Starting phenix.real_space_refine on Sat Feb 7 13:20:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ynd_73174/02_2026/9ynd_73174.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ynd_73174/02_2026/9ynd_73174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ynd_73174/02_2026/9ynd_73174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ynd_73174/02_2026/9ynd_73174.map" model { file = "/net/cci-nas-00/data/ceres_data/9ynd_73174/02_2026/9ynd_73174.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ynd_73174/02_2026/9ynd_73174.cif" } resolution = 4.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.031 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: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 2 5.21 5 S 161 5.16 5 C 20303 2.51 5 N 5633 2.21 5 O 6010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32118 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 24658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3065, 24658 Classifications: {'peptide': 3065} Link IDs: {'PTRANS': 134, 'TRANS': 2930} Chain breaks: 3 Chain: "B" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2557 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 12, 'TRANS': 309} Chain: "C" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2494 Classifications: {'peptide': 313} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "D" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 373 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'TRANS': 74} Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 5, 'ASP:plan': 4, 'GLU:plan': 11, 'ASN:plan1': 4, 'TYR:plan': 4, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 148 Chain: "E" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 373 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'TRANS': 74} Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 5, 'ASP:plan': 4, 'GLU:plan': 11, 'ASN:plan1': 4, 'TYR:plan': 4, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 148 Chain: "F" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 170 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'TRANS': 33} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 68 Chain: "G" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 170 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'TRANS': 33} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 68 Chain: "H" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 607 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'TRANS': 121} Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 479 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 12, 'GLU:plan': 22, 'ASP:plan': 8, 'ARG:plan': 10, 'ASN:plan1': 7, 'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 250 Chain: "I" Number of atoms: 602 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 120, 597 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'TRANS': 119} Unresolved non-hydrogen bonds: 375 Unresolved non-hydrogen angles: 473 Unresolved non-hydrogen dihedrals: 285 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLU:plan': 22, 'ASP:plan': 8, 'GLN:plan1': 11, 'ARG:plan': 10, 'ASN:plan1': 7, 'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 246 Conformer: "B" Number of residues, atoms: 120, 597 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'TRANS': 119} Unresolved non-hydrogen bonds: 375 Unresolved non-hydrogen angles: 473 Unresolved non-hydrogen dihedrals: 285 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLU:plan': 22, 'ASP:plan': 8, 'GLN:plan1': 11, 'ARG:plan': 10, 'ASN:plan1': 7, 'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 246 bond proxies already assigned to first conformer: 590 Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 114 Unusual residues: {' MG': 2, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLU I 533 " occ=0.49 ... (8 atoms not shown) pdb=" CB BGLU I 533 " occ=0.51 Time building chain proxies: 7.36, per 1000 atoms: 0.23 Number of scatterers: 32118 At special positions: 0 Unit cell: (112.84, 185.752, 220.472, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 161 16.00 P 9 15.00 Mg 2 11.99 O 6010 8.00 N 5633 7.00 C 20303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 991.5 milliseconds 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7934 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 35 sheets defined 58.7% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 1355 through 1372 removed outlier: 3.739A pdb=" N ASN A1362 " --> pdb=" O LYS A1358 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A1365 " --> pdb=" O GLN A1361 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A1366 " --> pdb=" O ASN A1362 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN A1369 " --> pdb=" O ALA A1365 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS A1371 " --> pdb=" O LEU A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1393 removed outlier: 4.268A pdb=" N GLU A1384 " --> pdb=" O TYR A1380 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLN A1387 " --> pdb=" O TYR A1383 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR A1393 " --> pdb=" O LEU A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1409 through 1416 removed outlier: 3.706A pdb=" N TRP A1413 " --> pdb=" O LYS A1409 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A1414 " --> pdb=" O ASP A1410 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A1416 " --> pdb=" O HIS A1412 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1437 removed outlier: 3.710A pdb=" N ILE A1434 " --> pdb=" O THR A1430 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TRP A1435 " --> pdb=" O LEU A1431 " (cutoff:3.500A) Processing helix chain 'A' and resid 1438 through 1473 removed outlier: 5.146A pdb=" N ALA A1444 " --> pdb=" O GLN A1440 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE A1445 " --> pdb=" O LYS A1441 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A1459 " --> pdb=" O GLY A1455 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1510 removed outlier: 3.749A pdb=" N LEU A1493 " --> pdb=" O GLY A1489 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A1506 " --> pdb=" O ASN A1502 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET A1507 " --> pdb=" O SER A1503 " (cutoff:3.500A) Processing helix chain 'A' and resid 1516 through 1554 removed outlier: 4.973A pdb=" N VAL A1536 " --> pdb=" O ALA A1532 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE A1550 " --> pdb=" O TYR A1546 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1561 removed outlier: 3.997A pdb=" N HIS A1559 " --> pdb=" O ALA A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1585 removed outlier: 3.634A pdb=" N THR A1565 " --> pdb=" O LEU A1561 " (cutoff:3.500A) Processing helix chain 'A' and resid 1587 through 1594 Processing helix chain 'A' and resid 1596 through 1614 Processing helix chain 'A' and resid 1615 through 1626 removed outlier: 3.532A pdb=" N ARG A1621 " --> pdb=" O GLU A1617 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A1622 " --> pdb=" O TYR A1618 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1632 Processing helix chain 'A' and resid 1633 through 1643 removed outlier: 3.516A pdb=" N LEU A1638 " --> pdb=" O ASP A1634 " (cutoff:3.500A) Processing helix chain 'A' and resid 1644 through 1645 No H-bonds generated for 'chain 'A' and resid 1644 through 1645' Processing helix chain 'A' and resid 1646 through 1657 removed outlier: 3.521A pdb=" N LYS A1649 " --> pdb=" O ASN A1646 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A1651 " --> pdb=" O ALA A1648 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS A1652 " --> pdb=" O LYS A1649 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE A1654 " --> pdb=" O GLN A1651 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYS A1655 " --> pdb=" O LYS A1652 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1728 removed outlier: 3.814A pdb=" N TRP A1701 " --> pdb=" O LYS A1697 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A1722 " --> pdb=" O ALA A1718 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N PHE A1727 " --> pdb=" O GLU A1723 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1743 Processing helix chain 'A' and resid 1746 through 1769 removed outlier: 3.801A pdb=" N VAL A1751 " --> pdb=" O ALA A1747 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A1752 " --> pdb=" O GLN A1748 " (cutoff:3.500A) Processing helix chain 'A' and resid 1777 through 1796 Processing helix chain 'A' and resid 1801 through 1829 Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1852 through 1855 Processing helix chain 'A' and resid 1882 through 1898 removed outlier: 3.520A pdb=" N LEU A1890 " --> pdb=" O ASP A1886 " (cutoff:3.500A) Processing helix chain 'A' and resid 1913 through 1924 removed outlier: 3.698A pdb=" N LYS A1917 " --> pdb=" O THR A1913 " (cutoff:3.500A) Processing helix chain 'A' and resid 1937 through 1952 Processing helix chain 'A' and resid 1959 through 1963 removed outlier: 3.706A pdb=" N LEU A1963 " --> pdb=" O PHE A1960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1964 through 1987 removed outlier: 3.949A pdb=" N GLN A1973 " --> pdb=" O SER A1969 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLN A1974 " --> pdb=" O ALA A1970 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN A1987 " --> pdb=" O ARG A1983 " (cutoff:3.500A) Processing helix chain 'A' and resid 2029 through 2034 Processing helix chain 'A' and resid 2045 through 2057 Processing helix chain 'A' and resid 2061 through 2080 Proline residue: A2071 - end of helix removed outlier: 3.505A pdb=" N LYS A2074 " --> pdb=" O VAL A2070 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A2080 " --> pdb=" O CYS A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2118 Processing helix chain 'A' and resid 2123 through 2130 removed outlier: 3.605A pdb=" N ILE A2127 " --> pdb=" O ASP A2123 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A2128 " --> pdb=" O GLU A2124 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A2129 " --> pdb=" O GLY A2125 " (cutoff:3.500A) Processing helix chain 'A' and resid 2132 through 2149 removed outlier: 3.522A pdb=" N THR A2144 " --> pdb=" O SER A2140 " (cutoff:3.500A) Proline residue: A2147 - end of helix Processing helix chain 'A' and resid 2153 through 2165 Processing helix chain 'A' and resid 2175 through 2189 removed outlier: 3.922A pdb=" N GLU A2181 " --> pdb=" O ALA A2177 " (cutoff:3.500A) Processing helix chain 'A' and resid 2200 through 2217 removed outlier: 3.624A pdb=" N GLN A2215 " --> pdb=" O TYR A2211 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A2216 " --> pdb=" O GLN A2212 " (cutoff:3.500A) Processing helix chain 'A' and resid 2229 through 2246 removed outlier: 3.602A pdb=" N TRP A2234 " --> pdb=" O LYS A2230 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A2235 " --> pdb=" O SER A2231 " (cutoff:3.500A) Processing helix chain 'A' and resid 2255 through 2259 Processing helix chain 'A' and resid 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2290 removed outlier: 3.510A pdb=" N VAL A2283 " --> pdb=" O LEU A2279 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A2284 " --> pdb=" O PHE A2280 " (cutoff:3.500A) Processing helix chain 'A' and resid 2293 through 2297 removed outlier: 3.832A pdb=" N GLN A2296 " --> pdb=" O GLY A2293 " (cutoff:3.500A) Processing helix chain 'A' and resid 2312 through 2314 No H-bonds generated for 'chain 'A' and resid 2312 through 2314' Processing helix chain 'A' and resid 2315 through 2320 Processing helix chain 'A' and resid 2352 through 2358 Processing helix chain 'A' and resid 2370 through 2385 removed outlier: 4.281A pdb=" N ILE A2374 " --> pdb=" O SER A2370 " (cutoff:3.500A) Processing helix chain 'A' and resid 2411 through 2423 removed outlier: 3.526A pdb=" N THR A2421 " --> pdb=" O ARG A2417 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A2422 " --> pdb=" O ASP A2418 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET A2423 " --> pdb=" O ALA A2419 " (cutoff:3.500A) Processing helix chain 'A' and resid 2431 through 2443 removed outlier: 3.549A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A2443 " --> pdb=" O HIS A2439 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 removed outlier: 3.621A pdb=" N CYS A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET A2461 " --> pdb=" O SER A2457 " (cutoff:3.500A) Processing helix chain 'A' and resid 2482 through 2504 Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2533 through 2535 No H-bonds generated for 'chain 'A' and resid 2533 through 2535' Processing helix chain 'A' and resid 2549 through 2552 Processing helix chain 'A' and resid 2558 through 2562 Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.546A pdb=" N ARG A2576 " --> pdb=" O LEU A2572 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2611 removed outlier: 3.807A pdb=" N ALA A2611 " --> pdb=" O SER A2607 " (cutoff:3.500A) Processing helix chain 'A' and resid 2628 through 2638 Processing helix chain 'A' and resid 2677 through 2690 Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2740 through 2757 removed outlier: 3.615A pdb=" N PHE A2751 " --> pdb=" O ILE A2747 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG A2757 " --> pdb=" O ARG A2753 " (cutoff:3.500A) Processing helix chain 'A' and resid 2758 through 2764 removed outlier: 6.608A pdb=" N SER A2761 " --> pdb=" O LEU A2758 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2784 Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.526A pdb=" N VAL A2803 " --> pdb=" O MET A2799 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A2806 " --> pdb=" O TRP A2802 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU A2808 " --> pdb=" O ARG A2804 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A2809 " --> pdb=" O GLY A2805 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2834 Processing helix chain 'A' and resid 2839 through 2858 removed outlier: 3.898A pdb=" N ARG A2843 " --> pdb=" O GLU A2839 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A2855 " --> pdb=" O ASP A2851 " (cutoff:3.500A) Processing helix chain 'A' and resid 2862 through 2867 removed outlier: 3.565A pdb=" N MET A2867 " --> pdb=" O ARG A2863 " (cutoff:3.500A) Processing helix chain 'A' and resid 2885 through 2904 removed outlier: 3.712A pdb=" N ALA A2895 " --> pdb=" O ASP A2891 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A2896 " --> pdb=" O TYR A2892 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS A2898 " --> pdb=" O LYS A2894 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A2902 " --> pdb=" O LYS A2898 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2927 removed outlier: 4.206A pdb=" N ILE A2925 " --> pdb=" O ARG A2921 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE A2926 " --> pdb=" O ILE A2922 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG A2927 " --> pdb=" O ASP A2923 " (cutoff:3.500A) Processing helix chain 'A' and resid 2942 through 2955 Processing helix chain 'A' and resid 2968 through 2986 Processing helix chain 'A' and resid 2997 through 2999 No H-bonds generated for 'chain 'A' and resid 2997 through 2999' Processing helix chain 'A' and resid 3001 through 3015 removed outlier: 3.915A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA A3013 " --> pdb=" O ASN A3009 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3041 removed outlier: 3.762A pdb=" N GLU A3035 " --> pdb=" O THR A3031 " (cutoff:3.500A) Processing helix chain 'A' and resid 3046 through 3062 removed outlier: 3.846A pdb=" N LEU A3050 " --> pdb=" O SER A3046 " (cutoff:3.500A) Processing helix chain 'A' and resid 3071 through 3082 removed outlier: 3.730A pdb=" N ALA A3080 " --> pdb=" O LYS A3076 " (cutoff:3.500A) Processing helix chain 'A' and resid 3082 through 3088 removed outlier: 3.961A pdb=" N PHE A3086 " --> pdb=" O SER A3082 " (cutoff:3.500A) Processing helix chain 'A' and resid 3098 through 3112 removed outlier: 3.931A pdb=" N LYS A3112 " --> pdb=" O GLU A3108 " (cutoff:3.500A) Processing helix chain 'A' and resid 3138 through 3164 removed outlier: 3.870A pdb=" N HIS A3155 " --> pdb=" O HIS A3151 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG A3164 " --> pdb=" O ARG A3160 " (cutoff:3.500A) Processing helix chain 'A' and resid 3172 through 3252 removed outlier: 3.518A pdb=" N HIS A3188 " --> pdb=" O ALA A3184 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS A3200 " --> pdb=" O GLU A3196 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS A3209 " --> pdb=" O LEU A3205 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG A3220 " --> pdb=" O GLU A3216 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN A3248 " --> pdb=" O VAL A3244 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A3249 " --> pdb=" O LYS A3245 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU A3251 " --> pdb=" O GLN A3247 " (cutoff:3.500A) Processing helix chain 'A' and resid 3440 through 3482 removed outlier: 3.946A pdb=" N LYS A3448 " --> pdb=" O ILE A3444 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU A3449 " --> pdb=" O ALA A3445 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU A3450 " --> pdb=" O ARG A3446 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N TYR A3451 " --> pdb=" O TYR A3447 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A3460 " --> pdb=" O SER A3456 " (cutoff:3.500A) Processing helix chain 'A' and resid 3482 through 3495 Processing helix chain 'A' and resid 3495 through 3502 removed outlier: 3.778A pdb=" N THR A3502 " --> pdb=" O ASN A3498 " (cutoff:3.500A) Processing helix chain 'A' and resid 3502 through 3517 Processing helix chain 'A' and resid 3521 through 3539 removed outlier: 3.501A pdb=" N HIS A3535 " --> pdb=" O THR A3531 " (cutoff:3.500A) Processing helix chain 'A' and resid 3548 through 3554 Processing helix chain 'A' and resid 3555 through 3565 Processing helix chain 'A' and resid 3570 through 3580 Processing helix chain 'A' and resid 3594 through 3604 removed outlier: 4.094A pdb=" N GLU A3598 " --> pdb=" O GLY A3594 " (cutoff:3.500A) Processing helix chain 'A' and resid 3618 through 3630 Processing helix chain 'A' and resid 3638 through 3641 Processing helix chain 'A' and resid 3645 through 3651 Processing helix chain 'A' and resid 3689 through 3696 Processing helix chain 'A' and resid 3704 through 3721 removed outlier: 3.561A pdb=" N ASN A3714 " --> pdb=" O SER A3710 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A3715 " --> pdb=" O GLN A3711 " (cutoff:3.500A) Processing helix chain 'A' and resid 3721 through 3755 Processing helix chain 'A' and resid 3759 through 3762 Processing helix chain 'A' and resid 3763 through 3799 removed outlier: 3.765A pdb=" N ILE A3767 " --> pdb=" O ASP A3763 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A3778 " --> pdb=" O LYS A3774 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU A3779 " --> pdb=" O ARG A3775 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A3780 " --> pdb=" O GLU A3776 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A3781 " --> pdb=" O ALA A3777 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU A3795 " --> pdb=" O MET A3791 " (cutoff:3.500A) Processing helix chain 'A' and resid 3801 through 3817 removed outlier: 3.676A pdb=" N SER A3805 " --> pdb=" O TYR A3801 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A3810 " --> pdb=" O THR A3806 " (cutoff:3.500A) Processing helix chain 'A' and resid 3818 through 3821 Processing helix chain 'A' and resid 3828 through 3842 Processing helix chain 'A' and resid 3843 through 3847 removed outlier: 3.930A pdb=" N LYS A3847 " --> pdb=" O PRO A3844 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3874 removed outlier: 3.538A pdb=" N PHE A3864 " --> pdb=" O THR A3860 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY A3874 " --> pdb=" O ARG A3870 " (cutoff:3.500A) Processing helix chain 'A' and resid 3876 through 3894 removed outlier: 4.026A pdb=" N ILE A3881 " --> pdb=" O HIS A3877 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THR A3882 " --> pdb=" O GLN A3878 " (cutoff:3.500A) Processing helix chain 'A' and resid 3901 through 3911 Processing helix chain 'A' and resid 3928 through 3939 removed outlier: 3.648A pdb=" N VAL A3936 " --> pdb=" O ALA A3932 " (cutoff:3.500A) Processing helix chain 'A' and resid 3940 through 3945 removed outlier: 6.115A pdb=" N ALA A3943 " --> pdb=" O CYS A3940 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS A3945 " --> pdb=" O PRO A3942 " (cutoff:3.500A) Processing helix chain 'A' and resid 3946 through 3954 Processing helix chain 'A' and resid 3956 through 3962 Processing helix chain 'A' and resid 3965 through 3970 removed outlier: 4.101A pdb=" N VAL A3970 " --> pdb=" O GLU A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3997 removed outlier: 3.589A pdb=" N HIS A3988 " --> pdb=" O GLY A3984 " (cutoff:3.500A) Processing helix chain 'A' and resid 4000 through 4014 removed outlier: 3.614A pdb=" N HIS A4006 " --> pdb=" O LEU A4002 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET A4007 " --> pdb=" O ALA A4003 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A4008 " --> pdb=" O MET A4004 " (cutoff:3.500A) Processing helix chain 'A' and resid 4015 through 4017 No H-bonds generated for 'chain 'A' and resid 4015 through 4017' Processing helix chain 'A' and resid 4018 through 4023 removed outlier: 3.839A pdb=" N GLU A4022 " --> pdb=" O MET A4018 " (cutoff:3.500A) Processing helix chain 'A' and resid 4026 through 4033 removed outlier: 3.795A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4062 Processing helix chain 'A' and resid 4073 through 4091 removed outlier: 3.854A pdb=" N LYS A4089 " --> pdb=" O ASN A4085 " (cutoff:3.500A) Processing helix chain 'A' and resid 4098 through 4101 Processing helix chain 'A' and resid 4102 through 4115 removed outlier: 3.724A pdb=" N MET A4107 " --> pdb=" O PRO A4103 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN A4108 " --> pdb=" O GLY A4104 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS A4114 " --> pdb=" O GLU A4110 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER A4115 " --> pdb=" O LYS A4111 " (cutoff:3.500A) Processing helix chain 'A' and resid 4135 through 4142 removed outlier: 4.004A pdb=" N LEU A4139 " --> pdb=" O PRO A4135 " (cutoff:3.500A) Processing helix chain 'A' and resid 4152 through 4164 removed outlier: 3.517A pdb=" N LEU A4158 " --> pdb=" O LYS A4154 " (cutoff:3.500A) Processing helix chain 'A' and resid 4165 through 4170 removed outlier: 3.512A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4175 through 4193 Processing helix chain 'A' and resid 4196 through 4201 Processing helix chain 'A' and resid 4208 through 4227 Processing helix chain 'A' and resid 4234 through 4238 Processing helix chain 'A' and resid 4239 through 4250 removed outlier: 3.583A pdb=" N LEU A4246 " --> pdb=" O ALA A4242 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A4248 " --> pdb=" O LYS A4244 " (cutoff:3.500A) Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4301 through 4312 removed outlier: 3.786A pdb=" N GLU A4310 " --> pdb=" O VAL A4306 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A4311 " --> pdb=" O GLN A4307 " (cutoff:3.500A) Processing helix chain 'A' and resid 4326 through 4347 removed outlier: 4.135A pdb=" N VAL A4330 " --> pdb=" O ASN A4326 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU A4331 " --> pdb=" O ALA A4327 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N MET A4343 " --> pdb=" O MET A4339 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A4344 " --> pdb=" O ILE A4340 " (cutoff:3.500A) Processing helix chain 'A' and resid 4375 through 4391 Processing helix chain 'A' and resid 4401 through 4406 removed outlier: 3.532A pdb=" N LYS A4406 " --> pdb=" O VAL A4402 " (cutoff:3.500A) Processing helix chain 'A' and resid 4407 through 4439 Processing helix chain 'A' and resid 4445 through 4457 removed outlier: 3.578A pdb=" N LYS A4457 " --> pdb=" O ASN A4453 " (cutoff:3.500A) Processing helix chain 'A' and resid 4474 through 4497 removed outlier: 3.502A pdb=" N ILE A4492 " --> pdb=" O GLN A4488 " (cutoff:3.500A) Processing helix chain 'A' and resid 4500 through 4507 Processing helix chain 'A' and resid 4516 through 4533 removed outlier: 3.765A pdb=" N TYR A4520 " --> pdb=" O VAL A4516 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A4521 " --> pdb=" O PRO A4517 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR A4522 " --> pdb=" O GLU A4518 " (cutoff:3.500A) Processing helix chain 'A' and resid 4535 through 4537 No H-bonds generated for 'chain 'A' and resid 4535 through 4537' Processing helix chain 'A' and resid 4631 through 4638 Processing helix chain 'B' and resid 288 through 297 removed outlier: 4.544A pdb=" N SER B 292 " --> pdb=" O SER B 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 94 removed outlier: 3.720A pdb=" N GLU C 93 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 297 removed outlier: 4.075A pdb=" N SER C 291 " --> pdb=" O GLU C 287 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER C 292 " --> pdb=" O SER C 288 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 22 Processing helix chain 'D' and resid 24 through 35 Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.607A pdb=" N LYS D 45 " --> pdb=" O GLU D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 49 through 75 removed outlier: 3.558A pdb=" N THR D 56 " --> pdb=" O GLU D 52 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE D 59 " --> pdb=" O TRP D 55 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG D 60 " --> pdb=" O THR D 56 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS D 63 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N MET D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 21 Processing helix chain 'E' and resid 24 through 35 Processing helix chain 'E' and resid 41 through 47 Processing helix chain 'E' and resid 49 through 75 Processing helix chain 'F' and resid 3 through 35 Processing helix chain 'G' and resid 3 through 35 Processing helix chain 'H' and resid 418 through 538 removed outlier: 3.739A pdb=" N ASP H 431 " --> pdb=" O LYS H 427 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU H 438 " --> pdb=" O LEU H 434 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N MET H 439 " --> pdb=" O GLY H 435 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU H 441 " --> pdb=" O GLU H 437 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA H 466 " --> pdb=" O GLY H 462 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET H 467 " --> pdb=" O ASP H 463 " (cutoff:3.500A) Processing helix chain 'I' and resid 420 through 433 removed outlier: 4.123A pdb=" N GLN I 429 " --> pdb=" O GLU I 425 " (cutoff:3.500A) Processing helix chain 'I' and resid 433 through 538 removed outlier: 3.858A pdb=" N GLU I 437 " --> pdb=" O ALA I 433 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY I 493 " --> pdb=" O LEU I 489 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA I 494 " --> pdb=" O ASP I 490 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS I 526 " --> pdb=" O GLN I 522 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1477 through 1480 removed outlier: 3.636A pdb=" N CYS A1484 " --> pdb=" O TYR A1480 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1661 through 1666 removed outlier: 7.845A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 10.862A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 11.925A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 11.775A pdb=" N PHE A1686 " --> pdb=" O SER A1677 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA4, first strand: chain 'A' and resid 1901 through 1905 removed outlier: 6.905A pdb=" N GLY A1901 " --> pdb=" O ARG A2037 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU A2039 " --> pdb=" O GLY A1901 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N SER A1903 " --> pdb=" O LEU A2039 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1931 removed outlier: 6.213A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ASP A1958 " --> pdb=" O LEU A1928 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N PHE A1930 " --> pdb=" O ASP A1958 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLY A1955 " --> pdb=" O PHE A2015 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1998 through 2001 Processing sheet with id=AA7, first strand: chain 'A' and resid 2249 through 2254 removed outlier: 6.734A pdb=" N VAL A2250 " --> pdb=" O TRP A2300 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL A2302 " --> pdb=" O VAL A2250 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N HIS A2252 " --> pdb=" O VAL A2302 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASP A2304 " --> pdb=" O HIS A2252 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ILE A2254 " --> pdb=" O ASP A2304 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N GLU A2344 " --> pdb=" O ILE A2301 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE A2303 " --> pdb=" O GLU A2344 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N MET A2221 " --> pdb=" O GLY A2360 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL A2362 " --> pdb=" O MET A2221 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2266 through 2268 Processing sheet with id=AA9, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AB1, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB2, first strand: chain 'A' and resid 2615 through 2620 removed outlier: 5.905A pdb=" N GLU A2616 " --> pdb=" O VAL A2660 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N PHE A2662 " --> pdb=" O GLU A2616 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL A2618 " --> pdb=" O PHE A2662 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A2591 " --> pdb=" O PHE A2708 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2639 through 2644 removed outlier: 3.675A pdb=" N ALA A2651 " --> pdb=" O GLU A2640 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR A2699 " --> pdb=" O ARG A2694 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2873 through 2874 Processing sheet with id=AB5, first strand: chain 'A' and resid 2957 through 2960 removed outlier: 6.150A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N ASP A2995 " --> pdb=" O TYR A2959 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE A2990 " --> pdb=" O HIS A3063 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL A3065 " --> pdb=" O ILE A2990 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N PHE A2992 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N THR A3067 " --> pdb=" O PHE A2992 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N MET A2994 " --> pdb=" O THR A3067 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY A2937 " --> pdb=" O MET A3068 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 5.950A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU A3633 " --> pdb=" O PHE A3678 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N SER A3680 " --> pdb=" O LEU A3633 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL A3635 " --> pdb=" O SER A3680 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU A3588 " --> pdb=" O VAL A3699 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3662 through 3664 Processing sheet with id=AB8, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.582A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL A4041 " --> pdb=" O LEU A4126 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N MET A4128 " --> pdb=" O VAL A4041 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N MET A4043 " --> pdb=" O MET A4128 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4283 through 4285 removed outlier: 4.224A pdb=" N ALA A4285 " --> pdb=" O ILE A4294 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 6.425A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU A4587 " --> pdb=" O THR A4546 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 4564 through 4571 removed outlier: 7.106A pdb=" N ILE A4581 " --> pdb=" O GLY A4567 " (cutoff:3.500A) removed outlier: 9.351A pdb=" N THR A4569 " --> pdb=" O ASN A4579 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N ASN A4579 " --> pdb=" O THR A4569 " (cutoff:3.500A) removed outlier: 10.016A pdb=" N ASN A4571 " --> pdb=" O LEU A4577 " (cutoff:3.500A) removed outlier: 10.052A pdb=" N LEU A4577 " --> pdb=" O ASN A4571 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL A4609 " --> pdb=" O ILE A4619 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N THR A4621 " --> pdb=" O LEU A4607 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU A4607 " --> pdb=" O THR A4621 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP A4623 " --> pdb=" O VAL A4605 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N VAL A4605 " --> pdb=" O ASP A4623 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 95 through 104 removed outlier: 10.460A pdb=" N ARG B 410 " --> pdb=" O PRO B 98 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU B 100 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLU B 408 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR B 102 " --> pdb=" O VAL B 406 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 111 through 116 removed outlier: 4.509A pdb=" N THR B 131 " --> pdb=" O SER B 127 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG B 144 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP B 136 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N PHE B 142 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 153 through 158 removed outlier: 3.633A pdb=" N ASP B 155 " --> pdb=" O CYS B 168 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG B 186 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASP B 178 " --> pdb=" O CYS B 184 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N CYS B 184 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 195 through 200 removed outlier: 3.610A pdb=" N SER B 211 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N THR B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLU B 220 " --> pdb=" O CYS B 226 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N CYS B 226 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 237 through 242 removed outlier: 3.503A pdb=" N ALA B 270 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL B 262 " --> pdb=" O CYS B 268 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N CYS B 268 " --> pdb=" O VAL B 262 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 279 through 284 removed outlier: 7.058A pdb=" N GLY B 314 " --> pdb=" O GLU B 280 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE B 282 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU B 312 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N TRP B 284 " --> pdb=" O PHE B 310 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N PHE B 310 " --> pdb=" O TRP B 284 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR B 319 " --> pdb=" O SER B 315 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET B 332 " --> pdb=" O MET B 322 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ASP B 324 " --> pdb=" O CYS B 330 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N CYS B 330 " --> pdb=" O ASP B 324 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 341 through 346 removed outlier: 3.607A pdb=" N ILE B 353 " --> pdb=" O TRP B 365 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 357 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR B 361 " --> pdb=" O ALA B 357 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU B 362 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N THR B 375 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL B 364 " --> pdb=" O MET B 373 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 95 through 96 Processing sheet with id=AD2, first strand: chain 'C' and resid 95 through 96 removed outlier: 4.532A pdb=" N THR C 403 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER C 399 " --> pdb=" O THR C 403 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 111 through 116 removed outlier: 6.081A pdb=" N ASP C 136 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N PHE C 142 " --> pdb=" O ASP C 136 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 153 through 158 removed outlier: 3.523A pdb=" N SER C 167 " --> pdb=" O LYS C 175 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ASP C 178 " --> pdb=" O CYS C 184 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS C 184 " --> pdb=" O ASP C 178 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 197 through 199 removed outlier: 6.064A pdb=" N ILE C 216 " --> pdb=" O THR C 229 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR C 229 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N MET C 218 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR C 225 " --> pdb=" O GLU C 220 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 237 through 242 removed outlier: 7.107A pdb=" N CYS C 252 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL C 240 " --> pdb=" O ALA C 250 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ALA C 250 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU C 248 " --> pdb=" O PRO C 242 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA C 270 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL C 262 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N CYS C 268 " --> pdb=" O VAL C 262 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 279 through 284 removed outlier: 3.606A pdb=" N SER C 283 " --> pdb=" O LEU C 312 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 315 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR C 319 " --> pdb=" O SER C 315 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ASP C 324 " --> pdb=" O CYS C 330 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N CYS C 330 " --> pdb=" O ASP C 324 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 341 through 346 removed outlier: 3.648A pdb=" N THR C 361 " --> pdb=" O ALA C 357 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS C 374 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASP C 366 " --> pdb=" O CYS C 372 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N CYS C 372 " --> pdb=" O ASP C 366 " (cutoff:3.500A) 1910 hydrogen bonds defined for protein. 5563 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: 10.61 Time building geometry restraints manager: 3.42 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: 10724 1.34 - 1.46: 7294 1.46 - 1.58: 14476 1.58 - 1.70: 13 1.70 - 1.82: 264 Bond restraints: 32771 Sorted by residual: bond pdb=" N VAL I 530 " pdb=" CA VAL I 530 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.43e+00 bond pdb=" N VAL H 530 " pdb=" CA VAL H 530 " ideal model delta sigma weight residual 1.462 1.492 -0.030 1.18e-02 7.18e+03 6.43e+00 bond pdb=" N ASN I 536 " pdb=" CA ASN I 536 " ideal model delta sigma weight residual 1.457 1.490 -0.034 1.33e-02 5.65e+03 6.38e+00 bond pdb=" N LEU I 534 " pdb=" CA LEU I 534 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.20e+00 bond pdb=" N ASP I 529 " pdb=" CA ASP I 529 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.56e+00 ... (remaining 32766 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 43515 1.62 - 3.25: 815 3.25 - 4.87: 132 4.87 - 6.50: 45 6.50 - 8.12: 9 Bond angle restraints: 44516 Sorted by residual: angle pdb=" CA BGLU I 533 " pdb=" C BGLU I 533 " pdb=" O BGLU I 533 " ideal model delta sigma weight residual 120.42 116.44 3.98 1.06e+00 8.90e-01 1.41e+01 angle pdb=" CA AGLU I 533 " pdb=" C AGLU I 533 " pdb=" O AGLU I 533 " ideal model delta sigma weight residual 120.42 116.44 3.98 1.06e+00 8.90e-01 1.41e+01 angle pdb=" N SER B 127 " pdb=" CA SER B 127 " pdb=" C SER B 127 " ideal model delta sigma weight residual 108.34 112.81 -4.47 1.31e+00 5.83e-01 1.16e+01 angle pdb=" O VAL I 530 " pdb=" C VAL I 530 " pdb=" N ASN I 531 " ideal model delta sigma weight residual 121.91 125.15 -3.24 9.80e-01 1.04e+00 1.09e+01 angle pdb=" CA ARG I 532 " pdb=" C ARG I 532 " pdb=" O ARG I 532 " ideal model delta sigma weight residual 120.82 117.58 3.24 1.05e+00 9.07e-01 9.53e+00 ... (remaining 44511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 18088 17.91 - 35.82: 1408 35.82 - 53.74: 176 53.74 - 71.65: 92 71.65 - 89.56: 20 Dihedral angle restraints: 19784 sinusoidal: 7603 harmonic: 12181 Sorted by residual: dihedral pdb=" CA MET A2867 " pdb=" C MET A2867 " pdb=" N SER A2868 " pdb=" CA SER A2868 " ideal model delta harmonic sigma weight residual 180.00 157.99 22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA MET A2615 " pdb=" C MET A2615 " pdb=" N GLU A2616 " pdb=" CA GLU A2616 " ideal model delta harmonic sigma weight residual 180.00 158.80 21.20 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA TRP C 323 " pdb=" C TRP C 323 " pdb=" N ASP C 324 " pdb=" CA ASP C 324 " ideal model delta harmonic sigma weight residual 180.00 161.58 18.42 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 19781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 3802 0.041 - 0.082: 947 0.082 - 0.123: 299 0.123 - 0.164: 23 0.164 - 0.204: 2 Chirality restraints: 5073 Sorted by residual: chirality pdb=" CA VAL H 530 " pdb=" N VAL H 530 " pdb=" C VAL H 530 " pdb=" CB VAL H 530 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA VAL I 530 " pdb=" N VAL I 530 " pdb=" C VAL I 530 " pdb=" CB VAL I 530 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.34e-01 chirality pdb=" CA VAL A4469 " pdb=" N VAL A4469 " pdb=" C VAL A4469 " pdb=" CB VAL A4469 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 5070 not shown) Planarity restraints: 5730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BGLU I 533 " -0.032 2.00e-02 2.50e+03 6.51e-02 4.24e+01 pdb=" C BGLU I 533 " 0.113 2.00e-02 2.50e+03 pdb=" O BGLU I 533 " -0.042 2.00e-02 2.50e+03 pdb=" N LEU I 534 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA AGLU I 533 " -0.031 2.00e-02 2.50e+03 6.49e-02 4.21e+01 pdb=" C AGLU I 533 " 0.112 2.00e-02 2.50e+03 pdb=" O AGLU I 533 " -0.042 2.00e-02 2.50e+03 pdb=" N LEU I 534 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG I 532 " 0.026 2.00e-02 2.50e+03 5.27e-02 2.77e+01 pdb=" C ARG I 532 " -0.091 2.00e-02 2.50e+03 pdb=" O ARG I 532 " 0.034 2.00e-02 2.50e+03 pdb=" N AGLU I 533 " 0.031 2.00e-02 2.50e+03 ... (remaining 5727 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 319 2.53 - 3.12: 25465 3.12 - 3.71: 55337 3.71 - 4.31: 73660 4.31 - 4.90: 119024 Nonbonded interactions: 273805 Sorted by model distance: nonbonded pdb=" O2B ADP A4701 " pdb="MG MG A4706 " model vdw 1.935 2.170 nonbonded pdb=" NH2 ARG A2965 " pdb=" O SER A3640 " model vdw 2.001 3.120 nonbonded pdb=" OG SER A2231 " pdb="MG MG A4705 " model vdw 2.016 2.170 nonbonded pdb=" O3B ATP A4702 " pdb="MG MG A4705 " model vdw 2.045 2.170 nonbonded pdb=" O2B ATP A4702 " pdb="MG MG A4705 " model vdw 2.065 2.170 ... (remaining 273800 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 'B' and (resid 89 through 297 or resid 307 through 410)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' } ncs_group { reference = (chain 'H' and (resid 419 through 532 or resid 534 through 538)) selection = (chain 'I' and (resid 419 through 532 or resid 534 through 538)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 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: 1.500 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: 0.420 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 32.890 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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 : 0.002 0.034 32774 Z= 0.120 Angle : 0.563 8.120 44516 Z= 0.291 Chirality : 0.039 0.204 5073 Planarity : 0.004 0.107 5730 Dihedral : 13.461 89.559 11850 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.78 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.13), residues: 4137 helix: 1.86 (0.11), residues: 2135 sheet: 0.00 (0.24), residues: 493 loop : -0.02 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 144 TYR 0.022 0.001 TYR A2748 PHE 0.022 0.001 PHE C 179 TRP 0.031 0.001 TRP B 94 HIS 0.006 0.001 HIS A2964 Details of bonding type rmsd covalent geometry : bond 0.00234 (32771) covalent geometry : angle 0.56339 (44516) hydrogen bonds : bond 0.25282 ( 1908) hydrogen bonds : angle 7.19019 ( 5563) Misc. bond : bond 0.00120 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1394 MET cc_start: 0.1778 (ttm) cc_final: 0.1293 (tpp) REVERT: A 1507 MET cc_start: 0.7866 (mmp) cc_final: 0.7584 (mmt) REVERT: A 1589 MET cc_start: 0.9021 (mpp) cc_final: 0.8751 (tpp) REVERT: A 1606 ASP cc_start: 0.9404 (m-30) cc_final: 0.9147 (m-30) REVERT: A 1941 MET cc_start: 0.9258 (mmp) cc_final: 0.8635 (mmm) REVERT: A 2373 MET cc_start: 0.9149 (pmm) cc_final: 0.8735 (pmm) REVERT: A 2412 MET cc_start: 0.9187 (tpp) cc_final: 0.8275 (tmm) REVERT: A 2475 ASN cc_start: 0.9457 (t0) cc_final: 0.9172 (t0) REVERT: A 2683 ILE cc_start: 0.9816 (mm) cc_final: 0.9599 (mm) REVERT: A 2708 PHE cc_start: 0.8734 (m-80) cc_final: 0.8435 (m-10) REVERT: A 2803 VAL cc_start: 0.9599 (p) cc_final: 0.9295 (m) REVERT: A 2994 MET cc_start: 0.8132 (pmm) cc_final: 0.7846 (pmm) REVERT: A 3030 MET cc_start: 0.8227 (tpt) cc_final: 0.7887 (tpt) REVERT: A 3489 TRP cc_start: 0.8474 (m-10) cc_final: 0.7746 (m-10) REVERT: A 3737 GLU cc_start: 0.9520 (pt0) cc_final: 0.9179 (tm-30) REVERT: A 3791 MET cc_start: 0.8834 (tpp) cc_final: 0.8241 (tpp) REVERT: A 4095 MET cc_start: 0.8788 (tmm) cc_final: 0.8243 (tmm) REVERT: A 4157 MET cc_start: 0.9285 (mpp) cc_final: 0.9066 (mpp) REVERT: C 104 LEU cc_start: 0.7879 (mt) cc_final: 0.7661 (mt) REVERT: C 144 ARG cc_start: 0.8690 (ttm110) cc_final: 0.8258 (ptp-170) REVERT: C 241 ARG cc_start: 0.8928 (mpt180) cc_final: 0.8665 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.1914 time to fit residues: 71.6359 Evaluate side-chains 179 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 50.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1349 GLN A1433 GLN ** A1454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1643 ASN A1931 ASN ** A2588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4477 GLN ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.050226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.036751 restraints weight = 334963.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.038114 restraints weight = 174307.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.039021 restraints weight = 109732.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.039602 restraints weight = 78089.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.040044 restraints weight = 61026.209| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 32774 Z= 0.235 Angle : 0.644 9.263 44516 Z= 0.343 Chirality : 0.042 0.197 5073 Planarity : 0.005 0.056 5730 Dihedral : 5.642 85.511 4535 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.14 % Favored : 96.83 % Rotamer: Outliers : 0.12 % Allowed : 3.07 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.13), residues: 4137 helix: 1.79 (0.11), residues: 2215 sheet: -0.10 (0.23), residues: 515 loop : -0.06 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A2804 TYR 0.033 0.002 TYR A2748 PHE 0.022 0.002 PHE A2635 TRP 0.027 0.002 TRP C 177 HIS 0.008 0.001 HIS C 117 Details of bonding type rmsd covalent geometry : bond 0.00477 (32771) covalent geometry : angle 0.64375 (44516) hydrogen bonds : bond 0.05500 ( 1908) hydrogen bonds : angle 5.15018 ( 5563) Misc. bond : bond 0.00071 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 213 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1578 LEU cc_start: 0.9055 (mm) cc_final: 0.8846 (pp) REVERT: A 1892 MET cc_start: 0.8498 (mmp) cc_final: 0.8214 (mmp) REVERT: A 1941 MET cc_start: 0.9302 (mmp) cc_final: 0.8661 (mmm) REVERT: A 2126 GLU cc_start: 0.8676 (pt0) cc_final: 0.8196 (pp20) REVERT: A 2175 MET cc_start: 0.8485 (mpp) cc_final: 0.8273 (mpp) REVERT: A 2373 MET cc_start: 0.9209 (pmm) cc_final: 0.8919 (pmm) REVERT: A 2475 ASN cc_start: 0.9422 (t0) cc_final: 0.9218 (t0) REVERT: A 2603 MET cc_start: 0.9196 (ttp) cc_final: 0.8844 (ptm) REVERT: A 2671 MET cc_start: 0.7427 (tpt) cc_final: 0.7206 (tpt) REVERT: A 2708 PHE cc_start: 0.8702 (m-80) cc_final: 0.8451 (m-10) REVERT: A 2855 LEU cc_start: 0.9546 (pp) cc_final: 0.9313 (pp) REVERT: A 2994 MET cc_start: 0.8237 (pmm) cc_final: 0.7885 (pmm) REVERT: A 3030 MET cc_start: 0.8156 (tpt) cc_final: 0.7839 (tpt) REVERT: A 3478 LEU cc_start: 0.8700 (tt) cc_final: 0.8427 (mt) REVERT: A 4095 MET cc_start: 0.8930 (tmm) cc_final: 0.8633 (tmm) REVERT: A 4157 MET cc_start: 0.9298 (mpp) cc_final: 0.9014 (mpp) REVERT: B 188 MET cc_start: 0.8589 (tpp) cc_final: 0.8028 (tpp) REVERT: C 205 ASP cc_start: 0.8741 (t70) cc_final: 0.8205 (t0) REVERT: C 332 MET cc_start: 0.9142 (tpt) cc_final: 0.8479 (tmm) outliers start: 4 outliers final: 0 residues processed: 215 average time/residue: 0.1906 time to fit residues: 68.0232 Evaluate side-chains 167 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 48 optimal weight: 0.9990 chunk 315 optimal weight: 0.0570 chunk 44 optimal weight: 7.9990 chunk 341 optimal weight: 8.9990 chunk 174 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 381 optimal weight: 20.0000 chunk 108 optimal weight: 7.9990 chunk 147 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 305 optimal weight: 0.6980 overall best weight: 1.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1931 ASN ** A2588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3158 ASN ** A3200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3535 HIS A3744 GLN ** A3751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4477 GLN ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.062514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.051281 restraints weight = 361137.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.052621 restraints weight = 164243.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.053535 restraints weight = 94303.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.054064 restraints weight = 63929.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.054329 restraints weight = 49489.265| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32774 Z= 0.124 Angle : 0.546 6.302 44516 Z= 0.284 Chirality : 0.041 0.164 5073 Planarity : 0.004 0.058 5730 Dihedral : 5.546 88.464 4535 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.44 % Favored : 97.53 % Rotamer: Outliers : 0.12 % Allowed : 2.55 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.13), residues: 4137 helix: 2.01 (0.11), residues: 2224 sheet: -0.06 (0.23), residues: 507 loop : -0.08 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A3549 TYR 0.024 0.001 TYR C 290 PHE 0.020 0.001 PHE C 179 TRP 0.020 0.001 TRP C 177 HIS 0.010 0.001 HIS B 277 Details of bonding type rmsd covalent geometry : bond 0.00257 (32771) covalent geometry : angle 0.54571 (44516) hydrogen bonds : bond 0.04494 ( 1908) hydrogen bonds : angle 4.61306 ( 5563) Misc. bond : bond 0.00047 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 223 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1892 MET cc_start: 0.8509 (mmp) cc_final: 0.8155 (mmp) REVERT: A 1941 MET cc_start: 0.9269 (mmp) cc_final: 0.8565 (mmm) REVERT: A 2126 GLU cc_start: 0.8487 (pt0) cc_final: 0.8220 (pp20) REVERT: A 2232 MET cc_start: 0.8758 (ptp) cc_final: 0.8424 (ptp) REVERT: A 2372 ASP cc_start: 0.8924 (p0) cc_final: 0.8683 (p0) REVERT: A 2423 MET cc_start: 0.9296 (pmm) cc_final: 0.8358 (pmm) REVERT: A 2447 MET cc_start: 0.8301 (mmm) cc_final: 0.8016 (mmm) REVERT: A 2475 ASN cc_start: 0.9443 (t0) cc_final: 0.9241 (t0) REVERT: A 2603 MET cc_start: 0.8949 (ttp) cc_final: 0.8727 (ptm) REVERT: A 2994 MET cc_start: 0.8041 (pmm) cc_final: 0.7796 (pmm) REVERT: A 3001 ASP cc_start: 0.9148 (t0) cc_final: 0.8936 (t0) REVERT: A 3030 MET cc_start: 0.8119 (tpt) cc_final: 0.7784 (tpt) REVERT: A 3113 MET cc_start: 0.9009 (mmm) cc_final: 0.8766 (mmm) REVERT: A 3478 LEU cc_start: 0.8724 (tt) cc_final: 0.8449 (mt) REVERT: A 3489 TRP cc_start: 0.8735 (m-10) cc_final: 0.8465 (m-10) REVERT: A 4021 MET cc_start: 0.8714 (mmp) cc_final: 0.8415 (mmp) REVERT: A 4095 MET cc_start: 0.8971 (tmm) cc_final: 0.8753 (tmm) REVERT: A 4157 MET cc_start: 0.9340 (mpp) cc_final: 0.8926 (mmt) REVERT: B 154 GLN cc_start: 0.7372 (mp10) cc_final: 0.6914 (mp10) REVERT: C 205 ASP cc_start: 0.8625 (t70) cc_final: 0.8058 (t0) REVERT: C 332 MET cc_start: 0.8963 (tpt) cc_final: 0.8591 (tmm) outliers start: 4 outliers final: 0 residues processed: 225 average time/residue: 0.1940 time to fit residues: 73.0834 Evaluate side-chains 171 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 94 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 242 optimal weight: 6.9990 chunk 332 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 367 optimal weight: 0.3980 chunk 97 optimal weight: 0.0370 chunk 257 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 250 optimal weight: 0.9980 overall best weight: 0.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1931 ASN A2588 HIS ** A3200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4477 GLN B 180 GLN B 189 HIS ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.051971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.037636 restraints weight = 362269.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.039133 restraints weight = 180990.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.040149 restraints weight = 111358.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.040820 restraints weight = 77677.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.041260 restraints weight = 59866.991| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 32774 Z= 0.108 Angle : 0.526 9.331 44516 Z= 0.269 Chirality : 0.040 0.167 5073 Planarity : 0.004 0.059 5730 Dihedral : 5.410 84.729 4535 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.61 % Favored : 97.36 % Rotamer: Outliers : 0.06 % Allowed : 2.16 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.13), residues: 4137 helix: 2.09 (0.11), residues: 2227 sheet: 0.04 (0.23), residues: 498 loop : -0.06 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2965 TYR 0.021 0.001 TYR C 290 PHE 0.024 0.001 PHE A1926 TRP 0.033 0.001 TRP B 135 HIS 0.009 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00223 (32771) covalent geometry : angle 0.52612 (44516) hydrogen bonds : bond 0.03964 ( 1908) hydrogen bonds : angle 4.36989 ( 5563) Misc. bond : bond 0.00104 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 221 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1578 LEU cc_start: 0.9233 (pp) cc_final: 0.8881 (mm) REVERT: A 1892 MET cc_start: 0.8268 (mmp) cc_final: 0.8001 (mmp) REVERT: A 1941 MET cc_start: 0.9239 (mmp) cc_final: 0.8562 (mmm) REVERT: A 1965 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8482 (mm-30) REVERT: A 2126 GLU cc_start: 0.8561 (pt0) cc_final: 0.8273 (pp20) REVERT: A 2232 MET cc_start: 0.9053 (ptp) cc_final: 0.8716 (ptp) REVERT: A 2423 MET cc_start: 0.9299 (pmm) cc_final: 0.8328 (pmm) REVERT: A 2447 MET cc_start: 0.8241 (mmm) cc_final: 0.8018 (mmm) REVERT: A 2603 MET cc_start: 0.8877 (ttp) cc_final: 0.8652 (ptm) REVERT: A 2671 MET cc_start: 0.8033 (tpt) cc_final: 0.7744 (tpt) REVERT: A 3030 MET cc_start: 0.8195 (tpt) cc_final: 0.7821 (tpt) REVERT: A 3113 MET cc_start: 0.9150 (mmm) cc_final: 0.8942 (mmm) REVERT: A 3478 LEU cc_start: 0.8508 (tt) cc_final: 0.8189 (mt) REVERT: A 3489 TRP cc_start: 0.8581 (m-10) cc_final: 0.8374 (m-10) REVERT: A 4021 MET cc_start: 0.8648 (mmp) cc_final: 0.8366 (mmp) REVERT: A 4095 MET cc_start: 0.8990 (tmm) cc_final: 0.8606 (tmm) REVERT: A 4157 MET cc_start: 0.9246 (mpp) cc_final: 0.9012 (mmm) REVERT: B 123 MET cc_start: 0.8860 (ppp) cc_final: 0.8483 (ppp) REVERT: B 154 GLN cc_start: 0.7340 (mp10) cc_final: 0.6887 (mp10) REVERT: C 205 ASP cc_start: 0.8638 (t70) cc_final: 0.8035 (t0) REVERT: C 239 MET cc_start: 0.6468 (ppp) cc_final: 0.5603 (ppp) REVERT: C 332 MET cc_start: 0.9256 (tpt) cc_final: 0.8893 (tmm) outliers start: 2 outliers final: 0 residues processed: 222 average time/residue: 0.1921 time to fit residues: 70.8737 Evaluate side-chains 171 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 272 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 346 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 324 optimal weight: 0.0870 chunk 166 optimal weight: 4.9990 chunk 355 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1931 ASN A1979 GLN A2707 GLN ** A3200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.050819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.036839 restraints weight = 376294.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.038293 restraints weight = 186494.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.039266 restraints weight = 114470.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.039915 restraints weight = 80067.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.040388 restraints weight = 61544.949| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 32774 Z= 0.154 Angle : 0.544 6.644 44516 Z= 0.281 Chirality : 0.040 0.216 5073 Planarity : 0.004 0.108 5730 Dihedral : 5.407 83.582 4535 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.06 % Allowed : 2.16 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.13), residues: 4137 helix: 2.18 (0.11), residues: 2231 sheet: -0.17 (0.23), residues: 519 loop : -0.05 (0.17), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2965 TYR 0.020 0.001 TYR C 290 PHE 0.020 0.002 PHE A1626 TRP 0.022 0.001 TRP B 135 HIS 0.005 0.001 HIS A3151 Details of bonding type rmsd covalent geometry : bond 0.00320 (32771) covalent geometry : angle 0.54420 (44516) hydrogen bonds : bond 0.03805 ( 1908) hydrogen bonds : angle 4.33000 ( 5563) Misc. bond : bond 0.00121 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 205 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1892 MET cc_start: 0.8333 (mmp) cc_final: 0.8070 (mmp) REVERT: A 1941 MET cc_start: 0.9306 (mmp) cc_final: 0.8587 (mmm) REVERT: A 1965 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8413 (mm-30) REVERT: A 1967 MET cc_start: 0.9432 (mmm) cc_final: 0.9223 (mmm) REVERT: A 2126 GLU cc_start: 0.8530 (pt0) cc_final: 0.8290 (pp20) REVERT: A 2175 MET cc_start: 0.8406 (mpp) cc_final: 0.8045 (mpp) REVERT: A 2232 MET cc_start: 0.8974 (ptp) cc_final: 0.8705 (ptp) REVERT: A 2773 MET cc_start: 0.9137 (ttm) cc_final: 0.8899 (ttp) REVERT: A 3030 MET cc_start: 0.8215 (tpt) cc_final: 0.7975 (tpt) REVERT: A 3478 LEU cc_start: 0.8679 (tt) cc_final: 0.8147 (mt) REVERT: A 3489 TRP cc_start: 0.8597 (m-10) cc_final: 0.8364 (m-10) REVERT: A 4095 MET cc_start: 0.8994 (tmm) cc_final: 0.8664 (tmm) REVERT: A 4157 MET cc_start: 0.9260 (mpp) cc_final: 0.8979 (mmm) REVERT: A 4377 MET cc_start: 0.8404 (mtp) cc_final: 0.7971 (mmm) REVERT: B 123 MET cc_start: 0.8811 (ppp) cc_final: 0.8496 (ppp) REVERT: B 154 GLN cc_start: 0.8084 (mp10) cc_final: 0.7708 (mp10) REVERT: B 367 TYR cc_start: 0.7195 (p90) cc_final: 0.6902 (p90) REVERT: C 205 ASP cc_start: 0.8735 (t70) cc_final: 0.8107 (t0) REVERT: C 332 MET cc_start: 0.9253 (tpt) cc_final: 0.8669 (tpt) outliers start: 2 outliers final: 0 residues processed: 206 average time/residue: 0.1916 time to fit residues: 67.0069 Evaluate side-chains 167 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 351 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 188 optimal weight: 40.0000 chunk 87 optimal weight: 3.9990 chunk 226 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 chunk 312 optimal weight: 10.0000 chunk 293 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 chunk 187 optimal weight: 5.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1653 HIS A1931 ASN A1979 GLN A2834 GLN ** A3200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3826 GLN A3830 GLN ** A4477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4597 ASN B 180 GLN ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.049762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.036722 restraints weight = 291714.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.037955 restraints weight = 159048.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.038783 restraints weight = 102935.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.039361 restraints weight = 74742.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.039774 restraints weight = 58931.747| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 32774 Z= 0.185 Angle : 0.571 6.943 44516 Z= 0.296 Chirality : 0.041 0.184 5073 Planarity : 0.004 0.127 5730 Dihedral : 5.560 88.779 4535 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.06 % Allowed : 1.98 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.13), residues: 4137 helix: 2.15 (0.11), residues: 2233 sheet: -0.15 (0.23), residues: 515 loop : -0.09 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 241 TYR 0.020 0.002 TYR C 290 PHE 0.018 0.002 PHE A2776 TRP 0.031 0.002 TRP B 323 HIS 0.007 0.001 HIS A3877 Details of bonding type rmsd covalent geometry : bond 0.00386 (32771) covalent geometry : angle 0.57110 (44516) hydrogen bonds : bond 0.03781 ( 1908) hydrogen bonds : angle 4.37382 ( 5563) Misc. bond : bond 0.00092 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 202 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1709 MET cc_start: 0.8438 (ptm) cc_final: 0.7579 (ppp) REVERT: A 1892 MET cc_start: 0.8414 (mmp) cc_final: 0.8138 (mmp) REVERT: A 1941 MET cc_start: 0.9217 (mmp) cc_final: 0.8663 (mmm) REVERT: A 1965 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8447 (mm-30) REVERT: A 1967 MET cc_start: 0.9514 (mmm) cc_final: 0.9263 (mmm) REVERT: A 2126 GLU cc_start: 0.8565 (pt0) cc_final: 0.8303 (pp20) REVERT: A 2175 MET cc_start: 0.8494 (mpp) cc_final: 0.8161 (mpp) REVERT: A 2232 MET cc_start: 0.8975 (ptp) cc_final: 0.8649 (ptp) REVERT: A 2447 MET cc_start: 0.8304 (mmm) cc_final: 0.7985 (mmm) REVERT: A 2773 MET cc_start: 0.9063 (ttm) cc_final: 0.8828 (ttp) REVERT: A 3478 LEU cc_start: 0.8905 (tt) cc_final: 0.8373 (mt) REVERT: A 3489 TRP cc_start: 0.8640 (m-10) cc_final: 0.8429 (m-10) REVERT: A 4021 MET cc_start: 0.8610 (mmp) cc_final: 0.8169 (mmp) REVERT: A 4095 MET cc_start: 0.8924 (tmm) cc_final: 0.8704 (tmm) REVERT: A 4157 MET cc_start: 0.9248 (mpp) cc_final: 0.8871 (mpp) REVERT: A 4377 MET cc_start: 0.8408 (mtp) cc_final: 0.8001 (mmm) REVERT: B 123 MET cc_start: 0.8822 (ppp) cc_final: 0.8493 (ppp) REVERT: B 154 GLN cc_start: 0.7979 (mp10) cc_final: 0.7691 (mp10) REVERT: B 322 MET cc_start: 0.9060 (tmm) cc_final: 0.8749 (tmm) REVERT: B 367 TYR cc_start: 0.7284 (p90) cc_final: 0.6958 (p90) REVERT: C 172 MET cc_start: 0.8823 (mmm) cc_final: 0.8572 (mmt) REVERT: C 205 ASP cc_start: 0.8695 (t70) cc_final: 0.8075 (t0) REVERT: C 332 MET cc_start: 0.9032 (tpt) cc_final: 0.8426 (tpt) REVERT: C 394 TYR cc_start: 0.7923 (m-10) cc_final: 0.7720 (m-10) outliers start: 2 outliers final: 0 residues processed: 204 average time/residue: 0.1798 time to fit residues: 62.1365 Evaluate side-chains 170 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 327 optimal weight: 0.3980 chunk 157 optimal weight: 0.9990 chunk 188 optimal weight: 40.0000 chunk 356 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 374 optimal weight: 0.8980 chunk 408 optimal weight: 3.9990 chunk 378 optimal weight: 50.0000 chunk 319 optimal weight: 4.9990 chunk 316 optimal weight: 20.0000 chunk 187 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1931 ASN A1979 GLN ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4477 GLN A4597 ASN ** B 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.050707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.037032 restraints weight = 340860.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.038411 restraints weight = 173668.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.039338 restraints weight = 108341.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.039984 restraints weight = 76258.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.040383 restraints weight = 58843.797| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32774 Z= 0.123 Angle : 0.538 7.151 44516 Z= 0.274 Chirality : 0.040 0.154 5073 Planarity : 0.004 0.078 5730 Dihedral : 5.494 88.164 4535 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.13), residues: 4137 helix: 2.27 (0.11), residues: 2221 sheet: -0.14 (0.23), residues: 505 loop : -0.03 (0.17), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2797 TYR 0.019 0.001 TYR A1546 PHE 0.024 0.001 PHE A4268 TRP 0.016 0.001 TRP B 323 HIS 0.006 0.001 HIS B 277 Details of bonding type rmsd covalent geometry : bond 0.00262 (32771) covalent geometry : angle 0.53778 (44516) hydrogen bonds : bond 0.03587 ( 1908) hydrogen bonds : angle 4.22538 ( 5563) Misc. bond : bond 0.00242 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1709 MET cc_start: 0.8372 (ptm) cc_final: 0.7398 (ppp) REVERT: A 1892 MET cc_start: 0.8384 (mmp) cc_final: 0.8162 (mmp) REVERT: A 1941 MET cc_start: 0.9126 (mmp) cc_final: 0.8581 (mmm) REVERT: A 1965 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8339 (mm-30) REVERT: A 1967 MET cc_start: 0.9479 (mmm) cc_final: 0.9221 (mmm) REVERT: A 2175 MET cc_start: 0.8460 (mpp) cc_final: 0.8122 (mpp) REVERT: A 2232 MET cc_start: 0.8991 (ptp) cc_final: 0.8662 (ptp) REVERT: A 2447 MET cc_start: 0.8281 (mmm) cc_final: 0.8000 (mmm) REVERT: A 2671 MET cc_start: 0.8804 (tpp) cc_final: 0.8390 (tpp) REVERT: A 3478 LEU cc_start: 0.8849 (tt) cc_final: 0.8444 (pp) REVERT: A 3946 ASP cc_start: 0.8218 (p0) cc_final: 0.7661 (t0) REVERT: A 4021 MET cc_start: 0.8570 (mmp) cc_final: 0.8117 (mmp) REVERT: A 4095 MET cc_start: 0.8950 (tmm) cc_final: 0.8683 (tmm) REVERT: A 4157 MET cc_start: 0.9161 (mpp) cc_final: 0.8953 (mmm) REVERT: A 4377 MET cc_start: 0.8389 (mtp) cc_final: 0.7993 (mmm) REVERT: B 123 MET cc_start: 0.8805 (ppp) cc_final: 0.8453 (ppp) REVERT: B 154 GLN cc_start: 0.8144 (mp10) cc_final: 0.7702 (mp10) REVERT: B 373 MET cc_start: 0.9239 (ppp) cc_final: 0.8523 (tmm) REVERT: C 205 ASP cc_start: 0.8695 (t70) cc_final: 0.8077 (t0) REVERT: C 394 TYR cc_start: 0.7882 (m-10) cc_final: 0.7626 (m-10) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.1749 time to fit residues: 62.6312 Evaluate side-chains 162 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 112 optimal weight: 1.9990 chunk 199 optimal weight: 0.6980 chunk 268 optimal weight: 0.2980 chunk 335 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 291 optimal weight: 5.9990 chunk 228 optimal weight: 7.9990 chunk 297 optimal weight: 5.9990 chunk 177 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 369 optimal weight: 30.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1931 ASN A1979 GLN A1987 ASN A2263 HIS ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4477 GLN ** B 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.050011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.036938 restraints weight = 298588.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.038208 restraints weight = 160233.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.039057 restraints weight = 102720.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.039650 restraints weight = 73931.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.040031 restraints weight = 57742.951| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32774 Z= 0.142 Angle : 0.547 7.370 44516 Z= 0.280 Chirality : 0.040 0.162 5073 Planarity : 0.004 0.108 5730 Dihedral : 5.479 89.597 4535 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.03 % Allowed : 0.88 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.13), residues: 4137 helix: 2.27 (0.11), residues: 2227 sheet: -0.19 (0.23), residues: 508 loop : -0.05 (0.17), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 241 TYR 0.018 0.001 TYR A1546 PHE 0.017 0.001 PHE A4515 TRP 0.036 0.001 TRP B 94 HIS 0.005 0.001 HIS A3877 Details of bonding type rmsd covalent geometry : bond 0.00301 (32771) covalent geometry : angle 0.54714 (44516) hydrogen bonds : bond 0.03548 ( 1908) hydrogen bonds : angle 4.23155 ( 5563) Misc. bond : bond 0.00169 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 199 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1709 MET cc_start: 0.8370 (ptm) cc_final: 0.7469 (ppp) REVERT: A 1892 MET cc_start: 0.8399 (mmp) cc_final: 0.8171 (mmp) REVERT: A 1941 MET cc_start: 0.9116 (mmp) cc_final: 0.8593 (mmm) REVERT: A 1967 MET cc_start: 0.9476 (mmm) cc_final: 0.9254 (mmt) REVERT: A 2175 MET cc_start: 0.8505 (mpp) cc_final: 0.8149 (mpp) REVERT: A 2232 MET cc_start: 0.8968 (ptp) cc_final: 0.8625 (ptp) REVERT: A 2447 MET cc_start: 0.8276 (mmm) cc_final: 0.8012 (mmm) REVERT: A 2671 MET cc_start: 0.8757 (tpp) cc_final: 0.8371 (tpp) REVERT: A 2773 MET cc_start: 0.9122 (ttm) cc_final: 0.8900 (ttp) REVERT: A 3478 LEU cc_start: 0.8729 (tt) cc_final: 0.8419 (pp) REVERT: A 3946 ASP cc_start: 0.8263 (p0) cc_final: 0.7680 (t0) REVERT: A 4021 MET cc_start: 0.8628 (mmp) cc_final: 0.8368 (mmp) REVERT: A 4095 MET cc_start: 0.8964 (tmm) cc_final: 0.8672 (tmm) REVERT: A 4157 MET cc_start: 0.9185 (mpp) cc_final: 0.8966 (mmm) REVERT: A 4377 MET cc_start: 0.8496 (mtp) cc_final: 0.8103 (mmm) REVERT: B 123 MET cc_start: 0.8811 (ppp) cc_final: 0.8433 (ppp) REVERT: B 154 GLN cc_start: 0.8060 (mp10) cc_final: 0.7767 (mp10) REVERT: B 367 TYR cc_start: 0.6922 (p90) cc_final: 0.6573 (p90) REVERT: B 373 MET cc_start: 0.9184 (ppp) cc_final: 0.8503 (tmm) REVERT: C 205 ASP cc_start: 0.8718 (t70) cc_final: 0.8094 (t0) REVERT: C 332 MET cc_start: 0.9300 (tpt) cc_final: 0.8950 (tmm) REVERT: C 394 TYR cc_start: 0.7987 (m-10) cc_final: 0.7697 (m-10) outliers start: 1 outliers final: 0 residues processed: 200 average time/residue: 0.1890 time to fit residues: 63.9416 Evaluate side-chains 164 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 78 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 365 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 238 optimal weight: 0.9990 chunk 196 optimal weight: 0.8980 chunk 339 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 316 optimal weight: 20.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1412 HIS A1931 ASN A1979 GLN A1987 ASN ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4477 GLN ** B 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.050534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.037352 restraints weight = 268966.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.038559 restraints weight = 148246.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.039394 restraints weight = 96708.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.039954 restraints weight = 70243.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.040281 restraints weight = 55845.429| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32774 Z= 0.125 Angle : 0.549 7.628 44516 Z= 0.279 Chirality : 0.040 0.175 5073 Planarity : 0.004 0.077 5730 Dihedral : 5.409 88.898 4535 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.03 % Allowed : 0.36 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.13), residues: 4137 helix: 2.33 (0.11), residues: 2224 sheet: -0.20 (0.23), residues: 514 loop : -0.01 (0.17), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A2804 TYR 0.019 0.001 TYR A1546 PHE 0.016 0.001 PHE A4515 TRP 0.036 0.001 TRP B 94 HIS 0.004 0.001 HIS A3877 Details of bonding type rmsd covalent geometry : bond 0.00266 (32771) covalent geometry : angle 0.54853 (44516) hydrogen bonds : bond 0.03506 ( 1908) hydrogen bonds : angle 4.16356 ( 5563) Misc. bond : bond 0.00043 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1709 MET cc_start: 0.8436 (ptm) cc_final: 0.7581 (ppp) REVERT: A 1892 MET cc_start: 0.8439 (mmp) cc_final: 0.8193 (mmp) REVERT: A 1941 MET cc_start: 0.9195 (mmp) cc_final: 0.8602 (mmm) REVERT: A 1967 MET cc_start: 0.9486 (mmm) cc_final: 0.9262 (mmt) REVERT: A 2175 MET cc_start: 0.8544 (mpp) cc_final: 0.8169 (mpp) REVERT: A 2361 MET cc_start: 0.8282 (mmm) cc_final: 0.8009 (mmm) REVERT: A 2447 MET cc_start: 0.8272 (mmm) cc_final: 0.8018 (mmm) REVERT: A 2671 MET cc_start: 0.8811 (tpp) cc_final: 0.8448 (tpp) REVERT: A 3047 HIS cc_start: 0.8881 (m-70) cc_final: 0.7721 (m-70) REVERT: A 3478 LEU cc_start: 0.8824 (tt) cc_final: 0.8476 (pp) REVERT: A 3946 ASP cc_start: 0.8333 (p0) cc_final: 0.7746 (t0) REVERT: A 4021 MET cc_start: 0.8639 (mmp) cc_final: 0.8379 (mmp) REVERT: A 4095 MET cc_start: 0.8971 (tmm) cc_final: 0.8654 (tmm) REVERT: A 4157 MET cc_start: 0.9220 (mpp) cc_final: 0.8971 (mmm) REVERT: A 4377 MET cc_start: 0.8475 (mtp) cc_final: 0.8084 (mmm) REVERT: B 123 MET cc_start: 0.8856 (ppp) cc_final: 0.8459 (ppp) REVERT: B 154 GLN cc_start: 0.8118 (mp10) cc_final: 0.7722 (mp10) REVERT: B 367 TYR cc_start: 0.7176 (p90) cc_final: 0.6966 (p90) REVERT: B 373 MET cc_start: 0.9193 (ppp) cc_final: 0.8550 (tmm) REVERT: C 205 ASP cc_start: 0.8740 (t70) cc_final: 0.8107 (t0) REVERT: C 332 MET cc_start: 0.9289 (tpt) cc_final: 0.8950 (tmm) REVERT: C 394 TYR cc_start: 0.8095 (m-10) cc_final: 0.7771 (m-10) outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.1868 time to fit residues: 64.0824 Evaluate side-chains 165 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 307 optimal weight: 4.9990 chunk 208 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 234 optimal weight: 4.9990 chunk 184 optimal weight: 0.6980 chunk 230 optimal weight: 0.6980 chunk 202 optimal weight: 2.9990 chunk 408 optimal weight: 5.9990 chunk 238 optimal weight: 0.7980 chunk 182 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1931 ASN A1979 GLN A1987 ASN ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4477 GLN ** B 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.050317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.037304 restraints weight = 277459.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.038527 restraints weight = 152343.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.039366 restraints weight = 99073.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.039949 restraints weight = 71699.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.040348 restraints weight = 56341.764| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32774 Z= 0.120 Angle : 0.547 7.879 44516 Z= 0.277 Chirality : 0.040 0.180 5073 Planarity : 0.004 0.085 5730 Dihedral : 5.435 86.894 4535 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.03 % Allowed : 0.30 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.13), residues: 4137 helix: 2.39 (0.11), residues: 2213 sheet: -0.23 (0.23), residues: 513 loop : 0.03 (0.17), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 241 TYR 0.019 0.001 TYR A1546 PHE 0.018 0.001 PHE B 158 TRP 0.036 0.001 TRP B 94 HIS 0.006 0.001 HIS A3047 Details of bonding type rmsd covalent geometry : bond 0.00255 (32771) covalent geometry : angle 0.54706 (44516) hydrogen bonds : bond 0.03434 ( 1908) hydrogen bonds : angle 4.13372 ( 5563) Misc. bond : bond 0.00043 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1709 MET cc_start: 0.8400 (ptm) cc_final: 0.7571 (ppp) REVERT: A 1892 MET cc_start: 0.8374 (mmp) cc_final: 0.8152 (mmp) REVERT: A 1941 MET cc_start: 0.9148 (mmp) cc_final: 0.8579 (mmm) REVERT: A 1967 MET cc_start: 0.9470 (mmm) cc_final: 0.9248 (mmt) REVERT: A 2175 MET cc_start: 0.8461 (mpp) cc_final: 0.8092 (mpp) REVERT: A 2232 MET cc_start: 0.8739 (ptp) cc_final: 0.8493 (ptp) REVERT: A 2361 MET cc_start: 0.8318 (mmm) cc_final: 0.8020 (mmm) REVERT: A 2423 MET cc_start: 0.9230 (pmm) cc_final: 0.9019 (pmm) REVERT: A 2447 MET cc_start: 0.8252 (mmm) cc_final: 0.7996 (mmm) REVERT: A 2671 MET cc_start: 0.8864 (tpp) cc_final: 0.8427 (tpp) REVERT: A 2808 GLU cc_start: 0.9345 (mp0) cc_final: 0.8954 (mp0) REVERT: A 3030 MET cc_start: 0.8958 (ttp) cc_final: 0.8695 (ttt) REVERT: A 3478 LEU cc_start: 0.8805 (tt) cc_final: 0.8465 (pp) REVERT: A 3946 ASP cc_start: 0.8246 (p0) cc_final: 0.7675 (t0) REVERT: A 4021 MET cc_start: 0.8584 (mmp) cc_final: 0.8322 (mmp) REVERT: A 4043 MET cc_start: 0.9573 (mmm) cc_final: 0.9287 (mmt) REVERT: A 4095 MET cc_start: 0.8965 (tmm) cc_final: 0.8661 (tmm) REVERT: A 4157 MET cc_start: 0.9169 (mpp) cc_final: 0.8953 (mmm) REVERT: A 4377 MET cc_start: 0.8465 (mtp) cc_final: 0.8103 (mmm) REVERT: B 123 MET cc_start: 0.8833 (ppp) cc_final: 0.8427 (ppp) REVERT: B 154 GLN cc_start: 0.7993 (mp10) cc_final: 0.7670 (mp10) REVERT: B 194 ASN cc_start: 0.9362 (t0) cc_final: 0.8905 (p0) REVERT: B 373 MET cc_start: 0.9145 (ppp) cc_final: 0.8516 (tmm) REVERT: C 205 ASP cc_start: 0.8569 (t70) cc_final: 0.7815 (t0) REVERT: C 332 MET cc_start: 0.9245 (tpt) cc_final: 0.8967 (tmm) REVERT: C 394 TYR cc_start: 0.8130 (m-10) cc_final: 0.7845 (m-10) outliers start: 1 outliers final: 0 residues processed: 202 average time/residue: 0.1940 time to fit residues: 66.2114 Evaluate side-chains 166 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 411 optimal weight: 10.0000 chunk 138 optimal weight: 0.7980 chunk 387 optimal weight: 10.0000 chunk 267 optimal weight: 0.9980 chunk 162 optimal weight: 6.9990 chunk 399 optimal weight: 5.9990 chunk 279 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 395 optimal weight: 9.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1931 ASN A1979 GLN ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4477 GLN ** B 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.050321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.037055 restraints weight = 291291.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.038309 restraints weight = 156406.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.039164 restraints weight = 100455.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.039753 restraints weight = 72484.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.040104 restraints weight = 56899.283| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32774 Z= 0.131 Angle : 0.550 7.954 44516 Z= 0.279 Chirality : 0.040 0.183 5073 Planarity : 0.004 0.077 5730 Dihedral : 5.425 86.010 4535 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.13), residues: 4137 helix: 2.40 (0.11), residues: 2221 sheet: -0.23 (0.23), residues: 507 loop : -0.05 (0.17), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 241 TYR 0.019 0.001 TYR A1546 PHE 0.015 0.001 PHE A4515 TRP 0.034 0.001 TRP B 94 HIS 0.005 0.001 HIS A3877 Details of bonding type rmsd covalent geometry : bond 0.00278 (32771) covalent geometry : angle 0.54967 (44516) hydrogen bonds : bond 0.03414 ( 1908) hydrogen bonds : angle 4.11931 ( 5563) Misc. bond : bond 0.00049 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5323.88 seconds wall clock time: 93 minutes 23.41 seconds (5603.41 seconds total)