Starting phenix.real_space_refine on Tue Apr 29 11:50:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ax5_43927/04_2025/9ax5_43927_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ax5_43927/04_2025/9ax5_43927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ax5_43927/04_2025/9ax5_43927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ax5_43927/04_2025/9ax5_43927.map" model { file = "/net/cci-nas-00/data/ceres_data/9ax5_43927/04_2025/9ax5_43927_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ax5_43927/04_2025/9ax5_43927_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 3 5.49 5 Mg 1 5.21 5 S 49 5.16 5 C 5423 2.51 5 N 1463 2.21 5 O 1603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8543 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 887, 7096 Classifications: {'peptide': 887} Link IDs: {'PTRANS': 47, 'TRANS': 839} Chain breaks: 6 Chain: "C" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1413 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 11, 'TRANS': 166} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.55, per 1000 atoms: 0.77 Number of scatterers: 8543 At special positions: 0 Unit cell: (82.739, 98.022, 132.804, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 S 49 16.00 P 3 15.00 Mg 1 11.99 O 1603 8.00 N 1463 7.00 C 5423 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 936.4 milliseconds 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2022 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 9 sheets defined 37.5% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 851 through 861 Processing helix chain 'A' and resid 949 through 958 Processing helix chain 'A' and resid 963 through 967 Processing helix chain 'A' and resid 988 through 1010 removed outlier: 3.756A pdb=" N MET A 994 " --> pdb=" O HIS A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1029 removed outlier: 3.587A pdb=" N LYS A1022 " --> pdb=" O GLN A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1046 Processing helix chain 'A' and resid 1195 through 1209 removed outlier: 3.886A pdb=" N SER A1205 " --> pdb=" O GLU A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1212 through 1222 removed outlier: 4.193A pdb=" N TYR A1221 " --> pdb=" O ILE A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1273 through 1288 Processing helix chain 'A' and resid 1306 through 1317 removed outlier: 3.629A pdb=" N ASN A1316 " --> pdb=" O ASP A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1335 Processing helix chain 'A' and resid 1337 through 1343 Processing helix chain 'A' and resid 1347 through 1356 Processing helix chain 'A' and resid 1357 through 1361 removed outlier: 3.824A pdb=" N PHE A1361 " --> pdb=" O LYS A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1373 through 1377 removed outlier: 3.706A pdb=" N GLN A1376 " --> pdb=" O LYS A1373 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU A1377 " --> pdb=" O ASP A1374 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1373 through 1377' Processing helix chain 'A' and resid 1378 through 1380 No H-bonds generated for 'chain 'A' and resid 1378 through 1380' Processing helix chain 'A' and resid 1404 through 1412 Processing helix chain 'A' and resid 1443 through 1454 removed outlier: 3.823A pdb=" N SER A1453 " --> pdb=" O ALA A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1471 through 1486 removed outlier: 3.802A pdb=" N ARG A1476 " --> pdb=" O LEU A1472 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS A1477 " --> pdb=" O PRO A1473 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE A1481 " --> pdb=" O LYS A1477 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A1482 " --> pdb=" O MET A1478 " (cutoff:3.500A) Processing helix chain 'A' and resid 1496 through 1501 Processing helix chain 'A' and resid 1645 through 1650 removed outlier: 3.807A pdb=" N LEU A1649 " --> pdb=" O GLU A1645 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL A1650 " --> pdb=" O LEU A1646 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1645 through 1650' Processing helix chain 'A' and resid 1741 through 1751 Processing helix chain 'A' and resid 1751 through 1760 removed outlier: 3.670A pdb=" N GLN A1757 " --> pdb=" O GLN A1753 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A1760 " --> pdb=" O ILE A1756 " (cutoff:3.500A) Processing helix chain 'A' and resid 1780 through 1785 Processing helix chain 'A' and resid 1799 through 1810 removed outlier: 3.734A pdb=" N ASN A1805 " --> pdb=" O PRO A1801 " (cutoff:3.500A) Processing helix chain 'A' and resid 1811 through 1815 removed outlier: 3.767A pdb=" N CYS A1815 " --> pdb=" O ASN A1812 " (cutoff:3.500A) Processing helix chain 'A' and resid 1936 through 1938 No H-bonds generated for 'chain 'A' and resid 1936 through 1938' Processing helix chain 'A' and resid 1978 through 1983 Processing helix chain 'A' and resid 1984 through 1991 removed outlier: 3.629A pdb=" N CYS A1989 " --> pdb=" O GLU A1985 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER A1990 " --> pdb=" O GLU A1986 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A1991 " --> pdb=" O ARG A1987 " (cutoff:3.500A) Processing helix chain 'A' and resid 2016 through 2028 removed outlier: 3.604A pdb=" N GLN A2022 " --> pdb=" O LYS A2018 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A2027 " --> pdb=" O GLN A2023 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP A2028 " --> pdb=" O ILE A2024 " (cutoff:3.500A) Processing helix chain 'A' and resid 2034 through 2038 Processing helix chain 'A' and resid 2068 through 2074 removed outlier: 3.914A pdb=" N ILE A2072 " --> pdb=" O ASP A2068 " (cutoff:3.500A) Processing helix chain 'A' and resid 2075 through 2076 No H-bonds generated for 'chain 'A' and resid 2075 through 2076' Processing helix chain 'A' and resid 2077 through 2081 Processing helix chain 'C' and resid 17 through 28 removed outlier: 3.734A pdb=" N LEU C 22 " --> pdb=" O LYS C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 68 removed outlier: 4.194A pdb=" N ARG C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'C' and resid 88 through 107 removed outlier: 3.895A pdb=" N LEU C 92 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU C 93 " --> pdb=" O PRO C 89 " (cutoff:3.500A) Proline residue: C 96 - end of helix Proline residue: C 101 - end of helix Processing helix chain 'C' and resid 119 through 123 removed outlier: 3.948A pdb=" N ASN C 123 " --> pdb=" O ASP C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 135 removed outlier: 3.753A pdb=" N ARG C 128 " --> pdb=" O ASP C 124 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS C 133 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 151 Processing helix chain 'C' and resid 166 through 180 removed outlier: 3.605A pdb=" N VAL C 170 " --> pdb=" O GLY C 166 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE C 171 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 179 " --> pdb=" O THR C 175 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 931 through 934 removed outlier: 3.582A pdb=" N GLY A 931 " --> pdb=" O TRP A 890 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP A 890 " --> pdb=" O GLY A 931 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP A 868 " --> pdb=" O LEU A 873 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N HIS A 984 " --> pdb=" O TYR A 867 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLY A 968 " --> pdb=" O MET A 943 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N MET A 943 " --> pdb=" O GLY A 968 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR A 970 " --> pdb=" O VAL A 941 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL A 941 " --> pdb=" O THR A 970 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU A 972 " --> pdb=" O LYS A 939 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1737 through 1740 removed outlier: 3.649A pdb=" N TYR A1767 " --> pdb=" O LEU A1739 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU A1764 " --> pdb=" O LEU A1790 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ALA A1792 " --> pdb=" O LEU A1764 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR A1766 " --> pdb=" O ALA A1792 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N VAL A1791 " --> pdb=" O TYR A1382 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE A1384 " --> pdb=" O VAL A1791 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU A1793 " --> pdb=" O ILE A1384 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER A1386 " --> pdb=" O LEU A1793 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1416 through 1419 removed outlier: 6.347A pdb=" N ILE A1417 " --> pdb=" O SER A1465 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1430 through 1431 Processing sheet with id=AA5, first strand: chain 'A' and resid 1845 through 1846 Processing sheet with id=AA6, first strand: chain 'A' and resid 1901 through 1907 removed outlier: 3.918A pdb=" N VAL A1907 " --> pdb=" O ALA A1848 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LEU A1852 " --> pdb=" O ARG A1965 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ARG A1965 " --> pdb=" O LEU A1852 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE A1854 " --> pdb=" O ASN A1963 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN A1963 " --> pdb=" O ILE A1854 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1884 through 1886 removed outlier: 4.067A pdb=" N ALA A1929 " --> pdb=" O VAL A1919 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLU A1921 " --> pdb=" O ILE A1927 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE A1927 " --> pdb=" O GLU A1921 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2006 through 2011 removed outlier: 12.636A pdb=" N GLY A2084 " --> pdb=" O LYS A1994 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N THR A1996 " --> pdb=" O GLY A2084 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE A2086 " --> pdb=" O THR A1996 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 40 through 48 removed outlier: 9.374A pdb=" N VAL C 79 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LYS C 7 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LEU C 81 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL C 9 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N CYS C 83 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL C 11 " --> pdb=" O CYS C 83 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N SER C 85 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ILE C 80 " --> pdb=" O ILE C 113 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N VAL C 115 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N MET C 82 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ASN C 117 " --> pdb=" O MET C 82 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE C 84 " --> pdb=" O ASN C 117 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY C 155 " --> pdb=" O ILE C 112 " (cutoff:3.500A) 300 hydrogen bonds defined for protein. 822 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: 2.93 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2803 1.34 - 1.46: 1824 1.46 - 1.58: 4024 1.58 - 1.69: 5 1.69 - 1.81: 73 Bond restraints: 8729 Sorted by residual: bond pdb=" N GLY A 839 " pdb=" CA GLY A 839 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.42e+00 bond pdb=" N ILE C 4 " pdb=" CA ILE C 4 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.73e+00 bond pdb=" C TYR C 74 " pdb=" N PRO C 75 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.13e+00 bond pdb=" CA VAL A1223 " pdb=" C VAL A1223 " ideal model delta sigma weight residual 1.516 1.526 -0.010 1.11e-02 8.12e+03 8.29e-01 bond pdb=" N GLY C 14 " pdb=" CA GLY C 14 " ideal model delta sigma weight residual 1.449 1.461 -0.012 1.45e-02 4.76e+03 6.65e-01 ... (remaining 8724 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 11562 1.17 - 2.33: 186 2.33 - 3.50: 51 3.50 - 4.67: 20 4.67 - 5.84: 4 Bond angle restraints: 11823 Sorted by residual: angle pdb=" CA VAL A1223 " pdb=" C VAL A1223 " pdb=" N PRO A1224 " ideal model delta sigma weight residual 116.57 119.48 -2.91 9.80e-01 1.04e+00 8.81e+00 angle pdb=" C VAL A1223 " pdb=" CA VAL A1223 " pdb=" CB VAL A1223 " ideal model delta sigma weight residual 109.33 111.49 -2.16 9.80e-01 1.04e+00 4.87e+00 angle pdb=" C2' GTP C 201 " pdb=" C3' GTP C 201 " pdb=" C4' GTP C 201 " ideal model delta sigma weight residual 111.00 105.16 5.84 3.00e+00 1.11e-01 3.78e+00 angle pdb=" N GLU A1467 " pdb=" CA GLU A1467 " pdb=" C GLU A1467 " ideal model delta sigma weight residual 109.62 106.82 2.80 1.50e+00 4.44e-01 3.48e+00 angle pdb=" C1' GTP C 201 " pdb=" C2' GTP C 201 " pdb=" C3' GTP C 201 " ideal model delta sigma weight residual 111.00 105.59 5.41 3.00e+00 1.11e-01 3.26e+00 ... (remaining 11818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.84: 5099 19.84 - 39.69: 177 39.69 - 59.53: 21 59.53 - 79.38: 3 79.38 - 99.22: 3 Dihedral angle restraints: 5303 sinusoidal: 2192 harmonic: 3111 Sorted by residual: dihedral pdb=" C8 GTP C 201 " pdb=" C1' GTP C 201 " pdb=" N9 GTP C 201 " pdb=" O4' GTP C 201 " ideal model delta sinusoidal sigma weight residual 104.59 5.37 99.22 1 2.00e+01 2.50e-03 2.78e+01 dihedral pdb=" C4' GTP C 201 " pdb=" C5' GTP C 201 " pdb=" O5' GTP C 201 " pdb=" PA GTP C 201 " ideal model delta sinusoidal sigma weight residual 260.87 163.01 97.86 1 2.00e+01 2.50e-03 2.73e+01 dihedral pdb=" CA PRO A 883 " pdb=" C PRO A 883 " pdb=" N ASP A 884 " pdb=" CA ASP A 884 " ideal model delta harmonic sigma weight residual 180.00 162.78 17.22 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 5300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 812 0.029 - 0.058: 346 0.058 - 0.087: 66 0.087 - 0.116: 78 0.116 - 0.145: 12 Chirality restraints: 1314 Sorted by residual: chirality pdb=" CA ILE C 4 " pdb=" N ILE C 4 " pdb=" C ILE C 4 " pdb=" CB ILE C 4 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" C1' GTP C 201 " pdb=" C2' GTP C 201 " pdb=" N9 GTP C 201 " pdb=" O4' GTP C 201 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA ILE A 843 " pdb=" N ILE A 843 " pdb=" C ILE A 843 " pdb=" CB ILE A 843 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 1311 not shown) Planarity restraints: 1525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A1878 " -0.017 5.00e-02 4.00e+02 2.51e-02 1.01e+00 pdb=" N PRO A1879 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO A1879 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A1879 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1658 " -0.014 5.00e-02 4.00e+02 2.05e-02 6.73e-01 pdb=" N PRO A1659 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO A1659 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO A1659 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1779 " 0.013 5.00e-02 4.00e+02 2.00e-02 6.39e-01 pdb=" N PRO A1780 " -0.035 5.00e-02 4.00e+02 pdb=" CA PRO A1780 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO A1780 " 0.011 5.00e-02 4.00e+02 ... (remaining 1522 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 51 2.44 - 3.05: 5903 3.05 - 3.67: 12153 3.67 - 4.28: 18889 4.28 - 4.90: 32405 Nonbonded interactions: 69401 Sorted by model distance: nonbonded pdb=" O3G GTP C 201 " pdb="MG MG C 202 " model vdw 1.823 2.170 nonbonded pdb=" OG1 THR C 19 " pdb="MG MG C 202 " model vdw 1.955 2.170 nonbonded pdb=" OG SER C 85 " pdb=" OD1 ASP C 87 " model vdw 2.026 3.040 nonbonded pdb=" OD2 ASP A1499 " pdb=" OH TYR A1652 " model vdw 2.031 3.040 nonbonded pdb=" OH TYR A1383 " pdb=" O TRP A1784 " model vdw 2.034 3.040 ... (remaining 69396 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: 7.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.030 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8729 Z= 0.117 Angle : 0.451 5.836 11823 Z= 0.228 Chirality : 0.040 0.145 1314 Planarity : 0.003 0.025 1525 Dihedral : 10.244 99.223 3281 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.05 % Allowed : 4.40 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.27), residues: 1049 helix: 0.39 (0.33), residues: 293 sheet: -0.12 (0.38), residues: 209 loop : -0.26 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1825 HIS 0.004 0.001 HIS A1469 PHE 0.008 0.001 PHE A1909 TYR 0.008 0.001 TYR A1028 ARG 0.002 0.000 ARG A1211 Details of bonding type rmsd hydrogen bonds : bond 0.26823 ( 300) hydrogen bonds : angle 9.11260 ( 822) covalent geometry : bond 0.00268 ( 8729) covalent geometry : angle 0.45144 (11823) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 177 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1049 ARG cc_start: 0.7476 (ttm-80) cc_final: 0.7218 (ttm110) REVERT: A 1392 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8637 (mt) REVERT: A 1636 LYS cc_start: 0.6826 (pttt) cc_final: 0.6576 (ptmt) REVERT: A 1983 ASN cc_start: 0.8207 (t0) cc_final: 0.7851 (t0) REVERT: A 2018 LYS cc_start: 0.8278 (mtmt) cc_final: 0.7991 (mtmm) REVERT: A 2066 GLU cc_start: 0.7182 (tm-30) cc_final: 0.6829 (tp30) REVERT: A 2071 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7980 (tm-30) REVERT: C 162 LYS cc_start: 0.4514 (mtpp) cc_final: 0.4249 (mmtt) outliers start: 10 outliers final: 4 residues processed: 185 average time/residue: 0.2459 time to fit residues: 60.6595 Evaluate side-chains 126 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 121 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1261 ASP Chi-restraints excluded: chain A residue 1345 LEU Chi-restraints excluded: chain A residue 1390 THR Chi-restraints excluded: chain A residue 1392 LEU Chi-restraints excluded: chain A residue 1436 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 9.9990 chunk 79 optimal weight: 0.0370 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 82 optimal weight: 0.0670 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1469 HIS A2022 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.190160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.135104 restraints weight = 10549.591| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 3.48 r_work: 0.3376 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8729 Z= 0.136 Angle : 0.593 6.668 11823 Z= 0.302 Chirality : 0.043 0.155 1314 Planarity : 0.004 0.045 1525 Dihedral : 7.023 97.056 1164 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.68 % Allowed : 9.85 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.27), residues: 1049 helix: 0.45 (0.29), residues: 328 sheet: -0.02 (0.37), residues: 209 loop : -0.20 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 58 HIS 0.004 0.001 HIS A1469 PHE 0.024 0.002 PHE A2059 TYR 0.010 0.001 TYR A1383 ARG 0.005 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 300) hydrogen bonds : angle 5.91524 ( 822) covalent geometry : bond 0.00314 ( 8729) covalent geometry : angle 0.59252 (11823) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 956 GLN cc_start: 0.7663 (mt0) cc_final: 0.7325 (mt0) REVERT: A 1328 LEU cc_start: 0.7521 (tp) cc_final: 0.7288 (tp) REVERT: A 1636 LYS cc_start: 0.6504 (pttt) cc_final: 0.6109 (ptmt) REVERT: A 2018 LYS cc_start: 0.8340 (mtmt) cc_final: 0.7928 (tmtt) REVERT: A 2022 GLN cc_start: 0.8471 (mp-120) cc_final: 0.8079 (mp10) REVERT: A 2043 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8020 (mt-10) REVERT: A 2071 GLN cc_start: 0.8346 (tm-30) cc_final: 0.7948 (tm-30) REVERT: C 8 LEU cc_start: 0.8169 (pp) cc_final: 0.7479 (pp) REVERT: C 32 GLU cc_start: 0.5412 (mm-30) cc_final: 0.4851 (pm20) REVERT: C 58 TRP cc_start: 0.6736 (m-10) cc_final: 0.5673 (m100) REVERT: C 64 GLU cc_start: 0.7338 (tp30) cc_final: 0.6439 (mp0) REVERT: C 102 GLU cc_start: 0.2951 (tt0) cc_final: 0.2611 (tm-30) outliers start: 16 outliers final: 9 residues processed: 161 average time/residue: 0.2158 time to fit residues: 48.3797 Evaluate side-chains 138 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 889 THR Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1390 THR Chi-restraints excluded: chain A residue 1421 CYS Chi-restraints excluded: chain A residue 1508 SER Chi-restraints excluded: chain A residue 1882 SER Chi-restraints excluded: chain A residue 1884 HIS Chi-restraints excluded: chain A residue 1984 THR Chi-restraints excluded: chain C residue 157 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 0.0570 chunk 29 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 0 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1318 GLN ** A1468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1993 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.182807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.131671 restraints weight = 10442.741| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 3.07 r_work: 0.3403 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8729 Z= 0.136 Angle : 0.539 7.394 11823 Z= 0.274 Chirality : 0.043 0.177 1314 Planarity : 0.004 0.033 1525 Dihedral : 6.372 91.096 1157 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.20 % Allowed : 10.90 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.27), residues: 1049 helix: 0.63 (0.29), residues: 327 sheet: -0.10 (0.36), residues: 204 loop : -0.19 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1825 HIS 0.003 0.001 HIS A 945 PHE 0.012 0.001 PHE A1199 TYR 0.009 0.001 TYR A1767 ARG 0.004 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 300) hydrogen bonds : angle 5.45646 ( 822) covalent geometry : bond 0.00325 ( 8729) covalent geometry : angle 0.53880 (11823) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 956 GLN cc_start: 0.7752 (mt0) cc_final: 0.7370 (mt0) REVERT: A 1328 LEU cc_start: 0.7608 (tp) cc_final: 0.7396 (tp) REVERT: A 1636 LYS cc_start: 0.6399 (pttt) cc_final: 0.5650 (ptmt) REVERT: A 1845 MET cc_start: 0.8336 (mtm) cc_final: 0.8126 (mtm) REVERT: A 2018 LYS cc_start: 0.8471 (mtmt) cc_final: 0.7863 (tmtt) REVERT: A 2022 GLN cc_start: 0.8589 (mp-120) cc_final: 0.8359 (mp10) REVERT: A 2043 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8089 (mt-10) REVERT: A 2071 GLN cc_start: 0.8489 (tm-30) cc_final: 0.8075 (tm-30) REVERT: C 28 ASP cc_start: 0.7392 (t70) cc_final: 0.7130 (t70) REVERT: C 58 TRP cc_start: 0.6793 (m100) cc_final: 0.5756 (m100) REVERT: C 64 GLU cc_start: 0.7308 (tp30) cc_final: 0.6418 (mp0) outliers start: 21 outliers final: 17 residues processed: 144 average time/residue: 0.2189 time to fit residues: 43.6766 Evaluate side-chains 140 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 889 THR Chi-restraints excluded: chain A residue 1213 ASP Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1390 THR Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1508 SER Chi-restraints excluded: chain A residue 1736 ILE Chi-restraints excluded: chain A residue 1737 SER Chi-restraints excluded: chain A residue 1882 SER Chi-restraints excluded: chain A residue 1884 HIS Chi-restraints excluded: chain A residue 1984 THR Chi-restraints excluded: chain A residue 2021 LEU Chi-restraints excluded: chain A residue 2087 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 157 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 66 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 24 optimal weight: 0.2980 chunk 99 optimal weight: 20.0000 chunk 32 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.183869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.132840 restraints weight = 10211.428| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 3.09 r_work: 0.3385 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8729 Z= 0.179 Angle : 0.556 7.767 11823 Z= 0.282 Chirality : 0.043 0.132 1314 Planarity : 0.004 0.030 1525 Dihedral : 6.291 87.865 1157 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.25 % Allowed : 11.32 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.27), residues: 1049 helix: 0.64 (0.29), residues: 327 sheet: 0.07 (0.36), residues: 212 loop : -0.23 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1825 HIS 0.006 0.001 HIS A1469 PHE 0.014 0.002 PHE A1199 TYR 0.013 0.001 TYR A2082 ARG 0.007 0.000 ARG A1277 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 300) hydrogen bonds : angle 5.20233 ( 822) covalent geometry : bond 0.00441 ( 8729) covalent geometry : angle 0.55624 (11823) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 956 GLN cc_start: 0.7677 (mt0) cc_final: 0.7289 (mt0) REVERT: A 1193 ASN cc_start: 0.8593 (m-40) cc_final: 0.8099 (p0) REVERT: A 1328 LEU cc_start: 0.7581 (tp) cc_final: 0.7368 (tp) REVERT: A 1636 LYS cc_start: 0.6508 (pttt) cc_final: 0.5906 (ptmt) REVERT: A 1641 GLN cc_start: 0.8510 (tp40) cc_final: 0.8278 (tp40) REVERT: A 1824 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7588 (mt) REVERT: A 1871 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8886 (mp) REVERT: A 2018 LYS cc_start: 0.8465 (mtmt) cc_final: 0.7843 (tmtt) REVERT: A 2022 GLN cc_start: 0.8529 (mp-120) cc_final: 0.8296 (mp10) REVERT: A 2043 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7900 (mt-10) REVERT: A 2071 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8025 (tm-30) REVERT: C 8 LEU cc_start: 0.8139 (pp) cc_final: 0.7363 (pp) REVERT: C 28 ASP cc_start: 0.7388 (t70) cc_final: 0.7101 (t70) REVERT: C 58 TRP cc_start: 0.6824 (m100) cc_final: 0.5981 (m100) REVERT: C 64 GLU cc_start: 0.7291 (tp30) cc_final: 0.6427 (mp0) outliers start: 31 outliers final: 21 residues processed: 146 average time/residue: 0.2048 time to fit residues: 41.5226 Evaluate side-chains 143 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 889 THR Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 1213 ASP Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1390 THR Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1421 CYS Chi-restraints excluded: chain A residue 1508 SER Chi-restraints excluded: chain A residue 1736 ILE Chi-restraints excluded: chain A residue 1737 SER Chi-restraints excluded: chain A residue 1824 LEU Chi-restraints excluded: chain A residue 1871 ILE Chi-restraints excluded: chain A residue 1882 SER Chi-restraints excluded: chain A residue 1884 HIS Chi-restraints excluded: chain A residue 1984 THR Chi-restraints excluded: chain A residue 2021 LEU Chi-restraints excluded: chain A residue 2087 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 157 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 82 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 23 optimal weight: 0.0020 chunk 48 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 33 optimal weight: 0.1980 chunk 5 optimal weight: 0.8980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.187676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.133184 restraints weight = 10480.527| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 3.31 r_work: 0.3398 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8729 Z= 0.106 Angle : 0.503 6.056 11823 Z= 0.254 Chirality : 0.041 0.129 1314 Planarity : 0.003 0.031 1525 Dihedral : 6.039 83.502 1157 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.62 % Allowed : 12.79 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.27), residues: 1049 helix: 0.87 (0.29), residues: 328 sheet: 0.08 (0.37), residues: 202 loop : -0.20 (0.29), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A1825 HIS 0.005 0.000 HIS A1469 PHE 0.009 0.001 PHE A1199 TYR 0.008 0.001 TYR A1767 ARG 0.002 0.000 ARG A1049 Details of bonding type rmsd hydrogen bonds : bond 0.02940 ( 300) hydrogen bonds : angle 4.97866 ( 822) covalent geometry : bond 0.00249 ( 8729) covalent geometry : angle 0.50338 (11823) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 956 GLN cc_start: 0.7699 (mt0) cc_final: 0.7280 (mt0) REVERT: A 1193 ASN cc_start: 0.8521 (m-40) cc_final: 0.8063 (p0) REVERT: A 1636 LYS cc_start: 0.6416 (pttt) cc_final: 0.6068 (ptmt) REVERT: A 1641 GLN cc_start: 0.8479 (tp40) cc_final: 0.8237 (tp40) REVERT: A 1824 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7413 (mt) REVERT: A 2018 LYS cc_start: 0.8451 (mtmt) cc_final: 0.7828 (tmtt) REVERT: A 2043 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7830 (mt-10) REVERT: A 2071 GLN cc_start: 0.8392 (tm-30) cc_final: 0.7983 (tm-30) REVERT: C 8 LEU cc_start: 0.8164 (pp) cc_final: 0.7885 (pp) REVERT: C 28 ASP cc_start: 0.7136 (t70) cc_final: 0.6843 (t70) REVERT: C 64 GLU cc_start: 0.7153 (tp30) cc_final: 0.6347 (mp0) outliers start: 25 outliers final: 18 residues processed: 149 average time/residue: 0.1940 time to fit residues: 40.4882 Evaluate side-chains 143 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 889 THR Chi-restraints excluded: chain A residue 1213 ASP Chi-restraints excluded: chain A residue 1390 THR Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1421 CYS Chi-restraints excluded: chain A residue 1430 ILE Chi-restraints excluded: chain A residue 1508 SER Chi-restraints excluded: chain A residue 1736 ILE Chi-restraints excluded: chain A residue 1737 SER Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1823 VAL Chi-restraints excluded: chain A residue 1824 LEU Chi-restraints excluded: chain A residue 1882 SER Chi-restraints excluded: chain A residue 1884 HIS Chi-restraints excluded: chain A residue 1984 THR Chi-restraints excluded: chain A residue 2021 LEU Chi-restraints excluded: chain A residue 2087 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 157 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 79 optimal weight: 0.9990 chunk 101 optimal weight: 0.0980 chunk 93 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 98 optimal weight: 0.0040 chunk 60 optimal weight: 0.5980 chunk 72 optimal weight: 0.0050 chunk 103 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.3406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1896 ASN A2022 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.188752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.135559 restraints weight = 10372.316| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.96 r_work: 0.3406 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8729 Z= 0.098 Angle : 0.495 6.086 11823 Z= 0.248 Chirality : 0.041 0.132 1314 Planarity : 0.003 0.032 1525 Dihedral : 5.805 80.023 1157 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.62 % Allowed : 13.52 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.27), residues: 1049 helix: 1.01 (0.29), residues: 328 sheet: 0.10 (0.37), residues: 206 loop : -0.18 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1825 HIS 0.006 0.000 HIS A1469 PHE 0.008 0.001 PHE A1199 TYR 0.007 0.001 TYR A1850 ARG 0.003 0.000 ARG A1277 Details of bonding type rmsd hydrogen bonds : bond 0.02765 ( 300) hydrogen bonds : angle 4.81471 ( 822) covalent geometry : bond 0.00229 ( 8729) covalent geometry : angle 0.49488 (11823) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1193 ASN cc_start: 0.8463 (m-40) cc_final: 0.8086 (p0) REVERT: A 1636 LYS cc_start: 0.6470 (pttt) cc_final: 0.6038 (ptmt) REVERT: A 1641 GLN cc_start: 0.8456 (tp40) cc_final: 0.8210 (tp40) REVERT: A 1824 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7461 (mt) REVERT: A 1871 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8757 (mp) REVERT: A 1983 ASN cc_start: 0.8053 (t0) cc_final: 0.7784 (t0) REVERT: A 2018 LYS cc_start: 0.8333 (mtmt) cc_final: 0.7831 (tmtt) REVERT: A 2022 GLN cc_start: 0.8334 (mp-120) cc_final: 0.7968 (mp10) REVERT: A 2043 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7730 (mt-10) REVERT: A 2071 GLN cc_start: 0.8405 (tm-30) cc_final: 0.7986 (tm-30) REVERT: C 8 LEU cc_start: 0.8221 (pp) cc_final: 0.7978 (pt) REVERT: C 28 ASP cc_start: 0.7127 (t70) cc_final: 0.6823 (t70) REVERT: C 58 TRP cc_start: 0.6638 (m100) cc_final: 0.6356 (m100) REVERT: C 64 GLU cc_start: 0.7051 (tp30) cc_final: 0.6271 (mp0) outliers start: 25 outliers final: 21 residues processed: 151 average time/residue: 0.1921 time to fit residues: 40.9170 Evaluate side-chains 146 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 889 THR Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 1213 ASP Chi-restraints excluded: chain A residue 1251 ASP Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1390 THR Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1421 CYS Chi-restraints excluded: chain A residue 1430 ILE Chi-restraints excluded: chain A residue 1508 SER Chi-restraints excluded: chain A residue 1736 ILE Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1823 VAL Chi-restraints excluded: chain A residue 1824 LEU Chi-restraints excluded: chain A residue 1871 ILE Chi-restraints excluded: chain A residue 1882 SER Chi-restraints excluded: chain A residue 1884 HIS Chi-restraints excluded: chain A residue 1984 THR Chi-restraints excluded: chain A residue 2021 LEU Chi-restraints excluded: chain A residue 2087 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 157 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 98 optimal weight: 0.0050 chunk 78 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 0.0970 chunk 67 optimal weight: 2.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1412 GLN ** A1468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.187100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.137687 restraints weight = 10369.492| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.79 r_work: 0.3440 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8729 Z= 0.108 Angle : 0.492 6.172 11823 Z= 0.247 Chirality : 0.041 0.129 1314 Planarity : 0.003 0.031 1525 Dihedral : 5.625 77.225 1157 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.73 % Allowed : 13.63 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.27), residues: 1049 helix: 1.09 (0.29), residues: 327 sheet: 0.10 (0.36), residues: 206 loop : -0.14 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1825 HIS 0.006 0.001 HIS A1469 PHE 0.014 0.001 PHE A 857 TYR 0.008 0.001 TYR A1767 ARG 0.002 0.000 ARG A1277 Details of bonding type rmsd hydrogen bonds : bond 0.02775 ( 300) hydrogen bonds : angle 4.71954 ( 822) covalent geometry : bond 0.00258 ( 8729) covalent geometry : angle 0.49159 (11823) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1193 ASN cc_start: 0.8400 (m-40) cc_final: 0.8088 (p0) REVERT: A 1636 LYS cc_start: 0.6469 (pttt) cc_final: 0.5879 (ptmt) REVERT: A 1824 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7482 (mt) REVERT: A 1871 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8757 (mp) REVERT: A 1983 ASN cc_start: 0.8088 (t0) cc_final: 0.7831 (m-40) REVERT: A 2018 LYS cc_start: 0.8403 (mtmt) cc_final: 0.7827 (tmtt) REVERT: A 2022 GLN cc_start: 0.8407 (mp-120) cc_final: 0.8159 (mp10) REVERT: A 2043 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7786 (mt-10) REVERT: A 2071 GLN cc_start: 0.8387 (tm-30) cc_final: 0.7963 (tm-30) REVERT: C 8 LEU cc_start: 0.8205 (pp) cc_final: 0.7902 (pt) REVERT: C 28 ASP cc_start: 0.7225 (t70) cc_final: 0.6944 (t70) REVERT: C 64 GLU cc_start: 0.7265 (tp30) cc_final: 0.6407 (mp0) outliers start: 26 outliers final: 21 residues processed: 146 average time/residue: 0.2257 time to fit residues: 46.4209 Evaluate side-chains 147 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 889 THR Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 1213 ASP Chi-restraints excluded: chain A residue 1251 ASP Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1390 THR Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1430 ILE Chi-restraints excluded: chain A residue 1508 SER Chi-restraints excluded: chain A residue 1736 ILE Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1823 VAL Chi-restraints excluded: chain A residue 1824 LEU Chi-restraints excluded: chain A residue 1871 ILE Chi-restraints excluded: chain A residue 1882 SER Chi-restraints excluded: chain A residue 1884 HIS Chi-restraints excluded: chain A residue 1890 ILE Chi-restraints excluded: chain A residue 1984 THR Chi-restraints excluded: chain A residue 2021 LEU Chi-restraints excluded: chain A residue 2087 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 157 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 74 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 96 optimal weight: 20.0000 chunk 104 optimal weight: 6.9990 chunk 15 optimal weight: 0.0970 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 103 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.187117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.137402 restraints weight = 10452.456| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 3.11 r_work: 0.3419 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8729 Z= 0.114 Angle : 0.508 7.081 11823 Z= 0.253 Chirality : 0.041 0.131 1314 Planarity : 0.004 0.046 1525 Dihedral : 5.539 75.820 1157 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.94 % Allowed : 13.94 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.27), residues: 1049 helix: 1.11 (0.29), residues: 327 sheet: 0.15 (0.37), residues: 206 loop : -0.13 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 58 HIS 0.006 0.001 HIS A1469 PHE 0.010 0.001 PHE A1199 TYR 0.009 0.001 TYR A2082 ARG 0.008 0.000 ARG A1277 Details of bonding type rmsd hydrogen bonds : bond 0.02774 ( 300) hydrogen bonds : angle 4.67795 ( 822) covalent geometry : bond 0.00275 ( 8729) covalent geometry : angle 0.50798 (11823) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1193 ASN cc_start: 0.8394 (m-40) cc_final: 0.8113 (p0) REVERT: A 1636 LYS cc_start: 0.6394 (pttt) cc_final: 0.6107 (ptmt) REVERT: A 1641 GLN cc_start: 0.8531 (tp40) cc_final: 0.8304 (tp40) REVERT: A 1824 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7539 (mt) REVERT: A 1871 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8779 (mp) REVERT: A 1983 ASN cc_start: 0.8158 (t0) cc_final: 0.7889 (m-40) REVERT: A 2018 LYS cc_start: 0.8439 (mtmt) cc_final: 0.8190 (tmtt) REVERT: A 2043 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7869 (mt-10) REVERT: A 2071 GLN cc_start: 0.8407 (tm-30) cc_final: 0.7989 (tm-30) REVERT: C 28 ASP cc_start: 0.7187 (t70) cc_final: 0.6910 (t70) REVERT: C 64 GLU cc_start: 0.7209 (tp30) cc_final: 0.6353 (mp0) outliers start: 28 outliers final: 25 residues processed: 144 average time/residue: 0.2704 time to fit residues: 56.1288 Evaluate side-chains 148 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 889 THR Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1213 ASP Chi-restraints excluded: chain A residue 1251 ASP Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1390 THR Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1421 CYS Chi-restraints excluded: chain A residue 1508 SER Chi-restraints excluded: chain A residue 1634 GLN Chi-restraints excluded: chain A residue 1736 ILE Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1823 VAL Chi-restraints excluded: chain A residue 1824 LEU Chi-restraints excluded: chain A residue 1871 ILE Chi-restraints excluded: chain A residue 1882 SER Chi-restraints excluded: chain A residue 1884 HIS Chi-restraints excluded: chain A residue 1890 ILE Chi-restraints excluded: chain A residue 1984 THR Chi-restraints excluded: chain A residue 2021 LEU Chi-restraints excluded: chain A residue 2087 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 157 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 19 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.188782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.132079 restraints weight = 10819.060| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 3.63 r_work: 0.3359 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8729 Z= 0.172 Angle : 0.559 8.560 11823 Z= 0.280 Chirality : 0.043 0.134 1314 Planarity : 0.004 0.029 1525 Dihedral : 5.603 75.034 1157 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.04 % Allowed : 14.15 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.27), residues: 1049 helix: 1.01 (0.29), residues: 326 sheet: 0.11 (0.36), residues: 214 loop : -0.17 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1422 HIS 0.006 0.001 HIS A1469 PHE 0.038 0.002 PHE A2059 TYR 0.013 0.001 TYR A1767 ARG 0.009 0.000 ARG A1277 Details of bonding type rmsd hydrogen bonds : bond 0.03126 ( 300) hydrogen bonds : angle 4.77807 ( 822) covalent geometry : bond 0.00423 ( 8729) covalent geometry : angle 0.55880 (11823) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1193 ASN cc_start: 0.8402 (m-40) cc_final: 0.8107 (p0) REVERT: A 1636 LYS cc_start: 0.6390 (pttt) cc_final: 0.5912 (ptmt) REVERT: A 1641 GLN cc_start: 0.8554 (tp40) cc_final: 0.8308 (tp40) REVERT: A 1824 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7491 (mt) REVERT: A 1845 MET cc_start: 0.8713 (mmt) cc_final: 0.8068 (mmt) REVERT: A 1871 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8804 (mp) REVERT: A 1983 ASN cc_start: 0.8188 (t0) cc_final: 0.7945 (m-40) REVERT: A 2018 LYS cc_start: 0.8368 (mtmt) cc_final: 0.8153 (tmtt) REVERT: A 2043 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7982 (mt-10) REVERT: A 2071 GLN cc_start: 0.8390 (tm-30) cc_final: 0.7980 (tm-30) REVERT: C 28 ASP cc_start: 0.7048 (t70) cc_final: 0.6775 (t70) REVERT: C 64 GLU cc_start: 0.7307 (tp30) cc_final: 0.6441 (mp0) REVERT: C 173 MET cc_start: 0.6077 (mmm) cc_final: 0.5843 (mmm) outliers start: 29 outliers final: 21 residues processed: 138 average time/residue: 0.2017 time to fit residues: 40.1782 Evaluate side-chains 142 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1213 ASP Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1360 ASN Chi-restraints excluded: chain A residue 1390 THR Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1421 CYS Chi-restraints excluded: chain A residue 1508 SER Chi-restraints excluded: chain A residue 1736 ILE Chi-restraints excluded: chain A residue 1737 SER Chi-restraints excluded: chain A residue 1823 VAL Chi-restraints excluded: chain A residue 1824 LEU Chi-restraints excluded: chain A residue 1871 ILE Chi-restraints excluded: chain A residue 1882 SER Chi-restraints excluded: chain A residue 1884 HIS Chi-restraints excluded: chain A residue 1984 THR Chi-restraints excluded: chain A residue 2021 LEU Chi-restraints excluded: chain A residue 2087 VAL Chi-restraints excluded: chain C residue 38 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 59 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 97 optimal weight: 0.2980 chunk 104 optimal weight: 0.2980 chunk 79 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 64 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 49 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 0.0040 overall best weight: 0.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.187865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.139259 restraints weight = 10282.172| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.87 r_work: 0.3470 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8729 Z= 0.098 Angle : 0.528 9.632 11823 Z= 0.261 Chirality : 0.041 0.133 1314 Planarity : 0.003 0.031 1525 Dihedral : 5.404 73.189 1157 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.20 % Allowed : 14.57 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.27), residues: 1049 helix: 1.16 (0.30), residues: 333 sheet: 0.16 (0.37), residues: 207 loop : -0.07 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 58 HIS 0.006 0.001 HIS A1469 PHE 0.009 0.001 PHE A1500 TYR 0.007 0.001 TYR A1767 ARG 0.010 0.000 ARG A1277 Details of bonding type rmsd hydrogen bonds : bond 0.02695 ( 300) hydrogen bonds : angle 4.64724 ( 822) covalent geometry : bond 0.00232 ( 8729) covalent geometry : angle 0.52774 (11823) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1193 ASN cc_start: 0.8439 (m-40) cc_final: 0.8212 (p0) REVERT: A 1636 LYS cc_start: 0.6446 (pttt) cc_final: 0.6158 (ptmt) REVERT: A 1641 GLN cc_start: 0.8634 (tp40) cc_final: 0.8407 (tp40) REVERT: A 1824 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7620 (mt) REVERT: A 1845 MET cc_start: 0.8769 (mmt) cc_final: 0.8341 (mmt) REVERT: A 1871 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8852 (mp) REVERT: A 1983 ASN cc_start: 0.8227 (t0) cc_final: 0.8001 (m-40) REVERT: A 2018 LYS cc_start: 0.8412 (mtmt) cc_final: 0.8179 (tmtt) REVERT: A 2043 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8065 (mt-10) REVERT: A 2071 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8102 (tm-30) REVERT: C 28 ASP cc_start: 0.7138 (t70) cc_final: 0.6868 (t70) REVERT: C 58 TRP cc_start: 0.6204 (m100) cc_final: 0.5211 (m100) REVERT: C 64 GLU cc_start: 0.7250 (tp30) cc_final: 0.6389 (mp0) REVERT: C 157 MET cc_start: 0.6446 (OUTLIER) cc_final: 0.5787 (mtt) outliers start: 21 outliers final: 16 residues processed: 135 average time/residue: 0.1899 time to fit residues: 36.6359 Evaluate side-chains 136 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 1213 ASP Chi-restraints excluded: chain A residue 1360 ASN Chi-restraints excluded: chain A residue 1390 THR Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1421 CYS Chi-restraints excluded: chain A residue 1508 SER Chi-restraints excluded: chain A residue 1736 ILE Chi-restraints excluded: chain A residue 1823 VAL Chi-restraints excluded: chain A residue 1824 LEU Chi-restraints excluded: chain A residue 1871 ILE Chi-restraints excluded: chain A residue 1882 SER Chi-restraints excluded: chain A residue 1884 HIS Chi-restraints excluded: chain A residue 1984 THR Chi-restraints excluded: chain A residue 2021 LEU Chi-restraints excluded: chain A residue 2087 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 157 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 59 optimal weight: 0.9980 chunk 104 optimal weight: 0.3980 chunk 102 optimal weight: 0.0980 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 32 optimal weight: 0.0980 chunk 20 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.187367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.135138 restraints weight = 10399.500| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.02 r_work: 0.3466 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8729 Z= 0.110 Angle : 0.527 8.929 11823 Z= 0.259 Chirality : 0.041 0.135 1314 Planarity : 0.003 0.031 1525 Dihedral : 5.300 71.980 1157 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.10 % Allowed : 14.99 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.27), residues: 1049 helix: 1.19 (0.30), residues: 333 sheet: 0.20 (0.37), residues: 207 loop : -0.05 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 58 HIS 0.006 0.001 HIS A1469 PHE 0.009 0.001 PHE A1199 TYR 0.008 0.001 TYR A1767 ARG 0.011 0.000 ARG A1277 Details of bonding type rmsd hydrogen bonds : bond 0.02709 ( 300) hydrogen bonds : angle 4.57563 ( 822) covalent geometry : bond 0.00265 ( 8729) covalent geometry : angle 0.52749 (11823) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5242.21 seconds wall clock time: 91 minutes 31.03 seconds (5491.03 seconds total)