Starting phenix.real_space_refine on Sat May 24 18:56:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oxq_17268/05_2025/8oxq_17268.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oxq_17268/05_2025/8oxq_17268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oxq_17268/05_2025/8oxq_17268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oxq_17268/05_2025/8oxq_17268.map" model { file = "/net/cci-nas-00/data/ceres_data/8oxq_17268/05_2025/8oxq_17268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oxq_17268/05_2025/8oxq_17268.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 6 5.49 5 Mg 2 5.21 5 S 174 5.16 5 C 15940 2.51 5 N 4288 2.21 5 O 4666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25078 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1550, 12506 Classifications: {'peptide': 1550} Link IDs: {'PTRANS': 46, 'TRANS': 1503} Chain breaks: 6 Chain: "B" Number of atoms: 12506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1550, 12506 Classifications: {'peptide': 1550} Link IDs: {'PTRANS': 46, 'TRANS': 1503} Chain breaks: 6 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3764 SG CYS A1899 73.433 40.750 29.954 1.00220.36 S ATOM 3770 SG CYS A1900 71.675 43.494 29.364 1.00216.15 S ATOM 16270 SG CYS B1899 90.081 126.253 29.972 1.00222.03 S ATOM 16276 SG CYS B1900 91.825 123.499 29.371 1.00219.12 S Time building chain proxies: 13.38, per 1000 atoms: 0.53 Number of scatterers: 25078 At special positions: 0 Unit cell: (164.374, 167.678, 118.944, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 174 16.00 P 6 15.00 Mg 2 11.99 O 4666 8.00 N 4288 7.00 C 15940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.98 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3103 " pdb="ZN ZN A3103 " - pdb=" SG CYS A1899 " pdb="ZN ZN A3103 " - pdb=" SG CYS A1900 " pdb="ZN ZN A3103 " - pdb=" ND1 HIS A1876 " pdb=" ZN B3103 " pdb="ZN ZN B3103 " - pdb=" SG CYS B1899 " pdb="ZN ZN B3103 " - pdb=" SG CYS B1900 " pdb="ZN ZN B3103 " - pdb=" ND1 HIS B1876 " 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5924 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 6 sheets defined 74.9% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.00 Creating SS restraints... Processing helix chain 'A' and resid 1412 through 1429 removed outlier: 4.214A pdb=" N GLN A1416 " --> pdb=" O PRO A1412 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR A1429 " --> pdb=" O GLN A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1451 Processing helix chain 'A' and resid 1460 through 1478 Processing helix chain 'A' and resid 1484 through 1509 Processing helix chain 'A' and resid 1512 through 1515 removed outlier: 4.319A pdb=" N ASN A1515 " --> pdb=" O ALA A1512 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1512 through 1515' Processing helix chain 'A' and resid 1516 through 1528 Proline residue: A1526 - end of helix Processing helix chain 'A' and resid 1531 through 1546 Processing helix chain 'A' and resid 1552 through 1561 removed outlier: 4.435A pdb=" N ILE A1557 " --> pdb=" O GLU A1553 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N THR A1558 " --> pdb=" O ASN A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1571 through 1583 Processing helix chain 'A' and resid 1589 through 1602 removed outlier: 3.646A pdb=" N VAL A1602 " --> pdb=" O LEU A1598 " (cutoff:3.500A) Processing helix chain 'A' and resid 1606 through 1609 Processing helix chain 'A' and resid 1610 through 1624 Processing helix chain 'A' and resid 1624 through 1635 removed outlier: 3.707A pdb=" N MET A1628 " --> pdb=" O HIS A1624 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A1629 " --> pdb=" O LYS A1625 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP A1630 " --> pdb=" O ASP A1626 " (cutoff:3.500A) Processing helix chain 'A' and resid 1642 through 1659 Processing helix chain 'A' and resid 1663 through 1678 removed outlier: 3.854A pdb=" N VAL A1667 " --> pdb=" O GLY A1663 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A1678 " --> pdb=" O CYS A1674 " (cutoff:3.500A) Processing helix chain 'A' and resid 1693 through 1703 removed outlier: 3.748A pdb=" N PHE A1703 " --> pdb=" O ALA A1699 " (cutoff:3.500A) Processing helix chain 'A' and resid 1705 through 1722 Processing helix chain 'A' and resid 1726 through 1743 removed outlier: 3.573A pdb=" N THR A1743 " --> pdb=" O ASN A1739 " (cutoff:3.500A) Processing helix chain 'A' and resid 1743 through 1754 Processing helix chain 'A' and resid 1758 through 1764 removed outlier: 4.000A pdb=" N ALA A1762 " --> pdb=" O ASP A1758 " (cutoff:3.500A) Processing helix chain 'A' and resid 1791 through 1796 Processing helix chain 'A' and resid 1801 through 1816 Processing helix chain 'A' and resid 1821 through 1826 removed outlier: 4.037A pdb=" N GLN A1825 " --> pdb=" O CYS A1821 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A1826 " --> pdb=" O GLU A1822 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1821 through 1826' Processing helix chain 'A' and resid 1827 through 1832 Processing helix chain 'A' and resid 1834 through 1852 Proline residue: A1843 - end of helix Processing helix chain 'A' and resid 1856 through 1875 Processing helix chain 'A' and resid 1902 through 1918 removed outlier: 3.545A pdb=" N GLN A1906 " --> pdb=" O ASP A1902 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A1907 " --> pdb=" O LYS A1903 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A1918 " --> pdb=" O ASP A1914 " (cutoff:3.500A) Processing helix chain 'A' and resid 1926 through 1931 Processing helix chain 'A' and resid 1937 through 1948 removed outlier: 3.622A pdb=" N VAL A1941 " --> pdb=" O ASN A1937 " (cutoff:3.500A) Processing helix chain 'A' and resid 1950 through 1974 Processing helix chain 'A' and resid 1985 through 1998 Processing helix chain 'A' and resid 2000 through 2013 Processing helix chain 'A' and resid 2015 through 2020 removed outlier: 3.605A pdb=" N LEU A2018 " --> pdb=" O PRO A2015 " (cutoff:3.500A) Processing helix chain 'A' and resid 2028 through 2039 Processing helix chain 'A' and resid 2041 through 2052 Processing helix chain 'A' and resid 2056 through 2071 Processing helix chain 'A' and resid 2073 through 2088 Processing helix chain 'A' and resid 2092 through 2106 Processing helix chain 'A' and resid 2123 through 2137 Processing helix chain 'A' and resid 2139 through 2160 removed outlier: 3.527A pdb=" N LYS A2160 " --> pdb=" O GLU A2156 " (cutoff:3.500A) Processing helix chain 'A' and resid 2165 through 2168 Processing helix chain 'A' and resid 2169 through 2191 removed outlier: 3.822A pdb=" N GLU A2187 " --> pdb=" O GLU A2183 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A2188 " --> pdb=" O SER A2184 " (cutoff:3.500A) Processing helix chain 'A' and resid 2194 through 2211 Processing helix chain 'A' and resid 2216 through 2237 Proline residue: A2222 - end of helix Processing helix chain 'A' and resid 2244 through 2265 Processing helix chain 'A' and resid 2268 through 2282 removed outlier: 3.576A pdb=" N TYR A2281 " --> pdb=" O GLN A2277 " (cutoff:3.500A) Processing helix chain 'A' and resid 2289 through 2302 removed outlier: 4.019A pdb=" N LEU A2293 " --> pdb=" O SER A2289 " (cutoff:3.500A) Processing helix chain 'A' and resid 2304 through 2323 Processing helix chain 'A' and resid 2327 through 2349 removed outlier: 4.120A pdb=" N LEU A2332 " --> pdb=" O PRO A2328 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR A2333 " --> pdb=" O SER A2329 " (cutoff:3.500A) Processing helix chain 'A' and resid 2352 through 2360 Processing helix chain 'A' and resid 2360 through 2371 removed outlier: 3.720A pdb=" N TYR A2371 " --> pdb=" O VAL A2367 " (cutoff:3.500A) Processing helix chain 'A' and resid 2376 through 2407 removed outlier: 3.687A pdb=" N ARG A2380 " --> pdb=" O SER A2376 " (cutoff:3.500A) Processing helix chain 'A' and resid 2407 through 2422 removed outlier: 3.523A pdb=" N GLU A2422 " --> pdb=" O LYS A2418 " (cutoff:3.500A) Processing helix chain 'A' and resid 2437 through 2476 removed outlier: 3.959A pdb=" N GLU A2449 " --> pdb=" O LEU A2445 " (cutoff:3.500A) Processing helix chain 'A' and resid 2480 through 2482 No H-bonds generated for 'chain 'A' and resid 2480 through 2482' Processing helix chain 'A' and resid 2483 through 2494 Processing helix chain 'A' and resid 2497 through 2508 Processing helix chain 'A' and resid 2509 through 2511 No H-bonds generated for 'chain 'A' and resid 2509 through 2511' Processing helix chain 'A' and resid 2512 through 2517 Processing helix chain 'A' and resid 2519 through 2526 removed outlier: 3.571A pdb=" N ARG A2526 " --> pdb=" O GLN A2522 " (cutoff:3.500A) Processing helix chain 'A' and resid 2536 through 2552 Processing helix chain 'A' and resid 2552 through 2565 removed outlier: 3.598A pdb=" N THR A2556 " --> pdb=" O HIS A2552 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N PHE A2558 " --> pdb=" O HIS A2554 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ILE A2559 " --> pdb=" O HIS A2555 " (cutoff:3.500A) Processing helix chain 'A' and resid 2567 through 2573 removed outlier: 3.772A pdb=" N PHE A2571 " --> pdb=" O ASN A2567 " (cutoff:3.500A) Processing helix chain 'A' and resid 2592 through 2613 removed outlier: 3.887A pdb=" N GLU A2596 " --> pdb=" O SER A2592 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG A2612 " --> pdb=" O THR A2608 " (cutoff:3.500A) Processing helix chain 'A' and resid 2613 through 2633 removed outlier: 3.593A pdb=" N VAL A2617 " --> pdb=" O ARG A2613 " (cutoff:3.500A) Processing helix chain 'A' and resid 2636 through 2641 removed outlier: 3.677A pdb=" N LYS A2639 " --> pdb=" O THR A2636 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N THR A2640 " --> pdb=" O GLN A2637 " (cutoff:3.500A) Processing helix chain 'A' and resid 2722 through 2741 Processing helix chain 'A' and resid 2742 through 2749 removed outlier: 3.610A pdb=" N ARG A2748 " --> pdb=" O GLU A2744 " (cutoff:3.500A) Processing helix chain 'A' and resid 2776 through 2781 Processing helix chain 'A' and resid 2786 through 2792 Processing helix chain 'A' and resid 2797 through 2808 Processing helix chain 'A' and resid 2809 through 2811 No H-bonds generated for 'chain 'A' and resid 2809 through 2811' Processing helix chain 'A' and resid 2812 through 2826 Processing helix chain 'A' and resid 2832 through 2839 removed outlier: 4.030A pdb=" N MET A2836 " --> pdb=" O ARG A2832 " (cutoff:3.500A) Processing helix chain 'A' and resid 2841 through 2867 Processing helix chain 'A' and resid 2872 through 2874 No H-bonds generated for 'chain 'A' and resid 2872 through 2874' Processing helix chain 'A' and resid 2911 through 2917 Processing helix chain 'A' and resid 2925 through 2941 Processing helix chain 'A' and resid 2941 through 2954 Processing helix chain 'A' and resid 2963 through 2971 Processing helix chain 'A' and resid 3002 through 3018 Processing helix chain 'A' and resid 3027 through 3041 Processing helix chain 'A' and resid 3041 through 3048 removed outlier: 3.582A pdb=" N ARG A3047 " --> pdb=" O LYS A3043 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A3048 " --> pdb=" O ASN A3044 " (cutoff:3.500A) Processing helix chain 'A' and resid 3049 through 3053 Processing helix chain 'B' and resid 1413 through 1429 removed outlier: 3.695A pdb=" N THR B1429 " --> pdb=" O GLN B1425 " (cutoff:3.500A) Processing helix chain 'B' and resid 1431 through 1451 Processing helix chain 'B' and resid 1460 through 1478 Processing helix chain 'B' and resid 1484 through 1509 Processing helix chain 'B' and resid 1512 through 1515 removed outlier: 4.322A pdb=" N ASN B1515 " --> pdb=" O ALA B1512 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1512 through 1515' Processing helix chain 'B' and resid 1516 through 1528 Proline residue: B1526 - end of helix Processing helix chain 'B' and resid 1531 through 1546 Processing helix chain 'B' and resid 1552 through 1561 removed outlier: 4.427A pdb=" N ILE B1557 " --> pdb=" O GLU B1553 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N THR B1558 " --> pdb=" O ASN B1554 " (cutoff:3.500A) Processing helix chain 'B' and resid 1571 through 1583 Processing helix chain 'B' and resid 1589 through 1602 removed outlier: 3.653A pdb=" N VAL B1602 " --> pdb=" O LEU B1598 " (cutoff:3.500A) Processing helix chain 'B' and resid 1606 through 1609 Processing helix chain 'B' and resid 1610 through 1624 Processing helix chain 'B' and resid 1624 through 1635 removed outlier: 3.706A pdb=" N MET B1628 " --> pdb=" O HIS B1624 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL B1629 " --> pdb=" O LYS B1625 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP B1630 " --> pdb=" O ASP B1626 " (cutoff:3.500A) Processing helix chain 'B' and resid 1642 through 1659 Processing helix chain 'B' and resid 1663 through 1678 removed outlier: 3.865A pdb=" N VAL B1667 " --> pdb=" O GLY B1663 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B1678 " --> pdb=" O CYS B1674 " (cutoff:3.500A) Processing helix chain 'B' and resid 1693 through 1703 removed outlier: 3.750A pdb=" N PHE B1703 " --> pdb=" O ALA B1699 " (cutoff:3.500A) Processing helix chain 'B' and resid 1705 through 1722 Processing helix chain 'B' and resid 1726 through 1743 removed outlier: 3.572A pdb=" N THR B1743 " --> pdb=" O ASN B1739 " (cutoff:3.500A) Processing helix chain 'B' and resid 1743 through 1754 Processing helix chain 'B' and resid 1758 through 1764 removed outlier: 3.999A pdb=" N ALA B1762 " --> pdb=" O ASP B1758 " (cutoff:3.500A) Processing helix chain 'B' and resid 1791 through 1796 Processing helix chain 'B' and resid 1801 through 1816 Processing helix chain 'B' and resid 1821 through 1826 removed outlier: 4.040A pdb=" N GLN B1825 " --> pdb=" O CYS B1821 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU B1826 " --> pdb=" O GLU B1822 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1821 through 1826' Processing helix chain 'B' and resid 1827 through 1832 Processing helix chain 'B' and resid 1834 through 1852 Proline residue: B1843 - end of helix Processing helix chain 'B' and resid 1856 through 1875 Processing helix chain 'B' and resid 1902 through 1918 removed outlier: 3.539A pdb=" N GLN B1906 " --> pdb=" O ASP B1902 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG B1907 " --> pdb=" O LYS B1903 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B1918 " --> pdb=" O ASP B1914 " (cutoff:3.500A) Processing helix chain 'B' and resid 1926 through 1931 Processing helix chain 'B' and resid 1937 through 1948 removed outlier: 3.619A pdb=" N VAL B1941 " --> pdb=" O ASN B1937 " (cutoff:3.500A) Processing helix chain 'B' and resid 1950 through 1974 Processing helix chain 'B' and resid 1985 through 1998 Processing helix chain 'B' and resid 2000 through 2013 Processing helix chain 'B' and resid 2015 through 2020 removed outlier: 3.606A pdb=" N LEU B2018 " --> pdb=" O PRO B2015 " (cutoff:3.500A) Processing helix chain 'B' and resid 2028 through 2039 Processing helix chain 'B' and resid 2041 through 2052 Processing helix chain 'B' and resid 2056 through 2071 Processing helix chain 'B' and resid 2073 through 2088 Processing helix chain 'B' and resid 2092 through 2106 Processing helix chain 'B' and resid 2123 through 2137 Processing helix chain 'B' and resid 2139 through 2160 removed outlier: 3.540A pdb=" N LYS B2160 " --> pdb=" O GLU B2156 " (cutoff:3.500A) Processing helix chain 'B' and resid 2165 through 2168 Processing helix chain 'B' and resid 2169 through 2191 removed outlier: 3.820A pdb=" N GLU B2187 " --> pdb=" O GLU B2183 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU B2188 " --> pdb=" O SER B2184 " (cutoff:3.500A) Processing helix chain 'B' and resid 2194 through 2211 Processing helix chain 'B' and resid 2216 through 2237 Proline residue: B2222 - end of helix Processing helix chain 'B' and resid 2244 through 2265 Processing helix chain 'B' and resid 2268 through 2282 removed outlier: 3.564A pdb=" N TYR B2281 " --> pdb=" O GLN B2277 " (cutoff:3.500A) Processing helix chain 'B' and resid 2289 through 2302 removed outlier: 4.023A pdb=" N LEU B2293 " --> pdb=" O SER B2289 " (cutoff:3.500A) Processing helix chain 'B' and resid 2304 through 2323 Processing helix chain 'B' and resid 2327 through 2349 removed outlier: 4.125A pdb=" N LEU B2332 " --> pdb=" O PRO B2328 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR B2333 " --> pdb=" O SER B2329 " (cutoff:3.500A) Processing helix chain 'B' and resid 2352 through 2360 Processing helix chain 'B' and resid 2360 through 2371 removed outlier: 3.729A pdb=" N TYR B2371 " --> pdb=" O VAL B2367 " (cutoff:3.500A) Processing helix chain 'B' and resid 2376 through 2407 removed outlier: 3.700A pdb=" N ARG B2380 " --> pdb=" O SER B2376 " (cutoff:3.500A) Processing helix chain 'B' and resid 2407 through 2422 removed outlier: 3.514A pdb=" N GLU B2422 " --> pdb=" O LYS B2418 " (cutoff:3.500A) Processing helix chain 'B' and resid 2437 through 2476 removed outlier: 3.945A pdb=" N GLU B2449 " --> pdb=" O LEU B2445 " (cutoff:3.500A) Processing helix chain 'B' and resid 2480 through 2482 No H-bonds generated for 'chain 'B' and resid 2480 through 2482' Processing helix chain 'B' and resid 2483 through 2494 Processing helix chain 'B' and resid 2497 through 2508 Processing helix chain 'B' and resid 2509 through 2511 No H-bonds generated for 'chain 'B' and resid 2509 through 2511' Processing helix chain 'B' and resid 2512 through 2517 Processing helix chain 'B' and resid 2519 through 2526 removed outlier: 3.562A pdb=" N ARG B2526 " --> pdb=" O GLN B2522 " (cutoff:3.500A) Processing helix chain 'B' and resid 2536 through 2552 Processing helix chain 'B' and resid 2552 through 2565 removed outlier: 3.593A pdb=" N THR B2556 " --> pdb=" O HIS B2552 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N PHE B2558 " --> pdb=" O HIS B2554 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ILE B2559 " --> pdb=" O HIS B2555 " (cutoff:3.500A) Processing helix chain 'B' and resid 2567 through 2573 removed outlier: 3.777A pdb=" N PHE B2571 " --> pdb=" O ASN B2567 " (cutoff:3.500A) Processing helix chain 'B' and resid 2592 through 2613 removed outlier: 3.881A pdb=" N GLU B2596 " --> pdb=" O SER B2592 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG B2612 " --> pdb=" O THR B2608 " (cutoff:3.500A) Processing helix chain 'B' and resid 2613 through 2633 removed outlier: 3.587A pdb=" N VAL B2617 " --> pdb=" O ARG B2613 " (cutoff:3.500A) Processing helix chain 'B' and resid 2636 through 2641 removed outlier: 3.676A pdb=" N LYS B2639 " --> pdb=" O THR B2636 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR B2640 " --> pdb=" O GLN B2637 " (cutoff:3.500A) Processing helix chain 'B' and resid 2722 through 2741 Processing helix chain 'B' and resid 2742 through 2749 removed outlier: 3.605A pdb=" N ARG B2748 " --> pdb=" O GLU B2744 " (cutoff:3.500A) Processing helix chain 'B' and resid 2776 through 2781 Processing helix chain 'B' and resid 2786 through 2792 Processing helix chain 'B' and resid 2797 through 2808 Processing helix chain 'B' and resid 2809 through 2811 No H-bonds generated for 'chain 'B' and resid 2809 through 2811' Processing helix chain 'B' and resid 2812 through 2826 Processing helix chain 'B' and resid 2832 through 2839 removed outlier: 3.989A pdb=" N MET B2836 " --> pdb=" O ARG B2832 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B2838 " --> pdb=" O PHE B2834 " (cutoff:3.500A) Processing helix chain 'B' and resid 2841 through 2867 Processing helix chain 'B' and resid 2872 through 2874 No H-bonds generated for 'chain 'B' and resid 2872 through 2874' Processing helix chain 'B' and resid 2911 through 2917 Processing helix chain 'B' and resid 2925 through 2941 Processing helix chain 'B' and resid 2941 through 2954 Processing helix chain 'B' and resid 2963 through 2971 Processing helix chain 'B' and resid 3002 through 3018 Processing helix chain 'B' and resid 3027 through 3041 Processing helix chain 'B' and resid 3041 through 3048 removed outlier: 3.582A pdb=" N ARG B3047 " --> pdb=" O LYS B3043 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B3048 " --> pdb=" O ASN B3044 " (cutoff:3.500A) Processing helix chain 'B' and resid 3049 through 3053 Processing sheet with id=AA1, first strand: chain 'A' and resid 2645 through 2646 removed outlier: 7.355A pdb=" N GLU A2689 " --> pdb=" O ASP A2703 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ASP A2703 " --> pdb=" O GLU A2689 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ASP A2703 " --> pdb=" O PHE A2686 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHE A2686 " --> pdb=" O ASP A2703 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL A2705 " --> pdb=" O GLN A2684 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL A2662 " --> pdb=" O ILE A2683 " (cutoff:3.500A) removed outlier: 11.138A pdb=" N SER A2685 " --> pdb=" O GLU A2660 " (cutoff:3.500A) removed outlier: 10.618A pdb=" N GLU A2660 " --> pdb=" O SER A2685 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2645 through 2646 removed outlier: 7.355A pdb=" N GLU A2689 " --> pdb=" O ASP A2703 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ASP A2703 " --> pdb=" O GLU A2689 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2773 through 2775 Processing sheet with id=AA4, first strand: chain 'B' and resid 2645 through 2646 removed outlier: 7.383A pdb=" N GLU B2689 " --> pdb=" O ASP B2703 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ASP B2703 " --> pdb=" O GLU B2689 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ASP B2703 " --> pdb=" O PHE B2686 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N PHE B2686 " --> pdb=" O ASP B2703 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL B2705 " --> pdb=" O GLN B2684 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL B2662 " --> pdb=" O ILE B2683 " (cutoff:3.500A) removed outlier: 11.129A pdb=" N SER B2685 " --> pdb=" O GLU B2660 " (cutoff:3.500A) removed outlier: 10.609A pdb=" N GLU B2660 " --> pdb=" O SER B2685 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2645 through 2646 removed outlier: 7.383A pdb=" N GLU B2689 " --> pdb=" O ASP B2703 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ASP B2703 " --> pdb=" O GLU B2689 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2773 through 2775 1615 hydrogen bonds defined for protein. 4761 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: 9.43 Time building geometry restraints manager: 6.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8186 1.34 - 1.46: 5057 1.46 - 1.58: 12023 1.58 - 1.69: 10 1.69 - 1.81: 264 Bond restraints: 25540 Sorted by residual: bond pdb=" N3B ANP B3101 " pdb=" PG ANP B3101 " ideal model delta sigma weight residual 1.795 1.630 0.165 2.00e-02 2.50e+03 6.81e+01 bond pdb=" N3B ANP A3101 " pdb=" PG ANP A3101 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.76e+01 bond pdb=" O3A ANP A3101 " pdb=" PB ANP A3101 " ideal model delta sigma weight residual 1.700 1.622 0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" O3A ANP B3101 " pdb=" PB ANP B3101 " ideal model delta sigma weight residual 1.700 1.622 0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" O5' ANP A3101 " pdb=" PA ANP A3101 " ideal model delta sigma weight residual 1.655 1.595 0.060 2.00e-02 2.50e+03 9.06e+00 ... (remaining 25535 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 34266 2.23 - 4.46: 195 4.46 - 6.70: 29 6.70 - 8.93: 4 8.93 - 11.16: 2 Bond angle restraints: 34496 Sorted by residual: angle pdb=" O1B ANP B3101 " pdb=" PB ANP B3101 " pdb=" O3A ANP B3101 " ideal model delta sigma weight residual 103.40 114.56 -11.16 3.00e+00 1.11e-01 1.38e+01 angle pdb=" O1B ANP A3101 " pdb=" PB ANP A3101 " pdb=" O3A ANP A3101 " ideal model delta sigma weight residual 103.40 114.54 -11.14 3.00e+00 1.11e-01 1.38e+01 angle pdb=" C ARG B1875 " pdb=" N HIS B1876 " pdb=" CA HIS B1876 " ideal model delta sigma weight residual 121.70 127.72 -6.02 1.80e+00 3.09e-01 1.12e+01 angle pdb=" C ARG A1875 " pdb=" N HIS A1876 " pdb=" CA HIS A1876 " ideal model delta sigma weight residual 121.70 127.67 -5.97 1.80e+00 3.09e-01 1.10e+01 angle pdb=" PA ANP A3101 " pdb=" O3A ANP A3101 " pdb=" PB ANP A3101 " ideal model delta sigma weight residual 125.41 134.25 -8.84 3.00e+00 1.11e-01 8.68e+00 ... (remaining 34491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 14119 17.89 - 35.79: 1252 35.79 - 53.68: 163 53.68 - 71.58: 55 71.58 - 89.47: 33 Dihedral angle restraints: 15622 sinusoidal: 6504 harmonic: 9118 Sorted by residual: dihedral pdb=" CA ASP B2841 " pdb=" CB ASP B2841 " pdb=" CG ASP B2841 " pdb=" OD1 ASP B2841 " ideal model delta sinusoidal sigma weight residual -30.00 -87.18 57.18 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CA ASP A2841 " pdb=" CB ASP A2841 " pdb=" CG ASP A2841 " pdb=" OD1 ASP A2841 " ideal model delta sinusoidal sigma weight residual -30.00 -87.14 57.14 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CG ARG A2263 " pdb=" CD ARG A2263 " pdb=" NE ARG A2263 " pdb=" CZ ARG A2263 " ideal model delta sinusoidal sigma weight residual -180.00 -136.54 -43.46 2 1.50e+01 4.44e-03 1.01e+01 ... (remaining 15619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3429 0.055 - 0.110: 455 0.110 - 0.166: 18 0.166 - 0.221: 0 0.221 - 0.276: 2 Chirality restraints: 3904 Sorted by residual: chirality pdb=" C3' ANP A3101 " pdb=" C2' ANP A3101 " pdb=" C4' ANP A3101 " pdb=" O3' ANP A3101 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C3' ANP B3101 " pdb=" C2' ANP B3101 " pdb=" C4' ANP B3101 " pdb=" O3' ANP B3101 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA ILE B2055 " pdb=" N ILE B2055 " pdb=" C ILE B2055 " pdb=" CB ILE B2055 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 3901 not shown) Planarity restraints: 4362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A2058 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.87e+00 pdb=" C SER A2058 " -0.038 2.00e-02 2.50e+03 pdb=" O SER A2058 " 0.014 2.00e-02 2.50e+03 pdb=" N THR A2059 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B2058 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.68e+00 pdb=" C SER B2058 " 0.037 2.00e-02 2.50e+03 pdb=" O SER B2058 " -0.014 2.00e-02 2.50e+03 pdb=" N THR B2059 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B2504 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" C MET B2504 " 0.037 2.00e-02 2.50e+03 pdb=" O MET B2504 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS B2505 " -0.012 2.00e-02 2.50e+03 ... (remaining 4359 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 206 2.66 - 3.22: 23330 3.22 - 3.78: 40042 3.78 - 4.34: 52833 4.34 - 4.90: 87645 Nonbonded interactions: 204056 Sorted by model distance: nonbonded pdb=" O ARG A1875 " pdb=" ND1 HIS A1876 " model vdw 2.094 3.120 nonbonded pdb=" O ARG B1875 " pdb=" ND1 HIS B1876 " model vdw 2.095 3.120 nonbonded pdb=" OD1 ASN A2875 " pdb="MG MG A3102 " model vdw 2.189 2.170 nonbonded pdb=" OD1 ASN B2875 " pdb="MG MG B3102 " model vdw 2.208 2.170 nonbonded pdb=" OH TYR B2969 " pdb=" O2G ANP B3101 " model vdw 2.212 3.040 ... (remaining 204051 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.540 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: 1.110 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 57.130 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.165 25546 Z= 0.132 Angle : 0.439 11.158 34496 Z= 0.217 Chirality : 0.035 0.276 3904 Planarity : 0.003 0.045 4362 Dihedral : 13.914 89.471 9698 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.15), residues: 3072 helix: 2.59 (0.11), residues: 2176 sheet: 1.45 (0.64), residues: 66 loop : 0.17 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2104 HIS 0.003 0.000 HIS A1951 PHE 0.014 0.001 PHE A2834 TYR 0.013 0.001 TYR B2129 ARG 0.007 0.000 ARG B1875 Details of bonding type rmsd hydrogen bonds : bond 0.11487 ( 1607) hydrogen bonds : angle 4.21094 ( 4761) metal coordination : bond 0.00356 ( 6) covalent geometry : bond 0.00259 (25540) covalent geometry : angle 0.43871 (34496) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 564 time to evaluate : 3.138 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 1437 ARG cc_start: 0.9056 (ttp80) cc_final: 0.8677 (tpt170) REVERT: A 1444 LEU cc_start: 0.9781 (tt) cc_final: 0.9507 (tm) REVERT: A 1489 ARG cc_start: 0.8895 (mtp180) cc_final: 0.8337 (mtp-110) REVERT: A 1518 HIS cc_start: 0.7455 (m-70) cc_final: 0.7182 (m90) REVERT: A 1559 ILE cc_start: 0.9386 (mt) cc_final: 0.9178 (mp) REVERT: A 1693 ASP cc_start: 0.8866 (m-30) cc_final: 0.8599 (t70) REVERT: A 2028 GLN cc_start: 0.9160 (mm110) cc_final: 0.8551 (mp10) REVERT: A 2030 ILE cc_start: 0.8486 (mp) cc_final: 0.8156 (mm) REVERT: A 2039 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8328 (mt-10) REVERT: A 2139 GLU cc_start: 0.8257 (mm-30) cc_final: 0.8017 (mm-30) REVERT: A 2476 SER cc_start: 0.8200 (m) cc_final: 0.7997 (t) REVERT: A 2668 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8531 (pp20) REVERT: A 2744 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8717 (mm-30) REVERT: A 2900 LEU cc_start: 0.8954 (mt) cc_final: 0.8635 (mt) REVERT: A 2905 THR cc_start: 0.8906 (p) cc_final: 0.8547 (p) REVERT: A 2954 TYR cc_start: 0.8901 (m-80) cc_final: 0.8585 (m-10) REVERT: A 3004 LYS cc_start: 0.9292 (mtpp) cc_final: 0.9014 (pttp) REVERT: A 3008 ARG cc_start: 0.8762 (tpt90) cc_final: 0.8483 (tpt170) REVERT: A 3043 LYS cc_start: 0.8579 (tptt) cc_final: 0.8324 (tptt) REVERT: A 3047 ARG cc_start: 0.8879 (mtt-85) cc_final: 0.8673 (mpp80) REVERT: B 1424 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8975 (mm-30) REVERT: B 1437 ARG cc_start: 0.9052 (ttp80) cc_final: 0.8577 (tpt170) REVERT: B 1444 LEU cc_start: 0.9786 (tt) cc_final: 0.9479 (tm) REVERT: B 1527 LEU cc_start: 0.9455 (mt) cc_final: 0.9183 (mm) REVERT: B 1544 TYR cc_start: 0.9045 (t80) cc_final: 0.8620 (t80) REVERT: B 1581 ILE cc_start: 0.9770 (mt) cc_final: 0.9556 (tp) REVERT: B 1604 ASP cc_start: 0.7771 (t0) cc_final: 0.7530 (t0) REVERT: B 1693 ASP cc_start: 0.8942 (m-30) cc_final: 0.8690 (t70) REVERT: B 2028 GLN cc_start: 0.9134 (mm110) cc_final: 0.8433 (mp10) REVERT: B 2030 ILE cc_start: 0.8518 (mp) cc_final: 0.8209 (mm) REVERT: B 2039 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8299 (mt-10) REVERT: B 2110 ASP cc_start: 0.8965 (m-30) cc_final: 0.8683 (p0) REVERT: B 2139 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8070 (mm-30) REVERT: B 2476 SER cc_start: 0.8410 (m) cc_final: 0.8091 (t) REVERT: B 2744 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8627 (mm-30) REVERT: B 2900 LEU cc_start: 0.8829 (mt) cc_final: 0.8471 (mt) REVERT: B 2954 TYR cc_start: 0.8885 (m-80) cc_final: 0.8572 (m-10) REVERT: B 3004 LYS cc_start: 0.9374 (mtpp) cc_final: 0.8844 (pttp) REVERT: B 3043 LYS cc_start: 0.8450 (tptt) cc_final: 0.8188 (tptt) outliers start: 0 outliers final: 0 residues processed: 564 average time/residue: 1.5715 time to fit residues: 1002.6570 Evaluate side-chains 299 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 6.9990 chunk 234 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 242 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 chunk 180 optimal weight: 3.9990 chunk 281 optimal weight: 0.1980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1867 GLN ** A1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2106 ASN A2197 GLN A2412 ASN A3014 GLN B1416 GLN B1443 HIS B1867 GLN ** B1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2197 GLN B2210 GLN B3014 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.094608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.064300 restraints weight = 52791.175| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.34 r_work: 0.2755 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25546 Z= 0.117 Angle : 0.528 9.961 34496 Z= 0.264 Chirality : 0.039 0.373 3904 Planarity : 0.004 0.049 4362 Dihedral : 4.588 88.810 3424 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.93 % Allowed : 10.39 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.16), residues: 3072 helix: 2.84 (0.11), residues: 2150 sheet: 1.04 (0.64), residues: 66 loop : 0.34 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A1461 HIS 0.004 0.001 HIS B2538 PHE 0.020 0.001 PHE A2571 TYR 0.018 0.001 TYR A1556 ARG 0.011 0.001 ARG A1585 Details of bonding type rmsd hydrogen bonds : bond 0.03392 ( 1607) hydrogen bonds : angle 3.54280 ( 4761) metal coordination : bond 0.00121 ( 6) covalent geometry : bond 0.00268 (25540) covalent geometry : angle 0.52789 (34496) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 335 time to evaluate : 2.817 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 1424 GLU cc_start: 0.9355 (OUTLIER) cc_final: 0.8752 (tp30) REVERT: A 1434 LYS cc_start: 0.9459 (tppt) cc_final: 0.9148 (tppt) REVERT: A 1437 ARG cc_start: 0.9176 (ttp80) cc_final: 0.8729 (tpt170) REVERT: A 1478 GLN cc_start: 0.9193 (pt0) cc_final: 0.8959 (pm20) REVERT: A 1489 ARG cc_start: 0.8892 (mtp-110) cc_final: 0.8469 (mtp-110) REVERT: A 1554 ASN cc_start: 0.9230 (m110) cc_final: 0.8924 (m110) REVERT: A 1693 ASP cc_start: 0.8794 (m-30) cc_final: 0.8453 (t0) REVERT: A 1701 LYS cc_start: 0.9357 (mtmm) cc_final: 0.9059 (mtmm) REVERT: A 1967 MET cc_start: 0.8408 (mmm) cc_final: 0.7997 (mmp) REVERT: A 1991 GLU cc_start: 0.8590 (tp30) cc_final: 0.8360 (tm-30) REVERT: A 2025 LYS cc_start: 0.8706 (mmpt) cc_final: 0.8453 (mmpt) REVERT: A 2028 GLN cc_start: 0.8953 (mm110) cc_final: 0.8329 (mp10) REVERT: A 2139 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8152 (mm-30) REVERT: A 2668 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8592 (pp20) REVERT: A 2744 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8768 (mm-30) REVERT: A 2900 LEU cc_start: 0.8892 (mt) cc_final: 0.8627 (mt) REVERT: A 2904 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8296 (mt-10) REVERT: A 2905 THR cc_start: 0.8871 (p) cc_final: 0.8497 (p) REVERT: A 2954 TYR cc_start: 0.8765 (m-80) cc_final: 0.8468 (m-10) REVERT: A 2962 MET cc_start: 0.9149 (tpp) cc_final: 0.8595 (tpp) REVERT: A 3004 LYS cc_start: 0.9285 (mtpp) cc_final: 0.8996 (pttp) REVERT: A 3008 ARG cc_start: 0.8774 (tpt90) cc_final: 0.8553 (tpt170) REVERT: A 3043 LYS cc_start: 0.8782 (tptt) cc_final: 0.8580 (tptt) REVERT: A 3047 ARG cc_start: 0.8894 (mtt-85) cc_final: 0.8616 (mtm-85) REVERT: B 1424 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8945 (mm-30) REVERT: B 1437 ARG cc_start: 0.9229 (ttp80) cc_final: 0.8732 (tpt170) REVERT: B 1544 TYR cc_start: 0.9063 (t80) cc_final: 0.8550 (t80) REVERT: B 1604 ASP cc_start: 0.7735 (t0) cc_final: 0.7488 (t0) REVERT: B 1693 ASP cc_start: 0.8910 (m-30) cc_final: 0.8564 (t0) REVERT: B 1836 ASP cc_start: 0.8989 (m-30) cc_final: 0.8530 (t0) REVERT: B 1991 GLU cc_start: 0.8588 (tp30) cc_final: 0.8367 (tt0) REVERT: B 2110 ASP cc_start: 0.9084 (m-30) cc_final: 0.8710 (p0) REVERT: B 2443 ARG cc_start: 0.8315 (mtp-110) cc_final: 0.8045 (ptm160) REVERT: B 2476 SER cc_start: 0.8368 (m) cc_final: 0.8086 (t) REVERT: B 2744 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8705 (mm-30) REVERT: B 2900 LEU cc_start: 0.8825 (mt) cc_final: 0.8447 (mt) REVERT: B 2904 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8242 (mt-10) REVERT: B 2954 TYR cc_start: 0.8673 (m-80) cc_final: 0.8391 (m-10) REVERT: B 3004 LYS cc_start: 0.9106 (mtpp) cc_final: 0.8878 (ptpp) outliers start: 54 outliers final: 11 residues processed: 363 average time/residue: 1.3901 time to fit residues: 581.4828 Evaluate side-chains 298 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 284 time to evaluate : 3.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1424 GLU Chi-restraints excluded: chain A residue 2310 SER Chi-restraints excluded: chain A residue 2417 LEU Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2904 GLU Chi-restraints excluded: chain A residue 2965 LEU Chi-restraints excluded: chain A residue 3037 GLN Chi-restraints excluded: chain B residue 1555 LEU Chi-restraints excluded: chain B residue 1608 LEU Chi-restraints excluded: chain B residue 2310 SER Chi-restraints excluded: chain B residue 2417 LEU Chi-restraints excluded: chain B residue 2447 LEU Chi-restraints excluded: chain B residue 2904 GLU Chi-restraints excluded: chain B residue 3037 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 294 optimal weight: 4.9990 chunk 270 optimal weight: 2.9990 chunk 156 optimal weight: 0.0980 chunk 163 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 266 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 29 optimal weight: 0.4980 chunk 298 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2002 GLN A2066 GLN A2070 ASN B1431 ASN ** B1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2241 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.092456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.062335 restraints weight = 52240.151| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.24 r_work: 0.2803 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25546 Z= 0.137 Angle : 0.516 10.388 34496 Z= 0.259 Chirality : 0.038 0.256 3904 Planarity : 0.003 0.050 4362 Dihedral : 4.637 87.885 3424 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.54 % Allowed : 11.25 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.23 (0.16), residues: 3072 helix: 2.87 (0.11), residues: 2148 sheet: 0.89 (0.63), residues: 66 loop : 0.33 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A1461 HIS 0.003 0.001 HIS A2538 PHE 0.017 0.001 PHE A1491 TYR 0.024 0.001 TYR A1508 ARG 0.008 0.001 ARG A2443 Details of bonding type rmsd hydrogen bonds : bond 0.03430 ( 1607) hydrogen bonds : angle 3.43251 ( 4761) metal coordination : bond 0.00284 ( 6) covalent geometry : bond 0.00318 (25540) covalent geometry : angle 0.51607 (34496) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 308 time to evaluate : 3.167 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 1424 GLU cc_start: 0.9328 (OUTLIER) cc_final: 0.8730 (tp30) REVERT: A 1434 LYS cc_start: 0.9494 (tppt) cc_final: 0.9242 (tppt) REVERT: A 1437 ARG cc_start: 0.9213 (ttp80) cc_final: 0.8809 (tpt170) REVERT: A 1449 LEU cc_start: 0.9245 (mp) cc_final: 0.9042 (mp) REVERT: A 1478 GLN cc_start: 0.9091 (pt0) cc_final: 0.8880 (pm20) REVERT: A 1489 ARG cc_start: 0.8961 (mtp-110) cc_final: 0.8477 (mtp-110) REVERT: A 1554 ASN cc_start: 0.9250 (m110) cc_final: 0.8923 (m110) REVERT: A 1693 ASP cc_start: 0.8817 (m-30) cc_final: 0.8462 (t0) REVERT: A 2139 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8284 (mm-30) REVERT: A 2443 ARG cc_start: 0.8414 (mtp-110) cc_final: 0.7958 (ptm160) REVERT: A 2479 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8480 (tp30) REVERT: A 2744 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8905 (mm-30) REVERT: A 2904 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8383 (mt-10) REVERT: A 2954 TYR cc_start: 0.8993 (m-80) cc_final: 0.8692 (m-10) REVERT: A 2962 MET cc_start: 0.9248 (tpp) cc_final: 0.8809 (tpp) REVERT: A 3004 LYS cc_start: 0.9347 (mtpp) cc_final: 0.9065 (pttp) REVERT: B 1424 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8957 (mm-30) REVERT: B 1434 LYS cc_start: 0.9480 (tppt) cc_final: 0.9228 (tppt) REVERT: B 1437 ARG cc_start: 0.9292 (ttp80) cc_final: 0.8831 (tpt170) REVERT: B 1484 MET cc_start: 0.8358 (pmm) cc_final: 0.8146 (pmm) REVERT: B 1604 ASP cc_start: 0.7775 (t0) cc_final: 0.7557 (t0) REVERT: B 1693 ASP cc_start: 0.8916 (m-30) cc_final: 0.8533 (t0) REVERT: B 1701 LYS cc_start: 0.9072 (pttp) cc_final: 0.8783 (pptt) REVERT: B 1836 ASP cc_start: 0.9035 (m-30) cc_final: 0.8595 (t0) REVERT: B 2028 GLN cc_start: 0.9110 (mm-40) cc_final: 0.8268 (mp10) REVERT: B 2110 ASP cc_start: 0.9032 (m-30) cc_final: 0.8738 (p0) REVERT: B 2139 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8134 (mm-30) REVERT: B 2443 ARG cc_start: 0.8488 (mtp-110) cc_final: 0.8273 (ptm160) REVERT: B 2668 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8629 (pp20) REVERT: B 2744 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8871 (mm-30) REVERT: B 2904 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8387 (mt-10) REVERT: B 3004 LYS cc_start: 0.9150 (mtpp) cc_final: 0.8909 (ptpp) outliers start: 71 outliers final: 22 residues processed: 351 average time/residue: 1.3421 time to fit residues: 544.6861 Evaluate side-chains 298 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 272 time to evaluate : 2.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1424 GLU Chi-restraints excluded: chain A residue 1444 LEU Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1827 LEU Chi-restraints excluded: chain A residue 2310 SER Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2479 GLU Chi-restraints excluded: chain A residue 2557 LEU Chi-restraints excluded: chain A residue 2904 GLU Chi-restraints excluded: chain A residue 2965 LEU Chi-restraints excluded: chain A residue 2970 LEU Chi-restraints excluded: chain B residue 1439 LEU Chi-restraints excluded: chain B residue 1556 TYR Chi-restraints excluded: chain B residue 1608 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1827 LEU Chi-restraints excluded: chain B residue 2163 LEU Chi-restraints excluded: chain B residue 2310 SER Chi-restraints excluded: chain B residue 2332 LEU Chi-restraints excluded: chain B residue 2417 LEU Chi-restraints excluded: chain B residue 2447 LEU Chi-restraints excluded: chain B residue 2557 LEU Chi-restraints excluded: chain B residue 2904 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 127 optimal weight: 2.9990 chunk 116 optimal weight: 0.0770 chunk 293 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 219 optimal weight: 3.9990 chunk 253 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 283 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 chunk 66 optimal weight: 0.0570 chunk 235 optimal weight: 0.9980 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1638 ASN ** A1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2241 ASN B1416 GLN ** B1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2070 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.092908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.062683 restraints weight = 52444.584| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.26 r_work: 0.2786 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 25546 Z= 0.101 Angle : 0.504 12.182 34496 Z= 0.248 Chirality : 0.038 0.455 3904 Planarity : 0.003 0.051 4362 Dihedral : 4.569 85.367 3424 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.44 % Allowed : 12.71 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.26 (0.16), residues: 3072 helix: 2.91 (0.11), residues: 2162 sheet: 0.82 (0.63), residues: 66 loop : 0.25 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A1461 HIS 0.004 0.001 HIS B1443 PHE 0.012 0.001 PHE B1445 TYR 0.017 0.001 TYR A1556 ARG 0.009 0.000 ARG A1585 Details of bonding type rmsd hydrogen bonds : bond 0.03013 ( 1607) hydrogen bonds : angle 3.35027 ( 4761) metal coordination : bond 0.00171 ( 6) covalent geometry : bond 0.00231 (25540) covalent geometry : angle 0.50385 (34496) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 299 time to evaluate : 2.862 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 1424 GLU cc_start: 0.9328 (OUTLIER) cc_final: 0.8742 (tp30) REVERT: A 1434 LYS cc_start: 0.9532 (tppt) cc_final: 0.9105 (tppp) REVERT: A 1437 ARG cc_start: 0.9203 (ttp80) cc_final: 0.8752 (tpt170) REVERT: A 1449 LEU cc_start: 0.9239 (mt) cc_final: 0.8949 (mp) REVERT: A 1489 ARG cc_start: 0.8966 (mtp-110) cc_final: 0.8472 (mtp-110) REVERT: A 1554 ASN cc_start: 0.9284 (m110) cc_final: 0.8960 (m110) REVERT: A 1693 ASP cc_start: 0.8837 (m-30) cc_final: 0.8530 (t0) REVERT: A 1836 ASP cc_start: 0.9062 (m-30) cc_final: 0.8674 (t70) REVERT: A 1988 SER cc_start: 0.9313 (t) cc_final: 0.9018 (p) REVERT: A 2028 GLN cc_start: 0.9147 (mm-40) cc_final: 0.8296 (mp10) REVERT: A 2139 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8272 (mm-30) REVERT: A 2193 VAL cc_start: 0.9280 (OUTLIER) cc_final: 0.9051 (p) REVERT: A 2443 ARG cc_start: 0.8486 (mtp-110) cc_final: 0.8083 (ttp80) REVERT: A 2479 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8415 (tp30) REVERT: A 2744 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8940 (mm-30) REVERT: A 2904 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8397 (mt-10) REVERT: A 2954 TYR cc_start: 0.8942 (m-80) cc_final: 0.8638 (m-10) REVERT: A 2962 MET cc_start: 0.9255 (tpp) cc_final: 0.8809 (tpp) REVERT: A 3004 LYS cc_start: 0.9356 (mtpp) cc_final: 0.9081 (pttp) REVERT: B 1424 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8933 (mm-30) REVERT: B 1434 LYS cc_start: 0.9503 (tppt) cc_final: 0.9184 (tppt) REVERT: B 1437 ARG cc_start: 0.9286 (ttp80) cc_final: 0.8785 (tpt170) REVERT: B 1585 ARG cc_start: 0.9020 (mmm160) cc_final: 0.8635 (tmm160) REVERT: B 1693 ASP cc_start: 0.8917 (m-30) cc_final: 0.8585 (t0) REVERT: B 1701 LYS cc_start: 0.9020 (pttp) cc_final: 0.8767 (pptt) REVERT: B 1836 ASP cc_start: 0.9038 (m-30) cc_final: 0.8618 (t0) REVERT: B 1988 SER cc_start: 0.9475 (t) cc_final: 0.9227 (p) REVERT: B 2007 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8651 (mt-10) REVERT: B 2028 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8237 (mp10) REVERT: B 2108 GLN cc_start: 0.8685 (mt0) cc_final: 0.8400 (mt0) REVERT: B 2110 ASP cc_start: 0.9057 (m-30) cc_final: 0.8743 (p0) REVERT: B 2157 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: B 2561 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9262 (mm) REVERT: B 2612 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8369 (ptp-170) REVERT: B 2668 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8655 (pp20) REVERT: B 2744 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8919 (mm-30) REVERT: B 2904 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8380 (mt-10) REVERT: B 2954 TYR cc_start: 0.8907 (m-80) cc_final: 0.8579 (m-10) outliers start: 68 outliers final: 25 residues processed: 338 average time/residue: 1.3062 time to fit residues: 513.3420 Evaluate side-chains 306 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 273 time to evaluate : 3.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1424 GLU Chi-restraints excluded: chain A residue 1438 ILE Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1827 LEU Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2310 SER Chi-restraints excluded: chain A residue 2379 LEU Chi-restraints excluded: chain A residue 2417 LEU Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2479 GLU Chi-restraints excluded: chain A residue 2557 LEU Chi-restraints excluded: chain A residue 2904 GLU Chi-restraints excluded: chain A residue 2965 LEU Chi-restraints excluded: chain A residue 2970 LEU Chi-restraints excluded: chain B residue 1438 ILE Chi-restraints excluded: chain B residue 1555 LEU Chi-restraints excluded: chain B residue 1556 TYR Chi-restraints excluded: chain B residue 1608 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1702 LEU Chi-restraints excluded: chain B residue 1827 LEU Chi-restraints excluded: chain B residue 2157 GLU Chi-restraints excluded: chain B residue 2310 SER Chi-restraints excluded: chain B residue 2417 LEU Chi-restraints excluded: chain B residue 2447 LEU Chi-restraints excluded: chain B residue 2482 MET Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2612 ARG Chi-restraints excluded: chain B residue 2904 GLU Chi-restraints excluded: chain B residue 2970 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 191 optimal weight: 0.7980 chunk 266 optimal weight: 9.9990 chunk 192 optimal weight: 4.9990 chunk 230 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 268 optimal weight: 0.7980 chunk 180 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 215 optimal weight: 0.6980 chunk 103 optimal weight: 0.0050 chunk 211 optimal weight: 0.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1638 ASN A1876 HIS A2066 GLN B1416 GLN B1638 ASN B1876 HIS ** B2002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2809 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.092637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.062256 restraints weight = 52869.591| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.28 r_work: 0.2767 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.458 25546 Z= 0.435 Angle : 0.518 14.410 34496 Z= 0.253 Chirality : 0.038 0.361 3904 Planarity : 0.003 0.052 4362 Dihedral : 4.538 84.367 3424 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.26 % Allowed : 13.47 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.30 (0.16), residues: 3072 helix: 2.95 (0.11), residues: 2162 sheet: 0.82 (0.62), residues: 66 loop : 0.25 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A1461 HIS 0.003 0.001 HIS A1443 PHE 0.011 0.001 PHE B2143 TYR 0.013 0.001 TYR B1415 ARG 0.007 0.000 ARG B2443 Details of bonding type rmsd hydrogen bonds : bond 0.02964 ( 1607) hydrogen bonds : angle 3.32714 ( 4761) metal coordination : bond 0.82696 ( 6) covalent geometry : bond 0.00236 (25540) covalent geometry : angle 0.51843 (34496) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 292 time to evaluate : 3.049 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 1424 GLU cc_start: 0.9330 (OUTLIER) cc_final: 0.8748 (tp30) REVERT: A 1434 LYS cc_start: 0.9538 (tppt) cc_final: 0.9117 (tppp) REVERT: A 1437 ARG cc_start: 0.9244 (ttp80) cc_final: 0.8759 (tpt170) REVERT: A 1449 LEU cc_start: 0.9216 (mt) cc_final: 0.8949 (mp) REVERT: A 1489 ARG cc_start: 0.8985 (mtp-110) cc_final: 0.8498 (mtp-110) REVERT: A 1554 ASN cc_start: 0.9269 (m110) cc_final: 0.8954 (m110) REVERT: A 1585 ARG cc_start: 0.9044 (mmm-85) cc_final: 0.8658 (tmm160) REVERT: A 1693 ASP cc_start: 0.8864 (m-30) cc_final: 0.8522 (t0) REVERT: A 1836 ASP cc_start: 0.9049 (m-30) cc_final: 0.8589 (t0) REVERT: A 2139 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8251 (mm-30) REVERT: A 2193 VAL cc_start: 0.9285 (OUTLIER) cc_final: 0.9052 (p) REVERT: A 2314 GLN cc_start: 0.9305 (tt0) cc_final: 0.8914 (tp-100) REVERT: A 2443 ARG cc_start: 0.8484 (mtp-110) cc_final: 0.8087 (ttp80) REVERT: A 2479 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8406 (tp30) REVERT: A 2561 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9308 (mm) REVERT: A 2744 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8944 (mm-30) REVERT: A 2954 TYR cc_start: 0.8930 (m-80) cc_final: 0.8623 (m-10) REVERT: A 2962 MET cc_start: 0.9241 (tpp) cc_final: 0.8789 (tpp) REVERT: A 3004 LYS cc_start: 0.9357 (mtpp) cc_final: 0.9084 (pttp) REVERT: B 1424 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8941 (mm-30) REVERT: B 1434 LYS cc_start: 0.9531 (tppt) cc_final: 0.9106 (tppp) REVERT: B 1437 ARG cc_start: 0.9287 (ttp80) cc_final: 0.8788 (tpt170) REVERT: B 1484 MET cc_start: 0.8450 (pmm) cc_final: 0.8244 (pmm) REVERT: B 1693 ASP cc_start: 0.8900 (m-30) cc_final: 0.8564 (t0) REVERT: B 1836 ASP cc_start: 0.9041 (m-30) cc_final: 0.8631 (t0) REVERT: B 2002 GLN cc_start: 0.8241 (tt0) cc_final: 0.8001 (tt0) REVERT: B 2110 ASP cc_start: 0.9081 (m-30) cc_final: 0.8764 (p0) REVERT: B 2157 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8052 (mp0) REVERT: B 2561 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9196 (mm) REVERT: B 2612 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8384 (ppp80) REVERT: B 2668 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8643 (pp20) REVERT: B 2744 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8937 (mm-30) REVERT: B 2904 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8378 (mt-10) REVERT: B 2943 GLU cc_start: 0.8586 (mp0) cc_final: 0.8248 (pm20) REVERT: B 2954 TYR cc_start: 0.8919 (m-80) cc_final: 0.8579 (m-10) outliers start: 63 outliers final: 23 residues processed: 332 average time/residue: 1.3629 time to fit residues: 524.2976 Evaluate side-chains 295 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 264 time to evaluate : 2.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1424 GLU Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1827 LEU Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2310 SER Chi-restraints excluded: chain A residue 2379 LEU Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2479 GLU Chi-restraints excluded: chain A residue 2561 LEU Chi-restraints excluded: chain A residue 2965 LEU Chi-restraints excluded: chain A residue 2970 LEU Chi-restraints excluded: chain B residue 1438 ILE Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1556 TYR Chi-restraints excluded: chain B residue 1608 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1827 LEU Chi-restraints excluded: chain B residue 2157 GLU Chi-restraints excluded: chain B residue 2310 SER Chi-restraints excluded: chain B residue 2379 LEU Chi-restraints excluded: chain B residue 2417 LEU Chi-restraints excluded: chain B residue 2447 LEU Chi-restraints excluded: chain B residue 2482 MET Chi-restraints excluded: chain B residue 2557 LEU Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2612 ARG Chi-restraints excluded: chain B residue 2904 GLU Chi-restraints excluded: chain B residue 2970 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 103 optimal weight: 0.2980 chunk 88 optimal weight: 0.6980 chunk 113 optimal weight: 0.0570 chunk 306 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 chunk 232 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 309 optimal weight: 2.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2066 GLN A2809 GLN B1416 GLN B1638 ASN B2002 GLN B2066 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.092823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.062419 restraints weight = 52648.746| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.29 r_work: 0.2770 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25546 Z= 0.101 Angle : 0.540 16.251 34496 Z= 0.261 Chirality : 0.039 0.401 3904 Planarity : 0.003 0.052 4362 Dihedral : 4.528 83.351 3424 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.22 % Allowed : 14.36 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.30 (0.16), residues: 3072 helix: 2.91 (0.11), residues: 2176 sheet: 0.89 (0.62), residues: 66 loop : 0.30 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP A1461 HIS 0.006 0.001 HIS A1876 PHE 0.012 0.001 PHE A1712 TYR 0.017 0.001 TYR A1556 ARG 0.011 0.000 ARG B1585 Details of bonding type rmsd hydrogen bonds : bond 0.02905 ( 1607) hydrogen bonds : angle 3.32344 ( 4761) metal coordination : bond 0.00970 ( 6) covalent geometry : bond 0.00234 (25540) covalent geometry : angle 0.53977 (34496) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 283 time to evaluate : 3.115 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 1424 GLU cc_start: 0.9319 (OUTLIER) cc_final: 0.8755 (tp30) REVERT: A 1434 LYS cc_start: 0.9552 (tppt) cc_final: 0.9139 (tppp) REVERT: A 1437 ARG cc_start: 0.9263 (ttp80) cc_final: 0.8784 (tpt170) REVERT: A 1449 LEU cc_start: 0.9260 (mt) cc_final: 0.8962 (mp) REVERT: A 1489 ARG cc_start: 0.9011 (mtp180) cc_final: 0.8526 (mtp-110) REVERT: A 1554 ASN cc_start: 0.9270 (m110) cc_final: 0.8977 (m110) REVERT: A 1693 ASP cc_start: 0.8861 (m-30) cc_final: 0.8516 (t0) REVERT: A 1836 ASP cc_start: 0.9064 (m-30) cc_final: 0.8621 (t0) REVERT: A 2139 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8242 (mm-30) REVERT: A 2157 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8225 (mp0) REVERT: A 2193 VAL cc_start: 0.9245 (OUTLIER) cc_final: 0.9028 (p) REVERT: A 2314 GLN cc_start: 0.9307 (tt0) cc_final: 0.8909 (tp-100) REVERT: A 2479 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8410 (tp30) REVERT: A 2561 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9210 (mm) REVERT: A 2744 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8910 (mm-30) REVERT: A 2943 GLU cc_start: 0.8580 (mp0) cc_final: 0.8250 (pm20) REVERT: A 2954 TYR cc_start: 0.8903 (m-80) cc_final: 0.8598 (m-10) REVERT: A 2962 MET cc_start: 0.9240 (tpp) cc_final: 0.8838 (tpp) REVERT: A 3004 LYS cc_start: 0.9365 (mtpp) cc_final: 0.9087 (pttp) REVERT: B 1424 GLU cc_start: 0.9220 (mt-10) cc_final: 0.8955 (mm-30) REVERT: B 1434 LYS cc_start: 0.9544 (tppt) cc_final: 0.9113 (tppp) REVERT: B 1437 ARG cc_start: 0.9276 (ttp80) cc_final: 0.8753 (tpt170) REVERT: B 1527 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9001 (mm) REVERT: B 1568 HIS cc_start: 0.8624 (m90) cc_final: 0.8337 (m90) REVERT: B 1585 ARG cc_start: 0.9005 (mmm160) cc_final: 0.8427 (tmm160) REVERT: B 1693 ASP cc_start: 0.8908 (m-30) cc_final: 0.8563 (t0) REVERT: B 1701 LYS cc_start: 0.9056 (pttp) cc_final: 0.8845 (pptt) REVERT: B 1836 ASP cc_start: 0.9047 (m-30) cc_final: 0.8642 (t0) REVERT: B 2002 GLN cc_start: 0.8262 (tt0) cc_final: 0.7974 (tt0) REVERT: B 2110 ASP cc_start: 0.9092 (m-30) cc_final: 0.8763 (p0) REVERT: B 2157 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: B 2479 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8426 (tp30) REVERT: B 2561 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9163 (mm) REVERT: B 2612 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8400 (ppp80) REVERT: B 2668 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8661 (pp20) REVERT: B 2744 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8918 (mm-30) REVERT: B 2904 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8400 (mt-10) REVERT: B 2943 GLU cc_start: 0.8584 (mp0) cc_final: 0.8215 (pm20) REVERT: B 2954 TYR cc_start: 0.8897 (m-80) cc_final: 0.8565 (m-10) outliers start: 62 outliers final: 18 residues processed: 321 average time/residue: 1.3716 time to fit residues: 511.2246 Evaluate side-chains 289 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 260 time to evaluate : 2.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1424 GLU Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1827 LEU Chi-restraints excluded: chain A residue 1876 HIS Chi-restraints excluded: chain A residue 2157 GLU Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2310 SER Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2479 GLU Chi-restraints excluded: chain A residue 2557 LEU Chi-restraints excluded: chain A residue 2561 LEU Chi-restraints excluded: chain A residue 2965 LEU Chi-restraints excluded: chain B residue 1438 ILE Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1527 LEU Chi-restraints excluded: chain B residue 1608 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1827 LEU Chi-restraints excluded: chain B residue 1876 HIS Chi-restraints excluded: chain B residue 1988 SER Chi-restraints excluded: chain B residue 2157 GLU Chi-restraints excluded: chain B residue 2310 SER Chi-restraints excluded: chain B residue 2479 GLU Chi-restraints excluded: chain B residue 2557 LEU Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2612 ARG Chi-restraints excluded: chain B residue 2904 GLU Chi-restraints excluded: chain B residue 2970 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 69 optimal weight: 0.0050 chunk 207 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 115 optimal weight: 0.0670 chunk 133 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 246 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 overall best weight: 1.0136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2066 GLN B2066 GLN B2108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.091387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.060880 restraints weight = 52745.630| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.27 r_work: 0.2727 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25546 Z= 0.128 Angle : 0.570 14.930 34496 Z= 0.274 Chirality : 0.040 0.390 3904 Planarity : 0.003 0.065 4362 Dihedral : 4.565 83.322 3424 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.18 % Allowed : 14.94 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.31 (0.16), residues: 3072 helix: 2.92 (0.11), residues: 2172 sheet: 0.94 (0.63), residues: 66 loop : 0.30 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP A1461 HIS 0.005 0.001 HIS A1443 PHE 0.014 0.001 PHE B1491 TYR 0.014 0.001 TYR B1415 ARG 0.016 0.000 ARG A1585 Details of bonding type rmsd hydrogen bonds : bond 0.03199 ( 1607) hydrogen bonds : angle 3.36750 ( 4761) metal coordination : bond 0.00636 ( 6) covalent geometry : bond 0.00305 (25540) covalent geometry : angle 0.56989 (34496) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 276 time to evaluate : 3.054 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 1424 GLU cc_start: 0.9349 (OUTLIER) cc_final: 0.8786 (tp30) REVERT: A 1434 LYS cc_start: 0.9567 (tppt) cc_final: 0.9142 (tppp) REVERT: A 1437 ARG cc_start: 0.9266 (ttp80) cc_final: 0.8807 (tpt170) REVERT: A 1449 LEU cc_start: 0.9300 (mt) cc_final: 0.8982 (mp) REVERT: A 1489 ARG cc_start: 0.9032 (mtp-110) cc_final: 0.8538 (mtp-110) REVERT: A 1554 ASN cc_start: 0.9293 (m110) cc_final: 0.9006 (m110) REVERT: A 1693 ASP cc_start: 0.8882 (m-30) cc_final: 0.8530 (t0) REVERT: A 1836 ASP cc_start: 0.9090 (m-30) cc_final: 0.8651 (t0) REVERT: A 2139 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8265 (mm-30) REVERT: A 2157 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8214 (mp0) REVERT: A 2193 VAL cc_start: 0.9252 (OUTLIER) cc_final: 0.9038 (p) REVERT: A 2314 GLN cc_start: 0.9309 (tt0) cc_final: 0.8863 (tp-100) REVERT: A 2443 ARG cc_start: 0.8502 (ptm160) cc_final: 0.8286 (ptm160) REVERT: A 2561 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9159 (mm) REVERT: A 2744 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8944 (mm-30) REVERT: A 2962 MET cc_start: 0.9251 (tpp) cc_final: 0.8824 (tpp) REVERT: A 3004 LYS cc_start: 0.9390 (mtpp) cc_final: 0.9107 (pttp) REVERT: B 1424 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8965 (mm-30) REVERT: B 1434 LYS cc_start: 0.9559 (tppt) cc_final: 0.9105 (tppp) REVERT: B 1437 ARG cc_start: 0.9288 (ttp80) cc_final: 0.8786 (tpt170) REVERT: B 1554 ASN cc_start: 0.9111 (m110) cc_final: 0.8763 (m110) REVERT: B 1585 ARG cc_start: 0.8982 (mmm160) cc_final: 0.8533 (tmm160) REVERT: B 1693 ASP cc_start: 0.8913 (m-30) cc_final: 0.8553 (t0) REVERT: B 1701 LYS cc_start: 0.9053 (pttp) cc_final: 0.8834 (pptt) REVERT: B 1836 ASP cc_start: 0.9069 (m-30) cc_final: 0.8637 (t0) REVERT: B 2002 GLN cc_start: 0.8299 (tt0) cc_final: 0.7980 (tt0) REVERT: B 2110 ASP cc_start: 0.9048 (m-30) cc_final: 0.8768 (p0) REVERT: B 2157 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8118 (mp0) REVERT: B 2479 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8462 (tp30) REVERT: B 2561 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9170 (mm) REVERT: B 2612 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8433 (ppp80) REVERT: B 2668 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8680 (pp20) REVERT: B 2744 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8919 (mm-30) REVERT: B 2904 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8442 (mt-10) REVERT: B 2943 GLU cc_start: 0.8598 (mp0) cc_final: 0.8236 (pm20) REVERT: B 3008 ARG cc_start: 0.9126 (ptm160) cc_final: 0.8735 (ptp-110) outliers start: 61 outliers final: 20 residues processed: 312 average time/residue: 1.3767 time to fit residues: 497.1087 Evaluate side-chains 286 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 257 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1424 GLU Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1827 LEU Chi-restraints excluded: chain A residue 1876 HIS Chi-restraints excluded: chain A residue 2157 GLU Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2310 SER Chi-restraints excluded: chain A residue 2379 LEU Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2557 LEU Chi-restraints excluded: chain A residue 2561 LEU Chi-restraints excluded: chain A residue 2965 LEU Chi-restraints excluded: chain A residue 2970 LEU Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1608 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1823 ILE Chi-restraints excluded: chain B residue 1827 LEU Chi-restraints excluded: chain B residue 1876 HIS Chi-restraints excluded: chain B residue 2157 GLU Chi-restraints excluded: chain B residue 2310 SER Chi-restraints excluded: chain B residue 2379 LEU Chi-restraints excluded: chain B residue 2479 GLU Chi-restraints excluded: chain B residue 2557 LEU Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2612 ARG Chi-restraints excluded: chain B residue 2904 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 46 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 210 optimal weight: 1.9990 chunk 283 optimal weight: 3.9990 chunk 197 optimal weight: 0.5980 chunk 303 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 235 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2066 GLN A2241 ASN B2066 GLN B2108 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.091523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.061122 restraints weight = 52578.973| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 3.24 r_work: 0.2719 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25546 Z= 0.119 Angle : 0.579 13.688 34496 Z= 0.276 Chirality : 0.040 0.391 3904 Planarity : 0.003 0.052 4362 Dihedral : 4.560 82.459 3424 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.65 % Allowed : 15.37 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.26 (0.15), residues: 3072 helix: 2.90 (0.11), residues: 2168 sheet: 0.97 (0.63), residues: 66 loop : 0.24 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP A1461 HIS 0.004 0.001 HIS A1443 PHE 0.012 0.001 PHE B2143 TYR 0.014 0.001 TYR A1556 ARG 0.007 0.000 ARG A2642 Details of bonding type rmsd hydrogen bonds : bond 0.03125 ( 1607) hydrogen bonds : angle 3.37363 ( 4761) metal coordination : bond 0.00428 ( 6) covalent geometry : bond 0.00283 (25540) covalent geometry : angle 0.57925 (34496) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 256 time to evaluate : 2.657 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 1424 GLU cc_start: 0.9355 (OUTLIER) cc_final: 0.8783 (tp30) REVERT: A 1434 LYS cc_start: 0.9568 (tppt) cc_final: 0.9150 (tppp) REVERT: A 1437 ARG cc_start: 0.9267 (ttp80) cc_final: 0.8789 (tpt170) REVERT: A 1449 LEU cc_start: 0.9313 (mt) cc_final: 0.8982 (mp) REVERT: A 1489 ARG cc_start: 0.9036 (mtp-110) cc_final: 0.8532 (mtp-110) REVERT: A 1554 ASN cc_start: 0.9286 (m110) cc_final: 0.9008 (m110) REVERT: A 1693 ASP cc_start: 0.8864 (m-30) cc_final: 0.8541 (t0) REVERT: A 1836 ASP cc_start: 0.9087 (m-30) cc_final: 0.8663 (t0) REVERT: A 2139 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8233 (mm-30) REVERT: A 2157 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8232 (mp0) REVERT: A 2193 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.9025 (p) REVERT: A 2314 GLN cc_start: 0.9303 (tt0) cc_final: 0.8856 (tp-100) REVERT: A 2443 ARG cc_start: 0.8525 (ptm160) cc_final: 0.8323 (ptm160) REVERT: A 2561 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9143 (mm) REVERT: A 2744 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8896 (mm-30) REVERT: A 2962 MET cc_start: 0.9254 (tpp) cc_final: 0.8832 (tpp) REVERT: A 3004 LYS cc_start: 0.9400 (mtpp) cc_final: 0.9105 (pttp) REVERT: B 1424 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8961 (mm-30) REVERT: B 1434 LYS cc_start: 0.9558 (tppt) cc_final: 0.9112 (tppp) REVERT: B 1437 ARG cc_start: 0.9292 (ttp80) cc_final: 0.8788 (tpt170) REVERT: B 1585 ARG cc_start: 0.8974 (mmm160) cc_final: 0.8531 (tmm160) REVERT: B 1693 ASP cc_start: 0.8907 (m-30) cc_final: 0.8558 (t0) REVERT: B 1701 LYS cc_start: 0.9054 (pttp) cc_final: 0.8821 (pptt) REVERT: B 1836 ASP cc_start: 0.9055 (m-30) cc_final: 0.8634 (t0) REVERT: B 2002 GLN cc_start: 0.8284 (tt0) cc_final: 0.7957 (tt0) REVERT: B 2110 ASP cc_start: 0.9085 (m-30) cc_final: 0.8774 (p0) REVERT: B 2139 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7908 (mm-30) REVERT: B 2157 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: B 2479 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8437 (tp30) REVERT: B 2561 LEU cc_start: 0.9582 (OUTLIER) cc_final: 0.9139 (mm) REVERT: B 2612 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8431 (ppp80) REVERT: B 2668 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8687 (pp20) REVERT: B 2943 GLU cc_start: 0.8591 (mp0) cc_final: 0.8219 (pm20) REVERT: B 2946 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9193 (mm) outliers start: 46 outliers final: 17 residues processed: 285 average time/residue: 1.3663 time to fit residues: 449.7817 Evaluate side-chains 272 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 246 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1424 GLU Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1876 HIS Chi-restraints excluded: chain A residue 2157 GLU Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2310 SER Chi-restraints excluded: chain A residue 2379 LEU Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2557 LEU Chi-restraints excluded: chain A residue 2561 LEU Chi-restraints excluded: chain A residue 2965 LEU Chi-restraints excluded: chain A residue 2970 LEU Chi-restraints excluded: chain B residue 1608 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1827 LEU Chi-restraints excluded: chain B residue 1876 HIS Chi-restraints excluded: chain B residue 2157 GLU Chi-restraints excluded: chain B residue 2310 SER Chi-restraints excluded: chain B residue 2379 LEU Chi-restraints excluded: chain B residue 2479 GLU Chi-restraints excluded: chain B residue 2557 LEU Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2612 ARG Chi-restraints excluded: chain B residue 2946 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 105 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 274 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 213 optimal weight: 0.0010 chunk 28 optimal weight: 4.9990 chunk 236 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 268 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2066 GLN B2066 GLN B2108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.091696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.061296 restraints weight = 52625.036| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.25 r_work: 0.2723 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25546 Z= 0.113 Angle : 0.587 14.907 34496 Z= 0.280 Chirality : 0.040 0.395 3904 Planarity : 0.003 0.052 4362 Dihedral : 4.553 81.901 3424 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.43 % Allowed : 15.54 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.26 (0.15), residues: 3072 helix: 2.89 (0.11), residues: 2168 sheet: 1.00 (0.63), residues: 66 loop : 0.25 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP A1461 HIS 0.004 0.001 HIS A1443 PHE 0.013 0.001 PHE B1491 TYR 0.015 0.001 TYR B1556 ARG 0.007 0.000 ARG A2642 Details of bonding type rmsd hydrogen bonds : bond 0.03069 ( 1607) hydrogen bonds : angle 3.36902 ( 4761) metal coordination : bond 0.00387 ( 6) covalent geometry : bond 0.00271 (25540) covalent geometry : angle 0.58705 (34496) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 258 time to evaluate : 2.829 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 1424 GLU cc_start: 0.9352 (OUTLIER) cc_final: 0.8782 (tp30) REVERT: A 1434 LYS cc_start: 0.9578 (tppt) cc_final: 0.9167 (tppp) REVERT: A 1437 ARG cc_start: 0.9282 (ttp80) cc_final: 0.8817 (tpt170) REVERT: A 1449 LEU cc_start: 0.9309 (mt) cc_final: 0.8982 (mp) REVERT: A 1489 ARG cc_start: 0.9034 (mtp-110) cc_final: 0.8527 (mtp-110) REVERT: A 1554 ASN cc_start: 0.9280 (m110) cc_final: 0.9011 (m110) REVERT: A 1693 ASP cc_start: 0.8851 (m-30) cc_final: 0.8537 (t0) REVERT: A 1836 ASP cc_start: 0.9069 (m-30) cc_final: 0.8646 (t0) REVERT: A 2139 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8210 (mm-30) REVERT: A 2157 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8228 (mp0) REVERT: A 2193 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.9025 (p) REVERT: A 2314 GLN cc_start: 0.9299 (tt0) cc_final: 0.8849 (tp-100) REVERT: A 2443 ARG cc_start: 0.8547 (ptm160) cc_final: 0.8166 (ptm160) REVERT: A 2532 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7267 (mmm) REVERT: A 2561 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9141 (mm) REVERT: A 2744 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8895 (mm-30) REVERT: A 2962 MET cc_start: 0.9251 (tpp) cc_final: 0.8835 (tpp) REVERT: A 3004 LYS cc_start: 0.9408 (mtpp) cc_final: 0.9111 (pttp) REVERT: B 1424 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8962 (mm-30) REVERT: B 1434 LYS cc_start: 0.9562 (tppt) cc_final: 0.9130 (tppp) REVERT: B 1437 ARG cc_start: 0.9293 (ttp80) cc_final: 0.8800 (tpt170) REVERT: B 1554 ASN cc_start: 0.9141 (m110) cc_final: 0.8816 (m110) REVERT: B 1568 HIS cc_start: 0.8792 (m-70) cc_final: 0.8543 (m-70) REVERT: B 1693 ASP cc_start: 0.8904 (m-30) cc_final: 0.8557 (t0) REVERT: B 1701 LYS cc_start: 0.9057 (pttp) cc_final: 0.8831 (pptt) REVERT: B 1836 ASP cc_start: 0.9043 (m-30) cc_final: 0.8612 (t0) REVERT: B 2002 GLN cc_start: 0.8278 (tt0) cc_final: 0.7959 (tt0) REVERT: B 2106 ASN cc_start: 0.8733 (t0) cc_final: 0.8470 (m-40) REVERT: B 2108 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8287 (mp10) REVERT: B 2110 ASP cc_start: 0.9088 (m-30) cc_final: 0.8772 (p0) REVERT: B 2157 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8098 (mp0) REVERT: B 2561 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9134 (mm) REVERT: B 2612 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8439 (ppp80) REVERT: B 2668 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8704 (pp20) REVERT: B 2943 GLU cc_start: 0.8583 (mp0) cc_final: 0.8212 (pm20) REVERT: B 3008 ARG cc_start: 0.9105 (ptm160) cc_final: 0.8708 (ptp-110) outliers start: 40 outliers final: 18 residues processed: 281 average time/residue: 1.3526 time to fit residues: 439.8991 Evaluate side-chains 275 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 248 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1424 GLU Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 2157 GLU Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2310 SER Chi-restraints excluded: chain A residue 2379 LEU Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2532 MET Chi-restraints excluded: chain A residue 2557 LEU Chi-restraints excluded: chain A residue 2561 LEU Chi-restraints excluded: chain A residue 2965 LEU Chi-restraints excluded: chain A residue 2970 LEU Chi-restraints excluded: chain B residue 1555 LEU Chi-restraints excluded: chain B residue 1608 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1827 LEU Chi-restraints excluded: chain B residue 1876 HIS Chi-restraints excluded: chain B residue 2108 GLN Chi-restraints excluded: chain B residue 2157 GLU Chi-restraints excluded: chain B residue 2310 SER Chi-restraints excluded: chain B residue 2379 LEU Chi-restraints excluded: chain B residue 2557 LEU Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2612 ARG Chi-restraints excluded: chain B residue 2806 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 46 optimal weight: 0.1980 chunk 176 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 252 optimal weight: 0.9990 chunk 201 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 186 optimal weight: 0.9990 chunk 83 optimal weight: 0.3980 chunk 250 optimal weight: 2.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2066 GLN B2066 GLN B2108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.091557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.061097 restraints weight = 52727.441| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.27 r_work: 0.2717 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25546 Z= 0.116 Angle : 0.609 16.504 34496 Z= 0.288 Chirality : 0.040 0.390 3904 Planarity : 0.003 0.067 4362 Dihedral : 4.566 81.619 3424 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.07 % Allowed : 16.15 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.24 (0.15), residues: 3072 helix: 2.88 (0.11), residues: 2168 sheet: 0.95 (0.62), residues: 66 loop : 0.26 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP A1461 HIS 0.009 0.001 HIS A1876 PHE 0.011 0.001 PHE A2143 TYR 0.019 0.001 TYR A2969 ARG 0.014 0.000 ARG B1585 Details of bonding type rmsd hydrogen bonds : bond 0.03078 ( 1607) hydrogen bonds : angle 3.38180 ( 4761) metal coordination : bond 0.00480 ( 6) covalent geometry : bond 0.00276 (25540) covalent geometry : angle 0.60917 (34496) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 256 time to evaluate : 2.944 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 1424 GLU cc_start: 0.9353 (OUTLIER) cc_final: 0.8783 (tp30) REVERT: A 1434 LYS cc_start: 0.9578 (tppt) cc_final: 0.9163 (tppp) REVERT: A 1437 ARG cc_start: 0.9287 (ttp80) cc_final: 0.8831 (tpt170) REVERT: A 1449 LEU cc_start: 0.9328 (mt) cc_final: 0.8981 (mp) REVERT: A 1489 ARG cc_start: 0.9024 (mtp-110) cc_final: 0.8513 (mtp-110) REVERT: A 1554 ASN cc_start: 0.9276 (m110) cc_final: 0.9011 (m110) REVERT: A 1693 ASP cc_start: 0.8860 (m-30) cc_final: 0.8556 (t0) REVERT: A 2139 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8205 (mm-30) REVERT: A 2157 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8228 (mp0) REVERT: A 2193 VAL cc_start: 0.9230 (OUTLIER) cc_final: 0.9016 (p) REVERT: A 2314 GLN cc_start: 0.9313 (tt0) cc_final: 0.8866 (tp-100) REVERT: A 2443 ARG cc_start: 0.8572 (ptm160) cc_final: 0.8205 (ptm160) REVERT: A 2532 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7380 (mmm) REVERT: A 2561 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9144 (mm) REVERT: A 2744 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8900 (mm-30) REVERT: A 2962 MET cc_start: 0.9241 (tpp) cc_final: 0.8883 (tpp) REVERT: A 3004 LYS cc_start: 0.9409 (mtpp) cc_final: 0.9116 (pttp) REVERT: B 1424 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8964 (mm-30) REVERT: B 1434 LYS cc_start: 0.9570 (tppt) cc_final: 0.9134 (tppp) REVERT: B 1437 ARG cc_start: 0.9289 (ttp80) cc_final: 0.8809 (tpt170) REVERT: B 1554 ASN cc_start: 0.9161 (m110) cc_final: 0.8842 (m110) REVERT: B 1568 HIS cc_start: 0.8807 (m-70) cc_final: 0.8549 (m-70) REVERT: B 1693 ASP cc_start: 0.8901 (m-30) cc_final: 0.8556 (t0) REVERT: B 1701 LYS cc_start: 0.9060 (pttp) cc_final: 0.8826 (pptt) REVERT: B 1836 ASP cc_start: 0.9053 (m-30) cc_final: 0.8617 (t0) REVERT: B 2002 GLN cc_start: 0.8271 (tt0) cc_final: 0.7952 (tt0) REVERT: B 2110 ASP cc_start: 0.9071 (m-30) cc_final: 0.8786 (p0) REVERT: B 2139 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7907 (mm-30) REVERT: B 2479 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8448 (tp30) REVERT: B 2561 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9127 (mm) REVERT: B 2612 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8446 (ppp80) REVERT: B 2668 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8716 (pp20) REVERT: B 2943 GLU cc_start: 0.8598 (mp0) cc_final: 0.8231 (pm20) REVERT: B 3008 ARG cc_start: 0.9099 (ptm160) cc_final: 0.8702 (ptp-110) outliers start: 30 outliers final: 17 residues processed: 275 average time/residue: 1.3676 time to fit residues: 434.4149 Evaluate side-chains 272 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 247 time to evaluate : 3.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1424 GLU Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 2157 GLU Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2310 SER Chi-restraints excluded: chain A residue 2379 LEU Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2532 MET Chi-restraints excluded: chain A residue 2557 LEU Chi-restraints excluded: chain A residue 2561 LEU Chi-restraints excluded: chain A residue 2965 LEU Chi-restraints excluded: chain A residue 2970 LEU Chi-restraints excluded: chain B residue 1555 LEU Chi-restraints excluded: chain B residue 1608 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1827 LEU Chi-restraints excluded: chain B residue 1876 HIS Chi-restraints excluded: chain B residue 2310 SER Chi-restraints excluded: chain B residue 2379 LEU Chi-restraints excluded: chain B residue 2479 GLU Chi-restraints excluded: chain B residue 2557 LEU Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2612 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 158 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 289 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2066 GLN B2066 GLN B2108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.089377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.058898 restraints weight = 52887.677| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.22 r_work: 0.2659 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25546 Z= 0.175 Angle : 0.641 14.965 34496 Z= 0.305 Chirality : 0.042 0.388 3904 Planarity : 0.003 0.053 4362 Dihedral : 4.655 82.013 3424 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.11 % Allowed : 16.05 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.16), residues: 3072 helix: 2.83 (0.11), residues: 2154 sheet: 0.89 (0.63), residues: 66 loop : 0.32 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.001 TRP A1461 HIS 0.009 0.001 HIS A1876 PHE 0.015 0.001 PHE B1491 TYR 0.018 0.001 TYR A2969 ARG 0.009 0.001 ARG B1585 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 1607) hydrogen bonds : angle 3.49755 ( 4761) metal coordination : bond 0.00243 ( 6) covalent geometry : bond 0.00421 (25540) covalent geometry : angle 0.64132 (34496) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19857.70 seconds wall clock time: 342 minutes 33.21 seconds (20553.21 seconds total)