Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 02:15:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nj1_12369/04_2023/7nj1_12369.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nj1_12369/04_2023/7nj1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nj1_12369/04_2023/7nj1_12369.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nj1_12369/04_2023/7nj1_12369.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nj1_12369/04_2023/7nj1_12369.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nj1_12369/04_2023/7nj1_12369.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Residue "A GLU 540": "OE1" <-> "OE2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A GLU 563": "OE1" <-> "OE2" Residue "A ARG 570": "NH1" <-> "NH2" Residue "A ARG 586": "NH1" <-> "NH2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A GLU 936": "OE1" <-> "OE2" Residue "A GLU 975": "OE1" <-> "OE2" Residue "A GLU 986": "OE1" <-> "OE2" Residue "A GLU 992": "OE1" <-> "OE2" Residue "A GLU 1013": "OE1" <-> "OE2" Residue "A GLU 1038": "OE1" <-> "OE2" Residue "A GLU 1196": "OE1" <-> "OE2" Residue "A GLU 1622": "OE1" <-> "OE2" Residue "A GLU 1756": "OE1" <-> "OE2" Residue "A GLU 1766": "OE1" <-> "OE2" Residue "A GLU 1811": "OE1" <-> "OE2" Residue "A GLU 1812": "OE1" <-> "OE2" Residue "A GLU 1824": "OE1" <-> "OE2" Residue "A GLU 1867": "OE1" <-> "OE2" Residue "A ARG 1868": "NH1" <-> "NH2" Residue "A GLU 1871": "OE1" <-> "OE2" Residue "A GLU 1905": "OE1" <-> "OE2" Residue "A GLU 1962": "OE1" <-> "OE2" Residue "A GLU 1963": "OE1" <-> "OE2" Residue "A ARG 2067": "NH1" <-> "NH2" Residue "A ARG 2101": "NH1" <-> "NH2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "B GLU 126": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 6.19, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 4.49 Conformation dependent library (CDL) restraints added in 1.7 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: 0.97 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: 4.20 Time building geometry restraints manager: 4.84 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: 99.71 - 106.59: 336 106.59 - 113.47: 6430 113.47 - 120.35: 4303 120.35 - 127.22: 4193 127.22 - 134.10: 135 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 2.440 nonbonded pdb=" O LYS A 755 " pdb=" OG1 THR A 759 " model vdw 2.223 2.440 nonbonded pdb=" O PRO A 500 " pdb=" ND1 HIS A 504 " model vdw 2.223 2.520 nonbonded pdb=" O GLN A1674 " pdb=" OG SER A1678 " model vdw 2.227 2.440 nonbonded pdb=" ND2 ASN A1953 " pdb=" OE1 GLU A1962 " model vdw 2.242 2.520 ... (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 ========== 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: 0.010 Normalize map: mean=0, sd=1: 1.350 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: 7.350 Check model and map are aligned: 0.170 Set scattering table: 0.090 Process input model: 32.490 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 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:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.820 ------------------------------------------------------------------------------- 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 11303 Z= 0.332 Angle : 0.697 10.639 15397 Z= 0.432 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 % 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 *********************** 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 fitting. rotamer outliers: 12 poor density : 256 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 266 average time/residue: 1.0569 time to fit residues: 306.5629 Evaluate side-chains 215 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 210 time to evaluate : 1.256 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0980 time to fit residues: 1.9750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 0.7980 chunk 112 optimal weight: 0.0670 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 76 optimal weight: 0.1980 chunk 60 optimal weight: 0.5980 chunk 116 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 135 optimal weight: 0.4980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN ** A 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 HIS A 694 GLN A 821 GLN A 866 GLN A 903 GLN A 933 GLN A1048 GLN A1176 HIS A1236 ASN ** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1874 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 11303 Z= 0.241 Angle : 0.659 13.076 15397 Z= 0.323 Chirality : 0.039 0.170 1824 Planarity : 0.005 0.045 1987 Dihedral : 4.514 19.601 1589 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.72 % Favored : 93.14 % Rotamer Outliers : 4.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.81 (0.21), residues: 1487 helix: 0.36 (0.16), residues: 1005 sheet: -0.56 (0.70), residues: 46 loop : -2.63 (0.28), residues: 436 *********************** 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 265 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 221 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 13 residues processed: 243 average time/residue: 1.1434 time to fit residues: 303.0585 Evaluate side-chains 219 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 206 time to evaluate : 1.359 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 5 average time/residue: 0.1517 time to fit residues: 3.1354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 75 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 112 optimal weight: 0.0170 chunk 92 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 HIS ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 HIS A 694 GLN A 997 HIS ** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1746 ASN B 135 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 11303 Z= 0.262 Angle : 0.650 11.216 15397 Z= 0.319 Chirality : 0.040 0.167 1824 Planarity : 0.005 0.044 1987 Dihedral : 4.473 21.870 1589 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.46 % Favored : 93.41 % Rotamer Outliers : 4.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.18 (0.22), residues: 1487 helix: 0.87 (0.16), residues: 1008 sheet: -0.35 (0.69), residues: 48 loop : -2.47 (0.29), residues: 431 *********************** 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 255 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 211 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 16 residues processed: 234 average time/residue: 1.1284 time to fit residues: 287.8495 Evaluate side-chains 218 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 202 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 9 residues processed: 7 average time/residue: 0.3861 time to fit residues: 5.0414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 133 optimal weight: 0.3980 chunk 101 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 0.1980 chunk 91 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 71 optimal weight: 0.0980 chunk 128 optimal weight: 0.0870 chunk 38 optimal weight: 1.9990 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 HIS ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 HIS A 694 GLN A1176 HIS ** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1746 ASN A1865 GLN B 135 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 11303 Z= 0.208 Angle : 0.620 11.138 15397 Z= 0.302 Chirality : 0.038 0.164 1824 Planarity : 0.004 0.043 1987 Dihedral : 4.348 19.165 1589 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.12 % Favored : 93.75 % Rotamer Outliers : 4.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.22), residues: 1487 helix: 1.31 (0.17), residues: 1008 sheet: -0.09 (0.67), residues: 56 loop : -2.42 (0.29), residues: 423 *********************** 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 262 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 217 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 17 residues processed: 239 average time/residue: 1.1038 time to fit residues: 288.3106 Evaluate side-chains 220 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 203 time to evaluate : 1.282 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 8 residues processed: 9 average time/residue: 0.5198 time to fit residues: 7.3322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 119 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 122 optimal weight: 0.2980 chunk 99 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 73 optimal weight: 0.1980 chunk 129 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 HIS A 872 GLN A1048 GLN A1225 GLN ** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2037 HIS B 135 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 11303 Z= 0.268 Angle : 0.651 11.164 15397 Z= 0.315 Chirality : 0.040 0.159 1824 Planarity : 0.004 0.044 1987 Dihedral : 4.349 20.986 1589 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.19 % Favored : 93.68 % Rotamer Outliers : 3.72 % 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: 0.44 (0.22), residues: 1487 helix: 1.37 (0.17), residues: 1005 sheet: -0.23 (0.72), residues: 48 loop : -2.29 (0.28), residues: 434 *********************** 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 247 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 206 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 21 residues processed: 229 average time/residue: 1.1675 time to fit residues: 291.2640 Evaluate side-chains 221 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 200 time to evaluate : 1.278 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 10 residues processed: 11 average time/residue: 0.4480 time to fit residues: 7.7695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 48 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 144 optimal weight: 0.0870 chunk 119 optimal weight: 0.8980 chunk 66 optimal weight: 0.0870 chunk 11 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN A 504 HIS A1225 GLN ** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2037 HIS B 135 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 11303 Z= 0.238 Angle : 0.638 10.797 15397 Z= 0.310 Chirality : 0.039 0.162 1824 Planarity : 0.004 0.050 1987 Dihedral : 4.299 19.378 1589 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.39 % Favored : 93.48 % Rotamer Outliers : 3.27 % 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: 0.61 (0.22), residues: 1487 helix: 1.51 (0.17), residues: 1011 sheet: -0.28 (0.71), residues: 48 loop : -2.28 (0.29), residues: 428 *********************** 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 240 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 204 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 18 residues processed: 221 average time/residue: 1.1265 time to fit residues: 272.3467 Evaluate side-chains 219 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 201 time to evaluate : 1.386 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 10 residues processed: 8 average time/residue: 0.6104 time to fit residues: 7.4780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 138 optimal weight: 0.5980 chunk 16 optimal weight: 0.0980 chunk 82 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 121 optimal weight: 0.0770 chunk 80 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 87 optimal weight: 0.0870 chunk 66 optimal weight: 0.0000 overall best weight: 0.1720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 HIS ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 GLN A1225 GLN ** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2037 HIS B 135 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 11303 Z= 0.190 Angle : 0.625 10.767 15397 Z= 0.302 Chirality : 0.037 0.159 1824 Planarity : 0.004 0.048 1987 Dihedral : 4.203 19.782 1589 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.85 % Favored : 94.01 % Rotamer Outliers : 3.09 % 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: 0.89 (0.23), residues: 1487 helix: 1.73 (0.17), residues: 1007 sheet: 0.11 (0.75), residues: 46 loop : -2.21 (0.29), residues: 434 *********************** 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 248 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 214 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 17 residues processed: 230 average time/residue: 1.1082 time to fit residues: 279.5683 Evaluate side-chains 217 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 200 time to evaluate : 1.150 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 11 residues processed: 6 average time/residue: 0.4243 time to fit residues: 4.8664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 85 optimal weight: 0.0050 chunk 43 optimal weight: 0.2980 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 97 optimal weight: 0.0970 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN A 504 HIS ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1200 GLN ** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1689 GLN ** A1874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2037 HIS B 135 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 11303 Z= 0.218 Angle : 0.651 12.521 15397 Z= 0.314 Chirality : 0.039 0.177 1824 Planarity : 0.004 0.055 1987 Dihedral : 4.203 19.292 1589 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.19 % Favored : 93.68 % Rotamer Outliers : 2.63 % 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: 0.94 (0.23), residues: 1487 helix: 1.75 (0.17), residues: 1010 sheet: -0.04 (0.74), residues: 48 loop : -2.15 (0.30), residues: 429 *********************** 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 225 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 196 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 15 residues processed: 213 average time/residue: 1.1365 time to fit residues: 264.7552 Evaluate side-chains 205 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 190 time to evaluate : 1.224 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 11 residues processed: 4 average time/residue: 0.6040 time to fit residues: 4.5320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 130 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 120 optimal weight: 0.9980 chunk 126 optimal weight: 0.2980 chunk 87 optimal weight: 0.0370 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 HIS ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1225 GLN ** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2037 HIS B 135 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 11303 Z= 0.236 Angle : 0.672 13.062 15397 Z= 0.324 Chirality : 0.041 0.300 1824 Planarity : 0.005 0.050 1987 Dihedral : 4.208 19.389 1589 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.99 % Favored : 93.88 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.92 (0.23), residues: 1487 helix: 1.69 (0.17), residues: 1021 sheet: 0.03 (0.74), residues: 48 loop : -2.13 (0.30), residues: 418 *********************** 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 217 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 196 time to evaluate : 1.201 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 15 residues processed: 210 average time/residue: 1.1480 time to fit residues: 262.9663 Evaluate side-chains 208 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 193 time to evaluate : 1.289 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 4 average time/residue: 0.5834 time to fit residues: 4.5526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 141 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 98 optimal weight: 0.5980 chunk 148 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 12 optimal weight: 0.0030 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 HIS A1225 GLN ** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2037 HIS B 135 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 11303 Z= 0.261 Angle : 0.708 14.388 15397 Z= 0.338 Chirality : 0.042 0.342 1824 Planarity : 0.005 0.050 1987 Dihedral : 4.289 29.304 1589 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.32 % Favored : 93.54 % Rotamer Outliers : 1.73 % 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: 0.90 (0.23), residues: 1487 helix: 1.66 (0.17), residues: 1019 sheet: -0.01 (0.73), residues: 48 loop : -2.07 (0.30), residues: 420 ********************** 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 218 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 199 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 15 residues processed: 212 average time/residue: 1.1891 time to fit residues: 275.4750 Evaluate side-chains 208 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 193 time to evaluate : 1.277 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 10 residues processed: 6 average time/residue: 0.4277 time to fit residues: 4.9905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 0.5980 chunk 36 optimal weight: 0.0670 chunk 108 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 121 optimal weight: 0.4980 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 HIS ** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2037 HIS B 135 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.160250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.134165 restraints weight = 14713.561| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 1.90 r_work: 0.3696 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 11303 Z= 0.254 Angle : 0.701 14.960 15397 Z= 0.337 Chirality : 0.042 0.311 1824 Planarity : 0.005 0.049 1987 Dihedral : 4.302 31.662 1589 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.12 % Favored : 93.75 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.95 (0.23), residues: 1487 helix: 1.69 (0.17), residues: 1019 sheet: 0.02 (0.73), residues: 48 loop : -2.04 (0.30), residues: 420 =============================================================================== Job complete usr+sys time: 4819.17 seconds wall clock time: 85 minutes 56.37 seconds (5156.37 seconds total)