Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 23:55:07 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjb_22205/12_2021/6xjb_22205.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjb_22205/12_2021/6xjb_22205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjb_22205/12_2021/6xjb_22205.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjb_22205/12_2021/6xjb_22205.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjb_22205/12_2021/6xjb_22205.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjb_22205/12_2021/6xjb_22205.pdb" } resolution = 3.8 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 1466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1555": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 10070 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1277, 10070 Classifications: {'peptide': 1277} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 33, 'TRANS': 1243} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 5.87, per 1000 atoms: 0.58 Number of scatterers: 10070 At special positions: 0 Unit cell: (94.176, 110.592, 125.28, 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 18 16.00 O 1989 8.00 N 1711 7.00 C 6352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo 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: 4.11 Conformation dependent library (CDL) restraints added in 1.5 seconds 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2380 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 17 sheets defined 33.7% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 782 through 793 removed outlier: 3.807A pdb=" N LYS A 788 " --> pdb=" O SER A 784 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN A 791 " --> pdb=" O VAL A 787 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN A 792 " --> pdb=" O LYS A 788 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1015 removed outlier: 4.326A pdb=" N GLY A1015 " --> pdb=" O GLU A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1083 removed outlier: 3.718A pdb=" N VAL A1082 " --> pdb=" O SER A1079 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER A1083 " --> pdb=" O GLN A1080 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1079 through 1083' Processing helix chain 'A' and resid 1119 through 1128 removed outlier: 3.593A pdb=" N LYS A1128 " --> pdb=" O LYS A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1143 Processing helix chain 'A' and resid 1169 through 1174 Processing helix chain 'A' and resid 1211 through 1213 No H-bonds generated for 'chain 'A' and resid 1211 through 1213' Processing helix chain 'A' and resid 1224 through 1238 removed outlier: 4.173A pdb=" N ILE A1228 " --> pdb=" O ASP A1224 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU A1231 " --> pdb=" O SER A1227 " (cutoff:3.500A) Proline residue: A1234 - end of helix removed outlier: 3.598A pdb=" N LYS A1238 " --> pdb=" O PRO A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1250 removed outlier: 3.540A pdb=" N ARG A1247 " --> pdb=" O SER A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1273 Processing helix chain 'A' and resid 1273 through 1286 removed outlier: 3.935A pdb=" N SER A1277 " --> pdb=" O ASN A1273 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ALA A1286 " --> pdb=" O LEU A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1292 through 1306 removed outlier: 4.482A pdb=" N ARG A1296 " --> pdb=" O ASN A1292 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN A1306 " --> pdb=" O LYS A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1321 Processing helix chain 'A' and resid 1330 through 1335 removed outlier: 3.640A pdb=" N MET A1335 " --> pdb=" O LYS A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1357 Processing helix chain 'A' and resid 1364 through 1366 No H-bonds generated for 'chain 'A' and resid 1364 through 1366' Processing helix chain 'A' and resid 1367 through 1375 removed outlier: 3.537A pdb=" N TYR A1372 " --> pdb=" O ASN A1368 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY A1373 " --> pdb=" O VAL A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1396 Processing helix chain 'A' and resid 1401 through 1410 Processing helix chain 'A' and resid 1421 through 1430 removed outlier: 3.501A pdb=" N GLY A1429 " --> pdb=" O LYS A1425 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A1430 " --> pdb=" O THR A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1438 through 1444 Processing helix chain 'A' and resid 1450 through 1452 No H-bonds generated for 'chain 'A' and resid 1450 through 1452' Processing helix chain 'A' and resid 1453 through 1459 removed outlier: 3.533A pdb=" N THR A1459 " --> pdb=" O LEU A1455 " (cutoff:3.500A) Processing helix chain 'A' and resid 1480 through 1482 No H-bonds generated for 'chain 'A' and resid 1480 through 1482' Processing helix chain 'A' and resid 1491 through 1519 removed outlier: 3.521A pdb=" N ASP A1495 " --> pdb=" O LYS A1491 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1527 Processing helix chain 'A' and resid 1558 through 1564 Processing helix chain 'A' and resid 1595 through 1610 removed outlier: 3.864A pdb=" N ALA A1599 " --> pdb=" O ASP A1595 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE A1600 " --> pdb=" O LYS A1596 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A1601 " --> pdb=" O ASP A1597 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS A1604 " --> pdb=" O ILE A1600 " (cutoff:3.500A) Processing helix chain 'A' and resid 1628 through 1633 removed outlier: 3.552A pdb=" N LYS A1632 " --> pdb=" O GLU A1628 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY A1633 " --> pdb=" O PHE A1629 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1628 through 1633' Processing helix chain 'A' and resid 1658 through 1662 removed outlier: 3.564A pdb=" N GLU A1661 " --> pdb=" O ASP A1658 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A1662 " --> pdb=" O SER A1659 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1658 through 1662' Processing helix chain 'A' and resid 1676 through 1705 Processing helix chain 'A' and resid 1707 through 1714 removed outlier: 3.628A pdb=" N ALA A1713 " --> pdb=" O TYR A1709 " (cutoff:3.500A) Processing helix chain 'A' and resid 1742 through 1749 removed outlier: 3.530A pdb=" N ASN A1748 " --> pdb=" O ALA A1744 " (cutoff:3.500A) Processing helix chain 'A' and resid 1751 through 1758 removed outlier: 3.546A pdb=" N ILE A1756 " --> pdb=" O PHE A1752 " (cutoff:3.500A) Processing helix chain 'A' and resid 1798 through 1812 removed outlier: 3.679A pdb=" N ARG A1803 " --> pdb=" O LEU A1799 " (cutoff:3.500A) Processing helix chain 'A' and resid 1817 through 1823 Processing helix chain 'A' and resid 1826 through 1834 Processing helix chain 'A' and resid 1848 through 1857 Processing helix chain 'A' and resid 1863 through 1880 Processing helix chain 'A' and resid 1904 through 1921 removed outlier: 3.656A pdb=" N LEU A1908 " --> pdb=" O ASN A1904 " (cutoff:3.500A) Processing helix chain 'A' and resid 1934 through 1951 removed outlier: 3.652A pdb=" N THR A1951 " --> pdb=" O TYR A1947 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 680 through 681 removed outlier: 6.262A pdb=" N LEU A 680 " --> pdb=" O GLN A 754 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N GLU A 756 " --> pdb=" O LEU A 680 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 699 through 700 removed outlier: 3.895A pdb=" N ARG A 699 " --> pdb=" O SER A 692 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 736 " --> pdb=" O VAL A 743 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 743 " --> pdb=" O GLU A 736 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE A 765 " --> pdb=" O ALA A 748 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 699 through 700 removed outlier: 3.895A pdb=" N ARG A 699 " --> pdb=" O SER A 692 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 797 through 799 removed outlier: 6.043A pdb=" N TYR A 798 " --> pdb=" O GLY A 829 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N THR A 853 " --> pdb=" O ILE A 828 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 804 through 805 removed outlier: 6.831A pdb=" N LEU A 804 " --> pdb=" O TYR A 839 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS A 860 " --> pdb=" O ILE A 838 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER A 858 " --> pdb=" O HIS A 887 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASP A 889 " --> pdb=" O SER A 858 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS A 860 " --> pdb=" O ASP A 889 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL A 891 " --> pdb=" O LYS A 860 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL A 862 " --> pdb=" O VAL A 891 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ALA A 893 " --> pdb=" O VAL A 862 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE A 864 " --> pdb=" O ALA A 893 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N VAL A 920 " --> pdb=" O GLY A 890 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU A 892 " --> pdb=" O VAL A 920 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ILE A 919 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ASP A 986 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER A 956 " --> pdb=" O ASP A 986 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 804 through 805 removed outlier: 6.831A pdb=" N LEU A 804 " --> pdb=" O TYR A 839 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS A 860 " --> pdb=" O ILE A 838 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER A 858 " --> pdb=" O HIS A 887 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASP A 889 " --> pdb=" O SER A 858 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS A 860 " --> pdb=" O ASP A 889 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL A 891 " --> pdb=" O LYS A 860 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL A 862 " --> pdb=" O VAL A 891 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ALA A 893 " --> pdb=" O VAL A 862 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE A 864 " --> pdb=" O ALA A 893 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 848 through 849 removed outlier: 6.935A pdb=" N ASN A 875 " --> pdb=" O LEU A 902 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 870 through 871 removed outlier: 6.412A pdb=" N ILE A 870 " --> pdb=" O GLY A 899 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 882 through 884 removed outlier: 6.353A pdb=" N ILE A 883 " --> pdb=" O ALA A 911 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE A 945 " --> pdb=" O GLN A 979 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 930 through 931 Processing sheet with id=AB2, first strand: chain 'A' and resid 1053 through 1055 Processing sheet with id=AB3, first strand: chain 'A' and resid 1159 through 1161 removed outlier: 3.765A pdb=" N LYS A1196 " --> pdb=" O ASN A1208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1324 through 1325 Processing sheet with id=AB5, first strand: chain 'A' and resid 1413 through 1417 removed outlier: 3.696A pdb=" N GLU A1417 " --> pdb=" O SER A1469 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1533 through 1534 removed outlier: 7.413A pdb=" N TYR A1534 " --> pdb=" O TYR A1588 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1734 through 1739 Processing sheet with id=AB8, first strand: chain 'A' and resid 1836 through 1839 323 hydrogen bonds defined for protein. 927 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: 3.88 Time building geometry restraints manager: 4.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3333 1.34 - 1.46: 1781 1.46 - 1.57: 5109 1.57 - 1.69: 0 1.69 - 1.80: 36 Bond restraints: 10259 Sorted by residual: bond pdb=" N THR A1057 " pdb=" CA THR A1057 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.72e+00 bond pdb=" N THR A1901 " pdb=" CA THR A1901 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.16e+00 bond pdb=" N VAL A1568 " pdb=" CA VAL A1568 " ideal model delta sigma weight residual 1.459 1.472 -0.013 1.25e-02 6.40e+03 1.07e+00 bond pdb=" N ALA A1113 " pdb=" CA ALA A1113 " ideal model delta sigma weight residual 1.459 1.470 -0.012 1.16e-02 7.43e+03 1.04e+00 bond pdb=" N PRO A1098 " pdb=" CA PRO A1098 " ideal model delta sigma weight residual 1.471 1.459 0.013 1.29e-02 6.01e+03 9.55e-01 ... (remaining 10254 not shown) Histogram of bond angle deviations from ideal: 100.59 - 107.28: 211 107.28 - 113.97: 5763 113.97 - 120.65: 4224 120.65 - 127.34: 3597 127.34 - 134.03: 70 Bond angle restraints: 13865 Sorted by residual: angle pdb=" N PRO A1094 " pdb=" CA PRO A1094 " pdb=" CB PRO A1094 " ideal model delta sigma weight residual 103.27 110.21 -6.94 9.00e-01 1.23e+00 5.94e+01 angle pdb=" N PRO A1090 " pdb=" CA PRO A1090 " pdb=" CB PRO A1090 " ideal model delta sigma weight residual 103.33 110.44 -7.11 9.30e-01 1.16e+00 5.84e+01 angle pdb=" N PRO A1098 " pdb=" CA PRO A1098 " pdb=" CB PRO A1098 " ideal model delta sigma weight residual 103.44 110.07 -6.63 1.12e+00 7.97e-01 3.50e+01 angle pdb=" C TYR A1928 " pdb=" CA TYR A1928 " pdb=" CB TYR A1928 " ideal model delta sigma weight residual 115.79 110.30 5.49 1.19e+00 7.06e-01 2.13e+01 angle pdb=" C PRO A1670 " pdb=" N THR A1671 " pdb=" CA THR A1671 " ideal model delta sigma weight residual 121.54 129.97 -8.43 1.91e+00 2.74e-01 1.95e+01 ... (remaining 13860 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 5634 17.56 - 35.12: 432 35.12 - 52.68: 76 52.68 - 70.25: 18 70.25 - 87.81: 7 Dihedral angle restraints: 6167 sinusoidal: 2437 harmonic: 3730 Sorted by residual: dihedral pdb=" CA ASP A1555 " pdb=" CB ASP A1555 " pdb=" CG ASP A1555 " pdb=" OD1 ASP A1555 " ideal model delta sinusoidal sigma weight residual -30.00 -90.08 60.08 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA ASP A1669 " pdb=" CB ASP A1669 " pdb=" CG ASP A1669 " pdb=" OD1 ASP A1669 " ideal model delta sinusoidal sigma weight residual -30.00 -88.11 58.11 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP A1609 " pdb=" CB ASP A1609 " pdb=" CG ASP A1609 " pdb=" OD1 ASP A1609 " ideal model delta sinusoidal sigma weight residual -30.00 -87.98 57.98 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 6164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1209 0.045 - 0.091: 242 0.091 - 0.136: 67 0.136 - 0.181: 2 0.181 - 0.226: 3 Chirality restraints: 1523 Sorted by residual: chirality pdb=" CA PRO A1098 " pdb=" N PRO A1098 " pdb=" C PRO A1098 " pdb=" CB PRO A1098 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA PRO A1090 " pdb=" N PRO A1090 " pdb=" C PRO A1090 " pdb=" CB PRO A1090 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA PRO A1094 " pdb=" N PRO A1094 " pdb=" C PRO A1094 " pdb=" CB PRO A1094 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.80e-01 ... (remaining 1520 not shown) Planarity restraints: 1803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 707 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO A 708 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 708 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 708 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A1892 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+00 pdb=" N PRO A1893 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A1893 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A1893 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1879 " -0.010 2.00e-02 2.50e+03 9.58e-03 1.61e+00 pdb=" CG PHE A1879 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE A1879 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A1879 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A1879 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A1879 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A1879 " 0.001 2.00e-02 2.50e+03 ... (remaining 1800 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 296 2.71 - 3.26: 10494 3.26 - 3.81: 15967 3.81 - 4.35: 20478 4.35 - 4.90: 34592 Nonbonded interactions: 81827 Sorted by model distance: nonbonded pdb=" O GLU A1059 " pdb=" ND2 ASN A1575 " model vdw 2.165 2.520 nonbonded pdb=" OG1 THR A 881 " pdb=" OG SER A 908 " model vdw 2.203 2.440 nonbonded pdb=" OG SER A1707 " pdb=" OE1 GLN A1710 " model vdw 2.218 2.440 nonbonded pdb=" O ASN A 793 " pdb=" OH TYR A 798 " model vdw 2.248 2.440 nonbonded pdb=" O SER A1751 " pdb=" OG SER A1754 " model vdw 2.258 2.440 ... (remaining 81822 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 6352 2.51 5 N 1711 2.21 5 O 1989 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue Write .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.420 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.090 Process input model: 30.060 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.040 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 41.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 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 : 0.002 0.047 10259 Z= 0.158 Angle : 0.561 8.428 13865 Z= 0.357 Chirality : 0.040 0.226 1523 Planarity : 0.003 0.037 1803 Dihedral : 13.146 87.806 3787 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer Outliers : 0.00 % 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: -3.06 (0.20), residues: 1273 helix: -1.26 (0.22), residues: 406 sheet: -1.53 (0.37), residues: 174 loop : -2.73 (0.19), residues: 693 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2441 time to fit residues: 51.9371 Evaluate side-chains 67 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.203 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 868 ASN ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1832 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.093 10259 Z= 0.502 Angle : 0.714 8.894 13865 Z= 0.379 Chirality : 0.046 0.155 1523 Planarity : 0.005 0.067 1803 Dihedral : 4.954 21.219 1394 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer Outliers : 3.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.29 (0.22), residues: 1273 helix: -0.20 (0.25), residues: 413 sheet: -1.36 (0.36), residues: 185 loop : -2.51 (0.21), residues: 675 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 68 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 26 residues processed: 97 average time/residue: 0.2207 time to fit residues: 31.3600 Evaluate side-chains 83 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 57 time to evaluate : 1.069 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1079 time to fit residues: 6.5028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1608 HIS ** A1927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 10259 Z= 0.175 Angle : 0.537 6.754 13865 Z= 0.287 Chirality : 0.040 0.137 1523 Planarity : 0.003 0.052 1803 Dihedral : 4.593 19.802 1394 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.22), residues: 1273 helix: 0.27 (0.26), residues: 413 sheet: -1.09 (0.37), residues: 166 loop : -2.38 (0.20), residues: 694 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 76 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 94 average time/residue: 0.2194 time to fit residues: 30.1812 Evaluate side-chains 76 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 1.104 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1315 time to fit residues: 3.6262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1654 HIS ** A1927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 10259 Z= 0.286 Angle : 0.574 7.013 13865 Z= 0.305 Chirality : 0.042 0.139 1523 Planarity : 0.004 0.060 1803 Dihedral : 4.705 21.146 1394 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.22), residues: 1273 helix: 0.46 (0.26), residues: 413 sheet: -1.17 (0.36), residues: 186 loop : -2.38 (0.21), residues: 674 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 68 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 18 residues processed: 86 average time/residue: 0.2185 time to fit residues: 28.0209 Evaluate side-chains 77 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 59 time to evaluate : 1.231 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1003 time to fit residues: 4.9878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1237 GLN ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1666 GLN A1884 GLN ** A1927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.074 10259 Z= 0.442 Angle : 0.678 8.923 13865 Z= 0.357 Chirality : 0.045 0.144 1523 Planarity : 0.004 0.075 1803 Dihedral : 5.172 23.047 1394 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer Outliers : 2.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.22), residues: 1273 helix: 0.46 (0.26), residues: 405 sheet: -1.19 (0.37), residues: 185 loop : -2.46 (0.21), residues: 683 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 59 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 16 residues processed: 83 average time/residue: 0.2172 time to fit residues: 27.0201 Evaluate side-chains 72 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 56 time to evaluate : 1.237 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0989 time to fit residues: 4.6149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 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 879 ASN ** A1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1337 HIS ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1608 HIS ** A1927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 10259 Z= 0.169 Angle : 0.544 9.710 13865 Z= 0.291 Chirality : 0.041 0.180 1523 Planarity : 0.003 0.049 1803 Dihedral : 4.785 20.959 1394 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer Outliers : 1.11 % 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: -1.73 (0.22), residues: 1273 helix: 0.58 (0.26), residues: 407 sheet: -1.06 (0.35), residues: 198 loop : -2.39 (0.21), residues: 668 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 76 average time/residue: 0.2278 time to fit residues: 25.6453 Evaluate side-chains 63 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 1.256 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1826 time to fit residues: 2.9635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 1.9990 chunk 13 optimal weight: 0.0870 chunk 70 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 122 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 879 ASN ** A1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1337 HIS ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 10259 Z= 0.233 Angle : 0.566 10.106 13865 Z= 0.298 Chirality : 0.041 0.159 1523 Planarity : 0.003 0.055 1803 Dihedral : 4.744 21.171 1394 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer Outliers : 1.39 % 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: -1.62 (0.23), residues: 1273 helix: 0.66 (0.26), residues: 409 sheet: -0.89 (0.37), residues: 183 loop : -2.33 (0.21), residues: 681 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 58 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 69 average time/residue: 0.2423 time to fit residues: 24.8251 Evaluate side-chains 64 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 1.242 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1055 time to fit residues: 3.6485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 96 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1337 HIS ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 10259 Z= 0.220 Angle : 0.562 10.637 13865 Z= 0.296 Chirality : 0.041 0.159 1523 Planarity : 0.003 0.051 1803 Dihedral : 4.709 20.880 1394 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.22), residues: 1273 helix: 0.66 (0.26), residues: 406 sheet: -0.90 (0.37), residues: 189 loop : -2.31 (0.21), residues: 678 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 67 average time/residue: 0.2367 time to fit residues: 23.2353 Evaluate side-chains 55 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 1.232 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0956 time to fit residues: 2.0672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 1.9990 chunk 117 optimal weight: 0.3980 chunk 106 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 0.0270 chunk 89 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1337 HIS A1367 ASN ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 10259 Z= 0.164 Angle : 0.568 10.793 13865 Z= 0.297 Chirality : 0.040 0.202 1523 Planarity : 0.003 0.044 1803 Dihedral : 4.576 20.233 1394 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.23), residues: 1273 helix: 0.62 (0.26), residues: 405 sheet: -0.78 (0.36), residues: 202 loop : -2.26 (0.22), residues: 666 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 72 average time/residue: 0.2251 time to fit residues: 24.1964 Evaluate side-chains 64 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 1.249 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0929 time to fit residues: 2.4813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 116 optimal weight: 0.3980 chunk 100 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 77 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1028 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1337 HIS A1367 ASN ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 10259 Z= 0.176 Angle : 0.567 11.339 13865 Z= 0.296 Chirality : 0.041 0.192 1523 Planarity : 0.003 0.046 1803 Dihedral : 4.549 21.083 1394 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.23), residues: 1273 helix: 0.63 (0.26), residues: 405 sheet: -0.71 (0.36), residues: 197 loop : -2.22 (0.22), residues: 671 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 69 average time/residue: 0.2430 time to fit residues: 24.8563 Evaluate side-chains 61 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 1.289 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1192 time to fit residues: 2.2094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN ** A1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1337 HIS ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.075516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.063566 restraints weight = 31124.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.065747 restraints weight = 15889.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.067226 restraints weight = 10028.608| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 10259 Z= 0.297 Angle : 0.633 13.027 13865 Z= 0.327 Chirality : 0.042 0.183 1523 Planarity : 0.004 0.056 1803 Dihedral : 4.751 21.350 1394 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.23), residues: 1273 helix: 0.49 (0.26), residues: 407 sheet: -0.97 (0.36), residues: 202 loop : -2.22 (0.22), residues: 664 =============================================================================== Job complete usr+sys time: 1762.19 seconds wall clock time: 34 minutes 16.04 seconds (2056.04 seconds total)