Starting phenix.real_space_refine on Sat Aug 23 16:36:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ki8_37254/08_2025/8ki8_37254.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ki8_37254/08_2025/8ki8_37254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ki8_37254/08_2025/8ki8_37254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ki8_37254/08_2025/8ki8_37254.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ki8_37254/08_2025/8ki8_37254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ki8_37254/08_2025/8ki8_37254.map" } resolution = 3.2 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= 0.109 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: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 92 5.16 5 C 8434 2.51 5 N 2193 2.21 5 O 2535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13264 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 13047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1621, 13047 Classifications: {'peptide': 1621} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 44, 'TRANS': 1576} Chain breaks: 8 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 217 Classifications: {'RNA': 10} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 7} Time building chain proxies: 2.89, per 1000 atoms: 0.22 Number of scatterers: 13264 At special positions: 0 Unit cell: (114.49, 108.07, 110.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 10 15.00 O 2535 8.00 N 2193 7.00 C 8434 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: 1.07 Conformation dependent library (CDL) restraints added in 606.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3128 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 6 sheets defined 59.5% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 337 through 345 removed outlier: 4.108A pdb=" N ARG A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 363 Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.651A pdb=" N ILE A 368 " --> pdb=" O CYS A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 390 Processing helix chain 'A' and resid 397 through 414 Processing helix chain 'A' and resid 415 through 434 removed outlier: 3.801A pdb=" N LYS A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 455 Processing helix chain 'A' and resid 462 through 466 removed outlier: 3.745A pdb=" N GLU A 465 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR A 466 " --> pdb=" O LEU A 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 466' Processing helix chain 'A' and resid 491 through 501 Processing helix chain 'A' and resid 521 through 536 Processing helix chain 'A' and resid 591 through 606 Processing helix chain 'A' and resid 663 through 682 removed outlier: 3.736A pdb=" N LEU A 667 " --> pdb=" O ASN A 663 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN A 682 " --> pdb=" O PHE A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 700 removed outlier: 3.581A pdb=" N VAL A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 705 removed outlier: 3.795A pdb=" N CYS A 704 " --> pdb=" O ASN A 701 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 705 " --> pdb=" O PRO A 702 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 701 through 705' Processing helix chain 'A' and resid 713 through 729 removed outlier: 3.968A pdb=" N GLU A 717 " --> pdb=" O LYS A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 748 Processing helix chain 'A' and resid 796 through 804 Processing helix chain 'A' and resid 828 through 837 Processing helix chain 'A' and resid 837 through 853 Proline residue: A 843 - end of helix Processing helix chain 'A' and resid 853 through 863 Processing helix chain 'A' and resid 874 through 893 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 921 through 928 removed outlier: 3.949A pdb=" N PHE A 928 " --> pdb=" O ILE A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 954 removed outlier: 3.695A pdb=" N LEU A 954 " --> pdb=" O ARG A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1005 removed outlier: 4.045A pdb=" N LEU A 995 " --> pdb=" O THR A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1036 Proline residue: A1024 - end of helix removed outlier: 3.840A pdb=" N PHE A1031 " --> pdb=" O TRP A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1075 Processing helix chain 'A' and resid 1077 through 1089 Processing helix chain 'A' and resid 1094 through 1098 Processing helix chain 'A' and resid 1114 through 1125 removed outlier: 3.503A pdb=" N ILE A1118 " --> pdb=" O SER A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1130 removed outlier: 3.863A pdb=" N ILE A1130 " --> pdb=" O ILE A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1151 Processing helix chain 'A' and resid 1151 through 1163 Processing helix chain 'A' and resid 1165 through 1178 Processing helix chain 'A' and resid 1190 through 1195 Processing helix chain 'A' and resid 1197 through 1209 removed outlier: 3.588A pdb=" N VAL A1201 " --> pdb=" O HIS A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1222 through 1235 removed outlier: 3.564A pdb=" N HIS A1235 " --> pdb=" O VAL A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1248 removed outlier: 4.030A pdb=" N VAL A1245 " --> pdb=" O ASP A1241 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET A1246 " --> pdb=" O LEU A1242 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU A1248 " --> pdb=" O SER A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1271 Processing helix chain 'A' and resid 1300 through 1314 Processing helix chain 'A' and resid 1314 through 1320 removed outlier: 3.629A pdb=" N ALA A1318 " --> pdb=" O PHE A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1353 removed outlier: 4.021A pdb=" N ARG A1335 " --> pdb=" O ASP A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1386 removed outlier: 3.566A pdb=" N ILE A1385 " --> pdb=" O VAL A1381 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU A1386 " --> pdb=" O LEU A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1393 through 1408 removed outlier: 3.611A pdb=" N LEU A1397 " --> pdb=" O GLY A1393 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1428 Processing helix chain 'A' and resid 1434 through 1439 Processing helix chain 'A' and resid 1460 through 1478 Processing helix chain 'A' and resid 1505 through 1513 Processing helix chain 'A' and resid 1517 through 1533 Processing helix chain 'A' and resid 1565 through 1575 removed outlier: 3.904A pdb=" N CYS A1573 " --> pdb=" O LEU A1569 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A1575 " --> pdb=" O ASN A1571 " (cutoff:3.500A) Processing helix chain 'A' and resid 1581 through 1598 removed outlier: 3.748A pdb=" N HIS A1591 " --> pdb=" O SER A1587 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1620 removed outlier: 4.460A pdb=" N PHE A1607 " --> pdb=" O GLU A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1638 Processing helix chain 'A' and resid 1647 through 1651 removed outlier: 3.523A pdb=" N GLY A1651 " --> pdb=" O THR A1648 " (cutoff:3.500A) Processing helix chain 'A' and resid 1657 through 1664 removed outlier: 3.618A pdb=" N LEU A1661 " --> pdb=" O PRO A1657 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1683 Processing helix chain 'A' and resid 1686 through 1696 removed outlier: 3.833A pdb=" N SER A1696 " --> pdb=" O ASP A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1714 Processing helix chain 'A' and resid 1717 through 1736 removed outlier: 3.963A pdb=" N SER A1734 " --> pdb=" O PHE A1730 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL A1735 " --> pdb=" O GLU A1731 " (cutoff:3.500A) Processing helix chain 'A' and resid 1764 through 1769 Processing helix chain 'A' and resid 1770 through 1780 Processing helix chain 'A' and resid 1781 through 1785 Processing helix chain 'A' and resid 1814 through 1829 removed outlier: 3.521A pdb=" N ASN A1829 " --> pdb=" O ILE A1825 " (cutoff:3.500A) Processing helix chain 'A' and resid 1830 through 1835 Processing helix chain 'A' and resid 1843 through 1850 Processing helix chain 'A' and resid 1866 through 1877 removed outlier: 4.291A pdb=" N LEU A1870 " --> pdb=" O GLU A1866 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP A1871 " --> pdb=" O LYS A1867 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS A1877 " --> pdb=" O VAL A1873 " (cutoff:3.500A) Processing helix chain 'A' and resid 1891 through 1904 Processing helix chain 'A' and resid 1910 through 1923 Processing helix chain 'A' and resid 1924 through 1936 Proline residue: A1932 - end of helix Processing helix chain 'A' and resid 1954 through 1959 removed outlier: 3.636A pdb=" N TRP A1958 " --> pdb=" O GLN A1954 " (cutoff:3.500A) Processing helix chain 'A' and resid 1960 through 1965 Processing helix chain 'A' and resid 1986 through 2008 Processing helix chain 'A' and resid 2018 through 2030 removed outlier: 4.230A pdb=" N ASN A2030 " --> pdb=" O PHE A2026 " (cutoff:3.500A) Processing helix chain 'A' and resid 2031 through 2043 removed outlier: 3.665A pdb=" N MET A2042 " --> pdb=" O ALA A2038 " (cutoff:3.500A) Processing helix chain 'A' and resid 2052 through 2058 removed outlier: 3.515A pdb=" N PHE A2056 " --> pdb=" O ILE A2052 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG A2058 " --> pdb=" O THR A2054 " (cutoff:3.500A) Processing helix chain 'A' and resid 2059 through 2064 Processing helix chain 'A' and resid 2065 through 2069 removed outlier: 3.857A pdb=" N ASN A2068 " --> pdb=" O SER A2065 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 508 through 509 removed outlier: 3.554A pdb=" N SER A 810 " --> pdb=" O ILE A 821 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ALA A 788 " --> pdb=" O MET A 822 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1109 through 1111 removed outlier: 4.310A pdb=" N VAL A1217 " --> pdb=" O ASN A1111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1295 through 1298 removed outlier: 6.561A pdb=" N VAL A1281 " --> pdb=" O CYS A1412 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1484 through 1492 removed outlier: 3.654A pdb=" N HIS A1492 " --> pdb=" O ASP A1495 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A1496 " --> pdb=" O ALA A1366 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1548 through 1549 Processing sheet with id=AA6, first strand: chain 'A' and resid 1973 through 1975 removed outlier: 3.530A pdb=" N VAL A1974 " --> pdb=" O ILE A2084 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE A2084 " --> pdb=" O VAL A1974 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 665 hydrogen bonds defined for protein. 1941 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: 2.18 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4125 1.34 - 1.46: 3092 1.46 - 1.59: 6143 1.59 - 1.71: 19 1.71 - 1.83: 151 Bond restraints: 13530 Sorted by residual: bond pdb=" C LEU A 912 " pdb=" N PRO A 913 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.54e+00 bond pdb=" C CYS A 982 " pdb=" N PRO A 983 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.48e+00 bond pdb=" C ILE A1931 " pdb=" N PRO A1932 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.20e-02 6.94e+03 3.01e+00 bond pdb=" CA PHE A1950 " pdb=" CB PHE A1950 " ideal model delta sigma weight residual 1.532 1.558 -0.026 1.51e-02 4.39e+03 2.87e+00 bond pdb=" C ILE A1988 " pdb=" N PRO A1989 " ideal model delta sigma weight residual 1.335 1.358 -0.022 1.36e-02 5.41e+03 2.73e+00 ... (remaining 13525 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 18106 3.43 - 6.86: 141 6.86 - 10.29: 22 10.29 - 13.71: 4 13.71 - 17.14: 3 Bond angle restraints: 18276 Sorted by residual: angle pdb=" CB MET A 951 " pdb=" CG MET A 951 " pdb=" SD MET A 951 " ideal model delta sigma weight residual 112.70 128.21 -15.51 3.00e+00 1.11e-01 2.67e+01 angle pdb=" CA LEU A2035 " pdb=" CB LEU A2035 " pdb=" CG LEU A2035 " ideal model delta sigma weight residual 116.30 133.44 -17.14 3.50e+00 8.16e-02 2.40e+01 angle pdb=" CA MET A 587 " pdb=" CB MET A 587 " pdb=" CG MET A 587 " ideal model delta sigma weight residual 114.10 123.24 -9.14 2.00e+00 2.50e-01 2.09e+01 angle pdb=" CA LEU A1337 " pdb=" CB LEU A1337 " pdb=" CG LEU A1337 " ideal model delta sigma weight residual 116.30 131.22 -14.92 3.50e+00 8.16e-02 1.82e+01 angle pdb=" CA MET A 875 " pdb=" CB MET A 875 " pdb=" CG MET A 875 " ideal model delta sigma weight residual 114.10 122.53 -8.43 2.00e+00 2.50e-01 1.78e+01 ... (remaining 18271 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 6876 16.44 - 32.89: 1016 32.89 - 49.33: 306 49.33 - 65.78: 65 65.78 - 82.22: 18 Dihedral angle restraints: 8281 sinusoidal: 3472 harmonic: 4809 Sorted by residual: dihedral pdb=" CA TYR A1044 " pdb=" C TYR A1044 " pdb=" N PRO A1045 " pdb=" CA PRO A1045 " ideal model delta harmonic sigma weight residual -180.00 -155.04 -24.96 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA SER A1965 " pdb=" C SER A1965 " pdb=" N PRO A1966 " pdb=" CA PRO A1966 " ideal model delta harmonic sigma weight residual 180.00 -155.31 -24.69 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA VAL A1962 " pdb=" C VAL A1962 " pdb=" N GLU A1963 " pdb=" CA GLU A1963 " ideal model delta harmonic sigma weight residual 180.00 157.21 22.79 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 8278 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1754 0.064 - 0.129: 281 0.129 - 0.193: 43 0.193 - 0.258: 2 0.258 - 0.322: 2 Chirality restraints: 2082 Sorted by residual: chirality pdb=" CB ILE A 423 " pdb=" CA ILE A 423 " pdb=" CG1 ILE A 423 " pdb=" CG2 ILE A 423 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB ILE A1043 " pdb=" CA ILE A1043 " pdb=" CG1 ILE A1043 " pdb=" CG2 ILE A1043 " both_signs ideal model delta sigma weight residual False 2.64 2.97 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CG LEU A1752 " pdb=" CB LEU A1752 " pdb=" CD1 LEU A1752 " pdb=" CD2 LEU A1752 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.82e-01 ... (remaining 2079 not shown) Planarity restraints: 2254 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A1043 " -0.022 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" C ILE A1043 " 0.077 2.00e-02 2.50e+03 pdb=" O ILE A1043 " -0.029 2.00e-02 2.50e+03 pdb=" N TYR A1044 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1952 " -0.015 2.00e-02 2.50e+03 1.86e-02 8.61e+00 pdb=" CG TRP A1952 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A1952 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A1952 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A1952 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1952 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1952 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1952 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1952 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A1952 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 587 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.10e+00 pdb=" C MET A 587 " -0.049 2.00e-02 2.50e+03 pdb=" O MET A 587 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS A 588 " 0.016 2.00e-02 2.50e+03 ... (remaining 2251 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3312 2.80 - 3.32: 11604 3.32 - 3.85: 21456 3.85 - 4.37: 23969 4.37 - 4.90: 42754 Nonbonded interactions: 103095 Sorted by model distance: nonbonded pdb=" OG SER A1372 " pdb=" O TRP A1453 " model vdw 2.271 3.040 nonbonded pdb=" OG SER A1372 " pdb=" OD1 ASN A1452 " model vdw 2.272 3.040 nonbonded pdb=" O LEU A1340 " pdb=" OG1 THR A1344 " model vdw 2.281 3.040 nonbonded pdb=" OD2 ASP A1740 " pdb=" OG SER A1855 " model vdw 2.284 3.040 nonbonded pdb=" OD2 ASP A 378 " pdb=" OG1 THR A1391 " model vdw 2.284 3.040 ... (remaining 103090 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.740 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 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 : 0.004 0.050 13530 Z= 0.190 Angle : 0.843 17.144 18276 Z= 0.440 Chirality : 0.049 0.322 2082 Planarity : 0.006 0.076 2254 Dihedral : 17.209 82.221 5153 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.86 % Favored : 93.01 % Rotamer: Outliers : 2.35 % Allowed : 20.58 % Favored : 77.08 % 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: -1.88 (0.19), residues: 1603 helix: -0.45 (0.16), residues: 868 sheet: 0.17 (0.57), residues: 85 loop : -2.56 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A1555 TYR 0.023 0.002 TYR A2064 PHE 0.041 0.002 PHE A1950 TRP 0.050 0.002 TRP A1952 HIS 0.004 0.001 HIS A1466 Details of bonding type rmsd covalent geometry : bond 0.00378 (13530) covalent geometry : angle 0.84342 (18276) hydrogen bonds : bond 0.08479 ( 665) hydrogen bonds : angle 4.80627 ( 1941) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6084 (OUTLIER) cc_final: 0.5283 (m-10) REVERT: A 809 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.6901 (t80) REVERT: A 922 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6922 (mp0) REVERT: A 972 ILE cc_start: 0.6238 (OUTLIER) cc_final: 0.5437 (mp) REVERT: A 1340 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7639 (mm) REVERT: A 1350 ASP cc_start: 0.7512 (m-30) cc_final: 0.7092 (m-30) REVERT: A 1769 LYS cc_start: 0.8430 (mmmt) cc_final: 0.8157 (mmmt) REVERT: A 1919 ASN cc_start: 0.7999 (m-40) cc_final: 0.7648 (m110) REVERT: A 2076 ASN cc_start: 0.6299 (p0) cc_final: 0.6051 (p0) outliers start: 35 outliers final: 27 residues processed: 198 average time/residue: 0.0908 time to fit residues: 27.8726 Evaluate side-chains 197 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 922 GLU Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1011 HIS Chi-restraints excluded: chain A residue 1022 ASN Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1715 THR Chi-restraints excluded: chain A residue 1754 GLN Chi-restraints excluded: chain A residue 1891 THR Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1953 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.0970 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.1980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 ASN A1213 ASN A2068 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.200502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.162823 restraints weight = 15598.856| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 1.83 r_work: 0.3717 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.0771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13530 Z= 0.117 Angle : 0.551 10.194 18276 Z= 0.288 Chirality : 0.041 0.255 2082 Planarity : 0.004 0.046 2254 Dihedral : 8.701 73.609 1930 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.86 % Favored : 94.01 % Rotamer: Outliers : 2.75 % Allowed : 20.78 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.65 (0.21), residues: 1603 helix: 0.84 (0.17), residues: 871 sheet: -0.04 (0.58), residues: 85 loop : -2.34 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1555 TYR 0.024 0.001 TYR A1044 PHE 0.031 0.001 PHE A1950 TRP 0.015 0.001 TRP A1952 HIS 0.004 0.001 HIS A1466 Details of bonding type rmsd covalent geometry : bond 0.00254 (13530) covalent geometry : angle 0.55086 (18276) hydrogen bonds : bond 0.04369 ( 665) hydrogen bonds : angle 3.97100 ( 1941) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 809 TYR cc_start: 0.7891 (OUTLIER) cc_final: 0.6912 (t80) REVERT: A 858 LYS cc_start: 0.7894 (ptmt) cc_final: 0.7472 (mtmt) REVERT: A 972 ILE cc_start: 0.5954 (OUTLIER) cc_final: 0.5197 (mp) REVERT: A 1091 PHE cc_start: 0.8119 (m-80) cc_final: 0.7909 (m-80) REVERT: A 1157 GLU cc_start: 0.6097 (OUTLIER) cc_final: 0.5655 (pm20) REVERT: A 1350 ASP cc_start: 0.8288 (m-30) cc_final: 0.7809 (m-30) REVERT: A 1713 LYS cc_start: 0.7324 (mmtm) cc_final: 0.7022 (ttpt) REVERT: A 1746 MET cc_start: 0.6138 (ptp) cc_final: 0.5900 (ptp) REVERT: A 1819 MET cc_start: 0.5298 (tpp) cc_final: 0.4687 (tpp) REVERT: A 1823 HIS cc_start: 0.7224 (m90) cc_final: 0.6525 (m-70) REVERT: A 1919 ASN cc_start: 0.7982 (m-40) cc_final: 0.7520 (m110) REVERT: A 2076 ASN cc_start: 0.6423 (p0) cc_final: 0.6098 (p0) outliers start: 41 outliers final: 21 residues processed: 212 average time/residue: 0.0903 time to fit residues: 28.7335 Evaluate side-chains 193 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1022 ASN Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1157 GLU Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1428 PHE Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1618 SER Chi-restraints excluded: chain A residue 1833 ILE Chi-restraints excluded: chain A residue 1953 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 0.0470 chunk 50 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 119 optimal weight: 0.0870 chunk 26 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1728 ASN ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2068 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.200100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.161739 restraints weight = 15561.010| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 1.88 r_work: 0.3731 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13530 Z= 0.102 Angle : 0.525 11.103 18276 Z= 0.272 Chirality : 0.040 0.204 2082 Planarity : 0.003 0.047 2254 Dihedral : 7.690 73.634 1892 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.80 % Favored : 94.07 % Rotamer: Outliers : 3.22 % Allowed : 20.44 % Favored : 76.34 % 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 (0.21), residues: 1603 helix: 1.32 (0.18), residues: 870 sheet: -0.04 (0.58), residues: 85 loop : -2.27 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1555 TYR 0.019 0.001 TYR A1044 PHE 0.028 0.001 PHE A1950 TRP 0.022 0.001 TRP A1952 HIS 0.003 0.001 HIS A1466 Details of bonding type rmsd covalent geometry : bond 0.00214 (13530) covalent geometry : angle 0.52484 (18276) hydrogen bonds : bond 0.03917 ( 665) hydrogen bonds : angle 3.80390 ( 1941) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 183 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 809 TYR cc_start: 0.7863 (OUTLIER) cc_final: 0.6981 (t80) REVERT: A 858 LYS cc_start: 0.7851 (ptmt) cc_final: 0.7414 (mtmt) REVERT: A 972 ILE cc_start: 0.5897 (OUTLIER) cc_final: 0.5144 (mp) REVERT: A 1157 GLU cc_start: 0.6033 (OUTLIER) cc_final: 0.5581 (pm20) REVERT: A 1350 ASP cc_start: 0.8299 (m-30) cc_final: 0.7827 (m-30) REVERT: A 1713 LYS cc_start: 0.7364 (mmtm) cc_final: 0.7081 (ttpt) REVERT: A 1819 MET cc_start: 0.5583 (tpp) cc_final: 0.4948 (tpp) REVERT: A 1823 HIS cc_start: 0.7197 (m90) cc_final: 0.6523 (m-70) REVERT: A 1919 ASN cc_start: 0.8011 (m-40) cc_final: 0.7552 (m110) REVERT: A 2076 ASN cc_start: 0.6337 (p0) cc_final: 0.6070 (p0) outliers start: 48 outliers final: 30 residues processed: 220 average time/residue: 0.1035 time to fit residues: 34.3880 Evaluate side-chains 204 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1022 ASN Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1157 GLU Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1428 PHE Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1566 CYS Chi-restraints excluded: chain A residue 1618 SER Chi-restraints excluded: chain A residue 1833 ILE Chi-restraints excluded: chain A residue 1891 THR Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1953 PHE Chi-restraints excluded: chain A residue 2050 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 30 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 68 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 120 optimal weight: 0.3980 chunk 70 optimal weight: 10.0000 chunk 137 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1420 ASN ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2068 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.199828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.161858 restraints weight = 15462.187| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 1.79 r_work: 0.3694 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13530 Z= 0.109 Angle : 0.524 11.053 18276 Z= 0.272 Chirality : 0.041 0.272 2082 Planarity : 0.003 0.041 2254 Dihedral : 7.574 73.651 1889 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.93 % Favored : 93.95 % Rotamer: Outliers : 3.28 % Allowed : 21.72 % Favored : 75.00 % 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: 0.04 (0.22), residues: 1603 helix: 1.52 (0.18), residues: 879 sheet: 0.04 (0.57), residues: 85 loop : -2.22 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1555 TYR 0.019 0.001 TYR A1044 PHE 0.028 0.001 PHE A1950 TRP 0.027 0.001 TRP A1952 HIS 0.004 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00240 (13530) covalent geometry : angle 0.52407 (18276) hydrogen bonds : bond 0.03983 ( 665) hydrogen bonds : angle 3.73953 ( 1941) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 175 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 LEU cc_start: 0.8356 (tt) cc_final: 0.8111 (tp) REVERT: A 809 TYR cc_start: 0.7939 (OUTLIER) cc_final: 0.7074 (t80) REVERT: A 858 LYS cc_start: 0.7726 (ptmt) cc_final: 0.7392 (mtmt) REVERT: A 972 ILE cc_start: 0.5887 (OUTLIER) cc_final: 0.5146 (mp) REVERT: A 1157 GLU cc_start: 0.5918 (OUTLIER) cc_final: 0.5513 (pm20) REVERT: A 1455 GLN cc_start: 0.7978 (tp40) cc_final: 0.7732 (tp40) REVERT: A 1494 ASP cc_start: 0.6654 (t0) cc_final: 0.6208 (t70) REVERT: A 1819 MET cc_start: 0.5352 (tpp) cc_final: 0.4700 (tpp) REVERT: A 1823 HIS cc_start: 0.7079 (m90) cc_final: 0.6391 (m-70) REVERT: A 1919 ASN cc_start: 0.7844 (m-40) cc_final: 0.7414 (m110) outliers start: 49 outliers final: 29 residues processed: 212 average time/residue: 0.0995 time to fit residues: 31.8394 Evaluate side-chains 201 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1011 HIS Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1157 GLU Chi-restraints excluded: chain A residue 1211 TYR Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1428 PHE Chi-restraints excluded: chain A residue 1468 CYS Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1618 SER Chi-restraints excluded: chain A residue 1833 ILE Chi-restraints excluded: chain A residue 1871 ASP Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1953 PHE Chi-restraints excluded: chain A residue 2050 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 0.0670 chunk 68 optimal weight: 20.0000 chunk 155 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 overall best weight: 1.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1022 ASN A1316 HIS ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1954 GLN A2068 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.197724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.158902 restraints weight = 15806.493| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 1.84 r_work: 0.3702 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13530 Z= 0.130 Angle : 0.561 11.527 18276 Z= 0.290 Chirality : 0.042 0.274 2082 Planarity : 0.003 0.042 2254 Dihedral : 7.607 73.743 1887 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.11 % Favored : 93.76 % Rotamer: Outliers : 4.22 % Allowed : 21.11 % Favored : 74.66 % 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: 0.04 (0.21), residues: 1603 helix: 1.52 (0.18), residues: 879 sheet: 0.03 (0.57), residues: 85 loop : -2.23 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1335 TYR 0.019 0.001 TYR A1044 PHE 0.030 0.001 PHE A1950 TRP 0.029 0.002 TRP A1952 HIS 0.006 0.001 HIS A1466 Details of bonding type rmsd covalent geometry : bond 0.00298 (13530) covalent geometry : angle 0.56122 (18276) hydrogen bonds : bond 0.04471 ( 665) hydrogen bonds : angle 3.78685 ( 1941) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 179 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6447 (OUTLIER) cc_final: 0.5526 (m-10) REVERT: A 425 LEU cc_start: 0.8382 (tt) cc_final: 0.8134 (tp) REVERT: A 602 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7791 (mp) REVERT: A 716 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6546 (mt) REVERT: A 809 TYR cc_start: 0.7973 (OUTLIER) cc_final: 0.7068 (t80) REVERT: A 858 LYS cc_start: 0.7814 (ptmt) cc_final: 0.7443 (mtmt) REVERT: A 953 ASP cc_start: 0.7679 (t0) cc_final: 0.7434 (t0) REVERT: A 972 ILE cc_start: 0.5662 (OUTLIER) cc_final: 0.4925 (mp) REVERT: A 1157 GLU cc_start: 0.6017 (OUTLIER) cc_final: 0.5566 (pm20) REVERT: A 1455 GLN cc_start: 0.8162 (tp40) cc_final: 0.7913 (tp40) REVERT: A 1494 ASP cc_start: 0.7030 (t0) cc_final: 0.6563 (t70) REVERT: A 1554 GLU cc_start: 0.5802 (OUTLIER) cc_final: 0.5506 (mt-10) REVERT: A 1713 LYS cc_start: 0.7311 (mmtm) cc_final: 0.6949 (ttpt) REVERT: A 1819 MET cc_start: 0.5611 (tpp) cc_final: 0.4996 (tpp) REVERT: A 1823 HIS cc_start: 0.7313 (m90) cc_final: 0.6688 (m90) outliers start: 63 outliers final: 38 residues processed: 225 average time/residue: 0.0901 time to fit residues: 30.8956 Evaluate side-chains 216 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 171 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1011 HIS Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1157 GLU Chi-restraints excluded: chain A residue 1211 TYR Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1428 PHE Chi-restraints excluded: chain A residue 1468 CYS Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1552 ILE Chi-restraints excluded: chain A residue 1554 GLU Chi-restraints excluded: chain A residue 1561 ILE Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1566 CYS Chi-restraints excluded: chain A residue 1618 SER Chi-restraints excluded: chain A residue 1783 LEU Chi-restraints excluded: chain A residue 1833 ILE Chi-restraints excluded: chain A residue 1871 ASP Chi-restraints excluded: chain A residue 1891 THR Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1953 PHE Chi-restraints excluded: chain A residue 2050 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 87 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 85 optimal weight: 9.9990 chunk 150 optimal weight: 0.9980 chunk 73 optimal weight: 30.0000 chunk 97 optimal weight: 0.6980 chunk 99 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1022 ASN A1213 ASN ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1954 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.193945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.152983 restraints weight = 15778.564| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.90 r_work: 0.3595 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13530 Z= 0.199 Angle : 0.645 11.452 18276 Z= 0.334 Chirality : 0.045 0.275 2082 Planarity : 0.004 0.046 2254 Dihedral : 7.892 73.928 1885 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.24 % Favored : 92.64 % Rotamer: Outliers : 4.02 % Allowed : 21.72 % Favored : 74.26 % 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: -0.24 (0.21), residues: 1603 helix: 1.21 (0.18), residues: 888 sheet: -0.15 (0.55), residues: 87 loop : -2.28 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 341 TYR 0.022 0.002 TYR A1044 PHE 0.037 0.002 PHE A1950 TRP 0.034 0.002 TRP A1952 HIS 0.008 0.001 HIS A1466 Details of bonding type rmsd covalent geometry : bond 0.00482 (13530) covalent geometry : angle 0.64502 (18276) hydrogen bonds : bond 0.05686 ( 665) hydrogen bonds : angle 4.01126 ( 1941) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 169 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6590 (OUTLIER) cc_final: 0.5775 (m-10) REVERT: A 425 LEU cc_start: 0.8459 (tt) cc_final: 0.8245 (tp) REVERT: A 716 LEU cc_start: 0.6798 (OUTLIER) cc_final: 0.6573 (mt) REVERT: A 809 TYR cc_start: 0.8062 (OUTLIER) cc_final: 0.7032 (t80) REVERT: A 858 LYS cc_start: 0.7874 (ptmt) cc_final: 0.7572 (mtmt) REVERT: A 873 MET cc_start: 0.7267 (mtt) cc_final: 0.7064 (mtt) REVERT: A 953 ASP cc_start: 0.7807 (t0) cc_final: 0.7350 (t0) REVERT: A 972 ILE cc_start: 0.5811 (OUTLIER) cc_final: 0.5078 (mp) REVERT: A 1157 GLU cc_start: 0.6010 (OUTLIER) cc_final: 0.5563 (pm20) REVERT: A 1490 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.8036 (mt) REVERT: A 1549 VAL cc_start: 0.8998 (OUTLIER) cc_final: 0.8698 (p) REVERT: A 1713 LYS cc_start: 0.7250 (mmtm) cc_final: 0.6923 (ttpt) REVERT: A 2080 LEU cc_start: 0.4784 (OUTLIER) cc_final: 0.4476 (mt) outliers start: 60 outliers final: 40 residues processed: 212 average time/residue: 0.0889 time to fit residues: 29.1427 Evaluate side-chains 210 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 162 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 855 GLU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1011 HIS Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1157 GLU Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1428 PHE Chi-restraints excluded: chain A residue 1468 CYS Chi-restraints excluded: chain A residue 1490 ILE Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1552 ILE Chi-restraints excluded: chain A residue 1561 ILE Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1566 CYS Chi-restraints excluded: chain A residue 1618 SER Chi-restraints excluded: chain A residue 1715 THR Chi-restraints excluded: chain A residue 1783 LEU Chi-restraints excluded: chain A residue 1833 ILE Chi-restraints excluded: chain A residue 1891 THR Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1953 PHE Chi-restraints excluded: chain A residue 1954 GLN Chi-restraints excluded: chain A residue 1955 THR Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 1963 GLU Chi-restraints excluded: chain A residue 2050 LEU Chi-restraints excluded: chain A residue 2080 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 105 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 29 optimal weight: 0.0010 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 0.0070 overall best weight: 0.7808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1022 ASN ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1954 GLN ** A2068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.195980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.156600 restraints weight = 15352.236| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 1.87 r_work: 0.3643 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13530 Z= 0.122 Angle : 0.574 11.866 18276 Z= 0.295 Chirality : 0.042 0.266 2082 Planarity : 0.004 0.045 2254 Dihedral : 7.760 73.799 1885 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.24 % Favored : 93.64 % Rotamer: Outliers : 3.82 % Allowed : 22.05 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.22), residues: 1603 helix: 1.49 (0.18), residues: 879 sheet: -0.06 (0.56), residues: 87 loop : -2.20 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1555 TYR 0.017 0.001 TYR A2064 PHE 0.030 0.001 PHE A1950 TRP 0.033 0.002 TRP A1952 HIS 0.005 0.001 HIS A1466 Details of bonding type rmsd covalent geometry : bond 0.00271 (13530) covalent geometry : angle 0.57365 (18276) hydrogen bonds : bond 0.04494 ( 665) hydrogen bonds : angle 3.85329 ( 1941) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 170 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6416 (OUTLIER) cc_final: 0.5555 (m-10) REVERT: A 425 LEU cc_start: 0.8400 (tt) cc_final: 0.8190 (tp) REVERT: A 472 MET cc_start: 0.6453 (OUTLIER) cc_final: 0.5013 (mmt) REVERT: A 809 TYR cc_start: 0.7979 (OUTLIER) cc_final: 0.7006 (t80) REVERT: A 858 LYS cc_start: 0.7776 (ptmt) cc_final: 0.7469 (mtmt) REVERT: A 953 ASP cc_start: 0.7849 (t0) cc_final: 0.7376 (t0) REVERT: A 972 ILE cc_start: 0.5765 (OUTLIER) cc_final: 0.5046 (mp) REVERT: A 1157 GLU cc_start: 0.6002 (OUTLIER) cc_final: 0.5562 (pm20) REVERT: A 1549 VAL cc_start: 0.8893 (OUTLIER) cc_final: 0.8605 (p) REVERT: A 1713 LYS cc_start: 0.7233 (mmtm) cc_final: 0.6924 (ttpt) outliers start: 57 outliers final: 42 residues processed: 212 average time/residue: 0.0982 time to fit residues: 31.4627 Evaluate side-chains 215 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 167 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 855 GLU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1011 HIS Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1157 GLU Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1428 PHE Chi-restraints excluded: chain A residue 1442 LEU Chi-restraints excluded: chain A residue 1468 CYS Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1552 ILE Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1566 CYS Chi-restraints excluded: chain A residue 1618 SER Chi-restraints excluded: chain A residue 1715 THR Chi-restraints excluded: chain A residue 1746 MET Chi-restraints excluded: chain A residue 1783 LEU Chi-restraints excluded: chain A residue 1833 ILE Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1891 THR Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1953 PHE Chi-restraints excluded: chain A residue 1954 GLN Chi-restraints excluded: chain A residue 1955 THR Chi-restraints excluded: chain A residue 1963 GLU Chi-restraints excluded: chain A residue 2050 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 102 optimal weight: 0.3980 chunk 157 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 64 optimal weight: 0.2980 chunk 5 optimal weight: 0.0770 chunk 103 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 GLN A1022 ASN ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1954 GLN ** A2068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.199113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.160600 restraints weight = 15745.870| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 1.84 r_work: 0.3701 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13530 Z= 0.102 Angle : 0.541 12.115 18276 Z= 0.276 Chirality : 0.040 0.261 2082 Planarity : 0.003 0.045 2254 Dihedral : 7.595 73.636 1885 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.11 % Favored : 93.76 % Rotamer: Outliers : 3.75 % Allowed : 22.25 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.23 (0.22), residues: 1603 helix: 1.67 (0.18), residues: 880 sheet: 0.15 (0.57), residues: 85 loop : -2.16 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1555 TYR 0.017 0.001 TYR A2064 PHE 0.026 0.001 PHE A1950 TRP 0.027 0.001 TRP A1952 HIS 0.004 0.001 HIS A1316 Details of bonding type rmsd covalent geometry : bond 0.00214 (13530) covalent geometry : angle 0.54112 (18276) hydrogen bonds : bond 0.03807 ( 665) hydrogen bonds : angle 3.73407 ( 1941) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 168 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6422 (OUTLIER) cc_final: 0.5567 (m-10) REVERT: A 425 LEU cc_start: 0.8377 (tt) cc_final: 0.8163 (tp) REVERT: A 472 MET cc_start: 0.6233 (OUTLIER) cc_final: 0.4863 (mmt) REVERT: A 809 TYR cc_start: 0.7953 (OUTLIER) cc_final: 0.7022 (t80) REVERT: A 858 LYS cc_start: 0.7714 (ptmt) cc_final: 0.7408 (mtmt) REVERT: A 953 ASP cc_start: 0.7772 (t0) cc_final: 0.7274 (t0) REVERT: A 972 ILE cc_start: 0.5728 (OUTLIER) cc_final: 0.5002 (mp) REVERT: A 1157 GLU cc_start: 0.6073 (OUTLIER) cc_final: 0.5565 (pm20) REVERT: A 1455 GLN cc_start: 0.8066 (tp40) cc_final: 0.7783 (tp40) REVERT: A 1713 LYS cc_start: 0.7281 (mmtm) cc_final: 0.6958 (ttpt) outliers start: 56 outliers final: 42 residues processed: 208 average time/residue: 0.1064 time to fit residues: 33.4013 Evaluate side-chains 211 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 164 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1011 HIS Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1157 GLU Chi-restraints excluded: chain A residue 1211 TYR Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1428 PHE Chi-restraints excluded: chain A residue 1468 CYS Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1566 CYS Chi-restraints excluded: chain A residue 1618 SER Chi-restraints excluded: chain A residue 1623 LEU Chi-restraints excluded: chain A residue 1715 THR Chi-restraints excluded: chain A residue 1746 MET Chi-restraints excluded: chain A residue 1783 LEU Chi-restraints excluded: chain A residue 1850 MET Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1891 THR Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1953 PHE Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 1963 GLU Chi-restraints excluded: chain A residue 2050 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 110 optimal weight: 3.9990 chunk 89 optimal weight: 0.1980 chunk 112 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 153 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 73 optimal weight: 30.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 GLN A1022 ASN ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.198616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.157469 restraints weight = 15832.861| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.99 r_work: 0.3655 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13530 Z= 0.119 Angle : 0.565 12.443 18276 Z= 0.287 Chirality : 0.042 0.276 2082 Planarity : 0.003 0.046 2254 Dihedral : 7.602 73.675 1885 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.11 % Favored : 93.76 % Rotamer: Outliers : 3.22 % Allowed : 22.18 % Favored : 74.60 % 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: 0.24 (0.22), residues: 1603 helix: 1.66 (0.18), residues: 881 sheet: 0.16 (0.56), residues: 85 loop : -2.11 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1555 TYR 0.015 0.001 TYR A1044 PHE 0.029 0.001 PHE A1950 TRP 0.028 0.001 TRP A1952 HIS 0.004 0.001 HIS A1466 Details of bonding type rmsd covalent geometry : bond 0.00270 (13530) covalent geometry : angle 0.56489 (18276) hydrogen bonds : bond 0.04234 ( 665) hydrogen bonds : angle 3.75316 ( 1941) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 171 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6424 (OUTLIER) cc_final: 0.5536 (m-10) REVERT: A 425 LEU cc_start: 0.8385 (tt) cc_final: 0.8173 (tp) REVERT: A 809 TYR cc_start: 0.7995 (OUTLIER) cc_final: 0.7032 (t80) REVERT: A 858 LYS cc_start: 0.7683 (ptmt) cc_final: 0.7388 (mtmt) REVERT: A 953 ASP cc_start: 0.7858 (t0) cc_final: 0.7391 (t0) REVERT: A 972 ILE cc_start: 0.5707 (OUTLIER) cc_final: 0.4989 (mp) REVERT: A 1157 GLU cc_start: 0.6077 (OUTLIER) cc_final: 0.5574 (pm20) REVERT: A 1455 GLN cc_start: 0.8137 (tp40) cc_final: 0.7855 (tp40) REVERT: A 1713 LYS cc_start: 0.7253 (mmtm) cc_final: 0.6946 (ttpt) REVERT: A 1982 ASN cc_start: 0.7129 (t0) cc_final: 0.6703 (t0) outliers start: 48 outliers final: 39 residues processed: 206 average time/residue: 0.1057 time to fit residues: 33.0349 Evaluate side-chains 212 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 169 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1011 HIS Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1157 GLU Chi-restraints excluded: chain A residue 1211 TYR Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1428 PHE Chi-restraints excluded: chain A residue 1468 CYS Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1566 CYS Chi-restraints excluded: chain A residue 1618 SER Chi-restraints excluded: chain A residue 1623 LEU Chi-restraints excluded: chain A residue 1715 THR Chi-restraints excluded: chain A residue 1746 MET Chi-restraints excluded: chain A residue 1783 LEU Chi-restraints excluded: chain A residue 1850 MET Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1891 THR Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1953 PHE Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 1963 GLU Chi-restraints excluded: chain A residue 2050 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 99 optimal weight: 7.9990 chunk 137 optimal weight: 0.0770 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 22 optimal weight: 0.0470 chunk 33 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 20.0000 overall best weight: 0.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1022 ASN ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2068 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 = 0.4300 r_free = 0.4300 target = 0.198826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.157304 restraints weight = 15757.308| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.04 r_work: 0.3655 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13530 Z= 0.117 Angle : 0.563 12.782 18276 Z= 0.286 Chirality : 0.041 0.279 2082 Planarity : 0.003 0.047 2254 Dihedral : 7.588 73.679 1885 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.43 % Favored : 93.45 % Rotamer: Outliers : 3.15 % Allowed : 22.32 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.22), residues: 1603 helix: 1.64 (0.18), residues: 883 sheet: 0.19 (0.57), residues: 85 loop : -2.10 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1555 TYR 0.017 0.001 TYR A2064 PHE 0.028 0.001 PHE A1950 TRP 0.026 0.001 TRP A1952 HIS 0.004 0.001 HIS A1466 Details of bonding type rmsd covalent geometry : bond 0.00263 (13530) covalent geometry : angle 0.56308 (18276) hydrogen bonds : bond 0.04153 ( 665) hydrogen bonds : angle 3.73640 ( 1941) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 172 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6475 (OUTLIER) cc_final: 0.5603 (m-10) REVERT: A 425 LEU cc_start: 0.8391 (tt) cc_final: 0.8174 (tp) REVERT: A 746 MET cc_start: 0.7921 (mtm) cc_final: 0.7610 (mtp) REVERT: A 809 TYR cc_start: 0.8004 (OUTLIER) cc_final: 0.6987 (t80) REVERT: A 858 LYS cc_start: 0.7683 (ptmt) cc_final: 0.7381 (mtmt) REVERT: A 953 ASP cc_start: 0.7889 (t0) cc_final: 0.7435 (t0) REVERT: A 972 ILE cc_start: 0.5671 (OUTLIER) cc_final: 0.4950 (mp) REVERT: A 1157 GLU cc_start: 0.6076 (OUTLIER) cc_final: 0.5578 (pm20) REVERT: A 1455 GLN cc_start: 0.8160 (tp40) cc_final: 0.7872 (tp40) REVERT: A 1549 VAL cc_start: 0.8817 (t) cc_final: 0.8572 (p) REVERT: A 1713 LYS cc_start: 0.7178 (mmtm) cc_final: 0.6910 (ttpt) REVERT: A 1982 ASN cc_start: 0.7136 (t0) cc_final: 0.6715 (t0) outliers start: 47 outliers final: 41 residues processed: 207 average time/residue: 0.0924 time to fit residues: 28.8353 Evaluate side-chains 214 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 169 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1011 HIS Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1157 GLU Chi-restraints excluded: chain A residue 1211 TYR Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1428 PHE Chi-restraints excluded: chain A residue 1468 CYS Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1566 CYS Chi-restraints excluded: chain A residue 1600 CYS Chi-restraints excluded: chain A residue 1618 SER Chi-restraints excluded: chain A residue 1623 LEU Chi-restraints excluded: chain A residue 1715 THR Chi-restraints excluded: chain A residue 1746 MET Chi-restraints excluded: chain A residue 1783 LEU Chi-restraints excluded: chain A residue 1850 MET Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1891 THR Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1953 PHE Chi-restraints excluded: chain A residue 1955 THR Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 1963 GLU Chi-restraints excluded: chain A residue 2050 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 26 optimal weight: 0.9990 chunk 146 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 84 optimal weight: 0.0030 chunk 145 optimal weight: 0.7980 chunk 160 optimal weight: 7.9990 chunk 101 optimal weight: 0.3980 chunk 73 optimal weight: 30.0000 chunk 63 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1022 ASN ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2068 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 = 0.4291 r_free = 0.4291 target = 0.198007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.159631 restraints weight = 15479.641| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 1.87 r_work: 0.3674 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13530 Z= 0.107 Angle : 0.548 12.670 18276 Z= 0.277 Chirality : 0.041 0.271 2082 Planarity : 0.003 0.046 2254 Dihedral : 7.502 73.632 1885 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.24 % Favored : 93.64 % Rotamer: Outliers : 3.08 % Allowed : 22.25 % Favored : 74.66 % 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: 0.30 (0.22), residues: 1603 helix: 1.71 (0.18), residues: 883 sheet: 0.01 (0.52), residues: 99 loop : -2.12 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1555 TYR 0.016 0.001 TYR A2064 PHE 0.027 0.001 PHE A1950 TRP 0.027 0.001 TRP A1952 HIS 0.004 0.001 HIS A1466 Details of bonding type rmsd covalent geometry : bond 0.00235 (13530) covalent geometry : angle 0.54800 (18276) hydrogen bonds : bond 0.03888 ( 665) hydrogen bonds : angle 3.71804 ( 1941) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2791.17 seconds wall clock time: 48 minutes 48.42 seconds (2928.42 seconds total)