Starting phenix.real_space_refine on Fri Jul 3 18:26:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vm2_65174/07_2026/9vm2_65174.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vm2_65174/07_2026/9vm2_65174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vm2_65174/07_2026/9vm2_65174.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vm2_65174/07_2026/9vm2_65174.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vm2_65174/07_2026/9vm2_65174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vm2_65174/07_2026/9vm2_65174.map" } resolution = 3.94 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 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= 0.004 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 66 5.16 5 C 9500 2.51 5 N 2552 2.21 5 O 2742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14860 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 13471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1688, 13471 Classifications: {'peptide': 1688} Link IDs: {'PCIS': 4, 'PTRANS': 99, 'TRANS': 1584} Chain breaks: 7 Chain: "B" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1389 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 12, 'TRANS': 165} Time building chain proxies: 3.64, per 1000 atoms: 0.24 Number of scatterers: 14860 At special positions: 0 Unit cell: (111.72, 129.01, 170.24, 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 66 16.00 O 2742 8.00 N 2552 7.00 C 9500 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: 1.12 Conformation dependent library (CDL) restraints added in 756.7 milliseconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3564 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 14 sheets defined 54.4% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 55 through 63 Processing helix chain 'A' and resid 72 through 77 removed outlier: 4.241A pdb=" N VAL A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 138 through 146 Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 211 through 224 Processing helix chain 'A' and resid 230 through 234 Processing helix chain 'A' and resid 303 through 309 Processing helix chain 'A' and resid 317 through 321 Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 401 through 407 Processing helix chain 'A' and resid 468 through 480 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 721 through 737 Processing helix chain 'A' and resid 749 through 751 No H-bonds generated for 'chain 'A' and resid 749 through 751' Processing helix chain 'A' and resid 752 through 764 removed outlier: 3.912A pdb=" N GLU A 756 " --> pdb=" O ASN A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 767 No H-bonds generated for 'chain 'A' and resid 765 through 767' Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 775 through 789 Processing helix chain 'A' and resid 800 through 819 Processing helix chain 'A' and resid 820 through 823 removed outlier: 3.511A pdb=" N GLN A 823 " --> pdb=" O GLU A 820 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 820 through 823' Processing helix chain 'A' and resid 829 through 838 Processing helix chain 'A' and resid 898 through 903 removed outlier: 4.670A pdb=" N ILE A 902 " --> pdb=" O GLU A 898 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 903 " --> pdb=" O VAL A 899 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 898 through 903' Processing helix chain 'A' and resid 907 through 918 removed outlier: 3.613A pdb=" N GLU A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 930 Processing helix chain 'A' and resid 930 through 949 removed outlier: 4.113A pdb=" N PHE A 934 " --> pdb=" O HIS A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 982 Processing helix chain 'A' and resid 986 through 1005 removed outlier: 3.931A pdb=" N ALA A 990 " --> pdb=" O ASP A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1030 removed outlier: 4.104A pdb=" N SER A1030 " --> pdb=" O THR A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1050 Processing helix chain 'A' and resid 1055 through 1059 Processing helix chain 'A' and resid 1090 through 1095 removed outlier: 3.525A pdb=" N THR A1094 " --> pdb=" O PRO A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1107 Processing helix chain 'A' and resid 1107 through 1120 Processing helix chain 'A' and resid 1128 through 1149 Processing helix chain 'A' and resid 1150 through 1153 removed outlier: 3.726A pdb=" N ALA A1153 " --> pdb=" O PRO A1150 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1150 through 1153' Processing helix chain 'A' and resid 1154 through 1166 removed outlier: 3.974A pdb=" N LEU A1164 " --> pdb=" O ARG A1160 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR A1165 " --> pdb=" O VAL A1161 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1174 removed outlier: 4.125A pdb=" N SER A1170 " --> pdb=" O LEU A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1179 Processing helix chain 'A' and resid 1246 through 1264 Processing helix chain 'A' and resid 1265 through 1275 Processing helix chain 'A' and resid 1277 through 1295 removed outlier: 3.696A pdb=" N PHE A1295 " --> pdb=" O CYS A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1305 removed outlier: 4.188A pdb=" N ARG A1305 " --> pdb=" O ALA A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1404 Processing helix chain 'A' and resid 1408 through 1426 removed outlier: 3.717A pdb=" N SER A1426 " --> pdb=" O TYR A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1429 through 1447 Processing helix chain 'A' and resid 1447 through 1453 removed outlier: 3.910A pdb=" N LEU A1451 " --> pdb=" O PHE A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1469 removed outlier: 4.509A pdb=" N CYS A1459 " --> pdb=" O ASP A1455 " (cutoff:3.500A) Processing helix chain 'A' and resid 1474 through 1495 Processing helix chain 'A' and resid 1499 through 1517 Processing helix chain 'A' and resid 1522 through 1538 Processing helix chain 'A' and resid 1540 through 1545 removed outlier: 3.877A pdb=" N ASP A1544 " --> pdb=" O GLY A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1571 Processing helix chain 'A' and resid 1574 through 1589 Processing helix chain 'A' and resid 1592 through 1609 Processing helix chain 'A' and resid 1612 through 1635 Processing helix chain 'A' and resid 1643 through 1648 removed outlier: 3.687A pdb=" N SER A1646 " --> pdb=" O GLY A1643 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN A1648 " --> pdb=" O VAL A1645 " (cutoff:3.500A) Processing helix chain 'A' and resid 1651 through 1657 removed outlier: 3.868A pdb=" N LEU A1655 " --> pdb=" O SER A1652 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU A1656 " --> pdb=" O ASN A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1679 through 1698 Processing helix chain 'A' and resid 1700 through 1716 Proline residue: A1712 - end of helix Processing helix chain 'A' and resid 1719 through 1740 removed outlier: 3.884A pdb=" N GLN A1740 " --> pdb=" O LYS A1736 " (cutoff:3.500A) Processing helix chain 'A' and resid 1758 through 1765 removed outlier: 5.913A pdb=" N ASP A1763 " --> pdb=" O HIS A1760 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A1764 " --> pdb=" O PHE A1761 " (cutoff:3.500A) Processing helix chain 'A' and resid 1778 through 1795 removed outlier: 3.596A pdb=" N ILE A1782 " --> pdb=" O LYS A1778 " (cutoff:3.500A) Processing helix chain 'A' and resid 1809 through 1813 removed outlier: 3.771A pdb=" N LYS A1812 " --> pdb=" O ASP A1809 " (cutoff:3.500A) Processing helix chain 'A' and resid 1832 through 1837 removed outlier: 3.876A pdb=" N ASP A1836 " --> pdb=" O TYR A1832 " (cutoff:3.500A) Processing helix chain 'A' and resid 1841 through 1845 Processing helix chain 'A' and resid 1865 through 1869 Processing helix chain 'A' and resid 1900 through 1921 Processing helix chain 'A' and resid 1926 through 1939 Processing helix chain 'A' and resid 1945 through 1955 removed outlier: 3.871A pdb=" N VAL A1949 " --> pdb=" O GLY A1945 " (cutoff:3.500A) Processing helix chain 'A' and resid 1960 through 1992 Processing helix chain 'A' and resid 1993 through 1995 No H-bonds generated for 'chain 'A' and resid 1993 through 1995' Processing helix chain 'A' and resid 1996 through 2019 Proline residue: A2016 - end of helix Processing helix chain 'B' and resid 15 through 25 removed outlier: 3.626A pdb=" N THR B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 removed outlier: 3.729A pdb=" N TYR B 64 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 72 removed outlier: 3.554A pdb=" N TYR B 72 " --> pdb=" O PRO B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 96 removed outlier: 4.205A pdb=" N LYS B 94 " --> pdb=" O PHE B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 105 removed outlier: 4.029A pdb=" N GLU B 100 " --> pdb=" O LYS B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 132 Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 164 through 176 removed outlier: 3.520A pdb=" N VAL B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 88 Processing sheet with id=AA2, first strand: chain 'A' and resid 495 through 499 removed outlier: 6.662A pdb=" N GLN A 495 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU A 268 " --> pdb=" O GLN A 495 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LYS A 497 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N SER A 324 " --> pdb=" O LYS A 530 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 296 through 298 removed outlier: 4.447A pdb=" N PHE A 298 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLY A 279 " --> pdb=" O PHE A 298 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 282 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL A 339 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 340 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA A 395 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 344 through 345 Processing sheet with id=AA5, first strand: chain 'A' and resid 619 through 622 removed outlier: 6.512A pdb=" N SER A 708 " --> pdb=" O HIS A 556 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 601 through 603 removed outlier: 3.783A pdb=" N VAL A 574 " --> pdb=" O ALA A 602 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 589 through 590 Processing sheet with id=AA8, first strand: chain 'A' and resid 662 through 663 Processing sheet with id=AA9, first strand: chain 'A' and resid 792 through 793 Processing sheet with id=AB1, first strand: chain 'A' and resid 1750 through 1752 Processing sheet with id=AB2, first strand: chain 'A' and resid 1767 through 1768 Processing sheet with id=AB3, first strand: chain 'A' and resid 1826 through 1827 removed outlier: 3.825A pdb=" N PHE A1850 " --> pdb=" O LEU A1876 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1826 through 1827 removed outlier: 3.825A pdb=" N PHE A1850 " --> pdb=" O LEU A1876 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 41 through 46 removed outlier: 5.997A pdb=" N ILE B 4 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N PHE B 56 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N CYS B 6 " --> pdb=" O PHE B 56 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU B 79 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N VAL B 7 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N CYS B 81 " --> pdb=" O VAL B 7 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL B 9 " --> pdb=" O CYS B 81 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N SER B 83 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL B 80 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N THR B 115 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE B 82 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU B 112 " --> pdb=" O VAL B 155 " (cutoff:3.500A) 767 hydrogen bonds defined for protein. 2157 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: 2.56 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4899 1.34 - 1.46: 3315 1.46 - 1.58: 6895 1.58 - 1.70: 0 1.70 - 1.82: 97 Bond restraints: 15206 Sorted by residual: bond pdb=" CB ILE A1047 " pdb=" CG2 ILE A1047 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.42e+00 bond pdb=" CB ARG A1046 " pdb=" CG ARG A1046 " ideal model delta sigma weight residual 1.520 1.458 0.062 3.00e-02 1.11e+03 4.25e+00 bond pdb=" CA GLU A1538 " pdb=" C GLU A1538 " ideal model delta sigma weight residual 1.523 1.495 0.028 1.41e-02 5.03e+03 3.94e+00 bond pdb=" CB LEU A1099 " pdb=" CG LEU A1099 " ideal model delta sigma weight residual 1.530 1.493 0.037 2.00e-02 2.50e+03 3.42e+00 bond pdb=" CG PRO A 69 " pdb=" CD PRO A 69 " ideal model delta sigma weight residual 1.503 1.441 0.062 3.40e-02 8.65e+02 3.36e+00 ... (remaining 15201 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 19755 1.96 - 3.92: 739 3.92 - 5.88: 103 5.88 - 7.85: 30 7.85 - 9.81: 11 Bond angle restraints: 20638 Sorted by residual: angle pdb=" CA PRO A 69 " pdb=" N PRO A 69 " pdb=" CD PRO A 69 " ideal model delta sigma weight residual 112.00 104.62 7.38 1.40e+00 5.10e-01 2.78e+01 angle pdb=" N PRO A 69 " pdb=" CD PRO A 69 " pdb=" CG PRO A 69 " ideal model delta sigma weight residual 103.20 96.34 6.86 1.50e+00 4.44e-01 2.09e+01 angle pdb=" C GLU A1959 " pdb=" N ASP A1960 " pdb=" CA ASP A1960 " ideal model delta sigma weight residual 120.67 125.68 -5.01 1.34e+00 5.57e-01 1.40e+01 angle pdb=" CB LEU A 912 " pdb=" CG LEU A 912 " pdb=" CD2 LEU A 912 " ideal model delta sigma weight residual 110.70 100.89 9.81 3.00e+00 1.11e-01 1.07e+01 angle pdb=" C HIS A1107 " pdb=" N PHE A1108 " pdb=" CA PHE A1108 " ideal model delta sigma weight residual 120.88 115.72 5.16 1.62e+00 3.81e-01 1.02e+01 ... (remaining 20633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 8239 17.85 - 35.69: 846 35.69 - 53.54: 123 53.54 - 71.38: 25 71.38 - 89.23: 11 Dihedral angle restraints: 9244 sinusoidal: 3765 harmonic: 5479 Sorted by residual: dihedral pdb=" CA ASN A1519 " pdb=" C ASN A1519 " pdb=" N PHE A1520 " pdb=" CA PHE A1520 " ideal model delta harmonic sigma weight residual -180.00 -151.51 -28.49 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA HIS A1717 " pdb=" C HIS A1717 " pdb=" N ARG A1718 " pdb=" CA ARG A1718 " ideal model delta harmonic sigma weight residual 180.00 154.49 25.51 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA ASP A 55 " pdb=" C ASP A 55 " pdb=" N PHE A 56 " pdb=" CA PHE A 56 " ideal model delta harmonic sigma weight residual -180.00 -154.77 -25.23 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 9241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1480 0.043 - 0.087: 634 0.087 - 0.130: 175 0.130 - 0.174: 42 0.174 - 0.217: 3 Chirality restraints: 2334 Sorted by residual: chirality pdb=" CG LEU A 912 " pdb=" CB LEU A 912 " pdb=" CD1 LEU A 912 " pdb=" CD2 LEU A 912 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB VAL A 244 " pdb=" CA VAL A 244 " pdb=" CG1 VAL A 244 " pdb=" CG2 VAL A 244 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.43e-01 chirality pdb=" CG LEU A1970 " pdb=" CB LEU A1970 " pdb=" CD1 LEU A1970 " pdb=" CD2 LEU A1970 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.17e-01 ... (remaining 2331 not shown) Planarity restraints: 2672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 68 " 0.056 5.00e-02 4.00e+02 8.08e-02 1.05e+01 pdb=" N PRO A 69 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 69 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 69 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A1765 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.23e+00 pdb=" CG ASP A1765 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASP A1765 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP A1765 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 501 " -0.037 5.00e-02 4.00e+02 5.68e-02 5.17e+00 pdb=" N PRO A 502 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 502 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 502 " -0.031 5.00e-02 4.00e+02 ... (remaining 2669 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 251 2.63 - 3.20: 14768 3.20 - 3.76: 23284 3.76 - 4.33: 31919 4.33 - 4.90: 50664 Nonbonded interactions: 120886 Sorted by model distance: nonbonded pdb=" O GLY A1111 " pdb=" OG1 THR A1115 " model vdw 2.061 3.040 nonbonded pdb=" O TYR A1054 " pdb=" ND2 ASN A1058 " model vdw 2.068 3.120 nonbonded pdb=" O PRO B 99 " pdb=" ND1 HIS B 103 " model vdw 2.107 3.120 nonbonded pdb=" O HIS A 837 " pdb=" NZ LYS A 940 " model vdw 2.131 3.120 nonbonded pdb=" O PHE A1012 " pdb=" OG SER A1015 " model vdw 2.136 3.040 ... (remaining 120881 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.110 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.630 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 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 : 0.008 0.069 15206 Z= 0.371 Angle : 0.920 9.807 20638 Z= 0.484 Chirality : 0.051 0.217 2334 Planarity : 0.006 0.081 2672 Dihedral : 14.555 89.229 5680 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.19), residues: 1848 helix: -0.38 (0.17), residues: 891 sheet: -1.11 (0.38), residues: 203 loop : -1.87 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 227 TYR 0.020 0.003 TYR B 23 PHE 0.023 0.003 PHE A1499 TRP 0.033 0.004 TRP B 97 HIS 0.011 0.002 HIS A1880 Details of bonding type rmsd/Z covalent geometry : bond 0.00839 / 0.37 (15206) covalent geometry : angle 0.92018 / 0.48 (20638) hydrogen bonds : bond 0.17475 / 11.06 ( 762) hydrogen bonds : angle 7.60104 / 5.44 ( 2157) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 PHE cc_start: 0.3314 (m-80) cc_final: 0.3010 (m-80) REVERT: A 1116 GLU cc_start: 0.7653 (tp30) cc_final: 0.7397 (tp30) REVERT: B 32 TYR cc_start: 0.6975 (p90) cc_final: 0.6710 (p90) REVERT: B 61 GLN cc_start: 0.6476 (mp10) cc_final: 0.5661 (mp10) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1061 time to fit residues: 30.1714 Evaluate side-chains 147 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.0970 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 3.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1107 HIS ** A1132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 ASN A1550 GLN ** A1602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1821 GLN A1863 HIS ** A1910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1967 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.131918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.093389 restraints weight = 38713.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.094654 restraints weight = 26722.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.095433 restraints weight = 19691.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.096020 restraints weight = 18625.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.096132 restraints weight = 17752.927| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15206 Z= 0.143 Angle : 0.676 9.848 20638 Z= 0.345 Chirality : 0.043 0.252 2334 Planarity : 0.005 0.052 2672 Dihedral : 5.597 24.158 2030 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.73 % Allowed : 6.98 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.20), residues: 1848 helix: 0.62 (0.17), residues: 918 sheet: -0.77 (0.38), residues: 207 loop : -1.43 (0.25), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1837 TYR 0.025 0.002 TYR A2007 PHE 0.026 0.002 PHE A 590 TRP 0.013 0.002 TRP B 97 HIS 0.016 0.001 HIS A1132 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (15206) covalent geometry : angle 0.67586 / 0.34 (20638) hydrogen bonds : bond 0.04876 / 3.19 ( 762) hydrogen bonds : angle 5.52455 / 3.97 ( 2157) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 191 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 PHE cc_start: 0.3372 (m-80) cc_final: 0.3044 (m-80) REVERT: A 1116 GLU cc_start: 0.7479 (tp30) cc_final: 0.7275 (tp30) REVERT: A 1763 ASP cc_start: 0.7602 (p0) cc_final: 0.7279 (p0) REVERT: A 1912 LYS cc_start: 0.8944 (mmtt) cc_final: 0.8425 (mmmt) REVERT: A 1965 ARG cc_start: 0.6661 (mmp-170) cc_final: 0.6376 (mmm160) REVERT: B 28 PHE cc_start: 0.7554 (m-80) cc_final: 0.7284 (m-80) REVERT: B 39 ASN cc_start: 0.6136 (m-40) cc_final: 0.5776 (m-40) REVERT: B 61 GLN cc_start: 0.6326 (mp10) cc_final: 0.5689 (mp10) REVERT: B 128 LYS cc_start: 0.6833 (tptm) cc_final: 0.6630 (tptp) outliers start: 12 outliers final: 7 residues processed: 194 average time/residue: 0.1035 time to fit residues: 31.2690 Evaluate side-chains 164 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 157 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1402 THR Chi-restraints excluded: chain A residue 1985 LEU Chi-restraints excluded: chain B residue 52 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 125 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 15 optimal weight: 0.0470 chunk 10 optimal weight: 0.0570 chunk 168 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 147 optimal weight: 0.0060 chunk 158 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 chunk 129 optimal weight: 10.0000 overall best weight: 0.3814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1910 GLN ** 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 = 0.4081 r_free = 0.4081 target = 0.132982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.093133 restraints weight = 38741.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.095115 restraints weight = 26977.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.097759 restraints weight = 19610.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.097721 restraints weight = 16964.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.097540 restraints weight = 16154.617| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15206 Z= 0.120 Angle : 0.616 13.276 20638 Z= 0.309 Chirality : 0.042 0.181 2334 Planarity : 0.005 0.053 2672 Dihedral : 5.079 20.530 2030 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.16 % Allowed : 10.10 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.20), residues: 1848 helix: 1.10 (0.17), residues: 923 sheet: -0.71 (0.37), residues: 211 loop : -1.33 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1861 TYR 0.032 0.002 TYR A2007 PHE 0.026 0.002 PHE A1432 TRP 0.016 0.002 TRP B 97 HIS 0.012 0.001 HIS A1132 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (15206) covalent geometry : angle 0.61611 / 0.31 (20638) hydrogen bonds : bond 0.04168 / 2.72 ( 762) hydrogen bonds : angle 5.11881 / 3.66 ( 2157) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7599 (tp30) cc_final: 0.7267 (tp30) REVERT: A 509 PHE cc_start: 0.3191 (m-80) cc_final: 0.2845 (m-80) REVERT: A 701 ASP cc_start: 0.7274 (m-30) cc_final: 0.6780 (t0) REVERT: A 1116 GLU cc_start: 0.7578 (tp30) cc_final: 0.7242 (tp30) REVERT: A 1654 VAL cc_start: 0.9065 (t) cc_final: 0.8694 (p) REVERT: A 1763 ASP cc_start: 0.7489 (p0) cc_final: 0.7140 (p0) REVERT: A 1803 LYS cc_start: 0.8001 (tttm) cc_final: 0.7697 (tttm) REVERT: A 1912 LYS cc_start: 0.8897 (mmtt) cc_final: 0.8496 (tptt) REVERT: A 1965 ARG cc_start: 0.6803 (mmp-170) cc_final: 0.6486 (mmm160) REVERT: B 61 GLN cc_start: 0.6291 (mp10) cc_final: 0.5643 (mp10) REVERT: B 95 GLU cc_start: 0.4896 (OUTLIER) cc_final: 0.4645 (tp30) REVERT: B 166 LYS cc_start: 0.6840 (tptt) cc_final: 0.6612 (tptt) outliers start: 19 outliers final: 9 residues processed: 198 average time/residue: 0.1040 time to fit residues: 32.2080 Evaluate side-chains 170 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1402 THR Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain A residue 1985 LEU Chi-restraints excluded: chain B residue 95 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 143 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 108 optimal weight: 0.5980 chunk 131 optimal weight: 0.4980 chunk 92 optimal weight: 0.6980 chunk 169 optimal weight: 0.0570 chunk 101 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 118 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1132 HIS A1497 HIS ** A1602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1931 GLN ** A1967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.133227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.096767 restraints weight = 37966.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.096198 restraints weight = 27546.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.097325 restraints weight = 21158.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.097372 restraints weight = 20801.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.097603 restraints weight = 17566.518| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15206 Z= 0.117 Angle : 0.603 14.501 20638 Z= 0.300 Chirality : 0.041 0.257 2334 Planarity : 0.004 0.054 2672 Dihedral : 4.760 18.688 2030 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.59 % Allowed : 11.81 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.20), residues: 1848 helix: 1.31 (0.17), residues: 926 sheet: -0.53 (0.37), residues: 207 loop : -1.25 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1914 TYR 0.037 0.001 TYR A2007 PHE 0.020 0.001 PHE A1432 TRP 0.009 0.001 TRP A 120 HIS 0.015 0.001 HIS A1497 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (15206) covalent geometry : angle 0.60307 / 0.30 (20638) hydrogen bonds : bond 0.03798 / 2.47 ( 762) hydrogen bonds : angle 4.90776 / 3.51 ( 2157) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7867 (tp30) cc_final: 0.7463 (tp30) REVERT: A 509 PHE cc_start: 0.2901 (m-80) cc_final: 0.2682 (m-80) REVERT: A 701 ASP cc_start: 0.7136 (m-30) cc_final: 0.6662 (t0) REVERT: A 1654 VAL cc_start: 0.9055 (t) cc_final: 0.8764 (p) REVERT: A 1912 LYS cc_start: 0.8856 (mmtt) cc_final: 0.8533 (tptt) REVERT: A 1965 ARG cc_start: 0.6789 (mmp-170) cc_final: 0.6457 (mmm160) REVERT: B 32 TYR cc_start: 0.7318 (p90) cc_final: 0.7081 (p90) REVERT: B 61 GLN cc_start: 0.6422 (mp10) cc_final: 0.6191 (mm-40) REVERT: B 92 ASN cc_start: 0.8306 (m110) cc_final: 0.7827 (m110) outliers start: 26 outliers final: 12 residues processed: 194 average time/residue: 0.1064 time to fit residues: 31.9887 Evaluate side-chains 171 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1402 THR Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain A residue 1902 VAL Chi-restraints excluded: chain A residue 1985 LEU Chi-restraints excluded: chain B residue 52 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 19 optimal weight: 7.9990 chunk 107 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 182 optimal weight: 7.9990 chunk 137 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 0.0670 chunk 2 optimal weight: 0.9980 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 GLN ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1497 HIS ** A1602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1967 HIS ** 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 = 0.4090 r_free = 0.4090 target = 0.133518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.101878 restraints weight = 38701.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.102859 restraints weight = 38780.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.103186 restraints weight = 39216.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.103654 restraints weight = 25231.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.104258 restraints weight = 22199.304| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15206 Z= 0.113 Angle : 0.604 13.841 20638 Z= 0.296 Chirality : 0.041 0.302 2334 Planarity : 0.004 0.053 2672 Dihedral : 4.590 18.145 2030 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.59 % Allowed : 13.22 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.20), residues: 1848 helix: 1.41 (0.18), residues: 929 sheet: -0.44 (0.37), residues: 207 loop : -1.14 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.025 0.001 TYR A2007 PHE 0.018 0.001 PHE A1432 TRP 0.010 0.001 TRP B 97 HIS 0.018 0.001 HIS A1497 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (15206) covalent geometry : angle 0.60437 / 0.30 (20638) hydrogen bonds : bond 0.03687 / 2.42 ( 762) hydrogen bonds : angle 4.82999 / 3.44 ( 2157) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7866 (tp30) cc_final: 0.7497 (tp30) REVERT: A 701 ASP cc_start: 0.6979 (m-30) cc_final: 0.6592 (t0) REVERT: A 1116 GLU cc_start: 0.7604 (tp30) cc_final: 0.7245 (tp30) REVERT: A 1654 VAL cc_start: 0.8990 (t) cc_final: 0.8676 (p) REVERT: A 1751 TYR cc_start: 0.8090 (m-80) cc_final: 0.7701 (m-10) REVERT: A 1912 LYS cc_start: 0.8879 (mmtt) cc_final: 0.8524 (tptt) REVERT: B 39 ASN cc_start: 0.7388 (m-40) cc_final: 0.7028 (m110) REVERT: B 61 GLN cc_start: 0.6534 (mp10) cc_final: 0.6309 (mm-40) REVERT: B 92 ASN cc_start: 0.8302 (m110) cc_final: 0.7852 (m110) outliers start: 26 outliers final: 16 residues processed: 189 average time/residue: 0.1072 time to fit residues: 32.1678 Evaluate side-chains 179 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1402 THR Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain A residue 1715 GLU Chi-restraints excluded: chain A residue 1985 LEU Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 93 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 57 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 166 optimal weight: 9.9990 chunk 74 optimal weight: 0.6980 chunk 146 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 151 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1280 GLN ** A1602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.132678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.097740 restraints weight = 38359.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.096019 restraints weight = 28647.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.096881 restraints weight = 23218.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.097239 restraints weight = 21197.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.097369 restraints weight = 19303.814| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15206 Z= 0.132 Angle : 0.621 14.171 20638 Z= 0.302 Chirality : 0.041 0.301 2334 Planarity : 0.004 0.057 2672 Dihedral : 4.592 19.724 2030 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.41 % Allowed : 14.38 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.20), residues: 1848 helix: 1.41 (0.18), residues: 928 sheet: -0.39 (0.37), residues: 207 loop : -1.11 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.019 0.001 TYR A1630 PHE 0.018 0.001 PHE A1432 TRP 0.010 0.001 TRP A1599 HIS 0.009 0.001 HIS A1132 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (15206) covalent geometry : angle 0.62099 / 0.30 (20638) hydrogen bonds : bond 0.03782 / 2.48 ( 762) hydrogen bonds : angle 4.85168 / 3.45 ( 2157) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7921 (tp30) cc_final: 0.7561 (tp30) REVERT: A 530 LYS cc_start: 0.8144 (mtpt) cc_final: 0.7182 (tppt) REVERT: A 701 ASP cc_start: 0.7092 (m-30) cc_final: 0.6637 (t0) REVERT: A 1116 GLU cc_start: 0.7567 (tp30) cc_final: 0.7191 (tp30) REVERT: A 1654 VAL cc_start: 0.8959 (t) cc_final: 0.8663 (p) REVERT: A 1739 HIS cc_start: 0.8469 (m90) cc_final: 0.8217 (m90) REVERT: A 1803 LYS cc_start: 0.7683 (tttm) cc_final: 0.7367 (tppt) REVERT: A 1912 LYS cc_start: 0.9011 (mmtt) cc_final: 0.8609 (tptt) REVERT: A 1965 ARG cc_start: 0.6755 (mmm160) cc_final: 0.6474 (mmm160) REVERT: B 61 GLN cc_start: 0.6492 (mp10) cc_final: 0.6262 (mm-40) REVERT: B 92 ASN cc_start: 0.8460 (m110) cc_final: 0.7960 (m110) REVERT: B 140 GLU cc_start: 0.5339 (mm-30) cc_final: 0.4837 (mp0) outliers start: 23 outliers final: 16 residues processed: 178 average time/residue: 0.1047 time to fit residues: 29.2002 Evaluate side-chains 178 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1290 LEU Chi-restraints excluded: chain A residue 1402 THR Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain A residue 1715 GLU Chi-restraints excluded: chain A residue 1902 VAL Chi-restraints excluded: chain A residue 1985 LEU Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 93 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 122 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 0.3980 chunk 50 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1497 HIS ** A1602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1988 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.132590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.097096 restraints weight = 38563.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.095052 restraints weight = 29841.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.095958 restraints weight = 23616.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.096226 restraints weight = 20697.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.096504 restraints weight = 19265.824| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15206 Z= 0.139 Angle : 0.622 14.356 20638 Z= 0.302 Chirality : 0.041 0.280 2334 Planarity : 0.004 0.053 2672 Dihedral : 4.562 17.829 2030 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.47 % Allowed : 15.06 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.20), residues: 1848 helix: 1.46 (0.18), residues: 922 sheet: -0.29 (0.37), residues: 207 loop : -1.02 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.021 0.001 TYR A2007 PHE 0.018 0.001 PHE A1432 TRP 0.009 0.001 TRP A1599 HIS 0.019 0.001 HIS A1497 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (15206) covalent geometry : angle 0.62210 / 0.30 (20638) hydrogen bonds : bond 0.03781 / 2.48 ( 762) hydrogen bonds : angle 4.82221 / 3.43 ( 2157) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7956 (tp30) cc_final: 0.7573 (tp30) REVERT: A 530 LYS cc_start: 0.8090 (mtpt) cc_final: 0.7114 (tppt) REVERT: A 701 ASP cc_start: 0.7122 (m-30) cc_final: 0.6650 (t0) REVERT: A 1042 MET cc_start: 0.7712 (tpt) cc_final: 0.7442 (tpt) REVERT: A 1116 GLU cc_start: 0.7468 (tp30) cc_final: 0.6965 (tp30) REVERT: A 1654 VAL cc_start: 0.8981 (t) cc_final: 0.8702 (p) REVERT: A 1739 HIS cc_start: 0.8507 (m90) cc_final: 0.8269 (m90) REVERT: A 1803 LYS cc_start: 0.7786 (tttm) cc_final: 0.7271 (tppt) REVERT: A 1912 LYS cc_start: 0.9060 (mmtt) cc_final: 0.8653 (tptt) REVERT: A 1965 ARG cc_start: 0.6822 (mmm160) cc_final: 0.6501 (mmm160) REVERT: B 61 GLN cc_start: 0.6499 (mp10) cc_final: 0.6251 (mm-40) REVERT: B 92 ASN cc_start: 0.8437 (m110) cc_final: 0.8110 (m-40) REVERT: B 140 GLU cc_start: 0.5252 (mm-30) cc_final: 0.4805 (mp0) outliers start: 24 outliers final: 19 residues processed: 174 average time/residue: 0.1049 time to fit residues: 29.1516 Evaluate side-chains 176 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1290 LEU Chi-restraints excluded: chain A residue 1402 THR Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain A residue 1497 HIS Chi-restraints excluded: chain A residue 1715 GLU Chi-restraints excluded: chain A residue 1902 VAL Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 93 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 0.5980 chunk 145 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 10 optimal weight: 0.0870 chunk 19 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 chunk 180 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1497 HIS ** A1602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1988 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.132252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.097896 restraints weight = 38546.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.095140 restraints weight = 28282.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.096205 restraints weight = 25732.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.096607 restraints weight = 21570.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.096819 restraints weight = 19703.498| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15206 Z= 0.142 Angle : 0.631 14.070 20638 Z= 0.305 Chirality : 0.041 0.297 2334 Planarity : 0.004 0.053 2672 Dihedral : 4.571 17.842 2030 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.47 % Allowed : 15.91 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.20), residues: 1848 helix: 1.48 (0.18), residues: 921 sheet: -0.33 (0.38), residues: 201 loop : -0.97 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.019 0.001 TYR A1630 PHE 0.018 0.001 PHE A1432 TRP 0.009 0.001 TRP B 97 HIS 0.030 0.001 HIS A1497 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (15206) covalent geometry : angle 0.63094 / 0.30 (20638) hydrogen bonds : bond 0.03803 / 2.48 ( 762) hydrogen bonds : angle 4.81661 / 3.42 ( 2157) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7931 (tp30) cc_final: 0.7579 (tp30) REVERT: A 530 LYS cc_start: 0.8016 (mtpt) cc_final: 0.7075 (tppt) REVERT: A 701 ASP cc_start: 0.7120 (m-30) cc_final: 0.6643 (t0) REVERT: A 1116 GLU cc_start: 0.7451 (tp30) cc_final: 0.7177 (tp30) REVERT: A 1654 VAL cc_start: 0.8975 (t) cc_final: 0.8637 (p) REVERT: A 1739 HIS cc_start: 0.8477 (m90) cc_final: 0.8275 (m90) REVERT: A 1803 LYS cc_start: 0.7783 (tttm) cc_final: 0.7241 (tppt) REVERT: A 1912 LYS cc_start: 0.9057 (mmtt) cc_final: 0.8626 (tptt) REVERT: A 1916 LEU cc_start: 0.6894 (pp) cc_final: 0.6529 (pp) REVERT: A 1965 ARG cc_start: 0.6800 (mmm160) cc_final: 0.6486 (mmm160) REVERT: B 61 GLN cc_start: 0.6501 (mp10) cc_final: 0.6243 (mm-40) REVERT: B 92 ASN cc_start: 0.8402 (m110) cc_final: 0.8105 (m-40) REVERT: B 140 GLU cc_start: 0.5247 (mm-30) cc_final: 0.4863 (mp0) outliers start: 24 outliers final: 20 residues processed: 174 average time/residue: 0.1053 time to fit residues: 28.8382 Evaluate side-chains 176 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1290 LEU Chi-restraints excluded: chain A residue 1402 THR Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain A residue 1497 HIS Chi-restraints excluded: chain A residue 1715 GLU Chi-restraints excluded: chain A residue 1902 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 93 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 119 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 174 optimal weight: 3.9990 chunk 136 optimal weight: 0.0670 chunk 100 optimal weight: 2.9990 chunk 146 optimal weight: 0.2980 chunk 164 optimal weight: 2.9990 chunk 182 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 chunk 109 optimal weight: 0.0070 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1497 HIS ** A1602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1988 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.133821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.102510 restraints weight = 38619.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.103970 restraints weight = 38150.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.103979 restraints weight = 40449.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.104644 restraints weight = 24472.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.105206 restraints weight = 21202.543| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15206 Z= 0.108 Angle : 0.619 15.425 20638 Z= 0.295 Chirality : 0.041 0.310 2334 Planarity : 0.004 0.053 2672 Dihedral : 4.407 16.951 2030 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.35 % Allowed : 16.03 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.20), residues: 1848 helix: 1.56 (0.18), residues: 925 sheet: -0.23 (0.40), residues: 190 loop : -0.94 (0.24), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.020 0.001 TYR A2007 PHE 0.016 0.001 PHE A1432 TRP 0.012 0.001 TRP A1599 HIS 0.034 0.001 HIS A1497 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (15206) covalent geometry : angle 0.61917 / 0.29 (20638) hydrogen bonds : bond 0.03522 / 2.31 ( 762) hydrogen bonds : angle 4.70818 / 3.35 ( 2157) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7861 (tp30) cc_final: 0.7586 (tp30) REVERT: A 530 LYS cc_start: 0.7723 (mtpt) cc_final: 0.6974 (tppt) REVERT: A 701 ASP cc_start: 0.6887 (m-30) cc_final: 0.6446 (t0) REVERT: A 1116 GLU cc_start: 0.7532 (tp30) cc_final: 0.7238 (tp30) REVERT: A 1654 VAL cc_start: 0.8963 (t) cc_final: 0.8623 (p) REVERT: A 1688 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7691 (mm-30) REVERT: A 1803 LYS cc_start: 0.7354 (tttm) cc_final: 0.7142 (tppt) REVERT: A 1912 LYS cc_start: 0.8919 (mmtt) cc_final: 0.8600 (tptt) REVERT: A 1916 LEU cc_start: 0.6848 (pp) cc_final: 0.6512 (pp) REVERT: A 1965 ARG cc_start: 0.6763 (mmm160) cc_final: 0.6542 (mmm160) REVERT: B 56 PHE cc_start: 0.6481 (m-80) cc_final: 0.6267 (m-80) REVERT: B 61 GLN cc_start: 0.6652 (mp10) cc_final: 0.6350 (mm-40) REVERT: B 92 ASN cc_start: 0.8350 (m110) cc_final: 0.7997 (m-40) REVERT: B 140 GLU cc_start: 0.4859 (mm-30) cc_final: 0.4389 (mp0) outliers start: 22 outliers final: 20 residues processed: 192 average time/residue: 0.1106 time to fit residues: 33.2726 Evaluate side-chains 186 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1290 LEU Chi-restraints excluded: chain A residue 1402 THR Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain A residue 1715 GLU Chi-restraints excluded: chain A residue 1902 VAL Chi-restraints excluded: chain A residue 1985 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 174 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 161 optimal weight: 9.9990 chunk 75 optimal weight: 0.0060 chunk 112 optimal weight: 1.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1497 HIS ** A1602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1988 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.133421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.102141 restraints weight = 38456.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.103333 restraints weight = 37712.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.103626 restraints weight = 38564.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.103988 restraints weight = 24686.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.104780 restraints weight = 21579.314| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15206 Z= 0.120 Angle : 0.632 14.717 20638 Z= 0.305 Chirality : 0.041 0.298 2334 Planarity : 0.004 0.052 2672 Dihedral : 4.394 17.675 2030 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.29 % Allowed : 16.77 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.20), residues: 1848 helix: 1.59 (0.18), residues: 923 sheet: -0.29 (0.39), residues: 191 loop : -0.91 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1160 TYR 0.019 0.001 TYR A1630 PHE 0.019 0.001 PHE A1556 TRP 0.010 0.001 TRP A1599 HIS 0.023 0.001 HIS A1497 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (15206) covalent geometry : angle 0.63168 / 0.31 (20638) hydrogen bonds : bond 0.03565 / 2.33 ( 762) hydrogen bonds : angle 4.73431 / 3.36 ( 2157) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7846 (tp30) cc_final: 0.7571 (tp30) REVERT: A 86 LEU cc_start: 0.8626 (mt) cc_final: 0.8405 (tt) REVERT: A 530 LYS cc_start: 0.7651 (mtpt) cc_final: 0.7196 (tppt) REVERT: A 598 PHE cc_start: 0.7256 (m-80) cc_final: 0.6631 (m-10) REVERT: A 701 ASP cc_start: 0.6888 (m-30) cc_final: 0.6433 (t0) REVERT: A 1654 VAL cc_start: 0.8976 (t) cc_final: 0.8636 (p) REVERT: A 1688 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7653 (mm-30) REVERT: A 1803 LYS cc_start: 0.7397 (tttm) cc_final: 0.6804 (tppt) REVERT: A 1912 LYS cc_start: 0.8910 (mmtt) cc_final: 0.8582 (tptt) REVERT: A 1965 ARG cc_start: 0.6772 (mmm160) cc_final: 0.6532 (mmm160) REVERT: B 56 PHE cc_start: 0.6369 (m-80) cc_final: 0.6091 (m-80) REVERT: B 61 GLN cc_start: 0.6669 (mp10) cc_final: 0.6372 (mm-40) REVERT: B 92 ASN cc_start: 0.8370 (m110) cc_final: 0.8014 (m-40) outliers start: 21 outliers final: 21 residues processed: 179 average time/residue: 0.1127 time to fit residues: 31.5549 Evaluate side-chains 182 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1290 LEU Chi-restraints excluded: chain A residue 1402 THR Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain A residue 1497 HIS Chi-restraints excluded: chain A residue 1715 GLU Chi-restraints excluded: chain A residue 1902 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 33 optimal weight: 0.0770 chunk 112 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 HIS ** A1132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1497 HIS ** A1602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1988 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 = 0.4073 r_free = 0.4073 target = 0.132437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.097445 restraints weight = 38745.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.095405 restraints weight = 27458.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.096194 restraints weight = 28262.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.096769 restraints weight = 22673.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.096957 restraints weight = 20788.690| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15206 Z= 0.159 Angle : 0.659 14.741 20638 Z= 0.318 Chirality : 0.042 0.298 2334 Planarity : 0.005 0.053 2672 Dihedral : 4.479 17.054 2030 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.35 % Allowed : 17.01 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.20), residues: 1848 helix: 1.52 (0.17), residues: 923 sheet: -0.38 (0.39), residues: 193 loop : -0.87 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1160 TYR 0.020 0.001 TYR A1630 PHE 0.018 0.001 PHE A1432 TRP 0.009 0.001 TRP B 97 HIS 0.023 0.001 HIS A1497 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (15206) covalent geometry : angle 0.65912 / 0.32 (20638) hydrogen bonds : bond 0.03816 / 2.49 ( 762) hydrogen bonds : angle 4.84535 / 3.43 ( 2157) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2176.02 seconds wall clock time: 38 minutes 39.88 seconds (2319.88 seconds total)