Starting phenix.real_space_refine on Thu May 15 16:21:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ki8_37254/05_2025/8ki8_37254.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ki8_37254/05_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_37254/05_2025/8ki8_37254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ki8_37254/05_2025/8ki8_37254.map" model { file = "/net/cci-nas-00/data/ceres_data/8ki8_37254/05_2025/8ki8_37254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ki8_37254/05_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 7.89, per 1000 atoms: 0.59 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: 3.33 Conformation dependent library (CDL) restraints added in 1.7 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: 1.62 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: 5.20 Time building geometry restraints manager: 3.91 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 32.990 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.460 ------------------------------------------------------------------------------- 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 : 1.568 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: 0.2258 time to fit residues: 68.1899 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 : 1.414 ------------------------------------------------------------------------------- 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 = 0.4282 r_free = 0.4282 target = 0.196576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.158142 restraints weight = 15735.357| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 1.82 r_work: 0.3661 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 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 : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6428 (OUTLIER) cc_final: 0.5402 (m-10) REVERT: A 809 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.6899 (t80) REVERT: A 858 LYS cc_start: 0.7774 (ptmt) cc_final: 0.7410 (mtmt) REVERT: A 953 ASP cc_start: 0.7668 (t0) cc_final: 0.7388 (t0) REVERT: A 972 ILE cc_start: 0.5973 (OUTLIER) cc_final: 0.5191 (mp) REVERT: A 1157 GLU cc_start: 0.6109 (OUTLIER) cc_final: 0.5660 (pm20) REVERT: A 1205 LEU cc_start: 0.6444 (tp) cc_final: 0.6238 (tt) REVERT: A 1713 LYS cc_start: 0.7440 (mmtm) cc_final: 0.7217 (ttpt) REVERT: A 2076 ASN cc_start: 0.6387 (p0) cc_final: 0.6068 (p0) outliers start: 52 outliers final: 30 residues processed: 221 average time/residue: 0.2442 time to fit residues: 80.6781 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 : 1.553 ------------------------------------------------------------------------------- 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: 0.9990 chunk 9 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 156 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4289 r_free = 0.4289 target = 0.197204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.158627 restraints weight = 15623.715| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 1.85 r_work: 0.3703 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13530 Z= 0.123 Angle : 0.555 10.899 18276 Z= 0.289 Chirality : 0.042 0.218 2082 Planarity : 0.004 0.048 2254 Dihedral : 8.149 73.761 1900 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.99 % Favored : 93.89 % Rotamer: Outliers : 3.35 % Allowed : 20.78 % Favored : 75.87 % 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: -0.34 (0.21), residues: 1603 helix: 1.20 (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 0.022 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 0.004 0.000 ARG A1555 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 665) hydrogen bonds : angle 3.90512 ( 1941) covalent geometry : bond 0.00274 (13530) covalent geometry : angle 0.55517 (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 224 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 174 time to evaluate : 1.595 Fit side-chains revert: symmetry clash REVERT: A 809 TYR cc_start: 0.7874 (OUTLIER) cc_final: 0.7034 (t80) REVERT: A 858 LYS cc_start: 0.7805 (ptmt) cc_final: 0.7438 (mtmt) REVERT: A 953 ASP cc_start: 0.7637 (t0) cc_final: 0.7174 (t0) REVERT: A 972 ILE cc_start: 0.5976 (OUTLIER) cc_final: 0.5211 (mp) REVERT: A 1091 PHE cc_start: 0.7976 (m-80) cc_final: 0.7739 (m-80) REVERT: A 1157 GLU cc_start: 0.5931 (OUTLIER) cc_final: 0.5504 (pm20) REVERT: A 1350 ASP cc_start: 0.7889 (m-30) cc_final: 0.7640 (m-30) REVERT: A 1713 LYS cc_start: 0.7333 (mmtm) cc_final: 0.7118 (ttpt) REVERT: A 2076 ASN cc_start: 0.6413 (p0) cc_final: 0.6144 (p0) outliers start: 50 outliers final: 23 residues processed: 214 average time/residue: 0.2356 time to fit residues: 76.3971 Evaluate side-chains 196 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 1.435 ------------------------------------------------------------------------------- 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 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 1031 PHE 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 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: 0.0170 chunk 149 optimal weight: 0.0020 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: 0.9980 chunk 100 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.5426 ------------------------------------------------------------------------------- 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 = 0.4316 r_free = 0.4316 target = 0.199645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.161196 restraints weight = 15278.548| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 1.86 r_work: 0.3695 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13530 Z= 0.104 Angle : 0.529 11.169 18276 Z= 0.274 Chirality : 0.041 0.276 2082 Planarity : 0.003 0.042 2254 Dihedral : 7.660 73.652 1888 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.11 % Favored : 93.76 % Rotamer: Outliers : 3.69 % Allowed : 21.65 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.02 (0.21), residues: 1603 helix: 1.52 (0.18), residues: 871 sheet: -0.04 (0.57), residues: 85 loop : -2.29 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A1952 HIS 0.005 0.001 HIS A 404 PHE 0.026 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 0.03903 ( 665) hydrogen bonds : angle 3.77605 ( 1941) covalent geometry : bond 0.00222 (13530) covalent geometry : angle 0.52895 (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 232 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 177 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 LEU cc_start: 0.8351 (tt) cc_final: 0.8101 (tp) REVERT: A 809 TYR cc_start: 0.7899 (OUTLIER) cc_final: 0.7073 (t80) REVERT: A 858 LYS cc_start: 0.7714 (ptmt) cc_final: 0.7429 (mtmt) REVERT: A 953 ASP cc_start: 0.7672 (t0) cc_final: 0.7180 (t0) REVERT: A 972 ILE cc_start: 0.5917 (OUTLIER) cc_final: 0.5148 (mp) REVERT: A 1157 GLU cc_start: 0.5920 (OUTLIER) cc_final: 0.5511 (pm20) REVERT: A 1494 ASP cc_start: 0.6892 (t0) cc_final: 0.6478 (t70) REVERT: A 1823 HIS cc_start: 0.7093 (m90) cc_final: 0.6440 (m-70) outliers start: 55 outliers final: 35 residues processed: 217 average time/residue: 0.2254 time to fit residues: 73.8081 Evaluate side-chains 204 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 1.434 ------------------------------------------------------------------------------- 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 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 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 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 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: 1.9990 chunk 117 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 120 optimal weight: 0.0270 chunk 21 optimal weight: 5.9990 chunk 1 optimal weight: 0.0020 chunk 69 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 overall best weight: 0.4646 ------------------------------------------------------------------------------- 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 = 0.4307 r_free = 0.4307 target = 0.199389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.160680 restraints weight = 15422.868| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.87 r_work: 0.3703 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1264 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= 0.100 Angle : 0.522 11.601 18276 Z= 0.270 Chirality : 0.040 0.259 2082 Planarity : 0.003 0.041 2254 Dihedral : 7.585 73.619 1887 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.68 % Favored : 94.20 % Rotamer: Outliers : 3.89 % Allowed : 21.98 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.10 (0.22), residues: 1603 helix: 1.61 (0.18), residues: 880 sheet: -0.18 (0.53), residues: 99 loop : -2.28 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A1952 HIS 0.003 0.001 HIS A1466 PHE 0.025 0.001 PHE A1950 TYR 0.016 0.001 TYR A1044 ARG 0.005 0.000 ARG A1555 Details of bonding type rmsd hydrogen bonds : bond 0.03785 ( 665) hydrogen bonds : angle 3.71090 ( 1941) covalent geometry : bond 0.00211 (13530) covalent geometry : angle 0.52237 (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 231 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 173 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6399 (OUTLIER) cc_final: 0.5493 (m-10) REVERT: A 425 LEU cc_start: 0.8343 (tt) cc_final: 0.8113 (tp) REVERT: A 602 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7709 (mp) REVERT: A 809 TYR cc_start: 0.7899 (OUTLIER) cc_final: 0.7053 (t80) REVERT: A 858 LYS cc_start: 0.7687 (ptmt) cc_final: 0.7409 (mtmt) REVERT: A 953 ASP cc_start: 0.7701 (t0) cc_final: 0.7194 (t0) REVERT: A 972 ILE cc_start: 0.5872 (OUTLIER) cc_final: 0.5137 (mp) REVERT: A 1157 GLU cc_start: 0.6006 (OUTLIER) cc_final: 0.5560 (pm20) REVERT: A 1455 GLN cc_start: 0.8050 (tp40) cc_final: 0.7766 (tp40) REVERT: A 1494 ASP cc_start: 0.6795 (t0) cc_final: 0.6346 (t70) REVERT: A 1713 LYS cc_start: 0.7212 (mmtm) cc_final: 0.6857 (ttpt) REVERT: A 1823 HIS cc_start: 0.7022 (m90) cc_final: 0.6398 (m-70) REVERT: A 1983 LEU cc_start: 0.4297 (OUTLIER) cc_final: 0.4092 (tt) outliers start: 58 outliers final: 36 residues processed: 214 average time/residue: 0.2357 time to fit residues: 76.2910 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 : 1.423 ------------------------------------------------------------------------------- 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 926 ASP Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1011 HIS Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1157 GLU Chi-restraints excluded: chain A residue 1211 TYR Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 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 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 1983 LEU 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: 2.9990 chunk 86 optimal weight: 2.9990 chunk 146 optimal weight: 0.0040 chunk 126 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 70 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 overall best weight: 1.1794 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.197290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.155247 restraints weight = 15877.742| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.05 r_work: 0.3627 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13530 Z= 0.140 Angle : 0.571 11.670 18276 Z= 0.295 Chirality : 0.042 0.262 2082 Planarity : 0.004 0.044 2254 Dihedral : 7.717 73.759 1887 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.61 % Favored : 93.26 % Rotamer: Outliers : 3.95 % Allowed : 22.12 % 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: 0.04 (0.22), residues: 1603 helix: 1.53 (0.18), residues: 880 sheet: -0.18 (0.52), residues: 99 loop : -2.26 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1952 HIS 0.006 0.001 HIS A1466 PHE 0.031 0.001 PHE A1950 TYR 0.019 0.001 TYR A1044 ARG 0.005 0.000 ARG A1555 Details of bonding type rmsd hydrogen bonds : bond 0.04715 ( 665) hydrogen bonds : angle 3.80583 ( 1941) covalent geometry : bond 0.00323 (13530) covalent geometry : angle 0.57099 (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 230 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 171 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6417 (OUTLIER) cc_final: 0.5516 (m-10) REVERT: A 425 LEU cc_start: 0.8416 (tt) cc_final: 0.8188 (tp) REVERT: A 809 TYR cc_start: 0.7995 (OUTLIER) cc_final: 0.7035 (t80) REVERT: A 858 LYS cc_start: 0.7722 (ptmt) cc_final: 0.7495 (mtmt) REVERT: A 873 MET cc_start: 0.7242 (mtt) cc_final: 0.6932 (mtt) REVERT: A 953 ASP cc_start: 0.7907 (t0) cc_final: 0.7445 (t0) REVERT: A 972 ILE cc_start: 0.5704 (OUTLIER) cc_final: 0.4972 (mp) REVERT: A 1157 GLU cc_start: 0.6001 (OUTLIER) cc_final: 0.5563 (pm20) REVERT: A 1455 GLN cc_start: 0.8134 (tp40) cc_final: 0.7837 (tp40) REVERT: A 1470 MET cc_start: 0.9046 (mmm) cc_final: 0.8838 (mmm) REVERT: A 1549 VAL cc_start: 0.8919 (OUTLIER) cc_final: 0.8664 (p) REVERT: A 1713 LYS cc_start: 0.7168 (mmtm) cc_final: 0.6860 (ttpt) REVERT: A 2080 LEU cc_start: 0.4779 (OUTLIER) cc_final: 0.4559 (mt) outliers start: 59 outliers final: 40 residues processed: 214 average time/residue: 0.2280 time to fit residues: 74.1153 Evaluate side-chains 209 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 163 time to evaluate : 1.382 ------------------------------------------------------------------------------- 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 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 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 1561 ILE Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1566 CYS Chi-restraints excluded: chain A residue 1618 SER Chi-restraints excluded: chain A residue 1715 THR Chi-restraints excluded: chain A residue 1783 LEU Chi-restraints excluded: chain A residue 1833 ILE Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1891 THR Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1953 PHE Chi-restraints excluded: chain A residue 1955 THR Chi-restraints excluded: chain A residue 1963 GLU Chi-restraints excluded: chain A residue 2050 LEU Chi-restraints excluded: chain A residue 2080 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 0.0770 chunk 143 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 91 optimal weight: 0.0010 chunk 78 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 112 optimal weight: 0.4980 chunk 69 optimal weight: 3.9990 overall best weight: 0.9146 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.196581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.157232 restraints weight = 15473.401| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 1.88 r_work: 0.3643 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13530 Z= 0.125 Angle : 0.561 11.827 18276 Z= 0.289 Chirality : 0.042 0.273 2082 Planarity : 0.003 0.042 2254 Dihedral : 7.716 73.733 1887 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.18 % Favored : 93.70 % Rotamer: Outliers : 3.89 % Allowed : 21.92 % Favored : 74.20 % 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 (0.22), residues: 1603 helix: 1.58 (0.18), residues: 879 sheet: -0.18 (0.52), residues: 99 loop : -2.25 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A1952 HIS 0.005 0.001 HIS A1466 PHE 0.028 0.001 PHE A1950 TYR 0.016 0.001 TYR A1044 ARG 0.005 0.000 ARG A1555 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 665) hydrogen bonds : angle 3.78224 ( 1941) covalent geometry : bond 0.00285 (13530) covalent geometry : angle 0.56072 (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 230 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 172 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6439 (OUTLIER) cc_final: 0.5552 (m-10) REVERT: A 425 LEU cc_start: 0.8410 (tt) cc_final: 0.8185 (tp) REVERT: A 472 MET cc_start: 0.6513 (OUTLIER) cc_final: 0.5113 (mmt) REVERT: A 809 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.7027 (t80) REVERT: A 858 LYS cc_start: 0.7706 (ptmt) cc_final: 0.7506 (mtmt) REVERT: A 873 MET cc_start: 0.7261 (mtt) cc_final: 0.6913 (mtt) REVERT: A 953 ASP cc_start: 0.7995 (t0) cc_final: 0.7538 (t0) REVERT: A 972 ILE cc_start: 0.5731 (OUTLIER) cc_final: 0.5010 (mp) REVERT: A 1157 GLU cc_start: 0.6079 (OUTLIER) cc_final: 0.5573 (pm20) REVERT: A 1549 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8640 (p) REVERT: A 1713 LYS cc_start: 0.7268 (mmtm) cc_final: 0.6939 (ttpt) REVERT: A 2080 LEU cc_start: 0.4721 (OUTLIER) cc_final: 0.4499 (mt) outliers start: 58 outliers final: 43 residues processed: 214 average time/residue: 0.2264 time to fit residues: 73.5038 Evaluate side-chains 218 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 168 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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 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 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 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 1833 ILE Chi-restraints excluded: chain A residue 1850 MET Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1891 THR Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1953 PHE Chi-restraints excluded: chain A residue 1955 THR Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 1963 GLU Chi-restraints excluded: chain A residue 2050 LEU Chi-restraints excluded: chain A residue 2080 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 132 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1022 ASN A1316 HIS ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4257 r_free = 0.4257 target = 0.193744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.154379 restraints weight = 15427.062| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.83 r_work: 0.3614 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13530 Z= 0.158 Angle : 0.605 12.056 18276 Z= 0.313 Chirality : 0.043 0.275 2082 Planarity : 0.004 0.048 2254 Dihedral : 7.876 73.891 1887 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.05 % Favored : 92.83 % Rotamer: Outliers : 3.82 % Allowed : 21.98 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.21), residues: 1603 helix: 1.46 (0.18), residues: 880 sheet: -0.38 (0.52), residues: 101 loop : -2.25 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A1952 HIS 0.006 0.001 HIS A1466 PHE 0.032 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 0.05075 ( 665) hydrogen bonds : angle 3.90169 ( 1941) covalent geometry : bond 0.00374 (13530) covalent geometry : angle 0.60471 (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 227 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 170 time to evaluate : 1.461 Fit side-chains revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6520 (OUTLIER) cc_final: 0.5718 (m-10) REVERT: A 472 MET cc_start: 0.6363 (OUTLIER) cc_final: 0.4922 (mmt) REVERT: A 584 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7427 (tm-30) REVERT: A 809 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.7011 (t80) REVERT: A 873 MET cc_start: 0.7312 (mtt) cc_final: 0.7046 (mtt) REVERT: A 953 ASP cc_start: 0.8046 (t0) cc_final: 0.7606 (t0) REVERT: A 972 ILE cc_start: 0.5769 (OUTLIER) cc_final: 0.5053 (mp) REVERT: A 1157 GLU cc_start: 0.6074 (OUTLIER) cc_final: 0.5546 (pm20) REVERT: A 1205 LEU cc_start: 0.6539 (tp) cc_final: 0.6338 (tt) REVERT: A 1239 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7281 (mm-30) REVERT: A 1490 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7960 (mt) REVERT: A 1713 LYS cc_start: 0.7202 (mmtm) cc_final: 0.6915 (ttpt) REVERT: A 2080 LEU cc_start: 0.4839 (OUTLIER) cc_final: 0.4585 (mt) outliers start: 57 outliers final: 44 residues processed: 211 average time/residue: 0.2359 time to fit residues: 75.6679 Evaluate side-chains 212 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 161 time to evaluate : 1.473 ------------------------------------------------------------------------------- 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 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 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 1490 ILE Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1561 ILE Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1566 CYS Chi-restraints excluded: chain A residue 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 1833 ILE 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 1955 THR Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 1963 GLU Chi-restraints excluded: chain A residue 2050 LEU Chi-restraints excluded: chain A residue 2080 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 107 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1022 ASN ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.192418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.152484 restraints weight = 15433.120| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.89 r_work: 0.3610 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13530 Z= 0.163 Angle : 0.616 12.420 18276 Z= 0.318 Chirality : 0.044 0.284 2082 Planarity : 0.004 0.045 2254 Dihedral : 7.932 73.848 1887 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.05 % Favored : 92.83 % Rotamer: Outliers : 3.69 % Allowed : 22.25 % 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: -0.14 (0.21), residues: 1603 helix: 1.36 (0.18), residues: 884 sheet: -0.37 (0.51), residues: 101 loop : -2.31 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A1952 HIS 0.007 0.001 HIS A1466 PHE 0.032 0.002 PHE A1950 TYR 0.020 0.001 TYR A1044 ARG 0.005 0.000 ARG A1555 Details of bonding type rmsd hydrogen bonds : bond 0.05126 ( 665) hydrogen bonds : angle 3.95751 ( 1941) covalent geometry : bond 0.00389 (13530) covalent geometry : angle 0.61583 (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 219 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 164 time to evaluate : 1.684 Fit side-chains revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6581 (OUTLIER) cc_final: 0.5850 (m-10) REVERT: A 472 MET cc_start: 0.6444 (OUTLIER) cc_final: 0.5016 (mmt) REVERT: A 873 MET cc_start: 0.7362 (mtt) cc_final: 0.7084 (mtt) REVERT: A 953 ASP cc_start: 0.8111 (t0) cc_final: 0.7678 (t0) REVERT: A 972 ILE cc_start: 0.5676 (OUTLIER) cc_final: 0.4942 (mp) REVERT: A 1157 GLU cc_start: 0.6062 (OUTLIER) cc_final: 0.5555 (pm20) REVERT: A 1239 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7341 (mm-30) REVERT: A 1490 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7966 (mt) REVERT: A 1549 VAL cc_start: 0.8926 (OUTLIER) cc_final: 0.8643 (p) REVERT: A 1982 ASN cc_start: 0.7136 (t0) cc_final: 0.6681 (t0) REVERT: A 2080 LEU cc_start: 0.5045 (OUTLIER) cc_final: 0.4758 (mt) outliers start: 55 outliers final: 45 residues processed: 204 average time/residue: 0.2432 time to fit residues: 75.5827 Evaluate side-chains 215 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 163 time to evaluate : 1.665 ------------------------------------------------------------------------------- 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 855 GLU 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 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 1490 ILE Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1561 ILE 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 1833 ILE 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 1955 THR Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 1963 GLU Chi-restraints excluded: chain A residue 2050 LEU Chi-restraints excluded: chain A residue 2080 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 113 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 118 optimal weight: 0.9990 chunk 152 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 44 optimal weight: 0.0970 chunk 130 optimal weight: 0.0870 chunk 63 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 GLN A1022 ASN A1420 ASN ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4294 r_free = 0.4294 target = 0.197768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.159266 restraints weight = 15335.671| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.84 r_work: 0.3670 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1718 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= 0.106 Angle : 0.559 12.808 18276 Z= 0.284 Chirality : 0.041 0.273 2082 Planarity : 0.003 0.041 2254 Dihedral : 7.760 73.657 1887 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.36 % Favored : 93.51 % Rotamer: Outliers : 3.49 % Allowed : 22.99 % 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: 0.15 (0.22), residues: 1603 helix: 1.63 (0.18), residues: 879 sheet: -0.30 (0.52), residues: 101 loop : -2.20 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A1952 HIS 0.004 0.001 HIS A1466 PHE 0.025 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 0.03927 ( 665) hydrogen bonds : angle 3.79656 ( 1941) covalent geometry : bond 0.00227 (13530) covalent geometry : angle 0.55896 (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: 52 poor density : 170 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6441 (OUTLIER) cc_final: 0.5712 (m-10) REVERT: A 472 MET cc_start: 0.6212 (OUTLIER) cc_final: 0.4738 (mmt) REVERT: A 584 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7387 (tm-30) REVERT: A 809 TYR cc_start: 0.7972 (OUTLIER) cc_final: 0.7016 (t80) REVERT: A 953 ASP cc_start: 0.8035 (t0) cc_final: 0.7647 (t0) REVERT: A 972 ILE cc_start: 0.5661 (OUTLIER) cc_final: 0.4929 (mp) REVERT: A 1157 GLU cc_start: 0.6058 (OUTLIER) cc_final: 0.5568 (pm20) REVERT: A 1239 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7379 (mm-30) REVERT: A 1490 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7716 (mt) REVERT: A 1819 MET cc_start: 0.5230 (tpp) cc_final: 0.4598 (tpp) REVERT: A 1823 HIS cc_start: 0.7149 (m90) cc_final: 0.6582 (m90) REVERT: A 1982 ASN cc_start: 0.7175 (t0) cc_final: 0.6763 (t0) outliers start: 52 outliers final: 37 residues processed: 209 average time/residue: 0.2474 time to fit residues: 78.1690 Evaluate side-chains 209 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 166 time to evaluate : 1.442 ------------------------------------------------------------------------------- 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 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 1022 ASN Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1157 GLU Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1428 PHE Chi-restraints excluded: chain A residue 1468 CYS Chi-restraints excluded: chain A residue 1490 ILE Chi-restraints excluded: chain A residue 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 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 1953 PHE Chi-restraints excluded: chain A residue 1963 GLU Chi-restraints excluded: chain A residue 2050 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 48 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 55 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 162 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 141 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1022 ASN ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.195613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.156163 restraints weight = 15493.270| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 1.87 r_work: 0.3649 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13530 Z= 0.121 Angle : 0.569 12.566 18276 Z= 0.290 Chirality : 0.042 0.279 2082 Planarity : 0.004 0.050 2254 Dihedral : 7.813 73.676 1887 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.67 % Favored : 93.20 % Rotamer: Outliers : 3.28 % Allowed : 22.65 % 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: 0.16 (0.22), residues: 1603 helix: 1.61 (0.18), residues: 882 sheet: -0.31 (0.52), residues: 101 loop : -2.16 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A1952 HIS 0.004 0.001 HIS A1466 PHE 0.039 0.001 PHE A1950 TYR 0.017 0.001 TYR A2064 ARG 0.007 0.000 ARG A1555 Details of bonding type rmsd hydrogen bonds : bond 0.04252 ( 665) hydrogen bonds : angle 3.82359 ( 1941) covalent geometry : bond 0.00276 (13530) covalent geometry : angle 0.56913 (18276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5965.45 seconds wall clock time: 104 minutes 34.82 seconds (6274.82 seconds total)