Starting phenix.real_space_refine on Fri Sep 11 16:55:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6cmx_7526/09_2026/6cmx_7526.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cmx_7526/09_2026/6cmx_7526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6cmx_7526/09_2026/6cmx_7526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cmx_7526/09_2026/6cmx_7526.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6cmx_7526/09_2026/6cmx_7526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cmx_7526/09_2026/6cmx_7526.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6cmx_7526/09_2026/6cmx_7526.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6cmx_7526/09_2026/6cmx_7526.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 6478 2.51 5 N 1740 2.21 5 O 1888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10139 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1300, 9919 Classifications: {'peptide': 1300} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'PTRANS': 46, 'TRANS': 1253} Chain breaks: 3 Unresolved non-hydrogen bonds: 530 Unresolved non-hydrogen angles: 659 Unresolved non-hydrogen dihedrals: 405 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'PHE:plan': 2, 'ASP:plan': 35, 'GLN:plan1': 18, 'ASN:plan1': 10, 'GLU:plan': 37, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 402 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'MAN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 159 Unusual residues: {'MAN': 3, 'NAG': 9} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 2.48, per 1000 atoms: 0.24 Number of scatterers: 10139 At special positions: 0 Unit cell: (80, 113, 111, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1888 8.00 N 1740 7.00 C 6478 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 Atom "HETATM10045 O5 NAG A2705 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-4 " NAG B 2 " - " MAN B 3 " ALPHA1-6 " MAN C 1 " - " MAN C 2 " BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A2701 " - " ASN A1490 " " NAG A2704 " - " ASN A1586 " " NAG A2708 " - " ASN A2071 " " NAG B 1 " - " ASN A1766 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 281.0 milliseconds 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 26 sheets defined 8.1% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 955 through 957 No H-bonds generated for 'chain 'A' and resid 955 through 957' Processing helix chain 'A' and resid 2318 through 2323 removed outlier: 3.900A pdb=" N GLY A2323 " --> pdb=" O TRP A2319 " (cutoff:3.500A) Processing helix chain 'A' and resid 2334 through 2338 Processing helix chain 'A' and resid 2345 through 2349 Processing helix chain 'A' and resid 2352 through 2360 Processing helix chain 'A' and resid 2382 through 2390 Processing helix chain 'A' and resid 2398 through 2412 Processing helix chain 'A' and resid 2464 through 2475 Processing helix chain 'A' and resid 2559 through 2591 removed outlier: 3.929A pdb=" N ASP A2563 " --> pdb=" O PRO A2559 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A2573 " --> pdb=" O VAL A2569 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN A2575 " --> pdb=" O ASP A2571 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A2576 " --> pdb=" O GLN A2572 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A2580 " --> pdb=" O ARG A2576 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A2584 " --> pdb=" O THR A2580 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A2587 " --> pdb=" O ALA A2583 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP A2591 " --> pdb=" O GLN A2587 " (cutoff:3.500A) Processing helix chain 'A' and resid 2603 through 2610 Processing sheet with id=AA1, first strand: chain 'A' and resid 911 through 914 removed outlier: 3.698A pdb=" N MET A 968 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LEU A1001 " --> pdb=" O MET A 968 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 930 through 931 Processing sheet with id=AA3, first strand: chain 'A' and resid 980 through 981 Processing sheet with id=AA4, first strand: chain 'A' and resid 984 through 985 Processing sheet with id=AA5, first strand: chain 'A' and resid 1067 through 1068 Processing sheet with id=AA6, first strand: chain 'A' and resid 1457 through 1461 removed outlier: 8.454A pdb=" N GLN A1477 " --> pdb=" O ASN A1490 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ASN A1490 " --> pdb=" O GLN A1477 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A1501 " --> pdb=" O THR A1492 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP A1504 " --> pdb=" O ASN A1508 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ASN A1508 " --> pdb=" O ASP A1504 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1522 through 1524 Processing sheet with id=AA8, first strand: chain 'A' and resid 1555 through 1556 Processing sheet with id=AA9, first strand: chain 'A' and resid 1607 through 1608 removed outlier: 3.909A pdb=" N ILE A1607 " --> pdb=" O VAL A1620 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER A1630 " --> pdb=" O ASN A1623 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A1644 " --> pdb=" O ALA A1629 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1652 through 1653 removed outlier: 7.078A pdb=" N SER A1692 " --> pdb=" O VAL A1715 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N VAL A1715 " --> pdb=" O SER A1692 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLU A1694 " --> pdb=" O LEU A1713 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU A1713 " --> pdb=" O GLU A1694 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ARG A1696 " --> pdb=" O ARG A1711 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ARG A1711 " --> pdb=" O ARG A1696 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ARG A1698 " --> pdb=" O PHE A1709 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE A1709 " --> pdb=" O ARG A1698 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU A1700 " --> pdb=" O THR A1707 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N THR A1707 " --> pdb=" O ASP A1726 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASP A1726 " --> pdb=" O THR A1707 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N PHE A1709 " --> pdb=" O ASP A1724 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASP A1724 " --> pdb=" O PHE A1709 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ARG A1711 " --> pdb=" O SER A1722 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER A1722 " --> pdb=" O ARG A1711 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU A1713 " --> pdb=" O LEU A1720 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1765 through 1766 removed outlier: 3.606A pdb=" N SER A1797 " --> pdb=" O ASP A1788 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1807 through 1809 removed outlier: 6.444A pdb=" N ILE A1826 " --> pdb=" O VAL A1838 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL A1838 " --> pdb=" O ILE A1826 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLU A1828 " --> pdb=" O LEU A1836 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1848 through 1853 removed outlier: 6.739A pdb=" N ILE A1871 " --> pdb=" O THR A1883 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR A1883 " --> pdb=" O ILE A1871 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP A1873 " --> pdb=" O LEU A1881 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU A1881 " --> pdb=" O TYR A1894 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS A1895 " --> pdb=" O GLU A1904 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLU A1904 " --> pdb=" O LYS A1895 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N SER A1903 " --> pdb=" O PHE A1914 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N PHE A1914 " --> pdb=" O SER A1903 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LYS A1924 " --> pdb=" O TYR A1939 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ASP A1947 " --> pdb=" O TYR A1965 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ASP A1964 " --> pdb=" O ILE A1977 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE A1977 " --> pdb=" O ASP A1964 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N THR A1966 " --> pdb=" O ALA A1975 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1848 through 1853 removed outlier: 6.739A pdb=" N ILE A1871 " --> pdb=" O THR A1883 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR A1883 " --> pdb=" O ILE A1871 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP A1873 " --> pdb=" O LEU A1881 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU A1881 " --> pdb=" O TYR A1894 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS A1895 " --> pdb=" O GLU A1904 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLU A1904 " --> pdb=" O LYS A1895 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N SER A1903 " --> pdb=" O PHE A1914 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N PHE A1914 " --> pdb=" O SER A1903 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LYS A1924 " --> pdb=" O TYR A1939 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ASP A1947 " --> pdb=" O TYR A1965 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A1981 " --> pdb=" O THR A1984 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1992 through 1993 Processing sheet with id=AB7, first strand: chain 'A' and resid 2007 through 2011 removed outlier: 3.771A pdb=" N ASN A2014 " --> pdb=" O TYR A2011 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN A2015 " --> pdb=" O LYS A2026 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A2038 " --> pdb=" O SER A2025 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLU A2036 " --> pdb=" O HIS A2027 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N LYS A2035 " --> pdb=" O VAL A2051 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL A2051 " --> pdb=" O LYS A2035 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASP A2054 " --> pdb=" O VAL A2059 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL A2059 " --> pdb=" O ASP A2054 " (cutoff:3.500A) removed outlier: 10.595A pdb=" N ARG A2058 " --> pdb=" O TYR A2079 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N TYR A2079 " --> pdb=" O ARG A2058 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE A2060 " --> pdb=" O TYR A2077 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A2075 " --> pdb=" O ARG A2062 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A2090 " --> pdb=" O PRO A2094 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2108 through 2109 Processing sheet with id=AB9, first strand: chain 'A' and resid 2130 through 2131 Processing sheet with id=AC1, first strand: chain 'A' and resid 2150 through 2151 Processing sheet with id=AC2, first strand: chain 'A' and resid 2219 through 2222 Processing sheet with id=AC3, first strand: chain 'A' and resid 2240 through 2243 removed outlier: 6.292A pdb=" N TYR A2240 " --> pdb=" O VAL A2252 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL A2252 " --> pdb=" O TYR A2240 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL A2252 " --> pdb=" O ILE A2260 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 2264 through 2266 removed outlier: 7.849A pdb=" N GLN A2264 " --> pdb=" O ILE A2271 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE A2271 " --> pdb=" O GLN A2264 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 2289 through 2290 Processing sheet with id=AC6, first strand: chain 'A' and resid 2449 through 2450 removed outlier: 3.572A pdb=" N ALA A2477 " --> pdb=" O VAL A2455 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 2485 through 2487 Processing sheet with id=AC8, first strand: chain 'A' and resid 2618 through 2620 309 hydrogen bonds defined for protein. 783 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: 2.97 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1547 1.31 - 1.43: 3044 1.43 - 1.56: 5723 1.56 - 1.68: 3 1.68 - 1.81: 62 Bond restraints: 10379 Sorted by residual: bond pdb=" C1 MAN A2703 " pdb=" O5 MAN A2703 " ideal model delta sigma weight residual 1.399 1.509 -0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C1 NAG B 1 " pdb=" C2 NAG B 1 " ideal model delta sigma weight residual 1.532 1.640 -0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C7 NAG A2702 " pdb=" N2 NAG A2702 " ideal model delta sigma weight residual 1.346 1.454 -0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" C1 MAN B 3 " pdb=" O5 MAN B 3 " ideal model delta sigma weight residual 1.399 1.507 -0.108 2.00e-02 2.50e+03 2.89e+01 bond pdb=" C7 NAG A2701 " pdb=" N2 NAG A2701 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.88e+01 ... (remaining 10374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 13860 3.19 - 6.38: 215 6.38 - 9.58: 38 9.58 - 12.77: 5 12.77 - 15.96: 1 Bond angle restraints: 14119 Sorted by residual: angle pdb=" CB HIS A 989 " pdb=" CG HIS A 989 " pdb=" CD2 HIS A 989 " ideal model delta sigma weight residual 131.20 122.42 8.78 1.30e+00 5.92e-01 4.56e+01 angle pdb=" CB HIS A2424 " pdb=" CG HIS A2424 " pdb=" CD2 HIS A2424 " ideal model delta sigma weight residual 131.20 122.63 8.57 1.30e+00 5.92e-01 4.35e+01 angle pdb=" CB HIS A2227 " pdb=" CG HIS A2227 " pdb=" CD2 HIS A2227 " ideal model delta sigma weight residual 131.20 122.64 8.56 1.30e+00 5.92e-01 4.34e+01 angle pdb=" CB HIS A2208 " pdb=" CG HIS A2208 " pdb=" CD2 HIS A2208 " ideal model delta sigma weight residual 131.20 122.69 8.51 1.30e+00 5.92e-01 4.29e+01 angle pdb=" C LYS A2137 " pdb=" N ILE A2138 " pdb=" CA ILE A2138 " ideal model delta sigma weight residual 120.34 130.65 -10.31 1.58e+00 4.01e-01 4.26e+01 ... (remaining 14114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.78: 5851 26.78 - 53.55: 76 53.55 - 80.32: 7 80.32 - 107.10: 2 107.10 - 133.87: 1 Dihedral angle restraints: 5937 sinusoidal: 2157 harmonic: 3780 Sorted by residual: dihedral pdb=" CA LYS A2137 " pdb=" C LYS A2137 " pdb=" N ILE A2138 " pdb=" CA ILE A2138 " ideal model delta harmonic sigma weight residual -180.00 -46.13 -133.87 0 5.00e+00 4.00e-02 7.17e+02 dihedral pdb=" CA ASP A2012 " pdb=" C ASP A2012 " pdb=" N ILE A2013 " pdb=" CA ILE A2013 " ideal model delta harmonic sigma weight residual 180.00 -143.50 -36.50 0 5.00e+00 4.00e-02 5.33e+01 dihedral pdb=" CA TYR A1907 " pdb=" C TYR A1907 " pdb=" N ASP A1908 " pdb=" CA ASP A1908 " ideal model delta harmonic sigma weight residual -180.00 -145.10 -34.90 0 5.00e+00 4.00e-02 4.87e+01 ... (remaining 5934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.615: 1618 0.615 - 1.231: 1 1.231 - 1.846: 1 1.846 - 2.462: 0 2.462 - 3.077: 3 Chirality restraints: 1623 Sorted by residual: chirality pdb=" C1 MAN B 3 " pdb=" O4 NAG B 2 " pdb=" C2 MAN B 3 " pdb=" O5 MAN B 3 " both_signs ideal model delta sigma weight residual False 2.40 2.88 -0.48 2.00e-02 2.50e+03 5.80e+02 chirality pdb=" C1 NAG A2704 " pdb=" ND2 ASN A1586 " pdb=" C2 NAG A2704 " pdb=" O5 NAG A2704 " both_signs ideal model delta sigma weight residual False -2.40 0.68 -3.08 2.00e-01 2.50e+01 2.37e+02 chirality pdb=" C1 NAG A2708 " pdb=" ND2 ASN A2071 " pdb=" C2 NAG A2708 " pdb=" O5 NAG A2708 " both_signs ideal model delta sigma weight residual False -2.40 0.18 -2.58 2.00e-01 2.50e+01 1.66e+02 ... (remaining 1620 not shown) Planarity restraints: 1772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2708 " -0.360 2.00e-02 2.50e+03 3.10e-01 1.20e+03 pdb=" C7 NAG A2708 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG A2708 " -0.122 2.00e-02 2.50e+03 pdb=" N2 NAG A2708 " 0.550 2.00e-02 2.50e+03 pdb=" O7 NAG A2708 " -0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2704 " -0.333 2.00e-02 2.50e+03 2.80e-01 9.77e+02 pdb=" C7 NAG A2704 " 0.090 2.00e-02 2.50e+03 pdb=" C8 NAG A2704 " -0.196 2.00e-02 2.50e+03 pdb=" N2 NAG A2704 " 0.481 2.00e-02 2.50e+03 pdb=" O7 NAG A2704 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2705 " 0.170 2.00e-02 2.50e+03 1.42e-01 2.51e+02 pdb=" C7 NAG A2705 " -0.045 2.00e-02 2.50e+03 pdb=" C8 NAG A2705 " 0.124 2.00e-02 2.50e+03 pdb=" N2 NAG A2705 " -0.232 2.00e-02 2.50e+03 pdb=" O7 NAG A2705 " -0.017 2.00e-02 2.50e+03 ... (remaining 1769 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.29: 44 2.29 - 2.94: 5209 2.94 - 3.60: 14584 3.60 - 4.25: 24488 4.25 - 4.90: 41902 Nonbonded interactions: 86227 Sorted by model distance: nonbonded pdb=" SG CYS A1645 " pdb=" O5 NAG A2705 " model vdw 1.638 2.720 nonbonded pdb=" OG1 THR A1888 " pdb=" OD2 ASP A2141 " model vdw 1.893 3.040 nonbonded pdb=" OG1 THR A1573 " pdb=" O LYS A2444 " model vdw 1.941 3.040 nonbonded pdb=" O ASN A1646 " pdb=" C1 NAG A2705 " model vdw 1.974 3.470 nonbonded pdb=" OD2 ASP A1917 " pdb=" OG1 THR A1920 " model vdw 1.975 3.040 ... (remaining 86222 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.500 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 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 : 0.009 0.248 10387 Z= 0.528 Angle : 1.257 50.913 14140 Z= 0.612 Chirality : 0.138 3.077 1623 Planarity : 0.012 0.310 1768 Dihedral : 10.092 133.872 3537 Min Nonbonded Distance : 1.638 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.60 % Favored : 90.17 % Rotamer: Outliers : 1.51 % Allowed : 4.04 % Favored : 94.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.85 (0.20), residues: 1292 helix: -1.75 (0.50), residues: 83 sheet: -3.12 (0.25), residues: 316 loop : -2.56 (0.18), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2428 TYR 0.028 0.003 TYR A2222 PHE 0.019 0.003 PHE A2360 TRP 0.016 0.002 TRP A2311 HIS 0.013 0.002 HIS A2212 Details of bonding type rmsd/Z covalent geometry : bond 0.00877 / 0.46 (10379) covalent geometry : angle 1.01070 / 0.56 (14119) hydrogen bonds : bond 0.24762 / 18.70 ( 269) hydrogen bonds : angle 11.67064 / 8.09 ( 783) Misc. bond : bond 0.24804 / 13.05 ( 1) link_ALPHA1-4 : bond 0.04744 / 2.50 ( 1) link_ALPHA1-4 : angle 9.50314 / 5.01 ( 3) link_ALPHA1-6 : bond 0.00165 / 0.09 ( 1) link_ALPHA1-6 : angle 1.46370 / 0.75 ( 3) link_BETA1-4 : bond 0.02035 / 1.07 ( 1) link_BETA1-4 : angle 5.05584 / 2.72 ( 3) link_NAG-ASN : bond 0.09646 / 4.76 ( 4) link_NAG-ASN : angle 25.08432 / 19.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 280 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 1031 TYR cc_start: 0.5823 (OUTLIER) cc_final: 0.5291 (t80) REVERT: A 1077 LYS cc_start: 0.8267 (mtpm) cc_final: 0.7997 (mtpt) REVERT: A 1779 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7495 (tt0) REVERT: A 1928 LEU cc_start: 0.8559 (tp) cc_final: 0.8323 (tp) REVERT: A 2005 LYS cc_start: 0.7775 (pttt) cc_final: 0.7410 (pttm) REVERT: A 2427 ILE cc_start: 0.7232 (mt) cc_final: 0.6732 (tp) REVERT: A 2594 GLU cc_start: 0.6732 (tp30) cc_final: 0.6334 (tp30) outliers start: 15 outliers final: 8 residues processed: 294 average time/residue: 0.1047 time to fit residues: 42.2971 Evaluate side-chains 163 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1477 GLN Chi-restraints excluded: chain A residue 1500 THR Chi-restraints excluded: chain A residue 1694 GLU Chi-restraints excluded: chain A residue 1778 LEU Chi-restraints excluded: chain A residue 1779 GLN Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 2310 ARG Chi-restraints excluded: chain A residue 2480 LEU Chi-restraints excluded: chain A residue 2491 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 989 HIS A1069 ASN A1083 GLN A1681 ASN A1716 HIS ** A2212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2276 ASN A2338 ASN A2424 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.167407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.145592 restraints weight = 11963.437| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.02 r_work: 0.3827 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3684 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10387 Z= 0.187 Angle : 0.824 12.359 14140 Z= 0.410 Chirality : 0.056 0.569 1623 Planarity : 0.005 0.041 1768 Dihedral : 7.442 65.991 1472 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.97 % Favored : 92.80 % Rotamer: Outliers : 2.62 % Allowed : 12.41 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.21), residues: 1292 helix: -1.32 (0.48), residues: 95 sheet: -2.78 (0.26), residues: 311 loop : -2.21 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A2043 TYR 0.024 0.002 TYR A2011 PHE 0.016 0.002 PHE A2253 TRP 0.019 0.001 TRP A1695 HIS 0.017 0.002 HIS A2212 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.19 (10379) covalent geometry : angle 0.79245 / 0.40 (14119) hydrogen bonds : bond 0.05143 / 3.92 ( 269) hydrogen bonds : angle 8.37938 / 5.74 ( 783) Misc. bond : bond 0.00100 / 0.05 ( 1) link_ALPHA1-4 : bond 0.01898 / 1.00 ( 1) link_ALPHA1-4 : angle 4.05144 / 2.15 ( 3) link_ALPHA1-6 : bond 0.00454 / 0.24 ( 1) link_ALPHA1-6 : angle 2.67799 / 1.05 ( 3) link_BETA1-4 : bond 0.00469 / 0.25 ( 1) link_BETA1-4 : angle 3.62758 / 1.62 ( 3) link_NAG-ASN : bond 0.01860 / 0.92 ( 4) link_NAG-ASN : angle 7.25687 / 5.45 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 964 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8611 (tt) REVERT: A 1031 TYR cc_start: 0.5017 (OUTLIER) cc_final: 0.4287 (t80) REVERT: A 1077 LYS cc_start: 0.8592 (mtpm) cc_final: 0.8385 (mtpt) REVERT: A 1634 VAL cc_start: 0.8871 (t) cc_final: 0.8670 (p) REVERT: A 1654 TYR cc_start: 0.8762 (m-80) cc_final: 0.8511 (m-80) REVERT: A 1677 ILE cc_start: 0.7069 (mt) cc_final: 0.6819 (tt) REVERT: A 1994 ASP cc_start: 0.7724 (t0) cc_final: 0.7350 (t0) REVERT: A 2080 ASP cc_start: 0.8198 (t0) cc_final: 0.7770 (m-30) REVERT: A 2239 TYR cc_start: 0.8044 (m-10) cc_final: 0.7023 (m-10) REVERT: A 2259 MET cc_start: 0.7900 (tpp) cc_final: 0.7642 (mmm) REVERT: A 2278 ASP cc_start: 0.8425 (m-30) cc_final: 0.8202 (m-30) REVERT: A 2594 GLU cc_start: 0.7026 (tp30) cc_final: 0.6819 (mm-30) outliers start: 26 outliers final: 11 residues processed: 181 average time/residue: 0.0895 time to fit residues: 23.7071 Evaluate side-chains 152 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1461 SER Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1624 LEU Chi-restraints excluded: chain A residue 1632 THR Chi-restraints excluded: chain A residue 1683 SER Chi-restraints excluded: chain A residue 1755 LEU Chi-restraints excluded: chain A residue 2117 LEU Chi-restraints excluded: chain A residue 2184 SER Chi-restraints excluded: chain A residue 2433 HIS Chi-restraints excluded: chain A residue 2456 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 63 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 98 optimal weight: 0.4980 chunk 78 optimal weight: 0.0980 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 0.2980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1851 HIS A2212 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.167128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.146715 restraints weight = 12044.721| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 1.85 r_work: 0.3829 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10387 Z= 0.163 Angle : 0.737 12.462 14140 Z= 0.371 Chirality : 0.052 0.455 1623 Planarity : 0.004 0.041 1768 Dihedral : 6.269 53.257 1450 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.82 % Favored : 92.03 % Rotamer: Outliers : 3.13 % Allowed : 12.82 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.21), residues: 1292 helix: -0.52 (0.50), residues: 95 sheet: -2.49 (0.28), residues: 288 loop : -2.07 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A2310 TYR 0.024 0.002 TYR A2222 PHE 0.017 0.002 PHE A1770 TRP 0.012 0.001 TRP A1695 HIS 0.008 0.001 HIS A2212 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (10379) covalent geometry : angle 0.71422 / 0.37 (14119) hydrogen bonds : bond 0.04074 / 3.11 ( 269) hydrogen bonds : angle 7.48749 / 5.15 ( 783) Misc. bond : bond 0.00004 / 0.00 ( 1) link_ALPHA1-4 : bond 0.02296 / 1.21 ( 1) link_ALPHA1-4 : angle 3.82005 / 2.03 ( 3) link_ALPHA1-6 : bond 0.00835 / 0.44 ( 1) link_ALPHA1-6 : angle 2.04671 / 0.83 ( 3) link_BETA1-4 : bond 0.00069 / 0.04 ( 1) link_BETA1-4 : angle 2.93525 / 1.20 ( 3) link_NAG-ASN : bond 0.00993 / 0.51 ( 4) link_NAG-ASN : angle 5.71961 / 4.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 964 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8557 (tt) REVERT: A 1031 TYR cc_start: 0.4757 (OUTLIER) cc_final: 0.3765 (t80) REVERT: A 1077 LYS cc_start: 0.8624 (mtpm) cc_final: 0.8409 (mtpt) REVERT: A 1497 ASN cc_start: 0.8349 (t0) cc_final: 0.8090 (t0) REVERT: A 1634 VAL cc_start: 0.8861 (t) cc_final: 0.8648 (p) REVERT: A 1677 ILE cc_start: 0.7312 (mt) cc_final: 0.6996 (tt) REVERT: A 1900 SER cc_start: 0.8534 (m) cc_final: 0.8239 (p) REVERT: A 2045 LEU cc_start: 0.7993 (tp) cc_final: 0.7773 (tp) REVERT: A 2080 ASP cc_start: 0.8192 (t0) cc_final: 0.7837 (m-30) REVERT: A 2135 GLN cc_start: 0.7997 (tm130) cc_final: 0.7745 (tm-30) REVERT: A 2239 TYR cc_start: 0.8072 (m-10) cc_final: 0.6851 (m-10) REVERT: A 2278 ASP cc_start: 0.8312 (m-30) cc_final: 0.7995 (m-30) REVERT: A 2594 GLU cc_start: 0.7018 (tp30) cc_final: 0.6812 (mm-30) REVERT: A 2619 TYR cc_start: 0.7974 (m-80) cc_final: 0.7438 (m-80) outliers start: 31 outliers final: 19 residues processed: 174 average time/residue: 0.0980 time to fit residues: 24.3260 Evaluate side-chains 143 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1069 ASN Chi-restraints excluded: chain A residue 1500 THR Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1586 ASN Chi-restraints excluded: chain A residue 1683 SER Chi-restraints excluded: chain A residue 1708 ILE Chi-restraints excluded: chain A residue 1755 LEU Chi-restraints excluded: chain A residue 1787 THR Chi-restraints excluded: chain A residue 1799 MET Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2217 ILE Chi-restraints excluded: chain A residue 2340 LEU Chi-restraints excluded: chain A residue 2433 HIS Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2456 THR Chi-restraints excluded: chain A residue 2457 THR Chi-restraints excluded: chain A residue 2462 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 115 optimal weight: 0.6980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2194 GLN A2212 HIS A2227 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.159619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.138773 restraints weight = 12343.351| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 1.86 r_work: 0.3732 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10387 Z= 0.237 Angle : 0.755 11.810 14140 Z= 0.382 Chirality : 0.053 0.477 1623 Planarity : 0.004 0.045 1768 Dihedral : 6.309 54.428 1450 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 4.54 % Allowed : 13.42 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.22), residues: 1292 helix: 0.26 (0.57), residues: 89 sheet: -2.49 (0.28), residues: 297 loop : -2.00 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A2310 TYR 0.025 0.002 TYR A1907 PHE 0.019 0.002 PHE A1770 TRP 0.009 0.002 TRP A1695 HIS 0.008 0.002 HIS A1846 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.24 (10379) covalent geometry : angle 0.73663 / 0.38 (14119) hydrogen bonds : bond 0.03887 / 2.91 ( 269) hydrogen bonds : angle 7.30248 / 5.00 ( 783) Misc. bond : bond 0.00003 / 0.00 ( 1) link_ALPHA1-4 : bond 0.02447 / 1.29 ( 1) link_ALPHA1-4 : angle 3.93187 / 2.07 ( 3) link_ALPHA1-6 : bond 0.00773 / 0.41 ( 1) link_ALPHA1-6 : angle 2.16459 / 0.89 ( 3) link_BETA1-4 : bond 0.00451 / 0.24 ( 1) link_BETA1-4 : angle 2.18306 / 0.83 ( 3) link_NAG-ASN : bond 0.00830 / 0.42 ( 4) link_NAG-ASN : angle 5.17393 / 3.54 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 0.368 Fit side-chains REVERT: A 1015 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7985 (mp10) REVERT: A 1031 TYR cc_start: 0.5007 (OUTLIER) cc_final: 0.4024 (t80) REVERT: A 1077 LYS cc_start: 0.8780 (mtpm) cc_final: 0.8556 (mtpt) REVERT: A 1651 ARG cc_start: 0.7825 (tpt90) cc_final: 0.7575 (tpt90) REVERT: A 1677 ILE cc_start: 0.7344 (mt) cc_final: 0.6997 (tt) REVERT: A 1900 SER cc_start: 0.8609 (m) cc_final: 0.8258 (p) REVERT: A 2080 ASP cc_start: 0.8206 (t0) cc_final: 0.7919 (m-30) REVERT: A 2239 TYR cc_start: 0.8107 (m-10) cc_final: 0.6707 (m-10) REVERT: A 2278 ASP cc_start: 0.8482 (m-30) cc_final: 0.8187 (m-30) REVERT: A 2358 VAL cc_start: 0.9203 (OUTLIER) cc_final: 0.8901 (m) REVERT: A 2483 MET cc_start: 0.7699 (mtt) cc_final: 0.7386 (mtp) REVERT: A 2594 GLU cc_start: 0.7131 (tp30) cc_final: 0.6544 (tp30) outliers start: 45 outliers final: 25 residues processed: 174 average time/residue: 0.0862 time to fit residues: 21.9970 Evaluate side-chains 160 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1015 GLN Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1069 ASN Chi-restraints excluded: chain A residue 1500 THR Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1632 THR Chi-restraints excluded: chain A residue 1683 SER Chi-restraints excluded: chain A residue 1755 LEU Chi-restraints excluded: chain A residue 1787 THR Chi-restraints excluded: chain A residue 1799 MET Chi-restraints excluded: chain A residue 1913 THR Chi-restraints excluded: chain A residue 2046 MET Chi-restraints excluded: chain A residue 2108 LEU Chi-restraints excluded: chain A residue 2117 LEU Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2212 HIS Chi-restraints excluded: chain A residue 2217 ILE Chi-restraints excluded: chain A residue 2340 LEU Chi-restraints excluded: chain A residue 2358 VAL Chi-restraints excluded: chain A residue 2433 HIS Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2457 THR Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2492 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 26 optimal weight: 0.0000 chunk 114 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 63 optimal weight: 0.6980 chunk 119 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.163820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.143362 restraints weight = 12141.624| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 1.85 r_work: 0.3783 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10387 Z= 0.150 Angle : 0.696 12.456 14140 Z= 0.351 Chirality : 0.050 0.433 1623 Planarity : 0.004 0.042 1768 Dihedral : 6.037 55.024 1450 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 3.53 % Allowed : 14.93 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.22), residues: 1292 helix: 0.45 (0.56), residues: 89 sheet: -2.30 (0.28), residues: 290 loop : -1.93 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2043 TYR 0.022 0.002 TYR A 952 PHE 0.017 0.001 PHE A1575 TRP 0.009 0.001 TRP A1695 HIS 0.012 0.001 HIS A2192 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (10379) covalent geometry : angle 0.67816 / 0.35 (14119) hydrogen bonds : bond 0.03538 / 2.66 ( 269) hydrogen bonds : angle 7.01149 / 4.79 ( 783) Misc. bond : bond 0.00002 / 0.00 ( 1) link_ALPHA1-4 : bond 0.02387 / 1.26 ( 1) link_ALPHA1-4 : angle 3.84385 / 2.02 ( 3) link_ALPHA1-6 : bond 0.00847 / 0.45 ( 1) link_ALPHA1-6 : angle 1.95076 / 0.82 ( 3) link_BETA1-4 : bond 0.00074 / 0.04 ( 1) link_BETA1-4 : angle 1.97107 / 0.75 ( 3) link_NAG-ASN : bond 0.01134 / 0.57 ( 4) link_NAG-ASN : angle 4.95797 / 3.01 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 1031 TYR cc_start: 0.4859 (OUTLIER) cc_final: 0.3852 (t80) REVERT: A 1077 LYS cc_start: 0.8713 (mtpm) cc_final: 0.8470 (mtpt) REVERT: A 1651 ARG cc_start: 0.7727 (tpt90) cc_final: 0.7434 (tpt90) REVERT: A 1677 ILE cc_start: 0.7322 (mt) cc_final: 0.6980 (tt) REVERT: A 1900 SER cc_start: 0.8585 (m) cc_final: 0.8219 (p) REVERT: A 2045 LEU cc_start: 0.8086 (tp) cc_final: 0.7759 (tp) REVERT: A 2239 TYR cc_start: 0.8027 (m-10) cc_final: 0.7655 (m-80) REVERT: A 2278 ASP cc_start: 0.8346 (m-30) cc_final: 0.8057 (m-30) REVERT: A 2310 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6457 (ptm160) REVERT: A 2358 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8835 (m) REVERT: A 2594 GLU cc_start: 0.7064 (tp30) cc_final: 0.6815 (mm-30) outliers start: 35 outliers final: 23 residues processed: 162 average time/residue: 0.0843 time to fit residues: 20.3977 Evaluate side-chains 157 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1069 ASN Chi-restraints excluded: chain A residue 1500 THR Chi-restraints excluded: chain A residue 1554 MET Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1586 ASN Chi-restraints excluded: chain A residue 1683 SER Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1755 LEU Chi-restraints excluded: chain A residue 1787 THR Chi-restraints excluded: chain A residue 1799 MET Chi-restraints excluded: chain A residue 2008 VAL Chi-restraints excluded: chain A residue 2046 MET Chi-restraints excluded: chain A residue 2108 LEU Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2217 ILE Chi-restraints excluded: chain A residue 2310 ARG Chi-restraints excluded: chain A residue 2340 LEU Chi-restraints excluded: chain A residue 2358 VAL Chi-restraints excluded: chain A residue 2433 HIS Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2456 THR Chi-restraints excluded: chain A residue 2457 THR Chi-restraints excluded: chain A residue 2462 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 86 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 103 optimal weight: 0.0170 chunk 31 optimal weight: 0.8980 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.164286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.143451 restraints weight = 12255.995| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 1.89 r_work: 0.3791 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10387 Z= 0.151 Angle : 0.683 11.975 14140 Z= 0.343 Chirality : 0.050 0.419 1623 Planarity : 0.004 0.042 1768 Dihedral : 5.872 56.068 1450 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 3.63 % Allowed : 14.93 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.22), residues: 1292 helix: 0.77 (0.55), residues: 89 sheet: -2.32 (0.28), residues: 281 loop : -1.88 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2043 TYR 0.021 0.002 TYR A1907 PHE 0.014 0.002 PHE A1575 TRP 0.007 0.001 TRP A1695 HIS 0.005 0.001 HIS A2407 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (10379) covalent geometry : angle 0.66575 / 0.34 (14119) hydrogen bonds : bond 0.03411 / 2.57 ( 269) hydrogen bonds : angle 6.76516 / 4.62 ( 783) Misc. bond : bond 0.00010 / 0.01 ( 1) link_ALPHA1-4 : bond 0.02396 / 1.26 ( 1) link_ALPHA1-4 : angle 3.88827 / 2.05 ( 3) link_ALPHA1-6 : bond 0.00676 / 0.36 ( 1) link_ALPHA1-6 : angle 1.83294 / 0.78 ( 3) link_BETA1-4 : bond 0.00000 / 0.00 ( 1) link_BETA1-4 : angle 2.01806 / 0.77 ( 3) link_NAG-ASN : bond 0.00783 / 0.40 ( 4) link_NAG-ASN : angle 4.74842 / 2.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 1031 TYR cc_start: 0.5088 (OUTLIER) cc_final: 0.4082 (t80) REVERT: A 1077 LYS cc_start: 0.8715 (mtpm) cc_final: 0.8494 (mtpt) REVERT: A 1651 ARG cc_start: 0.7726 (tpt90) cc_final: 0.7478 (tpt90) REVERT: A 1677 ILE cc_start: 0.7351 (mt) cc_final: 0.7035 (tt) REVERT: A 1900 SER cc_start: 0.8560 (m) cc_final: 0.8219 (p) REVERT: A 2358 VAL cc_start: 0.9216 (OUTLIER) cc_final: 0.8946 (m) outliers start: 36 outliers final: 25 residues processed: 164 average time/residue: 0.0893 time to fit residues: 21.5759 Evaluate side-chains 160 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1500 THR Chi-restraints excluded: chain A residue 1551 LEU Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1586 ASN Chi-restraints excluded: chain A residue 1683 SER Chi-restraints excluded: chain A residue 1693 ILE Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1755 LEU Chi-restraints excluded: chain A residue 1787 THR Chi-restraints excluded: chain A residue 1799 MET Chi-restraints excluded: chain A residue 2008 VAL Chi-restraints excluded: chain A residue 2046 MET Chi-restraints excluded: chain A residue 2108 LEU Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2184 SER Chi-restraints excluded: chain A residue 2217 ILE Chi-restraints excluded: chain A residue 2340 LEU Chi-restraints excluded: chain A residue 2358 VAL Chi-restraints excluded: chain A residue 2433 HIS Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2456 THR Chi-restraints excluded: chain A residue 2457 THR Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2570 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 121 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.163823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.142248 restraints weight = 12171.388| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 1.98 r_work: 0.3783 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10387 Z= 0.147 Angle : 0.674 11.963 14140 Z= 0.339 Chirality : 0.049 0.414 1623 Planarity : 0.004 0.059 1768 Dihedral : 5.796 56.230 1450 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 3.23 % Allowed : 15.64 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.22), residues: 1292 helix: 1.14 (0.54), residues: 89 sheet: -2.28 (0.28), residues: 281 loop : -1.86 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2043 TYR 0.019 0.002 TYR A1907 PHE 0.014 0.001 PHE A1575 TRP 0.007 0.001 TRP A2311 HIS 0.003 0.001 HIS A2407 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (10379) covalent geometry : angle 0.65787 / 0.34 (14119) hydrogen bonds : bond 0.03325 / 2.50 ( 269) hydrogen bonds : angle 6.66481 / 4.56 ( 783) Misc. bond : bond 0.00009 / 0.00 ( 1) link_ALPHA1-4 : bond 0.02441 / 1.28 ( 1) link_ALPHA1-4 : angle 3.92215 / 2.07 ( 3) link_ALPHA1-6 : bond 0.00654 / 0.34 ( 1) link_ALPHA1-6 : angle 1.80179 / 0.78 ( 3) link_BETA1-4 : bond 0.00027 / 0.01 ( 1) link_BETA1-4 : angle 1.80882 / 0.70 ( 3) link_NAG-ASN : bond 0.00780 / 0.40 ( 4) link_NAG-ASN : angle 4.56511 / 2.67 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 1015 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.8091 (mp10) REVERT: A 1031 TYR cc_start: 0.5031 (OUTLIER) cc_final: 0.3993 (t80) REVERT: A 1077 LYS cc_start: 0.8761 (mtpm) cc_final: 0.8530 (mtpt) REVERT: A 1651 ARG cc_start: 0.7672 (tpt90) cc_final: 0.7363 (tpt90) REVERT: A 1677 ILE cc_start: 0.7312 (mt) cc_final: 0.6993 (tt) REVERT: A 1900 SER cc_start: 0.8576 (m) cc_final: 0.8208 (p) REVERT: A 2045 LEU cc_start: 0.7886 (tp) cc_final: 0.7679 (tp) REVERT: A 2358 VAL cc_start: 0.9205 (OUTLIER) cc_final: 0.8915 (m) REVERT: A 2402 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7597 (mt0) outliers start: 32 outliers final: 21 residues processed: 161 average time/residue: 0.0855 time to fit residues: 20.4280 Evaluate side-chains 156 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1015 GLN Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1500 THR Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1586 ASN Chi-restraints excluded: chain A residue 1652 VAL Chi-restraints excluded: chain A residue 1693 ILE Chi-restraints excluded: chain A residue 1708 ILE Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1755 LEU Chi-restraints excluded: chain A residue 1799 MET Chi-restraints excluded: chain A residue 2008 VAL Chi-restraints excluded: chain A residue 2046 MET Chi-restraints excluded: chain A residue 2108 LEU Chi-restraints excluded: chain A residue 2117 LEU Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2217 ILE Chi-restraints excluded: chain A residue 2358 VAL Chi-restraints excluded: chain A residue 2402 GLN Chi-restraints excluded: chain A residue 2433 HIS Chi-restraints excluded: chain A residue 2457 THR Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2495 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 3 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 67 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.165455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.144527 restraints weight = 12164.505| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 1.90 r_work: 0.3803 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10387 Z= 0.144 Angle : 0.670 11.854 14140 Z= 0.335 Chirality : 0.049 0.403 1623 Planarity : 0.004 0.043 1768 Dihedral : 5.717 57.195 1450 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 3.13 % Allowed : 15.74 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.22), residues: 1292 helix: 1.47 (0.54), residues: 89 sheet: -2.09 (0.29), residues: 286 loop : -1.85 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2043 TYR 0.021 0.001 TYR A1907 PHE 0.014 0.001 PHE A1709 TRP 0.009 0.001 TRP A2311 HIS 0.005 0.001 HIS A1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (10379) covalent geometry : angle 0.65403 / 0.33 (14119) hydrogen bonds : bond 0.03319 / 2.49 ( 269) hydrogen bonds : angle 6.58760 / 4.50 ( 783) Misc. bond : bond 0.00002 / 0.00 ( 1) link_ALPHA1-4 : bond 0.02457 / 1.29 ( 1) link_ALPHA1-4 : angle 3.99106 / 2.10 ( 3) link_ALPHA1-6 : bond 0.00596 / 0.31 ( 1) link_ALPHA1-6 : angle 1.75573 / 0.77 ( 3) link_BETA1-4 : bond 0.00012 / 0.01 ( 1) link_BETA1-4 : angle 1.64566 / 0.64 ( 3) link_NAG-ASN : bond 0.00760 / 0.39 ( 4) link_NAG-ASN : angle 4.45332 / 2.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 1015 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.8059 (mp10) REVERT: A 1031 TYR cc_start: 0.5118 (OUTLIER) cc_final: 0.4056 (t80) REVERT: A 1077 LYS cc_start: 0.8786 (mtpm) cc_final: 0.8528 (mtpt) REVERT: A 1651 ARG cc_start: 0.7622 (tpt90) cc_final: 0.7292 (tpt90) REVERT: A 1654 TYR cc_start: 0.8777 (m-80) cc_final: 0.8551 (m-80) REVERT: A 1677 ILE cc_start: 0.7317 (mt) cc_final: 0.6977 (tt) REVERT: A 1715 VAL cc_start: 0.8982 (t) cc_final: 0.8761 (m) REVERT: A 1900 SER cc_start: 0.8573 (m) cc_final: 0.8202 (p) REVERT: A 2045 LEU cc_start: 0.7867 (tp) cc_final: 0.7636 (tp) REVERT: A 2358 VAL cc_start: 0.9202 (OUTLIER) cc_final: 0.8908 (m) REVERT: A 2406 ARG cc_start: 0.7714 (ttp-170) cc_final: 0.7480 (mtm-85) outliers start: 31 outliers final: 23 residues processed: 162 average time/residue: 0.0843 time to fit residues: 20.5540 Evaluate side-chains 162 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1015 GLN Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1500 THR Chi-restraints excluded: chain A residue 1554 MET Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1586 ASN Chi-restraints excluded: chain A residue 1652 VAL Chi-restraints excluded: chain A residue 1693 ILE Chi-restraints excluded: chain A residue 1721 LEU Chi-restraints excluded: chain A residue 1755 LEU Chi-restraints excluded: chain A residue 1787 THR Chi-restraints excluded: chain A residue 1799 MET Chi-restraints excluded: chain A residue 2008 VAL Chi-restraints excluded: chain A residue 2046 MET Chi-restraints excluded: chain A residue 2108 LEU Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2217 ILE Chi-restraints excluded: chain A residue 2358 VAL Chi-restraints excluded: chain A residue 2433 HIS Chi-restraints excluded: chain A residue 2456 THR Chi-restraints excluded: chain A residue 2457 THR Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2495 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 125 optimal weight: 10.0000 chunk 113 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 80 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 12 optimal weight: 0.0270 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2586 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.165285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.144349 restraints weight = 12080.024| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 1.90 r_work: 0.3795 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10387 Z= 0.151 Angle : 0.672 11.901 14140 Z= 0.337 Chirality : 0.049 0.399 1623 Planarity : 0.004 0.042 1768 Dihedral : 5.685 57.217 1450 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 3.13 % Allowed : 15.94 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.22), residues: 1292 helix: 1.67 (0.54), residues: 89 sheet: -2.26 (0.29), residues: 271 loop : -1.84 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2043 TYR 0.021 0.002 TYR A1907 PHE 0.011 0.001 PHE A1575 TRP 0.008 0.001 TRP A2311 HIS 0.004 0.001 HIS A1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (10379) covalent geometry : angle 0.65682 / 0.33 (14119) hydrogen bonds : bond 0.03289 / 2.47 ( 269) hydrogen bonds : angle 6.56454 / 4.49 ( 783) Misc. bond : bond 0.00001 / 0.00 ( 1) link_ALPHA1-4 : bond 0.02495 / 1.31 ( 1) link_ALPHA1-4 : angle 4.05153 / 2.13 ( 3) link_ALPHA1-6 : bond 0.00581 / 0.31 ( 1) link_ALPHA1-6 : angle 1.74644 / 0.77 ( 3) link_BETA1-4 : bond 0.00070 / 0.04 ( 1) link_BETA1-4 : angle 1.47244 / 0.57 ( 3) link_NAG-ASN : bond 0.00768 / 0.39 ( 4) link_NAG-ASN : angle 4.39117 / 2.55 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 1015 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.8083 (mp10) REVERT: A 1031 TYR cc_start: 0.5159 (OUTLIER) cc_final: 0.4059 (t80) REVERT: A 1077 LYS cc_start: 0.8801 (mtpm) cc_final: 0.8581 (mtpt) REVERT: A 1634 VAL cc_start: 0.8893 (t) cc_final: 0.8687 (p) REVERT: A 1651 ARG cc_start: 0.7640 (tpt90) cc_final: 0.7307 (tpt90) REVERT: A 1654 TYR cc_start: 0.8822 (m-80) cc_final: 0.8620 (m-80) REVERT: A 1677 ILE cc_start: 0.7353 (mt) cc_final: 0.7054 (tt) REVERT: A 1715 VAL cc_start: 0.8968 (t) cc_final: 0.8756 (m) REVERT: A 1900 SER cc_start: 0.8506 (m) cc_final: 0.8147 (p) REVERT: A 2045 LEU cc_start: 0.7924 (tp) cc_final: 0.7721 (tp) REVERT: A 2056 MET cc_start: 0.7313 (mtm) cc_final: 0.7020 (mtm) REVERT: A 2358 VAL cc_start: 0.9220 (OUTLIER) cc_final: 0.8925 (m) REVERT: A 2402 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7620 (mt0) outliers start: 31 outliers final: 25 residues processed: 158 average time/residue: 0.0793 time to fit residues: 19.1775 Evaluate side-chains 163 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1015 GLN Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1500 THR Chi-restraints excluded: chain A residue 1554 MET Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1586 ASN Chi-restraints excluded: chain A residue 1652 VAL Chi-restraints excluded: chain A residue 1683 SER Chi-restraints excluded: chain A residue 1693 ILE Chi-restraints excluded: chain A residue 1708 ILE Chi-restraints excluded: chain A residue 1721 LEU Chi-restraints excluded: chain A residue 1755 LEU Chi-restraints excluded: chain A residue 1787 THR Chi-restraints excluded: chain A residue 1799 MET Chi-restraints excluded: chain A residue 2008 VAL Chi-restraints excluded: chain A residue 2046 MET Chi-restraints excluded: chain A residue 2108 LEU Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2340 LEU Chi-restraints excluded: chain A residue 2358 VAL Chi-restraints excluded: chain A residue 2402 GLN Chi-restraints excluded: chain A residue 2433 HIS Chi-restraints excluded: chain A residue 2457 THR Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2495 PHE Chi-restraints excluded: chain A residue 2570 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 25 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2286 HIS A2366 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.161933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.140889 restraints weight = 12076.290| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.90 r_work: 0.3762 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10387 Z= 0.189 Angle : 0.704 12.458 14140 Z= 0.355 Chirality : 0.050 0.404 1623 Planarity : 0.004 0.042 1768 Dihedral : 5.834 57.476 1450 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 3.23 % Allowed : 16.25 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.22), residues: 1292 helix: 1.74 (0.54), residues: 89 sheet: -2.29 (0.29), residues: 266 loop : -1.89 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2043 TYR 0.021 0.002 TYR A1907 PHE 0.014 0.002 PHE A1709 TRP 0.009 0.001 TRP A2311 HIS 0.004 0.001 HIS A2493 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (10379) covalent geometry : angle 0.69031 / 0.35 (14119) hydrogen bonds : bond 0.03417 / 2.56 ( 269) hydrogen bonds : angle 6.69091 / 4.58 ( 783) Misc. bond : bond 0.00004 / 0.00 ( 1) link_ALPHA1-4 : bond 0.02417 / 1.27 ( 1) link_ALPHA1-4 : angle 4.14378 / 2.17 ( 3) link_ALPHA1-6 : bond 0.00491 / 0.26 ( 1) link_ALPHA1-6 : angle 1.78446 / 0.78 ( 3) link_BETA1-4 : bond 0.00026 / 0.01 ( 1) link_BETA1-4 : angle 1.50272 / 0.57 ( 3) link_NAG-ASN : bond 0.00689 / 0.35 ( 4) link_NAG-ASN : angle 4.28946 / 2.50 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 1015 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.8119 (mp10) REVERT: A 1031 TYR cc_start: 0.5316 (OUTLIER) cc_final: 0.4251 (t80) REVERT: A 1651 ARG cc_start: 0.7645 (tpt90) cc_final: 0.7291 (tpt90) REVERT: A 1677 ILE cc_start: 0.7387 (mt) cc_final: 0.7103 (tt) REVERT: A 1900 SER cc_start: 0.8522 (m) cc_final: 0.8149 (p) REVERT: A 2040 GLU cc_start: 0.8000 (pt0) cc_final: 0.7575 (tt0) REVERT: A 2056 MET cc_start: 0.7381 (mtm) cc_final: 0.6975 (mtp) REVERT: A 2239 TYR cc_start: 0.7879 (m-10) cc_final: 0.6397 (m-10) REVERT: A 2358 VAL cc_start: 0.9210 (OUTLIER) cc_final: 0.8924 (m) REVERT: A 2402 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7695 (mt0) REVERT: A 2406 ARG cc_start: 0.7706 (ttp-170) cc_final: 0.7490 (mtm-85) outliers start: 32 outliers final: 25 residues processed: 157 average time/residue: 0.0788 time to fit residues: 18.7906 Evaluate side-chains 159 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1015 GLN Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1500 THR Chi-restraints excluded: chain A residue 1554 MET Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1586 ASN Chi-restraints excluded: chain A residue 1652 VAL Chi-restraints excluded: chain A residue 1693 ILE Chi-restraints excluded: chain A residue 1708 ILE Chi-restraints excluded: chain A residue 1721 LEU Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1755 LEU Chi-restraints excluded: chain A residue 1787 THR Chi-restraints excluded: chain A residue 1799 MET Chi-restraints excluded: chain A residue 2008 VAL Chi-restraints excluded: chain A residue 2046 MET Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2217 ILE Chi-restraints excluded: chain A residue 2340 LEU Chi-restraints excluded: chain A residue 2358 VAL Chi-restraints excluded: chain A residue 2402 GLN Chi-restraints excluded: chain A residue 2433 HIS Chi-restraints excluded: chain A residue 2457 THR Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2495 PHE Chi-restraints excluded: chain A residue 2570 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 73 optimal weight: 0.4980 chunk 2 optimal weight: 0.0470 chunk 112 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 98 optimal weight: 0.0970 chunk 32 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.166382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.144550 restraints weight = 12079.383| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.01 r_work: 0.3815 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10387 Z= 0.126 Angle : 0.681 13.112 14140 Z= 0.341 Chirality : 0.048 0.375 1623 Planarity : 0.004 0.043 1768 Dihedral : 5.648 58.133 1450 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 2.62 % Allowed : 16.15 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.22), residues: 1292 helix: 1.97 (0.54), residues: 88 sheet: -2.22 (0.29), residues: 269 loop : -1.80 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2043 TYR 0.020 0.001 TYR A1907 PHE 0.014 0.001 PHE A2362 TRP 0.010 0.001 TRP A2311 HIS 0.004 0.001 HIS A1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (10379) covalent geometry : angle 0.66671 / 0.34 (14119) hydrogen bonds : bond 0.03166 / 2.40 ( 269) hydrogen bonds : angle 6.49779 / 4.45 ( 783) Misc. bond : bond 0.00014 / 0.01 ( 1) link_ALPHA1-4 : bond 0.02400 / 1.26 ( 1) link_ALPHA1-4 : angle 4.06226 / 2.13 ( 3) link_ALPHA1-6 : bond 0.00657 / 0.35 ( 1) link_ALPHA1-6 : angle 1.71578 / 0.76 ( 3) link_BETA1-4 : bond 0.00041 / 0.02 ( 1) link_BETA1-4 : angle 1.48252 / 0.57 ( 3) link_NAG-ASN : bond 0.00856 / 0.44 ( 4) link_NAG-ASN : angle 4.27950 / 2.43 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2387.48 seconds wall clock time: 41 minutes 57.26 seconds (2517.26 seconds total)