Starting phenix.real_space_refine on Wed Nov 20 03:20:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y0j_33547/11_2024/7y0j_33547.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y0j_33547/11_2024/7y0j_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y0j_33547/11_2024/7y0j_33547.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y0j_33547/11_2024/7y0j_33547.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y0j_33547/11_2024/7y0j_33547.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y0j_33547/11_2024/7y0j_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-5513/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: 14.98, per 1000 atoms: 0.72 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: 5.26 Conformation dependent library (CDL) restraints added in 2.8 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: 3.02 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: 7.96 Time building geometry restraints manager: 6.01 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: 5.870 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: 0.970 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 50.850 Find NCS groups from input model: 1.320 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.530 ------------------------------------------------------------------------------- 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 21224 Z= 0.214 Angle : 0.687 9.103 29000 Z= 0.359 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 *********************** 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 : 2.357 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: 0.2935 time to fit residues: 163.0699 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 : 2.124 ------------------------------------------------------------------------------- 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: 0.8980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 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 21224 Z= 0.188 Angle : 0.619 7.642 29000 Z= 0.325 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 *********************** 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 : 2.455 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: 0.8202 (m-80) cc_final: 0.7864 (m-80) REVERT: D 417 ASP cc_start: 0.7952 (t70) cc_final: 0.7739 (t70) REVERT: F 560 THR cc_start: 0.8099 (p) cc_final: 0.7883 (t) REVERT: H 489 MET cc_start: 0.8079 (tpp) cc_final: 0.7264 (mmt) REVERT: H 490 GLN cc_start: 0.7177 (tp40) cc_final: 0.6787 (tm-30) REVERT: K 464 LEU cc_start: 0.8778 (mt) cc_final: 0.8572 (mt) REVERT: K 483 ASP cc_start: 0.7219 (t0) cc_final: 0.6635 (t0) REVERT: L 493 GLN cc_start: 0.8662 (mp10) cc_final: 0.8360 (mp10) REVERT: L 499 LYS cc_start: 0.7762 (mmmt) cc_final: 0.7408 (mttt) outliers start: 24 outliers final: 13 residues processed: 332 average time/residue: 0.3462 time to fit residues: 173.7757 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 : 2.318 ------------------------------------------------------------------------------- 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 129 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 194 optimal weight: 0.4980 chunk 158 optimal weight: 0.0040 chunk 64 optimal weight: 6.9990 chunk 233 optimal weight: 0.0170 chunk 252 optimal weight: 0.5980 chunk 208 optimal weight: 0.9990 chunk 231 optimal weight: 30.0000 chunk 79 optimal weight: 20.0000 chunk 187 optimal weight: 5.9990 overall best weight: 0.4230 ------------------------------------------------------------------------------- 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 ** 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** ** K 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21224 Z= 0.171 Angle : 0.585 7.939 29000 Z= 0.304 Chirality : 0.046 0.380 3407 Planarity : 0.004 0.050 3693 Dihedral : 6.664 87.541 3062 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.23 % Allowed : 12.06 % Favored : 86.70 % 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: -0.77 (0.16), residues: 2574 helix: -0.34 (0.24), residues: 409 sheet: 0.12 (0.19), residues: 775 loop : -0.89 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP E 488 HIS 0.013 0.001 HIS G 393 PHE 0.024 0.002 PHE K 479 TYR 0.025 0.001 TYR C 375 ARG 0.010 0.000 ARG K 514 *********************** 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: 29 poor density : 312 time to evaluate : 2.413 Fit side-chains 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: 0.7878 (tp) cc_final: 0.7485 (tt) REVERT: D 417 ASP cc_start: 0.7919 (t70) cc_final: 0.7700 (t70) REVERT: D 489 MET cc_start: 0.7151 (mmt) cc_final: 0.6729 (mmm) REVERT: D 526 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7313 (tp30) REVERT: F 526 GLU cc_start: 0.8144 (mp0) cc_final: 0.7879 (mp0) REVERT: F 560 THR cc_start: 0.8024 (p) cc_final: 0.7802 (t) REVERT: H 463 GLN cc_start: 0.8620 (tt0) cc_final: 0.8408 (tt0) REVERT: H 489 MET cc_start: 0.7995 (tpp) cc_final: 0.7428 (mmt) REVERT: K 483 ASP cc_start: 0.7148 (t0) cc_final: 0.6551 (t0) REVERT: L 499 LYS cc_start: 0.7819 (mmmt) cc_final: 0.7386 (mttt) outliers start: 29 outliers final: 16 residues processed: 327 average time/residue: 0.3244 time to fit residues: 163.3935 Evaluate side-chains 295 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 278 time to evaluate : 2.718 ------------------------------------------------------------------------------- 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 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 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 K residue 555 SER Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain J residue 29 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 231 optimal weight: 20.0000 chunk 175 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 234 optimal weight: 20.0000 chunk 248 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 222 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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** A 487 GLN B 419 ASN ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 ASN ** F 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 393 HIS J 29 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 21224 Z= 0.330 Angle : 0.652 10.704 29000 Z= 0.341 Chirality : 0.049 0.429 3407 Planarity : 0.005 0.051 3693 Dihedral : 6.634 81.969 3062 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.12 % Allowed : 14.27 % Favored : 83.60 % 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: -0.89 (0.16), residues: 2574 helix: -0.26 (0.24), residues: 404 sheet: -0.11 (0.18), residues: 785 loop : -0.94 (0.16), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP E 488 HIS 0.008 0.001 HIS M1808 PHE 0.021 0.002 PHE L 348 TYR 0.022 0.002 TYR C 375 ARG 0.006 0.000 ARG L 384 *********************** 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 336 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 286 time to evaluate : 2.379 Fit side-chains TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: M 1608 TYR cc_start: 0.5311 (t80) cc_final: 0.4589 (t80) REVERT: M 1610 ASN cc_start: 0.7666 (OUTLIER) cc_final: 0.7069 (m110) REVERT: B 378 VAL cc_start: 0.6164 (OUTLIER) cc_final: 0.5601 (p) REVERT: F 526 GLU cc_start: 0.8214 (mp0) cc_final: 0.7966 (mp0) REVERT: H 463 GLN cc_start: 0.8638 (tt0) cc_final: 0.8416 (tt0) REVERT: H 489 MET cc_start: 0.8057 (tpp) cc_final: 0.7602 (tpp) REVERT: K 483 ASP cc_start: 0.7398 (t0) cc_final: 0.6865 (t0) REVERT: L 489 MET cc_start: 0.6419 (tpp) cc_final: 0.6195 (tpp) REVERT: L 493 GLN cc_start: 0.8509 (mp10) cc_final: 0.8215 (mp10) REVERT: L 499 LYS cc_start: 0.7764 (mmmt) cc_final: 0.7381 (mttt) outliers start: 50 outliers final: 34 residues processed: 314 average time/residue: 0.3296 time to fit residues: 160.0112 Evaluate side-chains 301 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 265 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1610 ASN Chi-restraints excluded: chain M residue 1911 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 417 ASP 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 453 ASP Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 535 THR Chi-restraints excluded: chain 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 370 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 555 SER Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain J residue 29 ASN Chi-restraints excluded: chain J residue 32 ILE 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 206 optimal weight: 40.0000 chunk 141 optimal weight: 20.0000 chunk 3 optimal weight: 0.7980 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 211 optimal weight: 40.0000 chunk 171 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 0.8980 chunk 222 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M1657 GLN ** M1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS ** 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** G 487 GLN H 385 GLN ** H 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21224 Z= 0.294 Angle : 0.637 14.220 29000 Z= 0.331 Chirality : 0.048 0.422 3407 Planarity : 0.005 0.052 3693 Dihedral : 6.452 77.480 3062 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.55 % Allowed : 15.29 % 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: -0.94 (0.16), residues: 2574 helix: -0.26 (0.24), residues: 407 sheet: -0.21 (0.18), residues: 796 loop : -0.93 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP E 488 HIS 0.012 0.001 HIS G 393 PHE 0.026 0.002 PHE L 354 TYR 0.019 0.002 TYR C 375 ARG 0.003 0.000 ARG H 443 *********************** 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 335 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 275 time to evaluate : 2.447 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: M 1608 TYR cc_start: 0.5438 (t80) cc_final: 0.5151 (t80) REVERT: B 378 VAL cc_start: 0.6150 (OUTLIER) cc_final: 0.5589 (p) REVERT: D 394 THR cc_start: 0.6518 (OUTLIER) cc_final: 0.6259 (p) REVERT: D 526 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7292 (tp30) REVERT: E 490 GLN cc_start: 0.7270 (tm-30) cc_final: 0.7038 (pp30) REVERT: F 526 GLU cc_start: 0.8238 (mp0) cc_final: 0.7967 (mp0) REVERT: H 463 GLN cc_start: 0.8571 (tt0) cc_final: 0.8357 (tt0) REVERT: H 489 MET cc_start: 0.8044 (tpp) cc_final: 0.7581 (tpp) REVERT: K 483 ASP cc_start: 0.7373 (t0) cc_final: 0.6868 (t0) REVERT: K 553 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7266 (m-30) REVERT: L 489 MET cc_start: 0.6605 (tpp) cc_final: 0.6400 (tpp) REVERT: L 493 GLN cc_start: 0.8402 (mp10) cc_final: 0.8184 (mp10) REVERT: L 499 LYS cc_start: 0.7733 (mmmt) cc_final: 0.7523 (mttt) REVERT: L 521 LEU cc_start: 0.7930 (tp) cc_final: 0.7698 (tp) outliers start: 60 outliers final: 39 residues processed: 317 average time/residue: 0.3250 time to fit residues: 160.9196 Evaluate side-chains 303 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 260 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1613 CYS Chi-restraints excluded: chain M residue 1911 VAL Chi-restraints excluded: chain M residue 1921 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 518 HIS Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 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 453 ASP Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 535 THR Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 393 HIS Chi-restraints excluded: chain G residue 487 GLN Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 370 THR 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 K residue 555 SER Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain J residue 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 83 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 206 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M1657 GLN ** M1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS C 419 ASN C 487 GLN ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 393 HIS G 487 GLN ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 393 HIS J 29 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 21224 Z= 0.327 Angle : 0.650 12.532 29000 Z= 0.339 Chirality : 0.049 0.435 3407 Planarity : 0.005 0.053 3693 Dihedral : 6.402 73.435 3062 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.76 % Allowed : 16.44 % Favored : 80.80 % 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: -0.99 (0.16), residues: 2574 helix: -0.30 (0.24), residues: 410 sheet: -0.25 (0.18), residues: 787 loop : -0.96 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP E 488 HIS 0.007 0.001 HIS M1808 PHE 0.026 0.002 PHE L 354 TYR 0.019 0.002 TYR C 375 ARG 0.004 0.000 ARG C 451 *********************** 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 331 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 266 time to evaluate : 2.569 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 1608 TYR cc_start: 0.5538 (t80) cc_final: 0.5255 (t80) REVERT: B 378 VAL cc_start: 0.6160 (OUTLIER) cc_final: 0.5602 (p) REVERT: C 423 ARG cc_start: 0.8190 (ttm110) cc_final: 0.7912 (tmm160) REVERT: D 394 THR cc_start: 0.6581 (OUTLIER) cc_final: 0.6307 (p) REVERT: H 463 GLN cc_start: 0.8576 (tt0) cc_final: 0.8365 (tt0) REVERT: H 489 MET cc_start: 0.8079 (tpp) cc_final: 0.7314 (mmt) REVERT: H 493 GLN cc_start: 0.7807 (tp-100) cc_final: 0.7258 (tp40) REVERT: K 483 ASP cc_start: 0.7464 (t0) cc_final: 0.6986 (t0) REVERT: K 553 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7332 (m-30) REVERT: L 424 PHE cc_start: 0.6360 (m-80) cc_final: 0.5884 (m-80) REVERT: L 489 MET cc_start: 0.6626 (tpp) cc_final: 0.6364 (tpp) REVERT: L 499 LYS cc_start: 0.7768 (mmmt) cc_final: 0.7506 (mttt) outliers start: 65 outliers final: 46 residues processed: 310 average time/residue: 0.3340 time to fit residues: 161.7971 Evaluate side-chains 307 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 258 time to evaluate : 3.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1613 CYS Chi-restraints excluded: chain M residue 1911 VAL Chi-restraints excluded: chain M residue 1921 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 528 TRP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 518 HIS Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 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 348 PHE Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 535 THR Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 393 HIS Chi-restraints excluded: chain G residue 419 ASN Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 480 SER Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain K residue 454 VAL Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 553 ASP Chi-restraints excluded: chain L residue 378 VAL 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 239 optimal weight: 0.0870 chunk 28 optimal weight: 6.9990 chunk 141 optimal weight: 0.9980 chunk 181 optimal weight: 5.9990 chunk 140 optimal weight: 20.0000 chunk 209 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 247 optimal weight: 7.9990 chunk 155 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M1610 ASN M1657 GLN B 393 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 393 HIS J 29 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21224 Z= 0.214 Angle : 0.614 14.295 29000 Z= 0.315 Chirality : 0.047 0.436 3407 Planarity : 0.005 0.052 3693 Dihedral : 6.041 66.737 3062 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.59 % Allowed : 17.33 % Favored : 80.08 % 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: -0.84 (0.16), residues: 2574 helix: -0.21 (0.24), residues: 415 sheet: -0.15 (0.18), residues: 796 loop : -0.85 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP E 488 HIS 0.004 0.001 HIS F 518 PHE 0.029 0.002 PHE L 354 TYR 0.019 0.001 TYR J 134 ARG 0.002 0.000 ARG H 461 *********************** 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 341 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 280 time to evaluate : 2.627 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: M 1608 TYR cc_start: 0.5530 (t80) cc_final: 0.4800 (t80) REVERT: M 1610 ASN cc_start: 0.7427 (OUTLIER) cc_final: 0.6785 (m110) REVERT: B 378 VAL cc_start: 0.6185 (OUTLIER) cc_final: 0.5613 (p) REVERT: D 394 THR cc_start: 0.6556 (OUTLIER) cc_final: 0.6287 (p) REVERT: D 526 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7274 (tp30) REVERT: H 463 GLN cc_start: 0.8502 (tt0) cc_final: 0.8297 (tt0) REVERT: H 489 MET cc_start: 0.7989 (tpp) cc_final: 0.7249 (mmt) REVERT: H 506 MET cc_start: 0.7180 (mmm) cc_final: 0.6420 (mpp) REVERT: K 483 ASP cc_start: 0.7396 (t0) cc_final: 0.6900 (t0) REVERT: L 405 PHE cc_start: 0.5472 (t80) cc_final: 0.5173 (t80) REVERT: L 424 PHE cc_start: 0.6505 (m-80) cc_final: 0.6168 (m-80) REVERT: L 489 MET cc_start: 0.6739 (tpp) cc_final: 0.6216 (mmm) REVERT: L 499 LYS cc_start: 0.7790 (mmmt) cc_final: 0.7495 (mttt) REVERT: L 521 LEU cc_start: 0.7765 (tp) cc_final: 0.7546 (tp) outliers start: 61 outliers final: 44 residues processed: 321 average time/residue: 0.3137 time to fit residues: 157.5537 Evaluate side-chains 306 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 258 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1610 ASN Chi-restraints excluded: chain M residue 1613 CYS Chi-restraints excluded: chain M residue 1688 ILE Chi-restraints excluded: chain M residue 1870 LYS Chi-restraints excluded: chain M residue 1911 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 528 TRP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 518 HIS Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 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 348 PHE Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 382 TRP Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 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 E residue 553 ASP Chi-restraints excluded: chain F residue 430 HIS 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 370 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 L residue 378 VAL Chi-restraints excluded: chain J residue 43 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 153 optimal weight: 0.0570 chunk 98 optimal weight: 30.0000 chunk 147 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 47 optimal weight: 0.0670 chunk 157 optimal weight: 0.6980 chunk 168 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 194 optimal weight: 0.0980 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M1657 GLN B 393 HIS E 385 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 J 29 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21224 Z= 0.171 Angle : 0.607 16.238 29000 Z= 0.310 Chirality : 0.046 0.380 3407 Planarity : 0.005 0.055 3693 Dihedral : 5.597 57.067 3062 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.46 % Allowed : 18.05 % Favored : 79.48 % 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: -0.64 (0.16), residues: 2574 helix: -0.07 (0.25), residues: 410 sheet: -0.04 (0.18), residues: 788 loop : -0.70 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP E 488 HIS 0.005 0.001 HIS D 400 PHE 0.025 0.002 PHE L 358 TYR 0.021 0.001 TYR J 134 ARG 0.006 0.000 ARG E 423 *********************** 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 337 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 279 time to evaluate : 2.384 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 530 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7790 (p) REVERT: B 378 VAL cc_start: 0.6060 (OUTLIER) cc_final: 0.5438 (p) REVERT: D 394 THR cc_start: 0.6504 (OUTLIER) cc_final: 0.6236 (p) REVERT: D 489 MET cc_start: 0.7451 (mmt) cc_final: 0.7235 (mmt) REVERT: D 526 GLU cc_start: 0.7573 (tp30) cc_final: 0.7159 (tp30) REVERT: F 491 ARG cc_start: 0.7698 (ttp-170) cc_final: 0.7384 (ttp-110) REVERT: H 489 MET cc_start: 0.7961 (tpp) cc_final: 0.7320 (mmt) REVERT: H 506 MET cc_start: 0.7048 (mmm) cc_final: 0.6524 (mpp) REVERT: K 466 LEU cc_start: 0.8214 (mp) cc_final: 0.7556 (tp) REVERT: K 483 ASP cc_start: 0.7346 (t0) cc_final: 0.6812 (t0) REVERT: L 424 PHE cc_start: 0.6365 (m-80) cc_final: 0.5993 (m-80) REVERT: L 499 LYS cc_start: 0.7795 (mmmt) cc_final: 0.7495 (mttt) REVERT: L 521 LEU cc_start: 0.7698 (tp) cc_final: 0.7470 (tp) outliers start: 58 outliers final: 39 residues processed: 317 average time/residue: 0.3127 time to fit residues: 154.7566 Evaluate side-chains 304 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 262 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1613 CYS Chi-restraints excluded: chain M residue 1688 ILE Chi-restraints excluded: chain M residue 1911 VAL Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain 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 C residue 370 THR Chi-restraints excluded: chain C residue 518 HIS Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 348 PHE 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 365 LEU Chi-restraints excluded: chain E residue 382 TRP Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 489 MET Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 535 THR Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain G residue 393 HIS Chi-restraints excluded: chain G residue 524 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 564 VAL Chi-restraints excluded: chain L residue 354 PHE Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 378 VAL 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 225 optimal weight: 0.0010 chunk 237 optimal weight: 6.9990 chunk 216 optimal weight: 4.9990 chunk 230 optimal weight: 50.0000 chunk 138 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 181 optimal weight: 2.9990 chunk 70 optimal weight: 0.0070 chunk 208 optimal weight: 50.0000 chunk 218 optimal weight: 3.9990 chunk 151 optimal weight: 0.1980 overall best weight: 0.8408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M1657 GLN B 393 HIS E 450 HIS ** 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 J 29 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21224 Z= 0.201 Angle : 0.620 17.543 29000 Z= 0.316 Chirality : 0.046 0.391 3407 Planarity : 0.005 0.054 3693 Dihedral : 5.437 59.118 3062 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.21 % Allowed : 18.65 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.17), residues: 2574 helix: -0.04 (0.25), residues: 415 sheet: -0.00 (0.18), residues: 790 loop : -0.73 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP E 488 HIS 0.005 0.001 HIS D 400 PHE 0.031 0.002 PHE L 358 TYR 0.024 0.001 TYR C 375 ARG 0.005 0.000 ARG E 423 *********************** 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 322 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 270 time to evaluate : 2.489 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: 0.8091 (OUTLIER) cc_final: 0.7795 (p) REVERT: B 378 VAL cc_start: 0.6092 (OUTLIER) cc_final: 0.5492 (p) REVERT: D 394 THR cc_start: 0.6497 (OUTLIER) cc_final: 0.6232 (p) REVERT: D 526 GLU cc_start: 0.7599 (tp30) cc_final: 0.7187 (tp30) REVERT: F 491 ARG cc_start: 0.7730 (ttp-170) cc_final: 0.7316 (ttm-80) REVERT: H 489 MET cc_start: 0.7952 (tpp) cc_final: 0.7338 (mmt) REVERT: H 506 MET cc_start: 0.7024 (mmm) cc_final: 0.6593 (mpp) REVERT: K 466 LEU cc_start: 0.8200 (mp) cc_final: 0.7573 (tp) REVERT: K 483 ASP cc_start: 0.7354 (t0) cc_final: 0.6800 (t0) REVERT: K 518 HIS cc_start: 0.7491 (t-170) cc_final: 0.7199 (t70) REVERT: L 354 PHE cc_start: 0.5838 (OUTLIER) cc_final: 0.5290 (m-80) REVERT: L 424 PHE cc_start: 0.6409 (m-80) cc_final: 0.5981 (m-80) REVERT: L 489 MET cc_start: 0.6500 (tpp) cc_final: 0.6182 (tpp) REVERT: L 499 LYS cc_start: 0.7815 (mmmt) cc_final: 0.7505 (mttt) REVERT: L 521 LEU cc_start: 0.7695 (tp) cc_final: 0.7448 (tp) outliers start: 52 outliers final: 41 residues processed: 307 average time/residue: 0.3239 time to fit residues: 156.0138 Evaluate side-chains 311 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 266 time to evaluate : 2.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1613 CYS Chi-restraints excluded: chain M residue 1870 LYS Chi-restraints excluded: chain M residue 1911 VAL Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 528 TRP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 518 HIS Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 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 365 LEU 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 E residue 553 ASP Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain G residue 393 HIS Chi-restraints excluded: chain G residue 524 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 480 SER Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain K residue 454 VAL Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 564 VAL Chi-restraints excluded: chain L residue 354 PHE Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 543 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 244 optimal weight: 7.9990 chunk 148 optimal weight: 0.0030 chunk 115 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 chunk 235 optimal weight: 5.9990 chunk 203 optimal weight: 30.0000 chunk 21 optimal weight: 0.9980 chunk 157 optimal weight: 0.7980 chunk 125 optimal weight: 0.0670 chunk 161 optimal weight: 10.0000 overall best weight: 0.5728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M1657 GLN B 393 HIS B 465 ASN C 400 HIS ** 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 430 HIS ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 393 HIS J 29 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21224 Z= 0.180 Angle : 0.614 17.369 29000 Z= 0.314 Chirality : 0.046 0.390 3407 Planarity : 0.005 0.054 3693 Dihedral : 5.253 59.092 3062 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.17 % Allowed : 18.86 % Favored : 78.97 % 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: -0.57 (0.17), residues: 2574 helix: -0.09 (0.25), residues: 418 sheet: 0.07 (0.19), residues: 782 loop : -0.67 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP M1860 HIS 0.008 0.001 HIS G 393 PHE 0.031 0.002 PHE L 358 TYR 0.028 0.001 TYR C 375 ARG 0.004 0.000 ARG F 384 ********************** 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 326 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 275 time to evaluate : 2.614 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: 0.8064 (OUTLIER) cc_final: 0.7768 (p) REVERT: B 378 VAL cc_start: 0.6049 (OUTLIER) cc_final: 0.5445 (p) REVERT: D 394 THR cc_start: 0.6470 (OUTLIER) cc_final: 0.6216 (p) REVERT: D 418 TRP cc_start: 0.7733 (t-100) cc_final: 0.7492 (t-100) REVERT: D 526 GLU cc_start: 0.7521 (tp30) cc_final: 0.7091 (tp30) REVERT: F 491 ARG cc_start: 0.7632 (ttp-170) cc_final: 0.7399 (ttp-110) REVERT: H 489 MET cc_start: 0.7927 (tpp) cc_final: 0.7268 (mmt) REVERT: H 506 MET cc_start: 0.7020 (mmm) cc_final: 0.6635 (mpp) REVERT: K 466 LEU cc_start: 0.8155 (mp) cc_final: 0.7553 (tp) REVERT: K 483 ASP cc_start: 0.7350 (t0) cc_final: 0.6792 (t0) REVERT: L 354 PHE cc_start: 0.5920 (OUTLIER) cc_final: 0.5370 (m-80) REVERT: L 424 PHE cc_start: 0.6441 (m-80) cc_final: 0.5987 (m-80) REVERT: L 489 MET cc_start: 0.6477 (tpp) cc_final: 0.6139 (tpp) REVERT: L 499 LYS cc_start: 0.7797 (mmmt) cc_final: 0.7507 (mttt) REVERT: L 521 LEU cc_start: 0.7671 (tp) cc_final: 0.7431 (tp) outliers start: 51 outliers final: 40 residues processed: 311 average time/residue: 0.3352 time to fit residues: 163.7649 Evaluate side-chains 311 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 267 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1613 CYS Chi-restraints excluded: chain M residue 1870 LYS Chi-restraints excluded: chain M residue 1911 VAL Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 528 TRP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 518 HIS Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 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 365 LEU 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 E residue 553 ASP Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain G residue 524 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 480 SER Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 564 VAL Chi-restraints excluded: chain L residue 354 PHE Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 378 VAL 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 217 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 187 optimal weight: 30.0000 chunk 30 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 204 optimal weight: 1.9990 chunk 85 optimal weight: 0.0040 chunk 209 optimal weight: 20.0000 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 179 optimal weight: 0.9980 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M1657 GLN M1743 HIS B 393 HIS B 465 ASN 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** ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 393 HIS ** K 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.182664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.114633 restraints weight = 27388.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.114085 restraints weight = 21305.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.115881 restraints weight = 17156.523| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21224 Z= 0.275 Angle : 0.652 17.173 29000 Z= 0.336 Chirality : 0.048 0.425 3407 Planarity : 0.005 0.057 3693 Dihedral : 5.407 59.373 3062 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.21 % Allowed : 18.78 % Favored : 79.01 % 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: -0.70 (0.16), residues: 2574 helix: -0.09 (0.25), residues: 412 sheet: -0.01 (0.18), residues: 792 loop : -0.80 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP E 488 HIS 0.007 0.001 HIS G 393 PHE 0.033 0.002 PHE B 358 TYR 0.026 0.002 TYR C 375 ARG 0.003 0.000 ARG F 384 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4790.41 seconds wall clock time: 182 minutes 49.63 seconds (10969.63 seconds total)