Starting phenix.real_space_refine on Thu Jul 31 09:52:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ki8_37254/07_2025/8ki8_37254.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ki8_37254/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ki8_37254/07_2025/8ki8_37254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ki8_37254/07_2025/8ki8_37254.map" model { file = "/net/cci-nas-00/data/ceres_data/8ki8_37254/07_2025/8ki8_37254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ki8_37254/07_2025/8ki8_37254.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.109 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'ARG:plan': 1, 'GLN:plan1': 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: 7.41, per 1000 atoms: 0.56 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: 2.81 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.43 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: 4.61 Time building geometry restraints manager: 3.41 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.010 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.540 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.050 0.002 TRP A1952 HIS 0.004 0.001 HIS A1466 PHE 0.041 0.002 PHE A1950 TYR 0.023 0.002 TYR A2064 ARG 0.016 0.001 ARG A1555 Details of bonding type rmsd hydrogen bonds : bond 0.08479 ( 665) hydrogen bonds : angle 4.80627 ( 1941) covalent geometry : bond 0.00378 (13530) covalent geometry : angle 0.84342 (18276) *********************** 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 : 1.382 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: 0.2248 time to fit residues: 68.0332 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 : 1.374 ------------------------------------------------------------------------------- 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 137 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 30.0000 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 127 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 ASN A2068 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.195455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.156333 restraints weight = 15425.958| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.85 r_work: 0.3649 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13530 Z= 0.170 Angle : 0.615 10.187 18276 Z= 0.322 Chirality : 0.044 0.266 2082 Planarity : 0.004 0.050 2254 Dihedral : 8.945 73.801 1930 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.61 % Favored : 93.26 % Rotamer: Outliers : 3.49 % Allowed : 19.91 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.21), residues: 1603 helix: 0.63 (0.17), residues: 880 sheet: -0.07 (0.57), residues: 85 loop : -2.37 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1952 HIS 0.007 0.001 HIS A1466 PHE 0.035 0.002 PHE A1950 TYR 0.026 0.001 TYR A1044 ARG 0.003 0.000 ARG A 498 Details of bonding type rmsd hydrogen bonds : bond 0.05355 ( 665) hydrogen bonds : angle 4.12616 ( 1941) covalent geometry : bond 0.00398 (13530) covalent geometry : angle 0.61494 (18276) *********************** 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 233 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 181 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6435 (OUTLIER) cc_final: 0.5406 (m-10) REVERT: A 809 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.6895 (t80) REVERT: A 858 LYS cc_start: 0.7789 (ptmt) cc_final: 0.7420 (mtmt) REVERT: A 953 ASP cc_start: 0.7675 (t0) cc_final: 0.7391 (t0) REVERT: A 972 ILE cc_start: 0.5948 (OUTLIER) cc_final: 0.5173 (mp) REVERT: A 1157 GLU cc_start: 0.6108 (OUTLIER) cc_final: 0.5657 (pm20) REVERT: A 1205 LEU cc_start: 0.6425 (tp) cc_final: 0.6216 (tt) REVERT: A 1713 LYS cc_start: 0.7402 (mmtm) cc_final: 0.7189 (ttpt) REVERT: A 2076 ASN cc_start: 0.6396 (p0) cc_final: 0.6080 (p0) outliers start: 52 outliers final: 30 residues processed: 221 average time/residue: 0.2614 time to fit residues: 86.3848 Evaluate side-chains 203 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 2.490 ------------------------------------------------------------------------------- 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 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 1260 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 1552 ILE Chi-restraints excluded: chain A residue 1561 ILE Chi-restraints excluded: chain A residue 1567 ARG 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 113 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 156 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1954 GLN A2068 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.198354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.159802 restraints weight = 15557.281| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 1.89 r_work: 0.3708 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1016 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= 0.120 Angle : 0.553 10.886 18276 Z= 0.288 Chirality : 0.041 0.220 2082 Planarity : 0.004 0.048 2254 Dihedral : 8.146 73.749 1900 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.11 % Favored : 93.76 % Rotamer: Outliers : 3.35 % Allowed : 20.64 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.21), residues: 1603 helix: 1.17 (0.18), residues: 870 sheet: -0.32 (0.57), residues: 87 loop : -2.31 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1952 HIS 0.005 0.001 HIS A1466 PHE 0.030 0.001 PHE A1950 TYR 0.021 0.001 TYR A1044 ARG 0.005 0.000 ARG A1555 Details of bonding type rmsd hydrogen bonds : bond 0.04444 ( 665) hydrogen bonds : angle 3.92003 ( 1941) covalent geometry : bond 0.00267 (13530) covalent geometry : angle 0.55326 (18276) *********************** 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 225 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 2.051 Fit side-chains revert: symmetry clash REVERT: A 809 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.7043 (t80) REVERT: A 858 LYS cc_start: 0.7951 (ptmt) cc_final: 0.7543 (mtmt) REVERT: A 953 ASP cc_start: 0.7773 (t0) cc_final: 0.7335 (t0) REVERT: A 972 ILE cc_start: 0.5901 (OUTLIER) cc_final: 0.5153 (mp) REVERT: A 1157 GLU cc_start: 0.6035 (OUTLIER) cc_final: 0.5582 (pm20) REVERT: A 1350 ASP cc_start: 0.8019 (m-30) cc_final: 0.7804 (m-30) REVERT: A 1713 LYS cc_start: 0.7291 (mmtm) cc_final: 0.7082 (ttpt) REVERT: A 2076 ASN cc_start: 0.6401 (p0) cc_final: 0.6127 (p0) outliers start: 50 outliers final: 28 residues processed: 214 average time/residue: 0.2538 time to fit residues: 82.4470 Evaluate side-chains 200 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ASP 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 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 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 1468 CYS Chi-restraints excluded: chain A residue 1549 VAL 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 1833 ILE 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 61 optimal weight: 0.0020 chunk 149 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.198573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.160392 restraints weight = 15278.986| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 1.80 r_work: 0.3684 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13530 Z= 0.111 Angle : 0.538 11.207 18276 Z= 0.278 Chirality : 0.041 0.274 2082 Planarity : 0.003 0.043 2254 Dihedral : 7.828 73.687 1892 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.05 % Favored : 93.82 % Rotamer: Outliers : 3.69 % Allowed : 21.25 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.21), residues: 1603 helix: 1.43 (0.18), residues: 877 sheet: -0.07 (0.57), residues: 85 loop : -2.29 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A1952 HIS 0.005 0.001 HIS A 404 PHE 0.027 0.001 PHE A1950 TYR 0.018 0.001 TYR A1044 ARG 0.004 0.000 ARG A1555 Details of bonding type rmsd hydrogen bonds : bond 0.04095 ( 665) hydrogen bonds : angle 3.81314 ( 1941) covalent geometry : bond 0.00243 (13530) covalent geometry : angle 0.53761 (18276) *********************** 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 229 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 174 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 809 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.7074 (t80) REVERT: A 858 LYS cc_start: 0.7716 (ptmt) cc_final: 0.7427 (mtmt) REVERT: A 953 ASP cc_start: 0.7686 (t0) cc_final: 0.7200 (t0) REVERT: A 972 ILE cc_start: 0.5796 (OUTLIER) cc_final: 0.5056 (mp) REVERT: A 1157 GLU cc_start: 0.5925 (OUTLIER) cc_final: 0.5536 (pm20) REVERT: A 1823 HIS cc_start: 0.7158 (m90) cc_final: 0.6480 (m-70) outliers start: 55 outliers final: 35 residues processed: 214 average time/residue: 0.3801 time to fit residues: 122.9530 Evaluate side-chains 207 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 2.032 ------------------------------------------------------------------------------- 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 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 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 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 1340 LEU Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1428 PHE Chi-restraints excluded: chain A residue 1468 CYS 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 2050 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 17 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 67 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 120 optimal weight: 0.0370 chunk 21 optimal weight: 0.9990 chunk 1 optimal weight: 0.0570 chunk 69 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 848 GLN A1022 ASN ** A1316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2068 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.199795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.161819 restraints weight = 15660.685| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.82 r_work: 0.3708 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13530 Z= 0.102 Angle : 0.525 11.558 18276 Z= 0.272 Chirality : 0.040 0.264 2082 Planarity : 0.003 0.042 2254 Dihedral : 7.703 73.637 1889 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.68 % Favored : 94.20 % Rotamer: Outliers : 3.89 % Allowed : 21.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.22), residues: 1603 helix: 1.56 (0.18), residues: 880 sheet: 0.05 (0.57), residues: 85 loop : -2.24 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A1952 HIS 0.004 0.001 HIS A1466 PHE 0.026 0.001 PHE A1950 TYR 0.017 0.001 TYR A1044 ARG 0.005 0.000 ARG A1555 Details of bonding type rmsd hydrogen bonds : bond 0.03858 ( 665) hydrogen bonds : angle 3.73642 ( 1941) covalent geometry : bond 0.00216 (13530) covalent geometry : angle 0.52482 (18276) *********************** 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 234 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 176 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6502 (OUTLIER) cc_final: 0.5570 (m-10) REVERT: A 602 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7769 (mp) REVERT: A 809 TYR cc_start: 0.7890 (OUTLIER) cc_final: 0.7051 (t80) REVERT: A 858 LYS cc_start: 0.7848 (ptmt) cc_final: 0.7545 (mtmt) REVERT: A 953 ASP cc_start: 0.7854 (t0) cc_final: 0.7355 (t0) REVERT: A 972 ILE cc_start: 0.5807 (OUTLIER) cc_final: 0.5088 (mp) REVERT: A 1157 GLU cc_start: 0.5959 (OUTLIER) cc_final: 0.5508 (pm20) REVERT: A 1455 GLN cc_start: 0.8178 (tp40) cc_final: 0.7927 (tp40) REVERT: A 1494 ASP cc_start: 0.7020 (t0) cc_final: 0.6590 (t70) REVERT: A 1713 LYS cc_start: 0.7204 (mmtm) cc_final: 0.6847 (ttpt) REVERT: A 1823 HIS cc_start: 0.7208 (m90) cc_final: 0.6567 (m-70) outliers start: 58 outliers final: 37 residues processed: 217 average time/residue: 0.2698 time to fit residues: 89.1334 Evaluate side-chains 211 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 1.736 ------------------------------------------------------------------------------- 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 468 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 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 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 1682 LEU 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 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 2050 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 138 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 70 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1022 ASN ** A1316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1728 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 = 0.4275 r_free = 0.4275 target = 0.195530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.156269 restraints weight = 15536.075| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 1.83 r_work: 0.3639 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1470 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= 0.148 Angle : 0.584 11.797 18276 Z= 0.302 Chirality : 0.043 0.277 2082 Planarity : 0.004 0.044 2254 Dihedral : 7.850 73.774 1889 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.80 % Favored : 93.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.22), residues: 1603 helix: 1.48 (0.18), residues: 880 sheet: 0.03 (0.57), residues: 85 loop : -2.22 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A1952 HIS 0.006 0.001 HIS A1466 PHE 0.031 0.002 PHE A1950 TYR 0.019 0.001 TYR A1044 ARG 0.005 0.000 ARG A1555 Details of bonding type rmsd hydrogen bonds : bond 0.04825 ( 665) hydrogen bonds : angle 3.83564 ( 1941) covalent geometry : bond 0.00346 (13530) covalent geometry : angle 0.58377 (18276) *********************** 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 : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6434 (OUTLIER) cc_final: 0.5527 (m-10) REVERT: A 809 TYR cc_start: 0.7990 (OUTLIER) cc_final: 0.7043 (t80) REVERT: A 858 LYS cc_start: 0.7723 (ptmt) cc_final: 0.7504 (mtmt) REVERT: A 873 MET cc_start: 0.7267 (mtt) cc_final: 0.6959 (mtt) REVERT: A 953 ASP cc_start: 0.7909 (t0) cc_final: 0.7452 (t0) REVERT: A 972 ILE cc_start: 0.5792 (OUTLIER) cc_final: 0.5052 (mp) REVERT: A 1157 GLU cc_start: 0.6006 (OUTLIER) cc_final: 0.5568 (pm20) REVERT: A 1470 MET cc_start: 0.9029 (mmm) cc_final: 0.8827 (mmm) REVERT: A 1549 VAL cc_start: 0.8920 (OUTLIER) cc_final: 0.8672 (p) REVERT: A 1713 LYS cc_start: 0.7276 (mmtm) cc_final: 0.6925 (ttpt) REVERT: A 2080 LEU cc_start: 0.4774 (OUTLIER) cc_final: 0.4553 (mt) outliers start: 60 outliers final: 41 residues processed: 214 average time/residue: 0.2302 time to fit residues: 75.6783 Evaluate side-chains 208 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 1.375 ------------------------------------------------------------------------------- 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 468 THR 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 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 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 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 1442 LEU 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 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 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 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 146 optimal weight: 0.0000 chunk 143 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 91 optimal weight: 0.0670 chunk 78 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 99 optimal weight: 0.1980 chunk 112 optimal weight: 0.6980 chunk 69 optimal weight: 0.0970 overall best weight: 0.2120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1022 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.201329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.163592 restraints weight = 15472.749| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 1.83 r_work: 0.3720 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13530 Z= 0.096 Angle : 0.525 12.107 18276 Z= 0.269 Chirality : 0.040 0.260 2082 Planarity : 0.003 0.043 2254 Dihedral : 7.555 73.587 1887 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.86 % Favored : 94.01 % Rotamer: Outliers : 3.42 % Allowed : 22.52 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.22), residues: 1603 helix: 1.73 (0.18), residues: 880 sheet: 0.03 (0.55), residues: 92 loop : -2.19 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A1952 HIS 0.004 0.001 HIS A 404 PHE 0.024 0.001 PHE A1950 TYR 0.014 0.001 TYR A2064 ARG 0.007 0.000 ARG A1555 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 665) hydrogen bonds : angle 3.67864 ( 1941) covalent geometry : bond 0.00192 (13530) covalent geometry : angle 0.52532 (18276) *********************** 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 224 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 173 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6382 (OUTLIER) cc_final: 0.5530 (m-10) REVERT: A 472 MET cc_start: 0.6412 (OUTLIER) cc_final: 0.5053 (mmt) REVERT: A 809 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.7008 (t80) REVERT: A 822 MET cc_start: 0.7679 (mmt) cc_final: 0.7095 (mmt) REVERT: A 858 LYS cc_start: 0.7633 (ptmt) cc_final: 0.7425 (mtmt) REVERT: A 953 ASP cc_start: 0.7856 (t0) cc_final: 0.7394 (t0) REVERT: A 972 ILE cc_start: 0.5856 (OUTLIER) cc_final: 0.5118 (mp) REVERT: A 977 ASP cc_start: 0.7948 (m-30) cc_final: 0.7676 (m-30) REVERT: A 1157 GLU cc_start: 0.6068 (OUTLIER) cc_final: 0.5565 (pm20) REVERT: A 1455 GLN cc_start: 0.8028 (tp40) cc_final: 0.7744 (tp40) REVERT: A 1470 MET cc_start: 0.9049 (mmm) cc_final: 0.8797 (mmm) REVERT: A 1494 ASP cc_start: 0.6809 (t0) cc_final: 0.6387 (t70) REVERT: A 1713 LYS cc_start: 0.7256 (mmtm) cc_final: 0.6939 (ttpt) REVERT: A 1823 HIS cc_start: 0.6958 (m90) cc_final: 0.6340 (m-70) outliers start: 51 outliers final: 32 residues processed: 209 average time/residue: 0.2328 time to fit residues: 73.5874 Evaluate side-chains 201 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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 413 GLU Chi-restraints excluded: chain A residue 468 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 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 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 1342 LEU Chi-restraints excluded: chain A residue 1428 PHE Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1566 CYS Chi-restraints excluded: chain A residue 1623 LEU Chi-restraints excluded: chain A residue 1715 THR Chi-restraints excluded: chain A residue 1783 LEU Chi-restraints excluded: chain A residue 1850 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 46 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 132 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 111 optimal weight: 0.0050 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1022 ASN ** A1316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4313 r_free = 0.4313 target = 0.199878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.158952 restraints weight = 15737.422| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 1.97 r_work: 0.3676 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13530 Z= 0.114 Angle : 0.548 12.291 18276 Z= 0.280 Chirality : 0.041 0.271 2082 Planarity : 0.003 0.047 2254 Dihedral : 7.553 73.643 1887 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.11 % Favored : 93.76 % Rotamer: Outliers : 3.15 % Allowed : 22.92 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.22), residues: 1603 helix: 1.75 (0.18), residues: 879 sheet: -0.10 (0.53), residues: 99 loop : -2.22 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A1952 HIS 0.004 0.001 HIS A1466 PHE 0.028 0.001 PHE A1950 TYR 0.015 0.001 TYR A1044 ARG 0.005 0.000 ARG A1555 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 665) hydrogen bonds : angle 3.68940 ( 1941) covalent geometry : bond 0.00256 (13530) covalent geometry : angle 0.54764 (18276) *********************** 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 220 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 173 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6437 (OUTLIER) cc_final: 0.5518 (m-10) REVERT: A 425 LEU cc_start: 0.8370 (tt) cc_final: 0.8103 (tp) REVERT: A 472 MET cc_start: 0.6509 (OUTLIER) cc_final: 0.5039 (mmt) REVERT: A 809 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.7034 (t80) REVERT: A 873 MET cc_start: 0.7257 (mtt) cc_final: 0.6920 (mtt) REVERT: A 953 ASP cc_start: 0.7919 (t0) cc_final: 0.7466 (t0) REVERT: A 972 ILE cc_start: 0.5827 (OUTLIER) cc_final: 0.5085 (mp) REVERT: A 1157 GLU cc_start: 0.6084 (OUTLIER) cc_final: 0.5572 (pm20) REVERT: A 1455 GLN cc_start: 0.8118 (tp40) cc_final: 0.7835 (tp40) REVERT: A 1549 VAL cc_start: 0.8789 (t) cc_final: 0.8554 (p) REVERT: A 1713 LYS cc_start: 0.7136 (mmtm) cc_final: 0.6879 (ttpt) REVERT: A 1823 HIS cc_start: 0.6976 (m90) cc_final: 0.6336 (m-70) outliers start: 47 outliers final: 35 residues processed: 208 average time/residue: 0.2484 time to fit residues: 78.3759 Evaluate side-chains 208 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 1.577 ------------------------------------------------------------------------------- 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 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 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 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 1623 LEU Chi-restraints excluded: chain A residue 1715 THR Chi-restraints excluded: chain A residue 1783 LEU Chi-restraints excluded: chain A residue 1880 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 1971 MET 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 107 optimal weight: 0.8980 chunk 45 optimal weight: 0.0170 chunk 91 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 100 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 113 optimal weight: 1.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 GLN A1022 ASN A1312 HIS ** A1316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2068 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.199689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.160884 restraints weight = 15384.081| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 1.88 r_work: 0.3705 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13530 Z= 0.099 Angle : 0.531 12.636 18276 Z= 0.270 Chirality : 0.040 0.267 2082 Planarity : 0.003 0.047 2254 Dihedral : 7.469 73.590 1887 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.68 % Favored : 94.20 % Rotamer: Outliers : 3.42 % Allowed : 22.92 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.22), residues: 1603 helix: 1.83 (0.18), residues: 880 sheet: -0.02 (0.53), residues: 99 loop : -2.18 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A1952 HIS 0.003 0.001 HIS A 404 PHE 0.024 0.001 PHE A1950 TYR 0.014 0.001 TYR A2064 ARG 0.007 0.000 ARG A1555 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 665) hydrogen bonds : angle 3.64716 ( 1941) covalent geometry : bond 0.00209 (13530) covalent geometry : angle 0.53111 (18276) *********************** 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 223 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 172 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6403 (OUTLIER) cc_final: 0.5556 (m-10) REVERT: A 425 LEU cc_start: 0.8342 (tt) cc_final: 0.8073 (tp) REVERT: A 472 MET cc_start: 0.6410 (OUTLIER) cc_final: 0.5051 (mmt) REVERT: A 809 TYR cc_start: 0.7908 (OUTLIER) cc_final: 0.7028 (t80) REVERT: A 822 MET cc_start: 0.7750 (mmt) cc_final: 0.7187 (mmt) REVERT: A 873 MET cc_start: 0.7201 (mtt) cc_final: 0.6845 (mtt) REVERT: A 953 ASP cc_start: 0.7937 (t0) cc_final: 0.7499 (t0) REVERT: A 972 ILE cc_start: 0.5838 (OUTLIER) cc_final: 0.5108 (mp) REVERT: A 1157 GLU cc_start: 0.6078 (OUTLIER) cc_final: 0.5575 (pm20) REVERT: A 1455 GLN cc_start: 0.8064 (tp40) cc_final: 0.7781 (tp40) REVERT: A 1470 MET cc_start: 0.9010 (mmm) cc_final: 0.8737 (mmm) REVERT: A 1494 ASP cc_start: 0.6783 (t0) cc_final: 0.6334 (t70) REVERT: A 1713 LYS cc_start: 0.7235 (mmtm) cc_final: 0.6909 (ttpt) REVERT: A 1823 HIS cc_start: 0.6862 (m90) cc_final: 0.6292 (m-70) REVERT: A 1919 ASN cc_start: 0.7854 (m-40) cc_final: 0.7312 (m110) outliers start: 51 outliers final: 42 residues processed: 209 average time/residue: 0.2373 time to fit residues: 75.4987 Evaluate side-chains 213 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 1.530 ------------------------------------------------------------------------------- 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 468 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 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 1783 LEU Chi-restraints excluded: chain A residue 1850 MET Chi-restraints excluded: chain A residue 1871 ASP 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 1971 MET 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 113 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 118 optimal weight: 0.6980 chunk 152 optimal weight: 7.9990 chunk 156 optimal weight: 6.9990 chunk 75 optimal weight: 0.0970 chunk 44 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 GLN A1022 ASN A1316 HIS ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2068 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.194894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.155249 restraints weight = 15346.261| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 1.86 r_work: 0.3619 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13530 Z= 0.158 Angle : 0.602 12.320 18276 Z= 0.309 Chirality : 0.043 0.286 2082 Planarity : 0.004 0.051 2254 Dihedral : 7.750 73.785 1887 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.99 % Favored : 92.89 % Rotamer: Outliers : 3.35 % Allowed : 22.99 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.22), residues: 1603 helix: 1.61 (0.18), residues: 883 sheet: 0.16 (0.56), residues: 85 loop : -2.13 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A1952 HIS 0.006 0.001 HIS A1492 PHE 0.032 0.002 PHE A1950 TYR 0.019 0.001 TYR A2064 ARG 0.006 0.000 ARG A1555 Details of bonding type rmsd hydrogen bonds : bond 0.04933 ( 665) hydrogen bonds : angle 3.83821 ( 1941) covalent geometry : bond 0.00378 (13530) covalent geometry : angle 0.60201 (18276) ********************** 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 222 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 172 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6561 (OUTLIER) cc_final: 0.5683 (m-10) REVERT: A 425 LEU cc_start: 0.8414 (tt) cc_final: 0.8151 (tp) REVERT: A 472 MET cc_start: 0.6443 (OUTLIER) cc_final: 0.4911 (mmt) REVERT: A 809 TYR cc_start: 0.8044 (OUTLIER) cc_final: 0.7031 (t80) REVERT: A 873 MET cc_start: 0.7217 (mtt) cc_final: 0.6946 (mtt) REVERT: A 953 ASP cc_start: 0.8057 (t0) cc_final: 0.7590 (t0) REVERT: A 972 ILE cc_start: 0.5650 (OUTLIER) cc_final: 0.4944 (mp) REVERT: A 1157 GLU cc_start: 0.6083 (OUTLIER) cc_final: 0.5565 (pm20) REVERT: A 1239 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7302 (mm-30) REVERT: A 1455 GLN cc_start: 0.8176 (tp40) cc_final: 0.7885 (tp40) REVERT: A 1549 VAL cc_start: 0.8874 (t) cc_final: 0.8649 (p) REVERT: A 1713 LYS cc_start: 0.7192 (mmtm) cc_final: 0.6914 (ttpt) REVERT: A 1982 ASN cc_start: 0.7203 (t0) cc_final: 0.6783 (t0) outliers start: 50 outliers final: 38 residues processed: 208 average time/residue: 0.2636 time to fit residues: 84.9340 Evaluate side-chains 211 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 2.175 ------------------------------------------------------------------------------- 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 468 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 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 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 1566 CYS Chi-restraints excluded: chain A residue 1600 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 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 2050 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 48 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 chunk 51 optimal weight: 0.0170 chunk 55 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 74 optimal weight: 0.0570 chunk 162 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.199646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.161068 restraints weight = 15471.507| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 1.86 r_work: 0.3689 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1679 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= 0.100 Angle : 0.539 12.759 18276 Z= 0.274 Chirality : 0.040 0.275 2082 Planarity : 0.003 0.045 2254 Dihedral : 7.585 73.612 1887 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.24 % Favored : 93.64 % Rotamer: Outliers : 3.28 % Allowed : 23.19 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.22), residues: 1603 helix: 1.78 (0.18), residues: 882 sheet: 0.24 (0.57), residues: 85 loop : -2.07 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A1952 HIS 0.003 0.001 HIS A1316 PHE 0.024 0.001 PHE A1950 TYR 0.017 0.001 TYR A2064 ARG 0.006 0.000 ARG A1555 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 665) hydrogen bonds : angle 3.70143 ( 1941) covalent geometry : bond 0.00209 (13530) covalent geometry : angle 0.53920 (18276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6822.04 seconds wall clock time: 122 minutes 8.91 seconds (7328.91 seconds total)