 0.1327 time to fit residues: 68.2711 Evaluate side-chains 314 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 272 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1612 ILE Chi-restraints excluded: chain M residue 1613 CYS Chi-restraints excluded: chain M residue 1921 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 528 TRP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 518 HIS Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 526 GLU Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 535 THR Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 393 HIS Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 480 SER Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain K residue 454 VAL Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 555 SER Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 520 ILE Chi-restraints excluded: chain J residue 101 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 91 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 208 optimal weight: 0.0970 chunk 204 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 236 optimal weight: 0.0970 chunk 176 optimal weight: 3.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M1610 ASN M1657 GLN M1910 ASN ** F 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 393 HIS G 487 GLN ** H 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 393 HIS J 29 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.184367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.116701 restraints weight = 27556.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.116783 restraints weight = 20896.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.118094 restraints weight = 15848.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.118473 restraints weight = 14832.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.118767 restraints weight = 14333.498| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21258 Z= 0.121 Angle : 0.616 12.483 29080 Z= 0.311 Chirality : 0.046 0.381 3407 Planarity : 0.005 0.053 3693 Dihedral : 4.679 23.755 2810 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.21 % Allowed : 17.50 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % 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: -0.86 (0.16), residues: 2574 helix: -0.16 (0.24), residues: 410 sheet: -0.15 (0.18), residues: 774 loop : -0.90 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 384 TYR 0.022 0.001 TYR C 375 PHE 0.018 0.002 PHE M1936 TRP 0.049 0.002 TRP E 488 HIS 0.005 0.001 HIS F 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (21224) covalent geometry : angle 0.60128 / 0.31 (29000) SS BOND : bond 0.00323 / 0.19 ( 22) SS BOND : angle 0.74442 / 0.48 ( 44) hydrogen bonds : bond 0.03746 / 2.50 ( 574) hydrogen bonds : angle 5.85066 / 4.15 ( 1485) link_BETA1-4 : bond 0.01100 / 0.58 ( 1) link_BETA1-4 : angle 1.83812 / 1.39 ( 3) link_NAG-ASN : bond 0.00504 / 0.27 ( 11) link_NAG-ASN : angle 3.96989 / 2.56 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 294 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 378 VAL cc_start: 0.6316 (OUTLIER) cc_final: 0.5747 (p) REVERT: C 419 ASN cc_start: 0.7974 (p0) cc_final: 0.7740 (m110) REVERT: D 394 THR cc_start: 0.6741 (OUTLIER) cc_final: 0.6456 (p) REVERT: D 489 MET cc_start: 0.7642 (mmt) cc_final: 0.7416 (mmt) REVERT: D 526 GLU cc_start: 0.7765 (tp30) cc_final: 0.7314 (tp30) REVERT: E 490 GLN cc_start: 0.7029 (pp30) cc_final: 0.6803 (pp30) REVERT: F 493 GLN cc_start: 0.7977 (pp30) cc_final: 0.7195 (pp30) REVERT: F 526 GLU cc_start: 0.8442 (mp0) cc_final: 0.8210 (mp0) REVERT: H 463 GLN cc_start: 0.8914 (tt0) cc_final: 0.8676 (tt0) REVERT: H 489 MET cc_start: 0.7811 (tpp) cc_final: 0.7157 (mmt) REVERT: H 490 GLN cc_start: 0.7176 (tp40) cc_final: 0.6923 (tm-30) REVERT: H 506 MET cc_start: 0.6312 (mpp) cc_final: 0.6045 (mpp) REVERT: K 463 GLN cc_start: 0.8919 (tp40) cc_final: 0.8651 (mm-40) REVERT: K 483 ASP cc_start: 0.7423 (t0) cc_final: 0.6820 (t0) REVERT: L 489 MET cc_start: 0.7110 (tpp) cc_final: 0.6524 (mmm) REVERT: L 499 LYS cc_start: 0.7785 (mmmt) cc_final: 0.7419 (mttt) REVERT: L 521 LEU cc_start: 0.7635 (tp) cc_final: 0.7326 (tp) REVERT: L 553 ASP cc_start: 0.7448 (t70) cc_final: 0.7084 (m-30) outliers start: 52 outliers final: 37 residues processed: 330 average time/residue: 0.1549 time to fit residues: 78.7572 Evaluate side-chains 310 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 271 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1613 CYS Chi-restraints excluded: chain M residue 1870 LYS Chi-restraints excluded: chain M residue 1911 VAL Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 528 TRP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 518 HIS Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 382 TRP Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 393 HIS Chi-restraints excluded: chain G residue 524 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 480 SER Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain K residue 454 VAL Chi-restraints excluded: chain K residue 499 LYS Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 564 VAL Chi-restraints excluded: chain L residue 520 ILE Chi-restraints excluded: chain J residue 101 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 54 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 221 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 251 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M1610 ASN M1657 GLN B 393 HIS ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 463 GLN ** H 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 393 HIS ** K 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.180815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.116221 restraints weight = 27720.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.113523 restraints weight = 20882.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.114028 restraints weight = 17337.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.114661 restraints weight = 16307.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.115021 restraints weight = 15150.110| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 21258 Z= 0.204 Angle : 0.667 14.330 29080 Z= 0.341 Chirality : 0.048 0.422 3407 Planarity : 0.005 0.054 3693 Dihedral : 4.904 26.309 2810 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.80 % Allowed : 18.05 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % 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: -0.98 (0.16), residues: 2574 helix: -0.18 (0.24), residues: 408 sheet: -0.29 (0.18), residues: 804 loop : -0.97 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 451 TYR 0.020 0.002 TYR C 375 PHE 0.018 0.002 PHE D 479 TRP 0.049 0.002 TRP E 488 HIS 0.007 0.001 HIS F 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.20 (21224) covalent geometry : angle 0.65188 / 0.34 (29000) SS BOND : bond 0.00484 / 0.33 ( 22) SS BOND : angle 0.89232 / 0.58 ( 44) hydrogen bonds : bond 0.04083 / 2.71 ( 574) hydrogen bonds : angle 5.94153 / 4.21 ( 1485) link_BETA1-4 : bond 0.01281 / 0.67 ( 1) link_BETA1-4 : angle 1.94944 / 1.39 ( 3) link_NAG-ASN : bond 0.00466 / 0.26 ( 11) link_NAG-ASN : angle 4.19312 / 2.63 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 266 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: M 1606 LYS cc_start: 0.5550 (tttm) cc_final: 0.5311 (tttm) REVERT: B 378 VAL cc_start: 0.6512 (OUTLIER) cc_final: 0.5944 (p) REVERT: B 562 TYR cc_start: 0.7725 (OUTLIER) cc_final: 0.6103 (m-10) REVERT: C 423 ARG cc_start: 0.8056 (ttm110) cc_final: 0.7663 (tmm160) REVERT: D 348 PHE cc_start: 0.7773 (m-80) cc_final: 0.7507 (m-80) REVERT: D 394 THR cc_start: 0.6722 (OUTLIER) cc_final: 0.6436 (p) REVERT: D 526 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7403 (tp30) REVERT: E 490 GLN cc_start: 0.7108 (pp30) cc_final: 0.6879 (pp30) REVERT: F 493 GLN cc_start: 0.7900 (pp30) cc_final: 0.7183 (pp30) REVERT: F 526 GLU cc_start: 0.8517 (mp0) cc_final: 0.8251 (mp0) REVERT: H 506 MET cc_start: 0.6420 (mpp) cc_final: 0.6153 (mpp) REVERT: K 463 GLN cc_start: 0.8939 (tp40) cc_final: 0.8662 (mm-40) REVERT: K 483 ASP cc_start: 0.7473 (t0) cc_final: 0.6881 (t0) REVERT: K 543 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8137 (mm) REVERT: K 553 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7483 (m-30) REVERT: L 405 PHE cc_start: 0.5509 (t80) cc_final: 0.5213 (t80) REVERT: L 499 LYS cc_start: 0.7787 (mmmt) cc_final: 0.7391 (mttt) outliers start: 66 outliers final: 46 residues processed: 314 average time/residue: 0.1583 time to fit residues: 76.6607 Evaluate side-chains 311 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 259 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1613 CYS Chi-restraints excluded: chain M residue 1870 LYS Chi-restraints excluded: chain M residue 1911 VAL Chi-restraints excluded: chain M residue 1921 VAL Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 528 TRP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 562 TYR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 518 HIS Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 526 GLU Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 382 TRP Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 535 THR Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 393 HIS Chi-restraints excluded: chain G residue 524 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 480 SER Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain K residue 454 VAL Chi-restraints excluded: chain K residue 543 LEU Chi-restraints excluded: chain K residue 553 ASP Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 520 ILE Chi-restraints excluded: chain J residue 101 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 144 optimal weight: 0.0170 chunk 27 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 202 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 227 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 177 optimal weight: 0.5980 chunk 50 optimal weight: 8.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M1610 ASN M1657 GLN B 393 HIS E 385 GLN ** F 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 393 HIS G 487 GLN ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 393 HIS ** K 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.184541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.118300 restraints weight = 27460.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.116772 restraints weight = 21148.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.117683 restraints weight = 16318.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.118323 restraints weight = 15415.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.118655 restraints weight = 14489.457| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21258 Z= 0.120 Angle : 0.627 17.478 29080 Z= 0.315 Chirality : 0.046 0.397 3407 Planarity : 0.005 0.052 3693 Dihedral : 4.624 23.838 2810 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.63 % Allowed : 18.69 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.16), residues: 2574 helix: -0.13 (0.25), residues: 414 sheet: -0.16 (0.18), residues: 794 loop : -0.83 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 384 TYR 0.020 0.001 TYR J 134 PHE 0.012 0.001 PHE L 348 TRP 0.058 0.002 TRP E 488 HIS 0.005 0.001 HIS D 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (21224) covalent geometry : angle 0.61359 / 0.31 (29000) SS BOND : bond 0.00239 / 0.15 ( 22) SS BOND : angle 0.74073 / 0.49 ( 44) hydrogen bonds : bond 0.03573 / 2.40 ( 574) hydrogen bonds : angle 5.66968 / 4.01 ( 1485) link_BETA1-4 : bond 0.01062 / 0.56 ( 1) link_BETA1-4 : angle 1.86960 / 1.45 ( 3) link_NAG-ASN : bond 0.00502 / 0.28 ( 11) link_NAG-ASN : angle 3.87488 / 2.47 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 279 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 378 VAL cc_start: 0.6209 (OUTLIER) cc_final: 0.5665 (p) REVERT: C 423 ARG cc_start: 0.7991 (ttm110) cc_final: 0.7523 (tmm160) REVERT: D 348 PHE cc_start: 0.7731 (m-80) cc_final: 0.7509 (m-80) REVERT: D 394 THR cc_start: 0.6666 (OUTLIER) cc_final: 0.6371 (p) REVERT: D 526 GLU cc_start: 0.7747 (tp30) cc_final: 0.7276 (tp30) REVERT: F 384 ARG cc_start: 0.8360 (mtp85) cc_final: 0.8118 (mtt90) REVERT: F 461 ARG cc_start: 0.6846 (ttp-110) cc_final: 0.6614 (mtm110) REVERT: F 526 GLU cc_start: 0.8459 (mp0) cc_final: 0.8172 (mp0) REVERT: H 489 MET cc_start: 0.7858 (tpp) cc_final: 0.7236 (mmt) REVERT: H 506 MET cc_start: 0.6249 (mpp) cc_final: 0.6027 (mpp) REVERT: K 463 GLN cc_start: 0.8924 (tp40) cc_final: 0.8718 (mm-40) REVERT: K 483 ASP cc_start: 0.7460 (t0) cc_final: 0.6824 (t0) REVERT: K 543 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8117 (mm) REVERT: L 489 MET cc_start: 0.6700 (tpp) cc_final: 0.6319 (tpp) REVERT: L 499 LYS cc_start: 0.7735 (mmmt) cc_final: 0.7496 (tptt) outliers start: 62 outliers final: 43 residues processed: 324 average time/residue: 0.1575 time to fit residues: 79.0979 Evaluate side-chains 316 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 270 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1613 CYS Chi-restraints excluded: chain M residue 1870 LYS Chi-restraints excluded: chain M residue 1911 VAL Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 528 TRP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 518 HIS Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 382 TRP Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 535 THR Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 393 HIS Chi-restraints excluded: chain G residue 524 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 480 SER Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 543 LEU Chi-restraints excluded: chain K residue 564 VAL Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 520 ILE Chi-restraints excluded: chain J residue 101 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 78 optimal weight: 8.9990 chunk 211 optimal weight: 20.0000 chunk 229 optimal weight: 10.0000 chunk 22 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 239 optimal weight: 8.9990 chunk 247 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 215 optimal weight: 6.9990 chunk 164 optimal weight: 20.0000 chunk 179 optimal weight: 2.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M1610 ASN M1657 GLN ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 GLN ** C 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 393 HIS K 393 HIS ** K 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.179771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.114415 restraints weight = 27976.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.112409 restraints weight = 22432.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.113292 restraints weight = 18728.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.113876 restraints weight = 17498.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.113971 restraints weight = 16701.514| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 21258 Z= 0.223 Angle : 0.702 16.702 29080 Z= 0.359 Chirality : 0.049 0.447 3407 Planarity : 0.005 0.054 3693 Dihedral : 5.019 27.258 2810 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.68 % Allowed : 19.37 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.16), residues: 2574 helix: -0.22 (0.24), residues: 410 sheet: -0.30 (0.18), residues: 805 loop : -1.00 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 451 TYR 0.020 0.002 TYR H 515 PHE 0.029 0.002 PHE B 358 TRP 0.062 0.002 TRP E 488 HIS 0.008 0.001 HIS G 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.22 (21224) covalent geometry : angle 0.68704 / 0.36 (29000) SS BOND : bond 0.00584 / 0.41 ( 22) SS BOND : angle 1.01726 / 0.69 ( 44) hydrogen bonds : bond 0.04124 / 2.74 ( 574) hydrogen bonds : angle 5.90545 / 4.18 ( 1485) link_BETA1-4 : bond 0.01164 / 0.61 ( 1) link_BETA1-4 : angle 2.22073 / 1.49 ( 3) link_NAG-ASN : bond 0.00571 / 0.31 ( 11) link_NAG-ASN : angle 4.19927 / 2.58 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 256 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 THR cc_start: 0.8191 (OUTLIER) cc_final: 0.7896 (p) REVERT: B 378 VAL cc_start: 0.6094 (OUTLIER) cc_final: 0.5470 (p) REVERT: B 562 TYR cc_start: 0.7744 (OUTLIER) cc_final: 0.6074 (m-10) REVERT: C 423 ARG cc_start: 0.8118 (ttm110) cc_final: 0.7807 (tmm160) REVERT: D 394 THR cc_start: 0.6616 (OUTLIER) cc_final: 0.6305 (p) REVERT: D 526 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7368 (tp30) REVERT: F 461 ARG cc_start: 0.6876 (ttp-110) cc_final: 0.6627 (mtm110) REVERT: F 493 GLN cc_start: 0.8250 (pm20) cc_final: 0.7826 (pm20) REVERT: F 526 GLU cc_start: 0.8356 (mp0) cc_final: 0.8093 (mp0) REVERT: K 483 ASP cc_start: 0.7490 (t0) cc_final: 0.6961 (t0) REVERT: K 543 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8088 (mm) outliers start: 63 outliers final: 44 residues processed: 302 average time/residue: 0.1611 time to fit residues: 75.0337 Evaluate side-chains 298 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 248 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1613 CYS Chi-restraints excluded: chain M residue 1870 LYS Chi-restraints excluded: chain M residue 1911 VAL Chi-restraints excluded: chain M residue 1921 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 528 TRP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 562 TYR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 518 HIS Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 526 GLU Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 382 TRP Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 535 THR Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 393 HIS Chi-restraints excluded: chain G residue 524 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 480 SER Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain K residue 454 VAL Chi-restraints excluded: chain K residue 543 LEU Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain J residue 101 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 203 optimal weight: 30.0000 chunk 107 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 chunk 80 optimal weight: 0.4980 chunk 238 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 28 optimal weight: 20.0000 chunk 200 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M1610 ASN M1657 GLN M1743 HIS B 393 HIS B 465 ASN C 487 GLN ** C 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 HIS ** F 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 393 HIS H 430 HIS K 393 HIS ** K 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.183663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.120369 restraints weight = 27619.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.115491 restraints weight = 20972.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.116980 restraints weight = 18761.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.117852 restraints weight = 16672.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.118510 restraints weight = 15039.155| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21258 Z= 0.127 Angle : 0.647 16.864 29080 Z= 0.326 Chirality : 0.047 0.418 3407 Planarity : 0.005 0.060 3693 Dihedral : 4.728 24.494 2810 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.42 % Allowed : 19.03 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % 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: -0.82 (0.16), residues: 2574 helix: -0.11 (0.25), residues: 411 sheet: -0.18 (0.18), residues: 806 loop : -0.84 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 384 TYR 0.021 0.001 TYR H 515 PHE 0.025 0.001 PHE B 358 TRP 0.050 0.002 TRP E 488 HIS 0.007 0.001 HIS H 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (21224) covalent geometry : angle 0.63298 / 0.32 (29000) SS BOND : bond 0.00254 / 0.15 ( 22) SS BOND : angle 1.01157 / 0.63 ( 44) hydrogen bonds : bond 0.03543 / 2.36 ( 574) hydrogen bonds : angle 5.61000 / 3.97 ( 1485) link_BETA1-4 : bond 0.01197 / 0.63 ( 1) link_BETA1-4 : angle 2.16326 / 1.66 ( 3) link_NAG-ASN : bond 0.00466 / 0.26 ( 11) link_NAG-ASN : angle 3.92707 / 2.47 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 271 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 530 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7885 (p) REVERT: B 378 VAL cc_start: 0.6132 (OUTLIER) cc_final: 0.5579 (p) REVERT: C 423 ARG cc_start: 0.8045 (ttm110) cc_final: 0.7620 (tmm160) REVERT: D 394 THR cc_start: 0.6651 (OUTLIER) cc_final: 0.6355 (p) REVERT: D 526 GLU cc_start: 0.7754 (tp30) cc_final: 0.7270 (tp30) REVERT: F 493 GLN cc_start: 0.8247 (pm20) cc_final: 0.7754 (pm20) REVERT: F 526 GLU cc_start: 0.8426 (mp0) cc_final: 0.8121 (mp0) REVERT: H 489 MET cc_start: 0.7890 (tpp) cc_final: 0.7220 (mmt) REVERT: K 483 ASP cc_start: 0.7440 (t0) cc_final: 0.6811 (t0) REVERT: K 543 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8129 (mm) REVERT: L 489 MET cc_start: 0.6703 (tpp) cc_final: 0.6340 (tpp) REVERT: L 499 LYS cc_start: 0.7649 (tppt) cc_final: 0.7101 (tppt) REVERT: J 4 ARG cc_start: 0.6154 (mpp80) cc_final: 0.5784 (mtt180) outliers start: 57 outliers final: 43 residues processed: 311 average time/residue: 0.1565 time to fit residues: 75.3511 Evaluate side-chains 314 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 267 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1613 CYS Chi-restraints excluded: chain M residue 1870 LYS Chi-restraints excluded: chain M residue 1911 VAL Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 528 TRP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 518 HIS Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 382 TRP Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 535 THR Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 524 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 480 SER Chi-restraints excluded: chain H residue 506 MET Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain K residue 543 LEU Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain J residue 101 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 208 optimal weight: 30.0000 chunk 110 optimal weight: 1.9990 chunk 164 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 206 optimal weight: 0.4980 chunk 221 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M1657 GLN M1743 HIS B 465 ASN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 HIS ** F 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 393 HIS K 393 HIS ** K 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.184171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.116337 restraints weight = 27553.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.116940 restraints weight = 20860.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.116973 restraints weight = 16309.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.117672 restraints weight = 16178.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.118323 restraints weight = 14720.671| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21258 Z= 0.128 Angle : 0.644 16.552 29080 Z= 0.325 Chirality : 0.046 0.386 3407 Planarity : 0.005 0.061 3693 Dihedral : 4.680 24.194 2810 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.25 % Allowed : 19.75 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % 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: -0.77 (0.16), residues: 2574 helix: -0.16 (0.25), residues: 412 sheet: -0.11 (0.19), residues: 783 loop : -0.80 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 384 TYR 0.021 0.001 TYR C 375 PHE 0.029 0.002 PHE B 358 TRP 0.062 0.002 TRP E 488 HIS 0.008 0.001 HIS D 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (21224) covalent geometry : angle 0.63094 / 0.32 (29000) SS BOND : bond 0.00292 / 0.18 ( 22) SS BOND : angle 0.94137 / 0.60 ( 44) hydrogen bonds : bond 0.03519 / 2.32 ( 574) hydrogen bonds : angle 5.55125 / 3.92 ( 1485) link_BETA1-4 : bond 0.01153 / 0.61 ( 1) link_BETA1-4 : angle 2.12071 / 1.61 ( 3) link_NAG-ASN : bond 0.00434 / 0.23 ( 11) link_NAG-ASN : angle 3.76990 / 2.39 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4754.38 seconds wall clock time: 82 minutes 41.76 seconds (4961.76 seconds total)