Starting phenix.real_space_refine on Wed Sep 17 12:24:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ax5_43927/09_2025/9ax5_43927_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ax5_43927/09_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_43927/09_2025/9ax5_43927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ax5_43927/09_2025/9ax5_43927.map" model { file = "/net/cci-nas-00/data/ceres_data/9ax5_43927/09_2025/9ax5_43927_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ax5_43927/09_2025/9ax5_43927_neut.cif" } resolution = 3.3 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= 0.009 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.09, per 1000 atoms: 0.24 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: 0.90 Conformation dependent library (CDL) restraints added in 323.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.37 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: 1.55 Time building geometry restraints manager: 1.13 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: 13.640 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.760 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.090 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A1211 TYR 0.008 0.001 TYR A1028 PHE 0.008 0.001 PHE A1909 TRP 0.005 0.001 TRP A1825 HIS 0.004 0.001 HIS A1469 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8729) covalent geometry : angle 0.45144 (11823) hydrogen bonds : bond 0.26823 ( 300) hydrogen bonds : angle 9.11260 ( 822) *********************** 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 : 0.366 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: 0.8638 (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: 0.7841 (t0) REVERT: A 2018 LYS cc_start: 0.8278 (mtmt) cc_final: 0.7990 (mtmm) REVERT: A 2066 GLU cc_start: 0.7182 (tm-30) cc_final: 0.6830 (tp30) REVERT: A 2071 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7979 (tm-30) REVERT: C 162 LYS cc_start: 0.4514 (mtpp) cc_final: 0.4250 (mmtt) outliers start: 10 outliers final: 4 residues processed: 185 average time/residue: 0.1174 time to fit residues: 28.9282 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 : 0.343 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.5980 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.0020 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- 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 = 0.4216 r_free = 0.4216 target = 0.185787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.133957 restraints weight = 10399.968| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.94 r_work: 0.3404 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8729 Z= 0.156 Angle : 0.599 6.416 11823 Z= 0.306 Chirality : 0.044 0.161 1314 Planarity : 0.004 0.045 1525 Dihedral : 7.071 97.494 1164 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.68 % Allowed : 9.96 % Favored : 88.36 % 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 aren not related in a simple way. whole: -0.07 (0.27), residues: 1049 helix: 0.41 (0.29), residues: 328 sheet: -0.04 (0.37), residues: 209 loop : -0.22 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 129 TYR 0.010 0.001 TYR A1767 PHE 0.023 0.002 PHE A2059 TRP 0.006 0.001 TRP A1784 HIS 0.004 0.001 HIS A1469 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 8729) covalent geometry : angle 0.59853 (11823) hydrogen bonds : bond 0.04383 ( 300) hydrogen bonds : angle 5.96074 ( 822) *********************** 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 : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 956 GLN cc_start: 0.7656 (mt0) cc_final: 0.7338 (mt0) REVERT: A 1287 SER cc_start: 0.8329 (m) cc_final: 0.8068 (t) REVERT: A 1328 LEU cc_start: 0.7543 (tp) cc_final: 0.7294 (tp) REVERT: A 1636 LYS cc_start: 0.6582 (pttt) cc_final: 0.6196 (ptmt) REVERT: A 2018 LYS cc_start: 0.8313 (mtmt) cc_final: 0.7955 (tmtt) REVERT: A 2022 GLN cc_start: 0.8407 (mp-120) cc_final: 0.8033 (mp10) REVERT: A 2043 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7970 (mt-10) REVERT: A 2071 GLN cc_start: 0.8353 (tm-30) cc_final: 0.7950 (tm-30) REVERT: C 8 LEU cc_start: 0.8155 (pp) cc_final: 0.7473 (pp) REVERT: C 58 TRP cc_start: 0.6817 (m-10) cc_final: 0.5759 (m100) REVERT: C 64 GLU cc_start: 0.7256 (tp30) cc_final: 0.6392 (mp0) REVERT: C 102 GLU cc_start: 0.2953 (tt0) cc_final: 0.2614 (tm-30) outliers start: 16 outliers final: 10 residues processed: 160 average time/residue: 0.0959 time to fit residues: 21.4966 Evaluate side-chains 140 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 22 LEU 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 52 optimal weight: 0.0470 chunk 10 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 101 optimal weight: 0.0970 chunk 49 optimal weight: 0.0170 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 0.0770 overall best weight: 0.1672 ------------------------------------------------------------------------------- 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 A1993 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.187308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.136457 restraints weight = 10349.870| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.94 r_work: 0.3449 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8729 Z= 0.104 Angle : 0.523 7.066 11823 Z= 0.264 Chirality : 0.042 0.199 1314 Planarity : 0.004 0.031 1525 Dihedral : 6.272 89.565 1157 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.20 % Allowed : 10.80 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.27), residues: 1049 helix: 0.77 (0.29), residues: 323 sheet: 0.05 (0.36), residues: 201 loop : -0.14 (0.29), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 129 TYR 0.007 0.001 TYR A1850 PHE 0.011 0.001 PHE A1443 TRP 0.005 0.001 TRP A2076 HIS 0.002 0.000 HIS A1435 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8729) covalent geometry : angle 0.52344 (11823) hydrogen bonds : bond 0.03304 ( 300) hydrogen bonds : angle 5.37383 ( 822) *********************** 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 172 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 956 GLN cc_start: 0.7607 (mt0) cc_final: 0.7250 (mt0) REVERT: A 1049 ARG cc_start: 0.7432 (ttm-80) cc_final: 0.7146 (mtm-85) REVERT: A 1400 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7752 (tt0) REVERT: A 1636 LYS cc_start: 0.6516 (pttt) cc_final: 0.5774 (ptmt) REVERT: A 2018 LYS cc_start: 0.8363 (mtmt) cc_final: 0.7860 (tmtt) REVERT: A 2043 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7804 (mt-10) REVERT: A 2071 GLN cc_start: 0.8348 (tm-30) cc_final: 0.7875 (tm-30) REVERT: C 8 LEU cc_start: 0.7917 (pp) cc_final: 0.7274 (pp) REVERT: C 58 TRP cc_start: 0.6667 (m100) cc_final: 0.5608 (m100) REVERT: C 64 GLU cc_start: 0.7221 (tp30) cc_final: 0.6354 (mp0) outliers start: 21 outliers final: 12 residues processed: 163 average time/residue: 0.1000 time to fit residues: 22.7086 Evaluate side-chains 142 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 1508 SER Chi-restraints excluded: chain A residue 1736 ILE Chi-restraints excluded: chain A residue 1737 SER Chi-restraints excluded: chain A residue 1884 HIS Chi-restraints excluded: chain A residue 1894 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 12 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 83 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1318 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.184514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.133309 restraints weight = 10487.336| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 3.14 r_work: 0.3423 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2606 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= 0.134 Angle : 0.533 8.038 11823 Z= 0.267 Chirality : 0.042 0.146 1314 Planarity : 0.004 0.032 1525 Dihedral : 6.171 86.537 1157 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.62 % Allowed : 11.74 % Favored : 85.64 % 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 aren not related in a simple way. whole: 0.26 (0.27), residues: 1049 helix: 0.84 (0.29), residues: 322 sheet: 0.07 (0.36), residues: 206 loop : -0.09 (0.29), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1277 TYR 0.010 0.001 TYR A2082 PHE 0.012 0.001 PHE A1199 TRP 0.007 0.001 TRP A1825 HIS 0.007 0.001 HIS A1469 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8729) covalent geometry : angle 0.53284 (11823) hydrogen bonds : bond 0.03200 ( 300) hydrogen bonds : angle 5.09746 ( 822) *********************** 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: 25 poor density : 134 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 956 GLN cc_start: 0.7777 (mt0) cc_final: 0.7372 (mt0) REVERT: A 1400 GLU cc_start: 0.8518 (mt-10) cc_final: 0.7990 (tt0) REVERT: A 1636 LYS cc_start: 0.6336 (pttt) cc_final: 0.5725 (ptmt) REVERT: A 2018 LYS cc_start: 0.8374 (mtmt) cc_final: 0.7869 (tmtt) REVERT: A 2022 GLN cc_start: 0.8524 (mp10) cc_final: 0.8200 (mp10) REVERT: A 2043 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8134 (mt-10) REVERT: A 2071 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8226 (tm-30) REVERT: C 8 LEU cc_start: 0.8134 (pp) cc_final: 0.7464 (pp) REVERT: C 28 ASP cc_start: 0.7442 (t70) cc_final: 0.7213 (t70) REVERT: C 58 TRP cc_start: 0.6845 (m100) cc_final: 0.5924 (m100) REVERT: C 64 GLU cc_start: 0.7189 (tp30) cc_final: 0.6330 (mp0) outliers start: 25 outliers final: 19 residues processed: 148 average time/residue: 0.0960 time to fit residues: 20.0314 Evaluate side-chains 147 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 889 THR Chi-restraints excluded: chain A residue 978 THR 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 1736 ILE Chi-restraints excluded: chain A residue 1882 SER Chi-restraints excluded: chain A residue 1884 HIS Chi-restraints excluded: chain A residue 1979 SER 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 22 LEU Chi-restraints excluded: chain C residue 38 VAL 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 87 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 40 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.4230 r_free = 0.4230 target = 0.187485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.136749 restraints weight = 10505.406| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 3.37 r_work: 0.3431 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2792 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= 0.109 Angle : 0.504 6.047 11823 Z= 0.252 Chirality : 0.042 0.131 1314 Planarity : 0.003 0.032 1525 Dihedral : 5.998 82.078 1157 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.94 % Allowed : 12.37 % Favored : 84.70 % 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 aren not related in a simple way. whole: 0.36 (0.27), residues: 1049 helix: 0.99 (0.30), residues: 321 sheet: 0.12 (0.36), residues: 205 loop : -0.07 (0.29), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1277 TYR 0.008 0.001 TYR A1767 PHE 0.010 0.001 PHE A1199 TRP 0.006 0.001 TRP A 890 HIS 0.007 0.001 HIS A1469 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8729) covalent geometry : angle 0.50371 (11823) hydrogen bonds : bond 0.02917 ( 300) hydrogen bonds : angle 4.88535 ( 822) *********************** 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 165 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1049 ARG cc_start: 0.7650 (ttm-80) cc_final: 0.7295 (ptp-170) REVERT: A 1193 ASN cc_start: 0.8619 (m-40) cc_final: 0.8132 (p0) REVERT: A 1400 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8039 (tt0) REVERT: A 1636 LYS cc_start: 0.6364 (pttt) cc_final: 0.5806 (ptmt) REVERT: A 1824 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7639 (mt) REVERT: A 1983 ASN cc_start: 0.8225 (t0) cc_final: 0.7951 (m-40) REVERT: A 2018 LYS cc_start: 0.8417 (mtmt) cc_final: 0.8149 (tmtt) REVERT: A 2043 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7868 (mt-10) REVERT: A 2071 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8074 (tm-30) REVERT: C 8 LEU cc_start: 0.8098 (pp) cc_final: 0.7419 (pp) REVERT: C 58 TRP cc_start: 0.6831 (m100) cc_final: 0.6102 (m100) REVERT: C 64 GLU cc_start: 0.7243 (tp30) cc_final: 0.6374 (mp0) outliers start: 28 outliers final: 21 residues processed: 153 average time/residue: 0.0948 time to fit residues: 20.3299 Evaluate side-chains 147 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 1213 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 1642 ILE 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 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 54 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 26 optimal weight: 0.0870 chunk 25 optimal weight: 0.8980 chunk 88 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 66 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- 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 = 0.4222 r_free = 0.4222 target = 0.186097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.135826 restraints weight = 10278.445| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 3.18 r_work: 0.3447 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2812 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= 0.139 Angle : 0.518 6.187 11823 Z= 0.260 Chirality : 0.042 0.134 1314 Planarity : 0.003 0.031 1525 Dihedral : 5.883 79.147 1157 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.25 % Allowed : 13.21 % Favored : 83.54 % 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 aren not related in a simple way. whole: 0.37 (0.27), residues: 1049 helix: 1.00 (0.30), residues: 321 sheet: 0.15 (0.36), residues: 211 loop : -0.08 (0.29), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1277 TYR 0.011 0.001 TYR A1767 PHE 0.012 0.001 PHE A1199 TRP 0.008 0.001 TRP A1422 HIS 0.007 0.001 HIS A1469 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8729) covalent geometry : angle 0.51751 (11823) hydrogen bonds : bond 0.03009 ( 300) hydrogen bonds : angle 4.80830 ( 822) *********************** 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 162 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1193 ASN cc_start: 0.8574 (m-40) cc_final: 0.8192 (p0) REVERT: A 1400 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8054 (tt0) REVERT: A 1636 LYS cc_start: 0.6322 (pttt) cc_final: 0.5825 (ptmt) REVERT: A 1641 GLN cc_start: 0.8614 (tp40) cc_final: 0.8355 (tp40) REVERT: A 1824 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7638 (mt) REVERT: A 1871 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8859 (mp) REVERT: A 1983 ASN cc_start: 0.8276 (t0) cc_final: 0.7999 (m-40) REVERT: A 2018 LYS cc_start: 0.8433 (mtmt) cc_final: 0.8225 (tmtt) REVERT: A 2043 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8012 (mt-10) REVERT: A 2071 GLN cc_start: 0.8489 (tm-30) cc_final: 0.8069 (tm-30) REVERT: C 8 LEU cc_start: 0.8103 (pp) cc_final: 0.7442 (pp) REVERT: C 58 TRP cc_start: 0.6838 (m100) cc_final: 0.6255 (m100) REVERT: C 64 GLU cc_start: 0.7240 (tp30) cc_final: 0.6381 (mp0) outliers start: 31 outliers final: 26 residues processed: 149 average time/residue: 0.0959 time to fit residues: 19.9571 Evaluate side-chains 156 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 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 1642 ILE 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 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 1979 SER 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 20 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 chunk 60 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4211 r_free = 0.4211 target = 0.185569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.135152 restraints weight = 10597.488| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 3.28 r_work: 0.3393 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2909 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= 0.133 Angle : 0.513 6.245 11823 Z= 0.258 Chirality : 0.042 0.134 1314 Planarity : 0.003 0.029 1525 Dihedral : 5.768 76.921 1157 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.35 % Allowed : 13.31 % Favored : 83.33 % 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 aren not related in a simple way. whole: 0.41 (0.27), residues: 1049 helix: 1.05 (0.29), residues: 327 sheet: 0.25 (0.36), residues: 216 loop : -0.13 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1277 TYR 0.010 0.001 TYR A1767 PHE 0.020 0.001 PHE A2059 TRP 0.007 0.001 TRP A1825 HIS 0.008 0.001 HIS A1469 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8729) covalent geometry : angle 0.51322 (11823) hydrogen bonds : bond 0.02931 ( 300) hydrogen bonds : angle 4.75046 ( 822) *********************** 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 160 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1193 ASN cc_start: 0.8567 (m-40) cc_final: 0.8208 (p0) REVERT: A 1400 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8051 (tt0) REVERT: A 1636 LYS cc_start: 0.6375 (pttt) cc_final: 0.5889 (ptmt) REVERT: A 1641 GLN cc_start: 0.8607 (tp40) cc_final: 0.8334 (tp40) REVERT: A 1824 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7677 (mt) REVERT: A 1871 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8857 (mp) REVERT: A 1983 ASN cc_start: 0.8287 (t0) cc_final: 0.8017 (m-40) REVERT: A 2018 LYS cc_start: 0.8431 (mtmt) cc_final: 0.8198 (tmtt) REVERT: A 2043 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8098 (mt-10) REVERT: A 2071 GLN cc_start: 0.8535 (tm-30) cc_final: 0.8123 (tm-30) REVERT: C 64 GLU cc_start: 0.7248 (tp30) cc_final: 0.6412 (mp0) outliers start: 32 outliers final: 25 residues processed: 148 average time/residue: 0.0813 time to fit residues: 16.9586 Evaluate side-chains 151 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 978 THR Chi-restraints excluded: chain A residue 1213 ASP Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1345 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 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 1871 ILE Chi-restraints excluded: chain A residue 1882 SER Chi-restraints excluded: chain A residue 1884 HIS Chi-restraints excluded: chain A residue 1979 SER 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 115 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 103 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 27 optimal weight: 0.0570 chunk 6 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 39 optimal weight: 0.0770 chunk 7 optimal weight: 1.9990 chunk 97 optimal weight: 0.1980 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 overall best weight: 0.3056 ------------------------------------------------------------------------------- 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 = 0.4269 r_free = 0.4269 target = 0.192886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.140335 restraints weight = 10508.849| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 3.14 r_work: 0.3461 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8729 Z= 0.095 Angle : 0.508 9.140 11823 Z= 0.252 Chirality : 0.042 0.170 1314 Planarity : 0.003 0.031 1525 Dihedral : 5.569 75.116 1157 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.62 % Allowed : 13.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.27), residues: 1049 helix: 1.20 (0.29), residues: 327 sheet: 0.18 (0.36), residues: 211 loop : -0.07 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1277 TYR 0.007 0.001 TYR A1850 PHE 0.009 0.001 PHE A1500 TRP 0.004 0.001 TRP A 890 HIS 0.008 0.001 HIS A1469 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 8729) covalent geometry : angle 0.50836 (11823) hydrogen bonds : bond 0.02721 ( 300) hydrogen bonds : angle 4.64032 ( 822) *********************** 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 156 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1049 ARG cc_start: 0.8176 (ptp-110) cc_final: 0.7797 (ptp-170) REVERT: A 1193 ASN cc_start: 0.8333 (m-40) cc_final: 0.8094 (p0) REVERT: A 1274 ASP cc_start: 0.7025 (m-30) cc_final: 0.6745 (p0) REVERT: A 1400 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7838 (tt0) REVERT: A 1636 LYS cc_start: 0.6546 (pttt) cc_final: 0.6159 (ptmt) REVERT: A 1641 GLN cc_start: 0.8454 (tp40) cc_final: 0.8209 (tp40) REVERT: A 1824 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7499 (mt) REVERT: A 1871 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8745 (mp) REVERT: A 1983 ASN cc_start: 0.8127 (t0) cc_final: 0.7886 (m-40) REVERT: A 2043 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7690 (mt-10) REVERT: A 2071 GLN cc_start: 0.8395 (tm-30) cc_final: 0.7976 (tm-30) REVERT: C 64 GLU cc_start: 0.7138 (tp30) cc_final: 0.6303 (mp0) REVERT: C 157 MET cc_start: 0.6540 (OUTLIER) cc_final: 0.6027 (mtt) outliers start: 25 outliers final: 22 residues processed: 148 average time/residue: 0.0967 time to fit residues: 20.0615 Evaluate side-chains 150 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 978 THR Chi-restraints excluded: chain A residue 1213 ASP Chi-restraints excluded: chain A residue 1345 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 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 1979 SER 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 57 LEU Chi-restraints excluded: chain C residue 115 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 73 optimal weight: 0.5980 chunk 55 optimal weight: 0.3980 chunk 57 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 0.2980 chunk 94 optimal weight: 0.2980 chunk 25 optimal weight: 0.0030 chunk 90 optimal weight: 4.9990 overall best weight: 0.3190 ------------------------------------------------------------------------------- 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 = 0.4231 r_free = 0.4231 target = 0.187124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.136879 restraints weight = 10261.200| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 3.10 r_work: 0.3449 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8729 Z= 0.103 Angle : 0.541 9.263 11823 Z= 0.267 Chirality : 0.042 0.194 1314 Planarity : 0.003 0.031 1525 Dihedral : 5.480 73.468 1157 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.62 % Allowed : 14.05 % Favored : 83.33 % 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 aren not related in a simple way. whole: 0.60 (0.27), residues: 1049 helix: 1.29 (0.29), residues: 332 sheet: 0.24 (0.36), residues: 212 loop : -0.02 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1277 TYR 0.007 0.001 TYR A1850 PHE 0.035 0.001 PHE A2059 TRP 0.009 0.001 TRP C 58 HIS 0.008 0.001 HIS A1469 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 8729) covalent geometry : angle 0.54084 (11823) hydrogen bonds : bond 0.02726 ( 300) hydrogen bonds : angle 4.61805 ( 822) *********************** 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 150 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1049 ARG cc_start: 0.8201 (ptp-110) cc_final: 0.7891 (ptp-170) REVERT: A 1400 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7833 (tt0) REVERT: A 1641 GLN cc_start: 0.8390 (tp40) cc_final: 0.8160 (tp40) REVERT: A 1824 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7526 (mt) REVERT: A 2043 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7730 (mt-10) REVERT: A 2071 GLN cc_start: 0.8380 (tm-30) cc_final: 0.7954 (tm-30) REVERT: C 58 TRP cc_start: 0.5948 (m100) cc_final: 0.4972 (m100) REVERT: C 64 GLU cc_start: 0.7184 (tp30) cc_final: 0.6340 (mp0) REVERT: C 82 MET cc_start: 0.7013 (ptp) cc_final: 0.6445 (ttm) REVERT: C 157 MET cc_start: 0.6480 (OUTLIER) cc_final: 0.6035 (mtt) outliers start: 25 outliers final: 21 residues processed: 142 average time/residue: 0.0897 time to fit residues: 17.9826 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 : 0.290 ------------------------------------------------------------------------------- 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 1328 LEU Chi-restraints excluded: chain A residue 1345 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 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 81 LEU 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 3 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4238 r_free = 0.4238 target = 0.189840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.136254 restraints weight = 10472.727| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 3.45 r_work: 0.3425 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3179 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= 0.161 Angle : 0.566 7.390 11823 Z= 0.283 Chirality : 0.043 0.135 1314 Planarity : 0.004 0.028 1525 Dihedral : 5.568 72.235 1157 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.52 % Allowed : 14.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.27), residues: 1049 helix: 1.17 (0.29), residues: 335 sheet: 0.32 (0.35), residues: 217 loop : -0.08 (0.30), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1277 TYR 0.012 0.001 TYR A1767 PHE 0.013 0.001 PHE A1199 TRP 0.011 0.001 TRP A1422 HIS 0.008 0.001 HIS A1469 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 8729) covalent geometry : angle 0.56552 (11823) hydrogen bonds : bond 0.03118 ( 300) hydrogen bonds : angle 4.71732 ( 822) ********************** 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 149 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1049 ARG cc_start: 0.8254 (ptp-110) cc_final: 0.7922 (ptp-170) REVERT: A 1400 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7877 (tt0) REVERT: A 1636 LYS cc_start: 0.6586 (pttt) cc_final: 0.6167 (ptmt) REVERT: A 1641 GLN cc_start: 0.8380 (tp40) cc_final: 0.8137 (tp40) REVERT: A 1824 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7558 (mt) REVERT: A 1993 HIS cc_start: 0.8228 (m170) cc_final: 0.7954 (m-70) REVERT: A 2043 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7888 (mt-10) REVERT: A 2071 GLN cc_start: 0.8441 (tm-30) cc_final: 0.8009 (tm-30) REVERT: C 58 TRP cc_start: 0.6255 (m100) cc_final: 0.5230 (m100) REVERT: C 64 GLU cc_start: 0.7200 (tp30) cc_final: 0.6363 (mp0) REVERT: C 157 MET cc_start: 0.6726 (OUTLIER) cc_final: 0.6154 (mtt) outliers start: 24 outliers final: 20 residues processed: 140 average time/residue: 0.1012 time to fit residues: 19.6459 Evaluate side-chains 146 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 978 THR Chi-restraints excluded: chain A residue 1213 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 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 81 LEU 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 37 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 88 optimal weight: 20.0000 chunk 47 optimal weight: 0.3980 chunk 70 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 63 optimal weight: 0.0970 chunk 23 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.188093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.138536 restraints weight = 10256.557| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 3.33 r_work: 0.3464 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3310 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= 0.105 Angle : 0.530 7.293 11823 Z= 0.264 Chirality : 0.042 0.134 1314 Planarity : 0.003 0.030 1525 Dihedral : 5.410 71.030 1157 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.52 % Allowed : 14.99 % Favored : 82.49 % 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 aren not related in a simple way. whole: 0.58 (0.27), residues: 1049 helix: 1.24 (0.29), residues: 335 sheet: 0.24 (0.36), residues: 212 loop : -0.03 (0.30), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1277 TYR 0.009 0.001 TYR A1034 PHE 0.008 0.001 PHE A1199 TRP 0.008 0.001 TRP C 58 HIS 0.008 0.001 HIS A1469 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 8729) covalent geometry : angle 0.52970 (11823) hydrogen bonds : bond 0.02746 ( 300) hydrogen bonds : angle 4.61300 ( 822) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2829.82 seconds wall clock time: 49 minutes 12.77 seconds (2952.77 seconds total)