Starting phenix.real_space_refine on Wed Jun 18 06:39:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y0j_33547/06_2025/7y0j_33547.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y0j_33547/06_2025/7y0j_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7y0j_33547/06_2025/7y0j_33547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y0j_33547/06_2025/7y0j_33547.map" model { file = "/net/cci-nas-00/data/ceres_data/7y0j_33547/06_2025/7y0j_33547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y0j_33547/06_2025/7y0j_33547.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 14.30, per 1000 atoms: 0.69 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: 4.54 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.96 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: 7.45 Time building geometry restraints manager: 5.52 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 - 22.19: 12122 22.19 - 44.39: 809 44.39 - 66.58: 82 66.58 - 88.78: 30 88.78 - 110.97: 6 Dihedral angle restraints: 13049 sinusoidal: 5333 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 13046 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 568 or res \ id 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 568 or res \ id 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 568 or res \ id 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 568 or resid 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 568 or res \ id 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: 4.100 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: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 48.900 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.090 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 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 : 14.370 110.972 7945 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.49 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.057 0.002 TRP E 488 HIS 0.006 0.001 HIS C 518 PHE 0.028 0.001 PHE G 405 TYR 0.028 0.001 TYR G 375 ARG 0.007 0.000 ARG C 423 Details of bonding type rmsd link_NAG-ASN : bond 0.00773 ( 11) link_NAG-ASN : angle 5.16883 ( 33) link_BETA1-4 : bond 0.01388 ( 1) link_BETA1-4 : angle 2.03007 ( 3) hydrogen bonds : bond 0.28727 ( 574) hydrogen bonds : angle 9.78765 ( 1485) SS BOND : bond 0.00247 ( 22) SS BOND : angle 0.81088 ( 44) covalent geometry : bond 0.00321 (21224) covalent geometry : angle 0.68692 (29000) *********************** 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 : 2.195 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: 0.3437 time to fit residues: 192.2084 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 : 2.209 ------------------------------------------------------------------------------- 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 217 optimal weight: 0.9990 chunk 194 optimal weight: 0.3980 chunk 108 optimal weight: 0.1980 chunk 66 optimal weight: 0.6980 chunk 131 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 201 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 233 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M1610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1657 GLN A 487 GLN B 419 ASN D 439 GLN E 493 GLN E 518 HIS ** F 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 393 HIS G 529 ASN H 385 GLN ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.188021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.126255 restraints weight = 27585.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.121732 restraints weight = 21638.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.123320 restraints weight = 19989.354| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21258 Z= 0.128 Angle : 0.636 10.773 29080 Z= 0.328 Chirality : 0.047 0.388 3407 Planarity : 0.005 0.056 3693 Dihedral : 7.183 95.251 3064 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.02 % Allowed : 8.58 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.16), residues: 2574 helix: -0.39 (0.24), residues: 408 sheet: -0.01 (0.18), residues: 793 loop : -0.93 (0.17), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP E 488 HIS 0.011 0.001 HIS M1808 PHE 0.019 0.002 PHE L 348 TYR 0.022 0.001 TYR A 500 ARG 0.006 0.000 ARG K 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00509 ( 11) link_NAG-ASN : angle 4.25987 ( 33) link_BETA1-4 : bond 0.00643 ( 1) link_BETA1-4 : angle 2.29136 ( 3) hydrogen bonds : bond 0.04970 ( 574) hydrogen bonds : angle 6.97189 ( 1485) SS BOND : bond 0.00263 ( 22) SS BOND : angle 0.86842 ( 44) covalent geometry : bond 0.00284 (21224) covalent geometry : angle 0.61876 (29000) *********************** 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 348 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 324 time to evaluate : 2.171 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: M 1792 TYR cc_start: 0.8338 (m-80) cc_final: 0.7959 (m-80) REVERT: B 417 ASP cc_start: 0.9128 (m-30) cc_final: 0.8896 (p0) REVERT: D 417 ASP cc_start: 0.8122 (t70) cc_final: 0.7878 (t70) REVERT: F 560 THR cc_start: 0.8098 (p) cc_final: 0.7884 (t) REVERT: H 489 MET cc_start: 0.8074 (tpp) cc_final: 0.7245 (mmt) REVERT: H 490 GLN cc_start: 0.7153 (tp40) cc_final: 0.6765 (tm-30) REVERT: H 545 ASN cc_start: 0.6985 (t0) cc_final: 0.6785 (t0) REVERT: H 554 LYS cc_start: 0.8344 (tmmt) cc_final: 0.8125 (ttpp) REVERT: K 464 LEU cc_start: 0.8894 (mt) cc_final: 0.8668 (mt) REVERT: K 483 ASP cc_start: 0.7214 (t0) cc_final: 0.6619 (t0) REVERT: L 493 GLN cc_start: 0.8668 (mp10) cc_final: 0.8352 (mp10) REVERT: L 499 LYS cc_start: 0.7782 (mmmt) cc_final: 0.7398 (mttt) outliers start: 24 outliers final: 13 residues processed: 332 average time/residue: 0.3444 time to fit residues: 173.4795 Evaluate side-chains 288 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 275 time to evaluate : 2.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1921 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 526 GLU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain E residue 382 TRP 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 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 8 optimal weight: 0.6980 chunk 215 optimal weight: 0.4980 chunk 244 optimal weight: 9.9990 chunk 133 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 231 optimal weight: 30.0000 chunk 126 optimal weight: 0.7980 chunk 204 optimal weight: 1.9990 chunk 154 optimal weight: 0.6980 chunk 237 optimal weight: 4.9990 chunk 232 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 463 GLN ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.187534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.121181 restraints weight = 27140.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.121126 restraints weight = 20229.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.122041 restraints weight = 16433.848| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21258 Z= 0.122 Angle : 0.606 10.764 29080 Z= 0.310 Chirality : 0.046 0.384 3407 Planarity : 0.005 0.050 3693 Dihedral : 6.695 87.837 3062 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.57 % Allowed : 12.02 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.16), residues: 2574 helix: -0.28 (0.24), residues: 407 sheet: 0.09 (0.19), residues: 775 loop : -0.90 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP E 488 HIS 0.010 0.001 HIS G 393 PHE 0.021 0.002 PHE B 405 TYR 0.025 0.001 TYR C 375 ARG 0.010 0.000 ARG K 514 Details of bonding type rmsd link_NAG-ASN : bond 0.00521 ( 11) link_NAG-ASN : angle 4.06731 ( 33) link_BETA1-4 : bond 0.00896 ( 1) link_BETA1-4 : angle 2.28040 ( 3) hydrogen bonds : bond 0.04391 ( 574) hydrogen bonds : angle 6.44435 ( 1485) SS BOND : bond 0.00228 ( 22) SS BOND : angle 0.78673 ( 44) covalent geometry : bond 0.00279 (21224) covalent geometry : angle 0.58944 (29000) *********************** 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 341 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 304 time to evaluate : 2.278 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: A 521 LEU cc_start: 0.8006 (tp) cc_final: 0.7617 (tt) REVERT: B 378 VAL cc_start: 0.6424 (OUTLIER) cc_final: 0.5869 (p) REVERT: D 417 ASP cc_start: 0.8108 (t70) cc_final: 0.7861 (t70) REVERT: D 489 MET cc_start: 0.7268 (mmt) cc_final: 0.6832 (mmm) REVERT: D 526 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7319 (tp30) REVERT: E 488 TRP cc_start: 0.7320 (m-10) cc_final: 0.7097 (m-10) REVERT: F 526 GLU cc_start: 0.8342 (mp0) cc_final: 0.8048 (mp0) REVERT: F 560 THR cc_start: 0.8025 (p) cc_final: 0.7808 (t) REVERT: H 463 GLN cc_start: 0.8709 (tt0) cc_final: 0.8484 (tt0) REVERT: H 489 MET cc_start: 0.8020 (tpp) cc_final: 0.7362 (mmt) REVERT: H 554 LYS cc_start: 0.8322 (tmmt) cc_final: 0.8033 (ttpp) REVERT: K 483 ASP cc_start: 0.7258 (t0) cc_final: 0.6593 (t0) REVERT: K 506 MET cc_start: 0.7610 (tpp) cc_final: 0.7318 (tpp) REVERT: L 489 MET cc_start: 0.6393 (tpp) cc_final: 0.6177 (tpp) REVERT: L 499 LYS cc_start: 0.7784 (mmmt) cc_final: 0.7462 (mttt) outliers start: 37 outliers final: 21 residues processed: 321 average time/residue: 0.3164 time to fit residues: 157.4539 Evaluate side-chains 301 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 278 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1911 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 C residue 370 THR Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 432 ASP 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 382 TRP Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 535 THR Chi-restraints excluded: chain F residue 430 HIS 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 H residue 473 THR 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 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 77 optimal weight: 9.9990 chunk 245 optimal weight: 7.9990 chunk 145 optimal weight: 50.0000 chunk 133 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 164 optimal weight: 0.0170 chunk 66 optimal weight: 2.9990 chunk 93 optimal weight: 0.0000 chunk 223 optimal weight: 0.0570 chunk 48 optimal weight: 7.9990 chunk 209 optimal weight: 30.0000 overall best weight: 0.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M1610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1657 GLN A 487 GLN ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 ASN ** F 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 393 HIS ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.187744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.120802 restraints weight = 27236.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.120902 restraints weight = 20174.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.121724 restraints weight = 16096.468| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21258 Z= 0.113 Angle : 0.590 10.427 29080 Z= 0.300 Chirality : 0.046 0.379 3407 Planarity : 0.004 0.049 3693 Dihedral : 6.198 79.459 3062 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.40 % Allowed : 14.15 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.16), residues: 2574 helix: -0.19 (0.24), residues: 405 sheet: 0.08 (0.18), residues: 798 loop : -0.76 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 488 HIS 0.009 0.001 HIS M1808 PHE 0.021 0.001 PHE L 348 TYR 0.021 0.001 TYR C 375 ARG 0.004 0.000 ARG F 461 Details of bonding type rmsd link_NAG-ASN : bond 0.00499 ( 11) link_NAG-ASN : angle 3.84378 ( 33) link_BETA1-4 : bond 0.01326 ( 1) link_BETA1-4 : angle 2.23483 ( 3) hydrogen bonds : bond 0.03766 ( 574) hydrogen bonds : angle 5.99633 ( 1485) SS BOND : bond 0.00220 ( 22) SS BOND : angle 0.72974 ( 44) covalent geometry : bond 0.00257 (21224) covalent geometry : angle 0.57518 (29000) *********************** 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 343 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 310 time to evaluate : 2.492 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: A 521 LEU cc_start: 0.7863 (tp) cc_final: 0.7634 (tt) REVERT: D 394 THR cc_start: 0.6563 (OUTLIER) cc_final: 0.6306 (p) REVERT: D 417 ASP cc_start: 0.7980 (t70) cc_final: 0.7771 (t70) REVERT: D 526 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7177 (tp30) REVERT: H 489 MET cc_start: 0.7993 (tpp) cc_final: 0.7392 (mmt) REVERT: H 554 LYS cc_start: 0.8235 (tmmt) cc_final: 0.7966 (ttpp) REVERT: K 483 ASP cc_start: 0.7213 (t0) cc_final: 0.6623 (t0) REVERT: L 354 PHE cc_start: 0.6128 (m-80) cc_final: 0.5842 (t80) REVERT: L 489 MET cc_start: 0.6566 (tpp) cc_final: 0.6352 (tpp) REVERT: L 493 GLN cc_start: 0.8474 (mp10) cc_final: 0.8229 (mp10) REVERT: L 499 LYS cc_start: 0.7801 (mmmt) cc_final: 0.7317 (mttt) REVERT: L 521 LEU cc_start: 0.7734 (tp) cc_final: 0.7525 (tp) outliers start: 33 outliers final: 20 residues processed: 327 average time/residue: 0.3330 time to fit residues: 169.9687 Evaluate side-chains 296 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 274 time to evaluate : 3.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1911 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 432 ASP 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 382 TRP 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 F residue 430 HIS 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 477 THR Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain J residue 29 ASN Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 101 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 97 optimal weight: 0.9990 chunk 185 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 202 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 74 optimal weight: 0.0980 chunk 72 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 242 optimal weight: 9.9990 chunk 207 optimal weight: 20.0000 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M1610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1657 GLN ** M1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 ASN ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 430 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** G 487 GLN ** H 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 393 HIS J 29 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.186874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.120420 restraints weight = 27210.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.119182 restraints weight = 20768.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.120720 restraints weight = 18837.219| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21258 Z= 0.122 Angle : 0.594 13.934 29080 Z= 0.301 Chirality : 0.046 0.382 3407 Planarity : 0.004 0.049 3693 Dihedral : 5.925 72.849 3062 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.87 % Allowed : 15.21 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.16), residues: 2574 helix: -0.15 (0.24), residues: 410 sheet: 0.12 (0.18), residues: 785 loop : -0.76 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP E 488 HIS 0.008 0.001 HIS M1808 PHE 0.020 0.001 PHE L 354 TYR 0.019 0.001 TYR J 134 ARG 0.006 0.000 ARG C 384 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 11) link_NAG-ASN : angle 3.76416 ( 33) link_BETA1-4 : bond 0.01148 ( 1) link_BETA1-4 : angle 2.24139 ( 3) hydrogen bonds : bond 0.03642 ( 574) hydrogen bonds : angle 5.79569 ( 1485) SS BOND : bond 0.00246 ( 22) SS BOND : angle 0.72303 ( 44) covalent geometry : bond 0.00285 (21224) covalent geometry : angle 0.58049 (29000) *********************** 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 321 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 277 time to evaluate : 2.385 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: B 378 VAL cc_start: 0.6497 (OUTLIER) cc_final: 0.5956 (p) REVERT: D 348 PHE cc_start: 0.7566 (m-80) cc_final: 0.7340 (m-80) REVERT: D 417 ASP cc_start: 0.8059 (t70) cc_final: 0.7854 (t70) REVERT: D 489 MET cc_start: 0.7428 (mmt) cc_final: 0.7195 (mmt) REVERT: D 526 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7232 (tp30) REVERT: F 491 ARG cc_start: 0.7836 (ttp-170) cc_final: 0.7465 (ttp-110) REVERT: H 489 MET cc_start: 0.7942 (tpp) cc_final: 0.7269 (mmt) REVERT: H 506 MET cc_start: 0.6820 (mmm) cc_final: 0.6472 (mpp) REVERT: K 418 TRP cc_start: 0.6290 (t-100) cc_final: 0.5711 (t-100) REVERT: K 483 ASP cc_start: 0.7278 (t0) cc_final: 0.6635 (t0) REVERT: L 489 MET cc_start: 0.6760 (tpp) cc_final: 0.6466 (tpp) REVERT: L 499 LYS cc_start: 0.7778 (mmmt) cc_final: 0.7411 (mttt) REVERT: L 521 LEU cc_start: 0.7678 (tp) cc_final: 0.7445 (tp) outliers start: 44 outliers final: 28 residues processed: 306 average time/residue: 0.3291 time to fit residues: 157.0969 Evaluate side-chains 289 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 259 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1613 CYS Chi-restraints excluded: chain M residue 1911 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 552 VAL Chi-restraints excluded: chain D residue 432 ASP 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 382 TRP Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 535 THR Chi-restraints excluded: chain F residue 430 HIS 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 480 SER Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 466 LEU Chi-restraints excluded: chain J residue 29 ASN Chi-restraints excluded: chain J residue 69 LYS 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 185 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 214 optimal weight: 0.0670 chunk 251 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 113 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 193 optimal weight: 0.0970 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M1610 ASN M1657 GLN ** M1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 393 HIS ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 393 HIS K 518 HIS J 29 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.186597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.120110 restraints weight = 27107.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.118913 restraints weight = 19621.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.120248 restraints weight = 16871.708| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21258 Z= 0.119 Angle : 0.588 12.383 29080 Z= 0.299 Chirality : 0.046 0.383 3407 Planarity : 0.004 0.049 3693 Dihedral : 5.695 65.931 3062 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.00 % Allowed : 15.85 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.16), residues: 2574 helix: -0.06 (0.25), residues: 409 sheet: 0.07 (0.18), residues: 785 loop : -0.71 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP E 488 HIS 0.008 0.001 HIS M1808 PHE 0.018 0.001 PHE L 354 TYR 0.023 0.001 TYR C 375 ARG 0.008 0.000 ARG C 384 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 11) link_NAG-ASN : angle 3.67271 ( 33) link_BETA1-4 : bond 0.00967 ( 1) link_BETA1-4 : angle 2.07237 ( 3) hydrogen bonds : bond 0.03521 ( 574) hydrogen bonds : angle 5.64518 ( 1485) SS BOND : bond 0.00256 ( 22) SS BOND : angle 0.72739 ( 44) covalent geometry : bond 0.00280 (21224) covalent geometry : angle 0.57497 (29000) *********************** 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 320 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 273 time to evaluate : 2.472 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: B 378 VAL cc_start: 0.6281 (OUTLIER) cc_final: 0.5774 (p) REVERT: D 348 PHE cc_start: 0.7579 (m-80) cc_final: 0.7343 (m-80) REVERT: D 394 THR cc_start: 0.6565 (OUTLIER) cc_final: 0.6305 (p) REVERT: D 489 MET cc_start: 0.7512 (mmt) cc_final: 0.7257 (mmt) REVERT: D 526 GLU cc_start: 0.7633 (tp30) cc_final: 0.7206 (tp30) REVERT: H 489 MET cc_start: 0.7924 (tpp) cc_final: 0.7240 (mmt) REVERT: H 493 GLN cc_start: 0.7812 (tp-100) cc_final: 0.7344 (tp40) REVERT: H 554 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8093 (tttt) REVERT: K 418 TRP cc_start: 0.6311 (t-100) cc_final: 0.5745 (t-100) REVERT: K 483 ASP cc_start: 0.7249 (t0) cc_final: 0.6606 (t0) REVERT: K 553 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7112 (m-30) REVERT: L 424 PHE cc_start: 0.6428 (m-80) cc_final: 0.5951 (m-80) REVERT: L 489 MET cc_start: 0.6842 (tpp) cc_final: 0.6299 (mmm) REVERT: L 499 LYS cc_start: 0.7778 (mmmt) cc_final: 0.7419 (mttt) REVERT: L 521 LEU cc_start: 0.7653 (tp) cc_final: 0.7395 (tp) outliers start: 47 outliers final: 30 residues processed: 302 average time/residue: 0.3136 time to fit residues: 149.2237 Evaluate side-chains 292 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 258 time to evaluate : 2.367 ------------------------------------------------------------------------------- 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 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 552 VAL Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain E residue 382 TRP 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 F residue 430 HIS 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 H residue 480 SER Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 554 LYS Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 553 ASP Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 466 LEU Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 69 LYS 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 176 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 212 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 194 optimal weight: 0.2980 chunk 77 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 141 optimal weight: 0.0970 chunk 218 optimal weight: 0.9990 chunk 189 optimal weight: 20.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M1610 ASN M1657 GLN ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 385 GLN ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 393 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.187416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.120277 restraints weight = 27186.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.119753 restraints weight = 21767.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.121157 restraints weight = 17440.472| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21258 Z= 0.113 Angle : 0.589 14.764 29080 Z= 0.297 Chirality : 0.046 0.376 3407 Planarity : 0.004 0.049 3693 Dihedral : 5.459 58.499 3062 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.17 % Allowed : 16.14 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.16), residues: 2574 helix: 0.01 (0.25), residues: 409 sheet: 0.07 (0.18), residues: 787 loop : -0.67 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP E 488 HIS 0.011 0.001 HIS G 393 PHE 0.024 0.001 PHE L 354 TYR 0.020 0.001 TYR J 134 ARG 0.007 0.000 ARG C 384 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 11) link_NAG-ASN : angle 3.55559 ( 33) link_BETA1-4 : bond 0.01107 ( 1) link_BETA1-4 : angle 2.10167 ( 3) hydrogen bonds : bond 0.03393 ( 574) hydrogen bonds : angle 5.51935 ( 1485) SS BOND : bond 0.00254 ( 22) SS BOND : angle 0.69349 ( 44) covalent geometry : bond 0.00263 (21224) covalent geometry : angle 0.57696 (29000) *********************** 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 325 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 274 time to evaluate : 2.570 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: M 1852 GLU cc_start: 0.8219 (mp0) cc_final: 0.7997 (mp0) REVERT: A 530 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7875 (p) REVERT: B 378 VAL cc_start: 0.6306 (OUTLIER) cc_final: 0.5773 (p) REVERT: D 370 THR cc_start: 0.5375 (OUTLIER) cc_final: 0.4906 (m) REVERT: D 394 THR cc_start: 0.6557 (OUTLIER) cc_final: 0.6299 (p) REVERT: D 489 MET cc_start: 0.7530 (mmt) cc_final: 0.7299 (mmt) REVERT: D 526 GLU cc_start: 0.7578 (tp30) cc_final: 0.7154 (tp30) REVERT: E 488 TRP cc_start: 0.7294 (m-10) cc_final: 0.7032 (m-10) REVERT: F 384 ARG cc_start: 0.8380 (mtp85) cc_final: 0.8105 (mtt90) REVERT: H 489 MET cc_start: 0.7952 (tpp) cc_final: 0.7295 (mmt) REVERT: H 493 GLN cc_start: 0.7812 (tp-100) cc_final: 0.7355 (tp40) REVERT: H 506 MET cc_start: 0.6957 (mmm) cc_final: 0.6278 (mpp) REVERT: H 554 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8050 (tttt) REVERT: K 418 TRP cc_start: 0.6250 (t-100) cc_final: 0.5727 (t-100) REVERT: K 466 LEU cc_start: 0.8418 (mp) cc_final: 0.7632 (tp) REVERT: K 483 ASP cc_start: 0.7273 (t0) cc_final: 0.6618 (t0) REVERT: K 553 ASP cc_start: 0.7533 (OUTLIER) cc_final: 0.7108 (m-30) REVERT: L 405 PHE cc_start: 0.5642 (t80) cc_final: 0.5362 (t80) REVERT: L 489 MET cc_start: 0.6928 (tpp) cc_final: 0.6355 (mmm) REVERT: L 499 LYS cc_start: 0.7773 (mmmt) cc_final: 0.7416 (mttt) REVERT: L 521 LEU cc_start: 0.7597 (tp) cc_final: 0.7309 (tp) outliers start: 51 outliers final: 32 residues processed: 311 average time/residue: 0.3108 time to fit residues: 152.4550 Evaluate side-chains 297 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 259 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1613 CYS Chi-restraints excluded: chain M residue 1911 VAL Chi-restraints excluded: chain A residue 530 THR 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 552 VAL Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain E residue 382 TRP Chi-restraints excluded: chain E residue 454 VAL 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 430 HIS Chi-restraints excluded: chain F residue 456 LEU 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 536 CYS Chi-restraints excluded: chain H residue 554 LYS Chi-restraints excluded: chain K residue 454 VAL Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 553 ASP Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 466 LEU Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 69 LYS 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 24 optimal weight: 4.9990 chunk 221 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 81 optimal weight: 0.0370 chunk 250 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 overall best weight: 1.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M1610 ASN M1657 GLN ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 GLN ** C 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 393 HIS ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 393 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.183446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.113428 restraints weight = 27539.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.115537 restraints weight = 20486.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.115895 restraints weight = 15922.051| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21258 Z= 0.170 Angle : 0.640 15.465 29080 Z= 0.326 Chirality : 0.047 0.410 3407 Planarity : 0.005 0.049 3693 Dihedral : 5.489 58.844 3062 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.29 % Allowed : 16.61 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.16), residues: 2574 helix: 0.02 (0.25), residues: 407 sheet: -0.07 (0.18), residues: 823 loop : -0.71 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP E 488 HIS 0.008 0.001 HIS G 393 PHE 0.022 0.002 PHE M1936 TYR 0.020 0.001 TYR J 134 ARG 0.006 0.000 ARG C 384 Details of bonding type rmsd link_NAG-ASN : bond 0.00477 ( 11) link_NAG-ASN : angle 3.83668 ( 33) link_BETA1-4 : bond 0.01269 ( 1) link_BETA1-4 : angle 2.11699 ( 3) hydrogen bonds : bond 0.03807 ( 574) hydrogen bonds : angle 5.64308 ( 1485) SS BOND : bond 0.00437 ( 22) SS BOND : angle 0.85127 ( 44) covalent geometry : bond 0.00409 (21224) covalent geometry : angle 0.62592 (29000) *********************** 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 323 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 269 time to evaluate : 2.581 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: M 1610 ASN cc_start: 0.7420 (m110) cc_final: 0.7186 (m-40) REVERT: M 1852 GLU cc_start: 0.8223 (mp0) cc_final: 0.7987 (mp0) REVERT: A 530 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7965 (p) REVERT: B 378 VAL cc_start: 0.6299 (OUTLIER) cc_final: 0.5764 (p) REVERT: D 394 THR cc_start: 0.6660 (OUTLIER) cc_final: 0.6392 (p) REVERT: D 526 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7307 (tp30) REVERT: F 384 ARG cc_start: 0.8379 (mtp85) cc_final: 0.8066 (mtt90) REVERT: H 471 THR cc_start: 0.8319 (p) cc_final: 0.8119 (p) REVERT: H 489 MET cc_start: 0.8003 (tpp) cc_final: 0.7257 (mmt) REVERT: H 493 GLN cc_start: 0.7743 (tp-100) cc_final: 0.7263 (tp40) REVERT: H 506 MET cc_start: 0.6944 (mmm) cc_final: 0.6412 (mpp) REVERT: K 418 TRP cc_start: 0.6276 (t-100) cc_final: 0.5801 (t-100) REVERT: K 466 LEU cc_start: 0.8507 (mp) cc_final: 0.7705 (tp) REVERT: K 483 ASP cc_start: 0.7443 (t0) cc_final: 0.6790 (t0) REVERT: K 506 MET cc_start: 0.7634 (tpp) cc_final: 0.7367 (tpp) REVERT: K 553 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7318 (m-30) REVERT: L 499 LYS cc_start: 0.7761 (mmmt) cc_final: 0.7398 (mttt) REVERT: L 521 LEU cc_start: 0.7506 (tp) cc_final: 0.7192 (tp) outliers start: 54 outliers final: 37 residues processed: 306 average time/residue: 0.3248 time to fit residues: 154.8434 Evaluate side-chains 298 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 256 time to evaluate : 2.250 ------------------------------------------------------------------------------- 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 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 D residue 354 PHE Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 432 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 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 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 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 K residue 454 VAL Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 553 ASP Chi-restraints excluded: chain L residue 354 PHE Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 466 LEU Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 69 LYS 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 231 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 237 optimal weight: 0.8980 chunk 93 optimal weight: 0.0870 chunk 197 optimal weight: 0.6980 chunk 168 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 95 optimal weight: 20.0000 chunk 156 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M1657 GLN C 400 HIS C 487 GLN ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 393 HIS H 463 GLN ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 393 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.185529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.118474 restraints weight = 27456.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.116984 restraints weight = 20114.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.118168 restraints weight = 16536.716| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21258 Z= 0.129 Angle : 0.625 17.107 29080 Z= 0.315 Chirality : 0.046 0.409 3407 Planarity : 0.004 0.049 3693 Dihedral : 5.262 59.632 3062 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.00 % Allowed : 17.46 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.16), residues: 2574 helix: 0.09 (0.25), residues: 407 sheet: -0.01 (0.18), residues: 788 loop : -0.67 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP E 488 HIS 0.004 0.001 HIS D 400 PHE 0.024 0.002 PHE L 354 TYR 0.020 0.001 TYR J 134 ARG 0.006 0.000 ARG C 384 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 11) link_NAG-ASN : angle 3.68725 ( 33) link_BETA1-4 : bond 0.01070 ( 1) link_BETA1-4 : angle 2.05086 ( 3) hydrogen bonds : bond 0.03474 ( 574) hydrogen bonds : angle 5.48526 ( 1485) SS BOND : bond 0.00294 ( 22) SS BOND : angle 0.75804 ( 44) covalent geometry : bond 0.00307 (21224) covalent geometry : angle 0.61276 (29000) *********************** 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 315 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 268 time to evaluate : 2.370 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 1852 GLU cc_start: 0.8172 (mp0) cc_final: 0.7963 (mp0) REVERT: A 530 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.7931 (p) REVERT: B 378 VAL cc_start: 0.6120 (OUTLIER) cc_final: 0.5555 (p) REVERT: D 394 THR cc_start: 0.6641 (OUTLIER) cc_final: 0.6371 (p) REVERT: D 526 GLU cc_start: 0.7644 (tp30) cc_final: 0.7177 (tp30) REVERT: F 384 ARG cc_start: 0.8393 (mtp85) cc_final: 0.8057 (mtt90) REVERT: H 489 MET cc_start: 0.7950 (tpp) cc_final: 0.7260 (mmt) REVERT: H 493 GLN cc_start: 0.7711 (tp-100) cc_final: 0.7238 (tp40) REVERT: H 506 MET cc_start: 0.6909 (mmm) cc_final: 0.6460 (mpp) REVERT: H 554 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8013 (ptmm) REVERT: K 466 LEU cc_start: 0.8474 (mp) cc_final: 0.7706 (tp) REVERT: K 483 ASP cc_start: 0.7338 (t0) cc_final: 0.6718 (t0) REVERT: K 553 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7233 (m-30) REVERT: L 354 PHE cc_start: 0.5574 (OUTLIER) cc_final: 0.4858 (m-80) REVERT: L 489 MET cc_start: 0.6588 (tpp) cc_final: 0.6250 (tpp) REVERT: L 499 LYS cc_start: 0.7793 (mmmt) cc_final: 0.7441 (mttt) REVERT: L 521 LEU cc_start: 0.7538 (tp) cc_final: 0.7219 (tp) outliers start: 47 outliers final: 36 residues processed: 301 average time/residue: 0.3201 time to fit residues: 149.9994 Evaluate side-chains 305 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 263 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1613 CYS Chi-restraints excluded: chain M residue 1655 LEU 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 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 D residue 354 PHE Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 432 ASP 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 369 VAL Chi-restraints excluded: chain E residue 382 TRP Chi-restraints excluded: chain E residue 454 VAL 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 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 536 CYS Chi-restraints excluded: chain H residue 554 LYS Chi-restraints excluded: chain K residue 454 VAL Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 553 ASP Chi-restraints excluded: chain L residue 354 PHE Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 466 LEU Chi-restraints excluded: chain J residue 69 LYS 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 175 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 251 optimal weight: 1.9990 chunk 211 optimal weight: 40.0000 chunk 101 optimal weight: 7.9990 chunk 201 optimal weight: 0.8980 chunk 256 optimal weight: 2.9990 chunk 39 optimal weight: 0.0370 chunk 225 optimal weight: 10.0000 overall best weight: 1.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M1657 GLN M1743 HIS B 465 ASN C 487 GLN ** C 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 385 GLN ** E 490 GLN ** 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 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4446 r_free = 0.4446 target = 0.184114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.117218 restraints weight = 27593.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.117430 restraints weight = 20862.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.117628 restraints weight = 16872.801| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21258 Z= 0.158 Angle : 0.653 17.322 29080 Z= 0.331 Chirality : 0.047 0.402 3407 Planarity : 0.005 0.050 3693 Dihedral : 5.288 59.226 3062 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.12 % Allowed : 17.67 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.16), residues: 2574 helix: 0.05 (0.25), residues: 413 sheet: -0.02 (0.18), residues: 790 loop : -0.73 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP E 488 HIS 0.005 0.001 HIS F 518 PHE 0.035 0.002 PHE C 405 TYR 0.023 0.001 TYR C 375 ARG 0.006 0.000 ARG C 384 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 11) link_NAG-ASN : angle 3.73990 ( 33) link_BETA1-4 : bond 0.00803 ( 1) link_BETA1-4 : angle 1.93286 ( 3) hydrogen bonds : bond 0.03617 ( 574) hydrogen bonds : angle 5.55031 ( 1485) SS BOND : bond 0.00369 ( 22) SS BOND : angle 0.81880 ( 44) covalent geometry : bond 0.00382 (21224) covalent geometry : angle 0.64038 (29000) ********************** 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 313 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 263 time to evaluate : 2.379 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: 0.8165 (OUTLIER) cc_final: 0.7873 (p) REVERT: B 378 VAL cc_start: 0.6035 (OUTLIER) cc_final: 0.5446 (p) REVERT: D 394 THR cc_start: 0.6549 (OUTLIER) cc_final: 0.6280 (p) REVERT: D 526 GLU cc_start: 0.7633 (tp30) cc_final: 0.7188 (tp30) REVERT: F 384 ARG cc_start: 0.8370 (mtp85) cc_final: 0.8120 (mtt90) REVERT: H 489 MET cc_start: 0.7962 (tpp) cc_final: 0.7343 (mmt) REVERT: H 493 GLN cc_start: 0.7756 (tp-100) cc_final: 0.7301 (tp40) REVERT: H 506 MET cc_start: 0.6948 (mmm) cc_final: 0.6549 (mpp) REVERT: K 466 LEU cc_start: 0.8414 (mp) cc_final: 0.7673 (tp) REVERT: K 483 ASP cc_start: 0.7392 (t0) cc_final: 0.6800 (t0) REVERT: K 553 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7306 (m-30) REVERT: L 354 PHE cc_start: 0.5718 (OUTLIER) cc_final: 0.4986 (m-80) REVERT: L 499 LYS cc_start: 0.7807 (mmmt) cc_final: 0.7483 (mttt) REVERT: L 521 LEU cc_start: 0.7578 (tp) cc_final: 0.7258 (tp) outliers start: 50 outliers final: 38 residues processed: 301 average time/residue: 0.3200 time to fit residues: 149.5900 Evaluate side-chains 298 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 255 time to evaluate : 2.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1613 CYS Chi-restraints excluded: chain M residue 1655 LEU 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 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 D residue 354 PHE Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 432 ASP 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 367 CYS Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 382 TRP Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 521 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 F residue 456 LEU Chi-restraints excluded: chain G residue 350 ILE 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 477 THR Chi-restraints excluded: chain K residue 553 ASP Chi-restraints excluded: chain L residue 354 PHE Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 466 LEU Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 69 LYS 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 148 optimal weight: 0.8980 chunk 240 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 200 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 203 optimal weight: 30.0000 chunk 85 optimal weight: 0.6980 chunk 207 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M1657 GLN M1743 HIS B 465 ASN ** C 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 463 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.184529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.114542 restraints weight = 27499.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.116500 restraints weight = 20236.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.118001 restraints weight = 15233.439| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21258 Z= 0.142 Angle : 0.649 17.321 29080 Z= 0.328 Chirality : 0.047 0.417 3407 Planarity : 0.005 0.054 3693 Dihedral : 5.213 58.990 3062 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.08 % Allowed : 17.76 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.16), residues: 2574 helix: 0.01 (0.25), residues: 413 sheet: 0.04 (0.18), residues: 791 loop : -0.71 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP E 488 HIS 0.006 0.001 HIS H 393 PHE 0.026 0.002 PHE L 354 TYR 0.019 0.001 TYR J 134 ARG 0.006 0.000 ARG C 384 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 11) link_NAG-ASN : angle 3.72170 ( 33) link_BETA1-4 : bond 0.00896 ( 1) link_BETA1-4 : angle 1.79008 ( 3) hydrogen bonds : bond 0.03552 ( 574) hydrogen bonds : angle 5.49818 ( 1485) SS BOND : bond 0.00321 ( 22) SS BOND : angle 0.78172 ( 44) covalent geometry : bond 0.00342 (21224) covalent geometry : angle 0.63625 (29000) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9510.15 seconds wall clock time: 164 minutes 42.34 seconds (9882.34 seconds total)