Starting phenix.real_space_refine on Tue Jul 29 09:27:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nj1_12369/07_2025/7nj1_12369.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nj1_12369/07_2025/7nj1_12369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nj1_12369/07_2025/7nj1_12369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nj1_12369/07_2025/7nj1_12369.map" model { file = "/net/cci-nas-00/data/ceres_data/7nj1_12369/07_2025/7nj1_12369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nj1_12369/07_2025/7nj1_12369.cif" } resolution = 2.9 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= 0.001 sd= 0.017 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: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 7043 2.51 5 N 1944 2.21 5 O 2057 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11096 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1448, 10660 Classifications: {'peptide': 1448} Incomplete info: {'truncation_to_alanine': 175} Link IDs: {'PTRANS': 67, 'TRANS': 1380} Chain breaks: 5 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 634 Unresolved non-hydrogen angles: 808 Unresolved non-hydrogen dihedrals: 531 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 5, 'TYR:plan': 8, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 10, 'PHE:plan': 9, 'GLU:plan': 10, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 352 Chain: "B" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 436 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 45} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 7.29, per 1000 atoms: 0.66 Number of scatterers: 11096 At special positions: 0 Unit cell: (89.25, 89.25, 185.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 2057 8.00 N 1944 7.00 C 7043 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 637 " - pdb=" SG CYS A 687 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.6 seconds 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2838 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 2 sheets defined 69.7% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 251 through 263 removed outlier: 3.759A pdb=" N THR A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N HIS A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 271 Processing helix chain 'A' and resid 277 through 291 removed outlier: 3.518A pdb=" N THR A 285 " --> pdb=" O TYR A 281 " (cutoff:3.500A) Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.633A pdb=" N ILE A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 346 removed outlier: 4.012A pdb=" N LEU A 333 " --> pdb=" O PRO A 329 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 367 Processing helix chain 'A' and resid 376 through 390 removed outlier: 4.057A pdb=" N ASP A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 400 through 418 removed outlier: 3.642A pdb=" N VAL A 406 " --> pdb=" O HIS A 402 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL A 408 " --> pdb=" O TYR A 404 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A 409 " --> pdb=" O THR A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 442 removed outlier: 4.525A pdb=" N LYS A 431 " --> pdb=" O VAL A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 469 removed outlier: 3.923A pdb=" N PHE A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 490 Proline residue: A 482 - end of helix Processing helix chain 'A' and resid 499 through 517 removed outlier: 3.602A pdb=" N LEU A 503 " --> pdb=" O PRO A 499 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU A 509 " --> pdb=" O ARG A 505 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN A 510 " --> pdb=" O CYS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 534 removed outlier: 3.560A pdb=" N GLY A 523 " --> pdb=" O LYS A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 560 removed outlier: 3.755A pdb=" N VAL A 546 " --> pdb=" O MET A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 573 Processing helix chain 'A' and resid 577 through 595 Processing helix chain 'A' and resid 599 through 614 Processing helix chain 'A' and resid 618 through 637 removed outlier: 4.040A pdb=" N TRP A 623 " --> pdb=" O PRO A 619 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA A 624 " --> pdb=" O ALA A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 663 removed outlier: 3.678A pdb=" N ARG A 654 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 702 Processing helix chain 'A' and resid 729 through 737 removed outlier: 3.988A pdb=" N LEU A 737 " --> pdb=" O ILE A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 759 removed outlier: 3.700A pdb=" N LYS A 745 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N CYS A 746 " --> pdb=" O ALA A 742 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 747 " --> pdb=" O GLN A 743 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 752 " --> pdb=" O ASP A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 Processing helix chain 'A' and resid 788 through 806 Processing helix chain 'A' and resid 808 through 826 Processing helix chain 'A' and resid 829 through 845 removed outlier: 3.672A pdb=" N GLN A 833 " --> pdb=" O PRO A 829 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 834 " --> pdb=" O SER A 830 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS A 835 " --> pdb=" O TYR A 831 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N HIS A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 871 Processing helix chain 'A' and resid 873 through 886 Processing helix chain 'A' and resid 887 through 892 removed outlier: 3.731A pdb=" N GLN A 891 " --> pdb=" O PRO A 888 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS A 892 " --> pdb=" O ALA A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 913 Processing helix chain 'A' and resid 920 through 929 Processing helix chain 'A' and resid 934 through 954 removed outlier: 3.610A pdb=" N ILE A 950 " --> pdb=" O LEU A 946 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 952 " --> pdb=" O SER A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 1001 removed outlier: 3.742A pdb=" N TRP A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU A 984 " --> pdb=" O LYS A 980 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A 985 " --> pdb=" O TRP A 981 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 998 " --> pdb=" O LEU A 994 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A1000 " --> pdb=" O CYS A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1022 Processing helix chain 'A' and resid 1023 through 1041 removed outlier: 3.601A pdb=" N ARG A1041 " --> pdb=" O LEU A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1062 Processing helix chain 'A' and resid 1147 through 1153 Processing helix chain 'A' and resid 1153 through 1174 removed outlier: 3.715A pdb=" N ALA A1168 " --> pdb=" O VAL A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1207 Proline residue: A1192 - end of helix Processing helix chain 'A' and resid 1217 through 1232 removed outlier: 4.106A pdb=" N GLU A1221 " --> pdb=" O SER A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1237 removed outlier: 4.335A pdb=" N ASN A1236 " --> pdb=" O LEU A1232 " (cutoff:3.500A) Processing helix chain 'A' and resid 1246 through 1257 removed outlier: 3.767A pdb=" N ARG A1257 " --> pdb=" O PHE A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1278 removed outlier: 4.008A pdb=" N GLY A1278 " --> pdb=" O LEU A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1573 through 1589 Processing helix chain 'A' and resid 1594 through 1608 removed outlier: 3.794A pdb=" N ALA A1598 " --> pdb=" O SER A1594 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS A1599 " --> pdb=" O GLY A1595 " (cutoff:3.500A) Processing helix chain 'A' and resid 1612 through 1623 Processing helix chain 'A' and resid 1625 through 1647 Processing helix chain 'A' and resid 1668 through 1678 Processing helix chain 'A' and resid 1688 through 1701 Processing helix chain 'A' and resid 1750 through 1768 removed outlier: 3.617A pdb=" N LYS A1765 " --> pdb=" O GLN A1761 " (cutoff:3.500A) Processing helix chain 'A' and resid 1772 through 1798 removed outlier: 3.527A pdb=" N GLU A1795 " --> pdb=" O ILE A1791 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1807 removed outlier: 3.609A pdb=" N LEU A1806 " --> pdb=" O LYS A1803 " (cutoff:3.500A) Processing helix chain 'A' and resid 1814 through 1830 Processing helix chain 'A' and resid 1836 through 1843 Processing helix chain 'A' and resid 1845 through 1849 Processing helix chain 'A' and resid 1850 through 1862 Processing helix chain 'A' and resid 1866 through 1880 Processing helix chain 'A' and resid 1903 through 1907 Processing helix chain 'A' and resid 1920 through 1934 removed outlier: 4.099A pdb=" N LEU A1924 " --> pdb=" O SER A1920 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A1925 " --> pdb=" O PHE A1921 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR A1933 " --> pdb=" O ILE A1929 " (cutoff:3.500A) Processing helix chain 'A' and resid 1936 through 1941 Processing helix chain 'A' and resid 1958 through 1972 removed outlier: 3.865A pdb=" N GLN A1964 " --> pdb=" O SER A1960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1984 through 1995 removed outlier: 3.681A pdb=" N HIS A1995 " --> pdb=" O ALA A1991 " (cutoff:3.500A) Processing helix chain 'A' and resid 2011 through 2017 Processing helix chain 'A' and resid 2044 through 2051 removed outlier: 3.785A pdb=" N LYS A2048 " --> pdb=" O GLY A2044 " (cutoff:3.500A) Processing helix chain 'A' and resid 2066 through 2084 removed outlier: 4.711A pdb=" N GLY A2082 " --> pdb=" O GLN A2078 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY A2084 " --> pdb=" O TRP A2080 " (cutoff:3.500A) Processing helix chain 'A' and resid 2088 through 2096 removed outlier: 3.679A pdb=" N TYR A2092 " --> pdb=" O PRO A2088 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN A2094 " --> pdb=" O LEU A2090 " (cutoff:3.500A) Processing helix chain 'A' and resid 2097 through 2099 No H-bonds generated for 'chain 'A' and resid 2097 through 2099' Processing helix chain 'B' and resid 121 through 126 removed outlier: 4.001A pdb=" N PHE B 125 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1737 through 1742 removed outlier: 4.458A pdb=" N THR A1724 " --> pdb=" O ALA A1714 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N THR A1707 " --> pdb=" O VAL A1892 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL A1894 " --> pdb=" O THR A1707 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N CYS A1709 " --> pdb=" O VAL A1894 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1978 through 1979 removed outlier: 7.771A pdb=" N VAL A1978 " --> pdb=" O THR A1948 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N TYR A1950 " --> pdb=" O VAL A1978 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TYR A1998 " --> pdb=" O LEU A2025 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE A2027 " --> pdb=" O TYR A1998 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR A2000 " --> pdb=" O PHE A2027 " (cutoff:3.500A) 730 hydrogen bonds defined for protein. 2154 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.18 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2409 1.33 - 1.46: 2594 1.46 - 1.58: 6235 1.58 - 1.71: 0 1.71 - 1.84: 65 Bond restraints: 11303 Sorted by residual: bond pdb=" N VAL A1246 " pdb=" CA VAL A1246 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.08e-02 8.57e+03 1.31e+01 bond pdb=" CA SER A1940 " pdb=" CB SER A1940 " ideal model delta sigma weight residual 1.535 1.483 0.052 1.69e-02 3.50e+03 9.33e+00 bond pdb=" N VAL A1885 " pdb=" CA VAL A1885 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.23e-02 6.61e+03 9.04e+00 bond pdb=" N LEU A1883 " pdb=" CA LEU A1883 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.16e-02 7.43e+03 8.83e+00 bond pdb=" N GLN B 135 " pdb=" CA GLN B 135 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.23e-02 6.61e+03 8.47e+00 ... (remaining 11298 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 15065 2.13 - 4.26: 290 4.26 - 6.38: 33 6.38 - 8.51: 7 8.51 - 10.64: 2 Bond angle restraints: 15397 Sorted by residual: angle pdb=" N GLU B 133 " pdb=" CA GLU B 133 " pdb=" C GLU B 133 " ideal model delta sigma weight residual 113.72 103.08 10.64 1.30e+00 5.92e-01 6.70e+01 angle pdb=" N PRO A 331 " pdb=" CA PRO A 331 " pdb=" CB PRO A 331 " ideal model delta sigma weight residual 103.08 110.20 -7.12 9.70e-01 1.06e+00 5.39e+01 angle pdb=" N PRO A 329 " pdb=" CA PRO A 329 " pdb=" CB PRO A 329 " ideal model delta sigma weight residual 103.25 110.22 -6.97 1.05e+00 9.07e-01 4.41e+01 angle pdb=" N PRO A 289 " pdb=" CA PRO A 289 " pdb=" CB PRO A 289 " ideal model delta sigma weight residual 103.25 110.07 -6.82 1.05e+00 9.07e-01 4.22e+01 angle pdb=" N PRO B 131 " pdb=" CA PRO B 131 " pdb=" C PRO B 131 " ideal model delta sigma weight residual 114.68 121.25 -6.57 1.04e+00 9.25e-01 3.99e+01 ... (remaining 15392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 6329 17.98 - 35.96: 402 35.96 - 53.94: 82 53.94 - 71.92: 21 71.92 - 89.89: 13 Dihedral angle restraints: 6847 sinusoidal: 2483 harmonic: 4364 Sorted by residual: dihedral pdb=" CB CYS A 637 " pdb=" SG CYS A 637 " pdb=" SG CYS A 687 " pdb=" CB CYS A 687 " ideal model delta sinusoidal sigma weight residual -86.00 -126.47 40.47 1 1.00e+01 1.00e-02 2.30e+01 dihedral pdb=" C ILE A1258 " pdb=" N ILE A1258 " pdb=" CA ILE A1258 " pdb=" CB ILE A1258 " ideal model delta harmonic sigma weight residual -122.00 -133.16 11.16 0 2.50e+00 1.60e-01 1.99e+01 dihedral pdb=" CA VAL B 144 " pdb=" C VAL B 144 " pdb=" N PRO B 145 " pdb=" CA PRO B 145 " ideal model delta harmonic sigma weight residual -180.00 -160.29 -19.71 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 6844 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1607 0.062 - 0.125: 188 0.125 - 0.187: 18 0.187 - 0.249: 5 0.249 - 0.311: 6 Chirality restraints: 1824 Sorted by residual: chirality pdb=" CA PRO B 131 " pdb=" N PRO B 131 " pdb=" C PRO B 131 " pdb=" CB PRO B 131 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA ILE A1258 " pdb=" N ILE A1258 " pdb=" C ILE A1258 " pdb=" CB ILE A1258 " both_signs ideal model delta sigma weight residual False 2.43 2.16 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA ARG A1257 " pdb=" N ARG A1257 " pdb=" C ARG A1257 " pdb=" CB ARG A1257 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 1821 not shown) Planarity restraints: 1987 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 131 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C PRO B 131 " -0.040 2.00e-02 2.50e+03 pdb=" O PRO B 131 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU B 132 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A1592 " 0.033 5.00e-02 4.00e+02 5.05e-02 4.08e+00 pdb=" N PRO A1593 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A1593 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1593 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A1961 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.82e+00 pdb=" C THR A1961 " 0.034 2.00e-02 2.50e+03 pdb=" O THR A1961 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU A1962 " -0.011 2.00e-02 2.50e+03 ... (remaining 1984 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1472 2.75 - 3.29: 11251 3.29 - 3.82: 18337 3.82 - 4.36: 21448 4.36 - 4.90: 36710 Nonbonded interactions: 89218 Sorted by model distance: nonbonded pdb=" O PHE A1585 " pdb=" OG SER A1589 " model vdw 2.211 3.040 nonbonded pdb=" O LYS A 755 " pdb=" OG1 THR A 759 " model vdw 2.223 3.040 nonbonded pdb=" O PRO A 500 " pdb=" ND1 HIS A 504 " model vdw 2.223 3.120 nonbonded pdb=" O GLN A1674 " pdb=" OG SER A1678 " model vdw 2.227 3.040 nonbonded pdb=" ND2 ASN A1953 " pdb=" OE1 GLU A1962 " model vdw 2.242 3.120 ... (remaining 89213 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.620 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.870 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 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 : 0.005 0.052 11304 Z= 0.272 Angle : 0.698 10.639 15399 Z= 0.433 Chirality : 0.046 0.311 1824 Planarity : 0.005 0.050 1987 Dihedral : 13.535 89.894 4006 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.40 % Favored : 92.40 % Rotamer: Outliers : 1.09 % Allowed : 10.35 % Favored : 88.56 % Cbeta Deviations : 0.07 % 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: -2.39 (0.19), residues: 1487 helix: -0.93 (0.14), residues: 985 sheet: -1.62 (0.66), residues: 48 loop : -2.85 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 932 HIS 0.007 0.001 HIS A1890 PHE 0.011 0.001 PHE B 117 TYR 0.014 0.001 TYR A1597 ARG 0.004 0.000 ARG A1774 Details of bonding type rmsd hydrogen bonds : bond 0.13657 ( 730) hydrogen bonds : angle 5.60583 ( 2154) SS BOND : bond 0.00805 ( 1) SS BOND : angle 3.41068 ( 2) covalent geometry : bond 0.00502 (11303) covalent geometry : angle 0.69662 (15397) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 256 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 ASN cc_start: 0.7793 (m110) cc_final: 0.7478 (m-40) REVERT: A 587 GLU cc_start: 0.6818 (mt-10) cc_final: 0.6607 (mt-10) REVERT: A 821 GLN cc_start: 0.6980 (tt0) cc_final: 0.6725 (tt0) REVERT: A 822 LEU cc_start: 0.7909 (tp) cc_final: 0.7645 (tt) REVERT: A 1054 VAL cc_start: 0.7859 (m) cc_final: 0.7651 (t) REVERT: A 1946 ARG cc_start: 0.7525 (mtt90) cc_final: 0.7010 (mtp-110) REVERT: A 2049 TYR cc_start: 0.7846 (m-80) cc_final: 0.7607 (m-80) REVERT: A 2069 ILE cc_start: 0.8045 (tp) cc_final: 0.7816 (mp) REVERT: A 2117 VAL cc_start: 0.8471 (m) cc_final: 0.8219 (t) outliers start: 12 outliers final: 5 residues processed: 266 average time/residue: 1.1165 time to fit residues: 323.9894 Evaluate side-chains 216 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 211 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 735 PHE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain B residue 155 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 76 optimal weight: 0.2980 chunk 60 optimal weight: 0.5980 chunk 116 optimal weight: 0.0060 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 HIS A 639 HIS A 694 GLN A 866 GLN A 933 GLN A1048 GLN A1176 HIS A1236 ASN ** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1874 ASN B 160 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.159230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.133700 restraints weight = 14771.656| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.91 r_work: 0.3690 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11304 Z= 0.163 Angle : 0.677 12.727 15399 Z= 0.333 Chirality : 0.040 0.175 1824 Planarity : 0.005 0.043 1987 Dihedral : 5.304 54.677 1597 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.99 % Favored : 93.95 % Rotamer: Outliers : 3.72 % Allowed : 16.80 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.21), residues: 1487 helix: 0.36 (0.16), residues: 1006 sheet: -0.55 (0.71), residues: 46 loop : -2.61 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A2080 HIS 0.015 0.001 HIS A1890 PHE 0.011 0.001 PHE A1603 TYR 0.020 0.001 TYR A 465 ARG 0.005 0.000 ARG A2101 Details of bonding type rmsd hydrogen bonds : bond 0.04585 ( 730) hydrogen bonds : angle 4.41768 ( 2154) SS BOND : bond 0.00668 ( 1) SS BOND : angle 2.75216 ( 2) covalent geometry : bond 0.00372 (11303) covalent geometry : angle 0.67658 (15397) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 227 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 ASN cc_start: 0.8051 (m110) cc_final: 0.7814 (m-40) REVERT: A 548 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.8041 (t80) REVERT: A 551 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7353 (ttm170) REVERT: A 631 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7501 (mp0) REVERT: A 875 THR cc_start: 0.7969 (OUTLIER) cc_final: 0.7753 (p) REVERT: A 1054 VAL cc_start: 0.7951 (m) cc_final: 0.7749 (t) REVERT: A 1151 CYS cc_start: 0.6423 (OUTLIER) cc_final: 0.6116 (t) REVERT: A 1207 ASN cc_start: 0.8039 (t0) cc_final: 0.7827 (m-40) REVERT: A 1232 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8214 (tt) REVERT: A 1252 LYS cc_start: 0.8508 (ttmm) cc_final: 0.8253 (mtpp) REVERT: A 1756 GLU cc_start: 0.7692 (tp30) cc_final: 0.7341 (tm-30) REVERT: A 1817 GLN cc_start: 0.6995 (mm-40) cc_final: 0.6715 (mm-40) REVERT: A 1825 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7484 (mm) REVERT: A 1946 ARG cc_start: 0.7778 (mtt90) cc_final: 0.7097 (mtt-85) REVERT: A 2049 TYR cc_start: 0.8274 (m-80) cc_final: 0.7970 (m-80) REVERT: A 2069 ILE cc_start: 0.8013 (tp) cc_final: 0.7661 (mm) REVERT: A 2117 VAL cc_start: 0.8754 (m) cc_final: 0.8546 (t) outliers start: 41 outliers final: 10 residues processed: 247 average time/residue: 1.4254 time to fit residues: 386.1159 Evaluate side-chains 222 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 735 PHE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 875 THR Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1151 CYS Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1704 SER Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1884 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 44 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 56 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 85 optimal weight: 0.2980 chunk 13 optimal weight: 4.9990 chunk 23 optimal weight: 0.4980 chunk 80 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 HIS A 639 HIS A 694 GLN A 903 GLN A 997 HIS A1176 HIS ** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1874 ASN B 135 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.159002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.133370 restraints weight = 15008.468| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.92 r_work: 0.3689 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11304 Z= 0.160 Angle : 0.654 11.011 15399 Z= 0.323 Chirality : 0.040 0.170 1824 Planarity : 0.005 0.043 1987 Dihedral : 4.823 52.565 1592 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.59 % Favored : 93.28 % Rotamer: Outliers : 3.36 % Allowed : 19.44 % Favored : 77.20 % 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: -0.13 (0.22), residues: 1487 helix: 0.91 (0.16), residues: 1008 sheet: -0.11 (0.72), residues: 46 loop : -2.51 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 869 HIS 0.018 0.001 HIS A1890 PHE 0.009 0.001 PHE A1679 TYR 0.013 0.001 TYR A 465 ARG 0.008 0.000 ARG A1868 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 730) hydrogen bonds : angle 4.20847 ( 2154) SS BOND : bond 0.00662 ( 1) SS BOND : angle 2.85272 ( 2) covalent geometry : bond 0.00365 (11303) covalent geometry : angle 0.65357 (15397) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 212 time to evaluate : 3.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 631 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7486 (mp0) REVERT: A 875 THR cc_start: 0.7978 (OUTLIER) cc_final: 0.7730 (m) REVERT: A 954 MET cc_start: 0.7805 (mmm) cc_final: 0.7356 (mmt) REVERT: A 1196 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7179 (tm-30) REVERT: A 1200 GLN cc_start: 0.7692 (mm110) cc_final: 0.7183 (mm-40) REVERT: A 1207 ASN cc_start: 0.8039 (t0) cc_final: 0.7797 (m-40) REVERT: A 1232 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8228 (tt) REVERT: A 1252 LYS cc_start: 0.8515 (ttmm) cc_final: 0.8254 (mtpp) REVERT: A 1672 ARG cc_start: 0.7931 (mtp85) cc_final: 0.7711 (mtp180) REVERT: A 1756 GLU cc_start: 0.7727 (tp30) cc_final: 0.7333 (tm-30) REVERT: A 1817 GLN cc_start: 0.7067 (mm-40) cc_final: 0.6792 (mm-40) REVERT: A 1849 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7857 (tt) REVERT: A 1874 ASN cc_start: 0.7433 (m-40) cc_final: 0.7133 (m-40) REVERT: A 1946 ARG cc_start: 0.7730 (mtt90) cc_final: 0.7086 (mtt-85) REVERT: A 1994 LYS cc_start: 0.7830 (ttpp) cc_final: 0.7491 (ttpp) REVERT: A 2049 TYR cc_start: 0.8248 (m-80) cc_final: 0.8003 (m-80) outliers start: 37 outliers final: 11 residues processed: 234 average time/residue: 1.6651 time to fit residues: 429.8024 Evaluate side-chains 217 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 203 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 735 PHE Chi-restraints excluded: chain A residue 875 THR Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1704 SER Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1849 LEU Chi-restraints excluded: chain A residue 2070 ASP Chi-restraints excluded: chain B residue 155 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 1 optimal weight: 5.9990 chunk 107 optimal weight: 0.2980 chunk 43 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 93 optimal weight: 0.0470 chunk 10 optimal weight: 3.9990 chunk 146 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 HIS ** A 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 HIS A 694 GLN A 821 GLN ** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1865 GLN A2060 ASN B 135 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.159334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.133494 restraints weight = 14844.414| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 1.93 r_work: 0.3689 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11304 Z= 0.148 Angle : 0.630 11.016 15399 Z= 0.308 Chirality : 0.039 0.165 1824 Planarity : 0.004 0.046 1987 Dihedral : 4.752 51.757 1592 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.05 % Favored : 93.81 % Rotamer: Outliers : 3.54 % Allowed : 20.62 % Favored : 75.84 % 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: 0.23 (0.22), residues: 1487 helix: 1.22 (0.16), residues: 1006 sheet: -0.04 (0.75), residues: 46 loop : -2.42 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 869 HIS 0.011 0.001 HIS A1890 PHE 0.015 0.001 PHE A1603 TYR 0.012 0.001 TYR A 911 ARG 0.010 0.000 ARG A 586 Details of bonding type rmsd hydrogen bonds : bond 0.04045 ( 730) hydrogen bonds : angle 4.07709 ( 2154) SS BOND : bond 0.00603 ( 1) SS BOND : angle 2.85198 ( 2) covalent geometry : bond 0.00341 (11303) covalent geometry : angle 0.62934 (15397) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 954 MET cc_start: 0.7841 (mmm) cc_final: 0.7435 (mmt) REVERT: A 1200 GLN cc_start: 0.7617 (mm110) cc_final: 0.7208 (mm-40) REVERT: A 1207 ASN cc_start: 0.8005 (t0) cc_final: 0.7799 (m-40) REVERT: A 1232 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8220 (tt) REVERT: A 1252 LYS cc_start: 0.8518 (ttmm) cc_final: 0.8266 (mtpp) REVERT: A 1756 GLU cc_start: 0.7757 (tp30) cc_final: 0.7311 (tm-30) REVERT: A 1825 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7594 (mm) REVERT: A 1840 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.7070 (tttm) REVERT: A 1946 ARG cc_start: 0.7691 (mtt90) cc_final: 0.7077 (mtt-85) REVERT: A 1994 LYS cc_start: 0.7804 (ttpp) cc_final: 0.7499 (ttpp) REVERT: A 2049 TYR cc_start: 0.8284 (m-80) cc_final: 0.8015 (m-80) outliers start: 39 outliers final: 14 residues processed: 234 average time/residue: 1.1882 time to fit residues: 302.0356 Evaluate side-chains 219 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 735 PHE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1704 SER Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1840 LYS Chi-restraints excluded: chain A residue 2065 THR Chi-restraints excluded: chain B residue 155 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 102 optimal weight: 0.4980 chunk 77 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 126 optimal weight: 0.8980 chunk 65 optimal weight: 0.1980 chunk 49 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 64 optimal weight: 0.0970 chunk 1 optimal weight: 7.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 HIS ** A 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 HIS A 872 GLN A1176 HIS A1225 GLN ** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2037 HIS B 135 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.159262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.133390 restraints weight = 14760.469| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.92 r_work: 0.3692 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11304 Z= 0.148 Angle : 0.634 11.186 15399 Z= 0.308 Chirality : 0.039 0.159 1824 Planarity : 0.004 0.051 1987 Dihedral : 4.693 51.758 1592 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.19 % Favored : 93.68 % Rotamer: Outliers : 3.54 % Allowed : 22.07 % Favored : 74.39 % 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: 0.45 (0.22), residues: 1487 helix: 1.38 (0.17), residues: 1010 sheet: -0.33 (0.72), residues: 48 loop : -2.34 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 869 HIS 0.011 0.001 HIS A1890 PHE 0.012 0.001 PHE B 128 TYR 0.012 0.001 TYR A 911 ARG 0.011 0.001 ARG A 586 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 730) hydrogen bonds : angle 4.02908 ( 2154) SS BOND : bond 0.00596 ( 1) SS BOND : angle 2.82931 ( 2) covalent geometry : bond 0.00339 (11303) covalent geometry : angle 0.63282 (15397) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 205 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.6562 (ptp) cc_final: 0.6065 (ptp) REVERT: A 587 GLU cc_start: 0.7761 (tt0) cc_final: 0.7494 (tt0) REVERT: A 639 HIS cc_start: 0.7795 (OUTLIER) cc_final: 0.7136 (t-90) REVERT: A 876 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8128 (mttt) REVERT: A 954 MET cc_start: 0.7867 (mmm) cc_final: 0.7391 (mmt) REVERT: A 1200 GLN cc_start: 0.7660 (mm110) cc_final: 0.7235 (mm110) REVERT: A 1207 ASN cc_start: 0.7995 (t0) cc_final: 0.7790 (m-40) REVERT: A 1232 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8193 (tt) REVERT: A 1252 LYS cc_start: 0.8502 (ttmm) cc_final: 0.8256 (mtpp) REVERT: A 1751 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7370 (mtp180) REVERT: A 1756 GLU cc_start: 0.7807 (tp30) cc_final: 0.7344 (tm-30) REVERT: A 1825 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7622 (mm) REVERT: A 1840 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7148 (tttm) REVERT: A 1946 ARG cc_start: 0.7681 (mtt90) cc_final: 0.7092 (mtt-85) REVERT: A 1994 LYS cc_start: 0.7786 (ttpp) cc_final: 0.7516 (ttpp) REVERT: A 2010 LEU cc_start: 0.7982 (tp) cc_final: 0.7718 (tp) REVERT: A 2049 TYR cc_start: 0.8235 (m-80) cc_final: 0.7992 (m-80) REVERT: A 2101 ARG cc_start: 0.7604 (mtt-85) cc_final: 0.7388 (mtt-85) outliers start: 39 outliers final: 15 residues processed: 230 average time/residue: 1.1274 time to fit residues: 282.2831 Evaluate side-chains 222 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 201 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 735 PHE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 876 LYS Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1176 HIS Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1694 SER Chi-restraints excluded: chain A residue 1704 SER Chi-restraints excluded: chain A residue 1751 ARG Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1840 LYS Chi-restraints excluded: chain A residue 1899 LEU Chi-restraints excluded: chain A residue 2065 THR Chi-restraints excluded: chain B residue 155 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 1 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 114 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 127 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 HIS ** A 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 HIS A 821 GLN A1048 GLN A1225 GLN ** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2037 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.157693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.131583 restraints weight = 14914.292| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.95 r_work: 0.3667 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11304 Z= 0.190 Angle : 0.668 11.822 15399 Z= 0.324 Chirality : 0.041 0.201 1824 Planarity : 0.005 0.048 1987 Dihedral : 4.738 53.504 1592 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.39 % Favored : 93.48 % Rotamer: Outliers : 3.72 % Allowed : 22.16 % Favored : 74.11 % 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: 0.39 (0.22), residues: 1487 helix: 1.32 (0.16), residues: 1012 sheet: -0.39 (0.71), residues: 48 loop : -2.33 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 869 HIS 0.014 0.001 HIS A1176 PHE 0.013 0.002 PHE B 128 TYR 0.015 0.002 TYR A 911 ARG 0.010 0.001 ARG A1868 Details of bonding type rmsd hydrogen bonds : bond 0.04275 ( 730) hydrogen bonds : angle 4.09691 ( 2154) SS BOND : bond 0.00729 ( 1) SS BOND : angle 2.82131 ( 2) covalent geometry : bond 0.00441 (11303) covalent geometry : angle 0.66723 (15397) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 209 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.6598 (ptp) cc_final: 0.5944 (ptp) REVERT: A 587 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7493 (tt0) REVERT: A 876 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8139 (mttt) REVERT: A 954 MET cc_start: 0.7850 (mmm) cc_final: 0.7420 (mmt) REVERT: A 1200 GLN cc_start: 0.7681 (mm110) cc_final: 0.7247 (mm110) REVERT: A 1207 ASN cc_start: 0.8012 (t0) cc_final: 0.7802 (m-40) REVERT: A 1252 LYS cc_start: 0.8525 (ttmm) cc_final: 0.8273 (mtpp) REVERT: A 1751 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7410 (mtp180) REVERT: A 1756 GLU cc_start: 0.7829 (tp30) cc_final: 0.7343 (tm-30) REVERT: A 1825 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7548 (mm) REVERT: A 1840 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7086 (tttm) REVERT: A 1946 ARG cc_start: 0.7608 (mtt90) cc_final: 0.7034 (mtt-85) REVERT: A 2010 LEU cc_start: 0.7997 (tp) cc_final: 0.7696 (tp) REVERT: A 2049 TYR cc_start: 0.8276 (m-80) cc_final: 0.8027 (m-80) REVERT: A 2101 ARG cc_start: 0.7658 (mtt-85) cc_final: 0.7426 (mtt-85) outliers start: 41 outliers final: 17 residues processed: 231 average time/residue: 1.3463 time to fit residues: 339.2335 Evaluate side-chains 224 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 735 PHE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 876 LYS Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1704 SER Chi-restraints excluded: chain A residue 1751 ARG Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1840 LYS Chi-restraints excluded: chain A residue 1899 LEU Chi-restraints excluded: chain A residue 2065 THR Chi-restraints excluded: chain B residue 155 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 43 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 HIS ** A 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 HIS A1176 HIS A1225 GLN ** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2037 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.156923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.130902 restraints weight = 15081.600| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.94 r_work: 0.3648 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11304 Z= 0.217 Angle : 0.698 11.519 15399 Z= 0.340 Chirality : 0.043 0.227 1824 Planarity : 0.005 0.049 1987 Dihedral : 4.830 54.724 1592 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.39 % Favored : 93.48 % Rotamer: Outliers : 3.54 % Allowed : 23.52 % Favored : 72.93 % 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: 0.29 (0.22), residues: 1487 helix: 1.22 (0.16), residues: 1010 sheet: -0.57 (0.70), residues: 48 loop : -2.25 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A2080 HIS 0.010 0.002 HIS A1890 PHE 0.017 0.002 PHE B 128 TYR 0.018 0.002 TYR A 911 ARG 0.013 0.001 ARG A1868 Details of bonding type rmsd hydrogen bonds : bond 0.04623 ( 730) hydrogen bonds : angle 4.19344 ( 2154) SS BOND : bond 0.00912 ( 1) SS BOND : angle 3.45393 ( 2) covalent geometry : bond 0.00503 (11303) covalent geometry : angle 0.69692 (15397) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.6631 (ptp) cc_final: 0.6295 (ptp) REVERT: A 587 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7497 (tt0) REVERT: A 876 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8136 (mttt) REVERT: A 954 MET cc_start: 0.7822 (mmm) cc_final: 0.7424 (mmt) REVERT: A 982 GLN cc_start: 0.7681 (mm110) cc_final: 0.7455 (mm-40) REVERT: A 1196 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7477 (tm-30) REVERT: A 1200 GLN cc_start: 0.7625 (mm110) cc_final: 0.7299 (mm-40) REVERT: A 1207 ASN cc_start: 0.8010 (t0) cc_final: 0.7805 (m-40) REVERT: A 1232 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8173 (tt) REVERT: A 1252 LYS cc_start: 0.8516 (ttmm) cc_final: 0.8278 (mtpp) REVERT: A 1756 GLU cc_start: 0.7854 (tp30) cc_final: 0.7328 (tm-30) REVERT: A 1786 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7078 (mtp85) REVERT: A 1817 GLN cc_start: 0.7240 (mm-40) cc_final: 0.6962 (mm-40) REVERT: A 1825 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7607 (mm) REVERT: A 1840 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7143 (tttm) REVERT: A 1946 ARG cc_start: 0.7597 (mtt90) cc_final: 0.6982 (mtt-85) REVERT: A 2010 LEU cc_start: 0.7992 (tp) cc_final: 0.7693 (tp) REVERT: A 2049 TYR cc_start: 0.8305 (m-80) cc_final: 0.8002 (m-80) outliers start: 39 outliers final: 18 residues processed: 228 average time/residue: 1.1652 time to fit residues: 288.9361 Evaluate side-chains 226 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 735 PHE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 876 LYS Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1704 SER Chi-restraints excluded: chain A residue 1786 ARG Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1840 LYS Chi-restraints excluded: chain A residue 1899 LEU Chi-restraints excluded: chain A residue 2065 THR Chi-restraints excluded: chain B residue 155 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 87 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 chunk 90 optimal weight: 0.6980 chunk 125 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 HIS ** A 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 HIS A1225 GLN ** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2037 HIS A2060 ASN B 135 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.157394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.131592 restraints weight = 14841.710| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.92 r_work: 0.3672 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11304 Z= 0.171 Angle : 0.682 11.901 15399 Z= 0.329 Chirality : 0.041 0.155 1824 Planarity : 0.005 0.054 1987 Dihedral : 4.798 53.363 1592 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.59 % Favored : 93.28 % Rotamer: Outliers : 3.09 % Allowed : 24.61 % Favored : 72.30 % 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: 0.43 (0.22), residues: 1487 helix: 1.32 (0.16), residues: 1019 sheet: -0.50 (0.72), residues: 48 loop : -2.27 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 869 HIS 0.013 0.001 HIS A1890 PHE 0.016 0.001 PHE A1603 TYR 0.021 0.001 TYR A2104 ARG 0.015 0.001 ARG A1868 Details of bonding type rmsd hydrogen bonds : bond 0.04264 ( 730) hydrogen bonds : angle 4.12783 ( 2154) SS BOND : bond 0.00694 ( 1) SS BOND : angle 3.02803 ( 2) covalent geometry : bond 0.00399 (11303) covalent geometry : angle 0.68093 (15397) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.6639 (ptp) cc_final: 0.6333 (ptp) REVERT: A 587 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7449 (tt0) REVERT: A 612 GLU cc_start: 0.7802 (tt0) cc_final: 0.7561 (tt0) REVERT: A 876 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8110 (mttt) REVERT: A 954 MET cc_start: 0.7769 (mmm) cc_final: 0.7345 (mmt) REVERT: A 1200 GLN cc_start: 0.7691 (mm110) cc_final: 0.7262 (mm110) REVERT: A 1232 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8169 (tt) REVERT: A 1252 LYS cc_start: 0.8500 (ttmm) cc_final: 0.8267 (mtpp) REVERT: A 1749 HIS cc_start: 0.7133 (m170) cc_final: 0.6889 (m170) REVERT: A 1756 GLU cc_start: 0.7789 (tp30) cc_final: 0.7344 (tm-30) REVERT: A 1817 GLN cc_start: 0.7193 (mm-40) cc_final: 0.6937 (mm-40) REVERT: A 1825 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7573 (mm) REVERT: A 1840 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7157 (tttm) REVERT: A 1946 ARG cc_start: 0.7631 (mtt90) cc_final: 0.7022 (mtt-85) REVERT: A 1993 THR cc_start: 0.7794 (m) cc_final: 0.7592 (m) REVERT: A 2010 LEU cc_start: 0.7953 (tp) cc_final: 0.7696 (tp) REVERT: A 2049 TYR cc_start: 0.8276 (m-80) cc_final: 0.8009 (m-80) outliers start: 34 outliers final: 18 residues processed: 223 average time/residue: 1.1308 time to fit residues: 273.9686 Evaluate side-chains 225 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 735 PHE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 876 LYS Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1704 SER Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1840 LYS Chi-restraints excluded: chain A residue 1899 LEU Chi-restraints excluded: chain A residue 2065 THR Chi-restraints excluded: chain A residue 2117 VAL Chi-restraints excluded: chain B residue 155 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 33 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 124 optimal weight: 0.0070 chunk 9 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 101 optimal weight: 0.0870 chunk 140 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 103 optimal weight: 0.3980 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 HIS ** A 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 HIS A 982 GLN A1225 GLN ** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2037 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.159668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.133586 restraints weight = 14899.948| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 1.93 r_work: 0.3688 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11304 Z= 0.145 Angle : 0.663 11.950 15399 Z= 0.321 Chirality : 0.040 0.213 1824 Planarity : 0.005 0.061 1987 Dihedral : 4.705 51.349 1592 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.39 % Favored : 93.48 % Rotamer: Outliers : 3.36 % Allowed : 24.34 % Favored : 72.30 % 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: 0.69 (0.23), residues: 1487 helix: 1.53 (0.17), residues: 1021 sheet: -0.37 (0.72), residues: 48 loop : -2.24 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 869 HIS 0.009 0.001 HIS A1890 PHE 0.013 0.001 PHE B 128 TYR 0.013 0.001 TYR A1933 ARG 0.015 0.001 ARG A1868 Details of bonding type rmsd hydrogen bonds : bond 0.03917 ( 730) hydrogen bonds : angle 4.04028 ( 2154) SS BOND : bond 0.00594 ( 1) SS BOND : angle 2.71645 ( 2) covalent geometry : bond 0.00333 (11303) covalent geometry : angle 0.66184 (15397) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.6602 (ptp) cc_final: 0.6326 (ptp) REVERT: A 587 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7415 (tt0) REVERT: A 639 HIS cc_start: 0.7867 (OUTLIER) cc_final: 0.7374 (t70) REVERT: A 954 MET cc_start: 0.7726 (mmm) cc_final: 0.7319 (mmt) REVERT: A 982 GLN cc_start: 0.7771 (tp40) cc_final: 0.7565 (mm-40) REVERT: A 1200 GLN cc_start: 0.7642 (mm110) cc_final: 0.7271 (mm110) REVERT: A 1232 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8076 (tt) REVERT: A 1252 LYS cc_start: 0.8497 (ttmm) cc_final: 0.8247 (mtpp) REVERT: A 1751 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7403 (mtp180) REVERT: A 1756 GLU cc_start: 0.7778 (tp30) cc_final: 0.7360 (tm-30) REVERT: A 1825 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7564 (mm) REVERT: A 1840 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.7198 (tttm) REVERT: A 1946 ARG cc_start: 0.7546 (mtt90) cc_final: 0.6954 (mtt-85) REVERT: A 1994 LYS cc_start: 0.7747 (ttpp) cc_final: 0.7397 (ttpp) REVERT: A 2010 LEU cc_start: 0.7972 (tp) cc_final: 0.7722 (tp) REVERT: A 2049 TYR cc_start: 0.8207 (m-80) cc_final: 0.7984 (m-80) REVERT: A 2104 TYR cc_start: 0.6459 (m-80) cc_final: 0.6196 (m-80) outliers start: 37 outliers final: 18 residues processed: 220 average time/residue: 1.1875 time to fit residues: 283.2256 Evaluate side-chains 222 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 735 PHE Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1176 HIS Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1704 SER Chi-restraints excluded: chain A residue 1751 ARG Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1840 LYS Chi-restraints excluded: chain A residue 1899 LEU Chi-restraints excluded: chain A residue 2018 LEU Chi-restraints excluded: chain A residue 2065 THR Chi-restraints excluded: chain A residue 2117 VAL Chi-restraints excluded: chain B residue 155 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 18 optimal weight: 0.1980 chunk 89 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 128 optimal weight: 0.0770 chunk 83 optimal weight: 0.2980 chunk 121 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 117 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 69 optimal weight: 0.0470 chunk 101 optimal weight: 0.7980 overall best weight: 0.2236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 HIS ** A 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 HIS A1048 GLN A1053 GLN A1225 GLN ** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2037 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.160494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.134583 restraints weight = 14967.061| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 1.94 r_work: 0.3701 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11304 Z= 0.134 Angle : 0.665 13.473 15399 Z= 0.320 Chirality : 0.040 0.225 1824 Planarity : 0.005 0.048 1987 Dihedral : 4.662 50.907 1592 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.19 % Favored : 93.68 % Rotamer: Outliers : 2.27 % Allowed : 25.79 % Favored : 71.93 % 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: 0.82 (0.23), residues: 1487 helix: 1.63 (0.17), residues: 1021 sheet: -0.27 (0.73), residues: 48 loop : -2.18 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A2080 HIS 0.017 0.001 HIS A 639 PHE 0.017 0.001 PHE A 641 TYR 0.014 0.001 TYR A 638 ARG 0.008 0.000 ARG A1868 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 730) hydrogen bonds : angle 4.00230 ( 2154) SS BOND : bond 0.00444 ( 1) SS BOND : angle 3.14108 ( 2) covalent geometry : bond 0.00310 (11303) covalent geometry : angle 0.66378 (15397) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.6582 (ptp) cc_final: 0.6319 (ptp) REVERT: A 513 SER cc_start: 0.8050 (t) cc_final: 0.7715 (p) REVERT: A 587 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7445 (tt0) REVERT: A 644 GLN cc_start: 0.6873 (mp10) cc_final: 0.6547 (mp10) REVERT: A 894 SER cc_start: 0.7844 (t) cc_final: 0.7576 (m) REVERT: A 954 MET cc_start: 0.7703 (mmm) cc_final: 0.7268 (mmt) REVERT: A 1200 GLN cc_start: 0.7647 (mm110) cc_final: 0.7293 (mm110) REVERT: A 1252 LYS cc_start: 0.8496 (ttmm) cc_final: 0.8257 (mtpp) REVERT: A 1756 GLU cc_start: 0.7784 (tp30) cc_final: 0.7364 (tm-30) REVERT: A 1807 LEU cc_start: 0.8768 (mm) cc_final: 0.8485 (mp) REVERT: A 1825 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7584 (mm) REVERT: A 1840 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7315 (tttm) REVERT: A 1946 ARG cc_start: 0.7585 (mtt90) cc_final: 0.7000 (mtt-85) REVERT: A 1994 LYS cc_start: 0.7679 (ttpp) cc_final: 0.7370 (ttpp) REVERT: A 2049 TYR cc_start: 0.8233 (m-80) cc_final: 0.8009 (m-80) REVERT: B 121 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7556 (m-40) outliers start: 25 outliers final: 20 residues processed: 218 average time/residue: 1.3580 time to fit residues: 323.3516 Evaluate side-chains 217 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 735 PHE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1176 HIS Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1704 SER Chi-restraints excluded: chain A residue 1728 THR Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1840 LYS Chi-restraints excluded: chain A residue 1899 LEU Chi-restraints excluded: chain A residue 2018 LEU Chi-restraints excluded: chain A residue 2065 THR Chi-restraints excluded: chain A residue 2117 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 155 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 47 optimal weight: 0.0670 chunk 0 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 124 optimal weight: 0.0970 chunk 80 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 639 HIS A1053 GLN ** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2037 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.158986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.132804 restraints weight = 14730.086| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.92 r_work: 0.3677 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11304 Z= 0.174 Angle : 0.688 14.319 15399 Z= 0.333 Chirality : 0.042 0.230 1824 Planarity : 0.005 0.047 1987 Dihedral : 4.691 52.707 1592 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.52 % Favored : 93.34 % Rotamer: Outliers : 2.72 % Allowed : 25.16 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.22), residues: 1487 helix: 1.52 (0.16), residues: 1019 sheet: -0.28 (0.72), residues: 48 loop : -2.19 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A2080 HIS 0.027 0.002 HIS A 628 PHE 0.016 0.001 PHE A1603 TYR 0.014 0.001 TYR A 911 ARG 0.008 0.001 ARG A1868 Details of bonding type rmsd hydrogen bonds : bond 0.04138 ( 730) hydrogen bonds : angle 4.07382 ( 2154) SS BOND : bond 0.00799 ( 1) SS BOND : angle 3.10031 ( 2) covalent geometry : bond 0.00409 (11303) covalent geometry : angle 0.68752 (15397) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9849.60 seconds wall clock time: 174 minutes 41.42 seconds (10481.42 seconds total)