Starting phenix.real_space_refine on Wed Sep 25 11:12:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjb_22205/09_2024/6xjb_22205.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjb_22205/09_2024/6xjb_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_22205/09_2024/6xjb_22205.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjb_22205/09_2024/6xjb_22205.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjb_22205/09_2024/6xjb_22205.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjb_22205/09_2024/6xjb_22205.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 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. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 6.16, per 1000 atoms: 0.61 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.2 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: 1.45 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: 4.69 Time building geometry restraints manager: 2.83 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: 0.00 - 1.69: 13630 1.69 - 3.37: 201 3.37 - 5.06: 25 5.06 - 6.74: 6 6.74 - 8.43: 3 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: 433 35.12 - 52.68: 76 52.68 - 70.25: 17 70.25 - 87.81: 7 Dihedral angle restraints: 6167 sinusoidal: 2437 harmonic: 3730 Sorted by residual: 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 dihedral pdb=" CB GLU A1850 " pdb=" CG GLU A1850 " pdb=" CD GLU A1850 " pdb=" OE1 GLU A1850 " ideal model delta sinusoidal sigma weight residual 0.00 87.81 -87.81 1 3.00e+01 1.11e-03 1.03e+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 3.120 nonbonded pdb=" OG1 THR A 881 " pdb=" OG SER A 908 " model vdw 2.203 3.040 nonbonded pdb=" OG SER A1707 " pdb=" OE1 GLN A1710 " model vdw 2.218 3.040 nonbonded pdb=" O ASN A 793 " pdb=" OH TYR A 798 " model vdw 2.248 3.040 nonbonded pdb=" O SER A1751 " pdb=" OG SER A1754 " model vdw 2.258 3.040 ... (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 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 Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.710 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 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 : 13.114 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 % Allowed : 4.17 % Favored : 95.83 % 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: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1405 HIS 0.003 0.001 HIS A1604 PHE 0.021 0.001 PHE A1879 TYR 0.010 0.001 TYR A1512 ARG 0.003 0.000 ARG A1225 *********************** 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 : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 977 HIS cc_start: 0.7961 (p90) cc_final: 0.7659 (p90) REVERT: A 1594 LEU cc_start: 0.8792 (mp) cc_final: 0.8567 (mp) REVERT: A 1800 MET cc_start: 0.7970 (tpp) cc_final: 0.7719 (tpp) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2584 time to fit residues: 54.4844 Evaluate side-chains 67 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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: 1.9990 chunk 96 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 868 ASN A 879 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 10259 Z= 0.439 Angle : 0.693 7.527 13865 Z= 0.367 Chirality : 0.046 0.151 1523 Planarity : 0.004 0.063 1803 Dihedral : 4.879 21.109 1394 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.69 % Allowed : 12.06 % Favored : 85.25 % 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: -2.25 (0.22), residues: 1273 helix: -0.14 (0.25), residues: 413 sheet: -1.41 (0.34), residues: 197 loop : -2.49 (0.21), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1448 HIS 0.008 0.001 HIS A1654 PHE 0.028 0.002 PHE A1879 TYR 0.031 0.002 TYR A 982 ARG 0.010 0.001 ARG A1072 *********************** 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 102 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 73 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 977 HIS cc_start: 0.8071 (p90) cc_final: 0.7744 (p90) REVERT: A 1594 LEU cc_start: 0.9110 (mp) cc_final: 0.8808 (mp) REVERT: A 1800 MET cc_start: 0.7959 (tpp) cc_final: 0.7629 (tpp) outliers start: 29 outliers final: 17 residues processed: 100 average time/residue: 0.2194 time to fit residues: 31.9670 Evaluate side-chains 76 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 59 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 948 SER Chi-restraints excluded: chain A residue 986 ASP Chi-restraints excluded: chain A residue 1111 LYS Chi-restraints excluded: chain A residue 1164 ASP Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1252 ILE Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1535 ASP Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1654 HIS Chi-restraints excluded: chain A residue 1701 SER Chi-restraints excluded: chain A residue 1894 TRP Chi-restraints excluded: chain A residue 1927 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 124 optimal weight: 0.0060 chunk 102 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1608 HIS A1654 HIS A1730 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10259 Z= 0.201 Angle : 0.557 7.277 13865 Z= 0.298 Chirality : 0.041 0.153 1523 Planarity : 0.004 0.057 1803 Dihedral : 4.626 20.180 1394 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.60 % Allowed : 13.27 % Favored : 84.14 % 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: -1.90 (0.22), residues: 1273 helix: 0.33 (0.26), residues: 410 sheet: -1.26 (0.35), residues: 197 loop : -2.38 (0.21), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1405 HIS 0.003 0.001 HIS A1604 PHE 0.026 0.001 PHE A1879 TYR 0.019 0.001 TYR A 982 ARG 0.005 0.001 ARG A1072 *********************** 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 101 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 73 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 977 HIS cc_start: 0.8093 (p90) cc_final: 0.7752 (p90) REVERT: A 1193 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8514 (m-80) REVERT: A 1594 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8725 (mp) REVERT: A 1605 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7622 (mm-30) REVERT: A 1800 MET cc_start: 0.7843 (tpp) cc_final: 0.7522 (tpp) outliers start: 28 outliers final: 17 residues processed: 95 average time/residue: 0.2489 time to fit residues: 34.3293 Evaluate side-chains 83 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 64 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 867 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 979 GLN Chi-restraints excluded: chain A residue 1164 ASP Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1193 PHE Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1252 ILE Chi-restraints excluded: chain A residue 1383 THR Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1535 ASP Chi-restraints excluded: chain A residue 1594 LEU Chi-restraints excluded: chain A residue 1701 SER Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 1779 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10259 Z= 0.323 Angle : 0.603 6.868 13865 Z= 0.320 Chirality : 0.043 0.153 1523 Planarity : 0.004 0.063 1803 Dihedral : 4.817 21.269 1394 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 3.80 % Allowed : 13.45 % Favored : 82.75 % 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: -1.78 (0.22), residues: 1273 helix: 0.50 (0.26), residues: 412 sheet: -1.25 (0.37), residues: 187 loop : -2.34 (0.21), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1515 HIS 0.003 0.001 HIS A1685 PHE 0.024 0.002 PHE A1879 TYR 0.019 0.002 TYR A 982 ARG 0.004 0.000 ARG A1529 *********************** 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 108 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 67 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 757 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8595 (tp) REVERT: A 977 HIS cc_start: 0.8188 (p90) cc_final: 0.7806 (p90) REVERT: A 1193 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8397 (m-80) REVERT: A 1594 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8796 (mp) REVERT: A 1605 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7602 (mm-30) REVERT: A 1800 MET cc_start: 0.8070 (tpp) cc_final: 0.7697 (tpp) outliers start: 41 outliers final: 29 residues processed: 100 average time/residue: 0.2308 time to fit residues: 33.7396 Evaluate side-chains 88 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 56 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 979 GLN Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1164 ASP Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1193 PHE Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1252 ILE Chi-restraints excluded: chain A residue 1272 GLN Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1294 VAL Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1535 ASP Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 1594 LEU Chi-restraints excluded: chain A residue 1648 ILE Chi-restraints excluded: chain A residue 1701 SER Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 1779 ILE Chi-restraints excluded: chain A residue 1836 THR Chi-restraints excluded: chain A residue 1894 TRP Chi-restraints excluded: chain A residue 1899 THR Chi-restraints excluded: chain A residue 1947 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10259 Z= 0.301 Angle : 0.589 7.076 13865 Z= 0.314 Chirality : 0.042 0.161 1523 Planarity : 0.004 0.071 1803 Dihedral : 4.853 21.681 1394 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 4.36 % Allowed : 14.10 % Favored : 81.54 % 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: -1.72 (0.22), residues: 1273 helix: 0.57 (0.26), residues: 413 sheet: -1.17 (0.38), residues: 176 loop : -2.33 (0.21), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1515 HIS 0.003 0.001 HIS A1685 PHE 0.024 0.002 PHE A1879 TYR 0.018 0.002 TYR A1197 ARG 0.011 0.001 ARG A1225 *********************** 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 111 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 64 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 977 HIS cc_start: 0.8236 (p90) cc_final: 0.7831 (p90) REVERT: A 1193 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8411 (m-80) REVERT: A 1241 TYR cc_start: 0.8476 (t80) cc_final: 0.8270 (t80) REVERT: A 1594 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8816 (mp) REVERT: A 1605 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7680 (mm-30) REVERT: A 1800 MET cc_start: 0.8004 (tpp) cc_final: 0.7632 (tpp) REVERT: A 1953 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7855 (m-30) outliers start: 47 outliers final: 35 residues processed: 103 average time/residue: 0.2095 time to fit residues: 32.0646 Evaluate side-chains 95 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 57 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 867 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 979 GLN Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1164 ASP Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1193 PHE Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1252 ILE Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1272 GLN Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1294 VAL Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1383 THR Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1535 ASP Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 1594 LEU Chi-restraints excluded: chain A residue 1648 ILE Chi-restraints excluded: chain A residue 1701 SER Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 1779 ILE Chi-restraints excluded: chain A residue 1836 THR Chi-restraints excluded: chain A residue 1894 TRP Chi-restraints excluded: chain A residue 1899 THR Chi-restraints excluded: chain A residue 1947 TYR Chi-restraints excluded: chain A residue 1953 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 72 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 0.0870 chunk 40 optimal weight: 0.0370 chunk 64 optimal weight: 0.7980 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10259 Z= 0.149 Angle : 0.528 7.772 13865 Z= 0.284 Chirality : 0.040 0.154 1523 Planarity : 0.003 0.044 1803 Dihedral : 4.521 19.550 1394 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 3.15 % Allowed : 15.86 % Favored : 80.98 % 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: -1.58 (0.22), residues: 1273 helix: 0.76 (0.27), residues: 403 sheet: -1.01 (0.37), residues: 189 loop : -2.29 (0.21), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1405 HIS 0.003 0.000 HIS A1604 PHE 0.022 0.001 PHE A1879 TYR 0.017 0.001 TYR A1197 ARG 0.006 0.000 ARG A1052 *********************** 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 105 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 71 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 757 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8601 (tp) REVERT: A 977 HIS cc_start: 0.8114 (p90) cc_final: 0.7765 (p-80) REVERT: A 1594 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8796 (mp) REVERT: A 1605 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7721 (mm-30) REVERT: A 1800 MET cc_start: 0.7951 (tpp) cc_final: 0.7532 (tpp) outliers start: 34 outliers final: 27 residues processed: 100 average time/residue: 0.2212 time to fit residues: 32.6268 Evaluate side-chains 92 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 63 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 867 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1252 ILE Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1272 GLN Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1383 THR Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1454 VAL Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1535 ASP Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 1594 LEU Chi-restraints excluded: chain A residue 1648 ILE Chi-restraints excluded: chain A residue 1654 HIS Chi-restraints excluded: chain A residue 1701 SER Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 1779 ILE Chi-restraints excluded: chain A residue 1836 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 122 optimal weight: 7.9990 chunk 76 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1237 GLN ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10259 Z= 0.214 Angle : 0.561 10.052 13865 Z= 0.295 Chirality : 0.041 0.182 1523 Planarity : 0.003 0.043 1803 Dihedral : 4.558 19.860 1394 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 3.34 % Allowed : 16.05 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.23), residues: 1273 helix: 0.77 (0.27), residues: 409 sheet: -1.06 (0.38), residues: 179 loop : -2.22 (0.21), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1515 HIS 0.002 0.000 HIS A1604 PHE 0.022 0.002 PHE A1879 TYR 0.014 0.001 TYR A1197 ARG 0.006 0.000 ARG A1052 *********************** 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 99 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 63 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 757 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8571 (tp) REVERT: A 977 HIS cc_start: 0.8169 (p90) cc_final: 0.7778 (p90) REVERT: A 1594 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8826 (mp) REVERT: A 1605 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7749 (mm-30) REVERT: A 1800 MET cc_start: 0.7973 (tpp) cc_final: 0.7598 (tpp) outliers start: 36 outliers final: 28 residues processed: 93 average time/residue: 0.2232 time to fit residues: 30.4628 Evaluate side-chains 90 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 60 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 867 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1252 ILE Chi-restraints excluded: chain A residue 1272 GLN Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1294 VAL Chi-restraints excluded: chain A residue 1383 THR Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1535 ASP Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 1594 LEU Chi-restraints excluded: chain A residue 1648 ILE Chi-restraints excluded: chain A residue 1701 SER Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 1779 ILE Chi-restraints excluded: chain A residue 1836 THR Chi-restraints excluded: chain A residue 1894 TRP 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: 4.9990 chunk 73 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.0040 chunk 23 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1950 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2751 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= 0.226 Angle : 0.575 10.297 13865 Z= 0.302 Chirality : 0.041 0.178 1523 Planarity : 0.003 0.043 1803 Dihedral : 4.571 19.872 1394 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 3.71 % Allowed : 15.96 % Favored : 80.33 % 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: -1.54 (0.22), residues: 1273 helix: 0.75 (0.26), residues: 409 sheet: -1.09 (0.38), residues: 179 loop : -2.21 (0.21), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1515 HIS 0.002 0.001 HIS A1604 PHE 0.022 0.002 PHE A1879 TYR 0.014 0.001 TYR A1197 ARG 0.005 0.000 ARG A1052 *********************** 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 101 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 61 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 757 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8588 (tp) REVERT: A 977 HIS cc_start: 0.8201 (p90) cc_final: 0.7803 (p90) REVERT: A 1594 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8818 (mp) REVERT: A 1605 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7765 (mm-30) REVERT: A 1800 MET cc_start: 0.8002 (tpp) cc_final: 0.7608 (tpp) outliers start: 40 outliers final: 33 residues processed: 94 average time/residue: 0.2246 time to fit residues: 31.2319 Evaluate side-chains 92 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 57 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 867 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 979 GLN Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1252 ILE Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1272 GLN Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1294 VAL Chi-restraints excluded: chain A residue 1383 THR Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1454 VAL Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1535 ASP Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 1594 LEU Chi-restraints excluded: chain A residue 1648 ILE Chi-restraints excluded: chain A residue 1701 SER Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 1779 ILE Chi-restraints excluded: chain A residue 1836 THR Chi-restraints excluded: chain A residue 1894 TRP Chi-restraints excluded: chain A residue 1953 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 89 optimal weight: 0.4980 chunk 35 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 113 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10259 Z= 0.173 Angle : 0.567 10.886 13865 Z= 0.294 Chirality : 0.041 0.168 1523 Planarity : 0.003 0.044 1803 Dihedral : 4.461 19.509 1394 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 3.34 % Allowed : 16.42 % Favored : 80.24 % 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: -1.46 (0.22), residues: 1273 helix: 0.82 (0.27), residues: 409 sheet: -0.94 (0.39), residues: 173 loop : -2.19 (0.20), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1405 HIS 0.003 0.001 HIS A 937 PHE 0.021 0.001 PHE A1879 TYR 0.015 0.001 TYR A1197 ARG 0.006 0.000 ARG A1052 *********************** 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 99 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 63 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 757 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8592 (tp) REVERT: A 977 HIS cc_start: 0.8177 (p90) cc_final: 0.7786 (p90) REVERT: A 1594 LEU cc_start: 0.9042 (mp) cc_final: 0.8796 (mp) REVERT: A 1605 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7716 (mm-30) REVERT: A 1800 MET cc_start: 0.7989 (tpp) cc_final: 0.7576 (tpp) outliers start: 36 outliers final: 32 residues processed: 94 average time/residue: 0.2303 time to fit residues: 32.2617 Evaluate side-chains 91 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 58 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 867 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 979 GLN Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1252 ILE Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1272 GLN Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1294 VAL Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1383 THR Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1454 VAL Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1535 ASP Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 1648 ILE Chi-restraints excluded: chain A residue 1701 SER Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 1779 ILE Chi-restraints excluded: chain A residue 1836 THR Chi-restraints excluded: chain A residue 1894 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 2.9990 chunk 120 optimal weight: 0.3980 chunk 73 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 0.0570 chunk 61 optimal weight: 0.9980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1198 GLN ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10259 Z= 0.167 Angle : 0.575 10.921 13865 Z= 0.297 Chirality : 0.041 0.164 1523 Planarity : 0.003 0.044 1803 Dihedral : 4.414 19.272 1394 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.25 % Allowed : 16.79 % Favored : 79.96 % 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: -1.43 (0.22), residues: 1273 helix: 0.85 (0.26), residues: 402 sheet: -0.85 (0.39), residues: 174 loop : -2.17 (0.20), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1405 HIS 0.006 0.001 HIS A 937 PHE 0.021 0.001 PHE A1879 TYR 0.014 0.001 TYR A1197 ARG 0.005 0.000 ARG A1052 ********************** 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 99 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 64 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 757 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8625 (tp) REVERT: A 977 HIS cc_start: 0.8175 (p90) cc_final: 0.7806 (p90) REVERT: A 1594 LEU cc_start: 0.9055 (mp) cc_final: 0.8814 (mp) REVERT: A 1605 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7654 (mm-30) REVERT: A 1800 MET cc_start: 0.8003 (tpp) cc_final: 0.7579 (tpp) outliers start: 35 outliers final: 32 residues processed: 95 average time/residue: 0.2080 time to fit residues: 29.5135 Evaluate side-chains 92 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 59 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 867 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 979 GLN Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1252 ILE Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1272 GLN Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1294 VAL Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1332 ASP Chi-restraints excluded: chain A residue 1383 THR Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1454 VAL Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1535 ASP Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 1648 ILE Chi-restraints excluded: chain A residue 1701 SER Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 1779 ILE Chi-restraints excluded: chain A residue 1836 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.074807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.062778 restraints weight = 30059.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.065002 restraints weight = 15382.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.066527 restraints weight = 9718.471| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10259 Z= 0.276 Angle : 0.611 10.812 13865 Z= 0.316 Chirality : 0.042 0.241 1523 Planarity : 0.003 0.043 1803 Dihedral : 4.613 20.281 1394 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.43 % Allowed : 16.70 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.22), residues: 1273 helix: 0.78 (0.26), residues: 410 sheet: -1.02 (0.39), residues: 174 loop : -2.18 (0.20), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1515 HIS 0.005 0.001 HIS A 937 PHE 0.021 0.002 PHE A1879 TYR 0.016 0.001 TYR A 982 ARG 0.006 0.000 ARG A1072 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1971.64 seconds wall clock time: 36 minutes 46.54 seconds (2206.54 seconds total)