Starting phenix.real_space_refine on Fri Jul 3 18:40:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vm4_65176/07_2026/9vm4_65176.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vm4_65176/07_2026/9vm4_65176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vm4_65176/07_2026/9vm4_65176.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vm4_65176/07_2026/9vm4_65176.map" model { file = "/net/cci-nas-00/data/ceres_data/9vm4_65176/07_2026/9vm4_65176.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vm4_65176/07_2026/9vm4_65176.cif" } resolution = 4.2 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= 0.003 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 67 5.16 5 C 9496 2.51 5 N 2559 2.21 5 O 2734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 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: 14856 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: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1385 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 165} Time building chain proxies: 3.49, per 1000 atoms: 0.23 Number of scatterers: 14856 At special positions: 0 Unit cell: (113.05, 129.01, 171.57, 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 67 16.00 O 2734 8.00 N 2559 7.00 C 9496 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: 1.49 Conformation dependent library (CDL) restraints added in 736.7 milliseconds 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3558 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 14 sheets defined 54.2% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 55 through 62 Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.685A pdb=" N ASP A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 138 through 146 removed outlier: 3.551A pdb=" N GLN A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 removed outlier: 3.934A pdb=" N LEU A 207 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 224 Processing helix chain 'A' and resid 230 through 235 removed outlier: 4.270A pdb=" N LEU A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 230 through 235' Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 303 through 309 Processing helix chain 'A' and resid 317 through 321 Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 401 through 408 removed outlier: 3.975A pdb=" N ALA A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 481 Processing helix chain 'A' and resid 581 through 585 removed outlier: 3.638A pdb=" N ALA A 585 " --> pdb=" O PRO A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 737 Processing helix chain 'A' and resid 752 through 765 removed outlier: 3.752A pdb=" N GLU A 756 " --> pdb=" O ASN A 752 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 789 removed outlier: 3.561A pdb=" N PHE A 775 " --> pdb=" O PRO A 771 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N HIS A 777 " --> pdb=" O VAL A 773 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N HIS A 778 " --> pdb=" O ALA A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 819 Processing helix chain 'A' and resid 820 through 823 Processing helix chain 'A' and resid 829 through 838 Processing helix chain 'A' and resid 899 through 904 removed outlier: 3.931A pdb=" N LEU A 903 " --> pdb=" O VAL A 899 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA A 904 " --> pdb=" O SER A 900 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 899 through 904' Processing helix chain 'A' and resid 907 through 918 removed outlier: 3.508A pdb=" N GLU A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 928 Processing helix chain 'A' and resid 930 through 949 removed outlier: 4.100A pdb=" N PHE A 934 " --> pdb=" O HIS A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 959 removed outlier: 3.634A pdb=" N ARG A 959 " --> pdb=" O ARG A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 982 Processing helix chain 'A' and resid 986 through 1005 Processing helix chain 'A' and resid 1009 through 1030 removed outlier: 3.601A pdb=" N VAL A1013 " --> pdb=" O ASP A1009 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER A1030 " --> pdb=" O THR A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1050 removed outlier: 4.527A pdb=" N LEU A1037 " --> pdb=" O ASN A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1059 Processing helix chain 'A' and resid 1090 through 1097 removed outlier: 3.915A pdb=" N PHE A1097 " --> pdb=" O VAL A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1107 Processing helix chain 'A' and resid 1108 through 1122 Processing helix chain 'A' and resid 1128 through 1149 Processing helix chain 'A' and resid 1150 through 1153 removed outlier: 3.677A 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 1163 Processing helix chain 'A' and resid 1166 through 1174 removed outlier: 4.382A pdb=" N SER A1170 " --> pdb=" O LEU A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1179 removed outlier: 3.834A pdb=" N ARG A1178 " --> pdb=" O THR A1175 " (cutoff:3.500A) 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 1296 removed outlier: 3.855A pdb=" N PHE A1295 " --> pdb=" O CYS A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1305 removed outlier: 3.946A pdb=" N ARG A1305 " --> pdb=" O LYS A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1404 Processing helix chain 'A' and resid 1409 through 1426 removed outlier: 4.028A 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 1448 through 1453 Processing helix chain 'A' and resid 1455 through 1471 removed outlier: 4.279A pdb=" N CYS A1459 " --> pdb=" O ASP A1455 " (cutoff:3.500A) Processing helix chain 'A' and resid 1474 through 1496 Processing helix chain 'A' and resid 1499 through 1517 Processing helix chain 'A' and resid 1521 through 1538 removed outlier: 3.894A pdb=" N LEU A1525 " --> pdb=" O SER A1521 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1571 Processing helix chain 'A' and resid 1576 through 1589 Processing helix chain 'A' and resid 1592 through 1609 removed outlier: 3.567A pdb=" N ARG A1596 " --> pdb=" O SER A1592 " (cutoff:3.500A) Processing helix chain 'A' and resid 1613 through 1633 Processing helix chain 'A' and resid 1642 through 1648 removed outlier: 3.573A pdb=" N VAL A1645 " --> pdb=" O VAL A1642 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER A1646 " --> pdb=" O GLY A1643 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A1648 " --> pdb=" O VAL A1645 " (cutoff:3.500A) Processing helix chain 'A' and resid 1651 through 1658 removed outlier: 3.959A pdb=" N GLU A1656 " --> pdb=" O ASN A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1698 Processing helix chain 'A' and resid 1699 through 1718 removed outlier: 4.160A pdb=" N GLU A1705 " --> pdb=" O GLU A1701 " (cutoff:3.500A) Proline residue: A1712 - end of helix Processing helix chain 'A' and resid 1719 through 1740 Processing helix chain 'A' and resid 1761 through 1765 removed outlier: 3.559A pdb=" N LEU A1764 " --> pdb=" O PHE A1761 " (cutoff:3.500A) Processing helix chain 'A' and resid 1778 through 1795 removed outlier: 5.124A pdb=" N ARG A1793 " --> pdb=" O PHE A1789 " (cutoff:3.500A) Processing helix chain 'A' and resid 1830 through 1837 Processing helix chain 'A' and resid 1840 through 1844 Processing helix chain 'A' and resid 1900 through 1921 Processing helix chain 'A' and resid 1926 through 1939 removed outlier: 3.828A pdb=" N LEU A1930 " --> pdb=" O ASP A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1945 through 1955 removed outlier: 4.261A pdb=" N VAL A1949 " --> pdb=" O GLY A1945 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A1955 " --> pdb=" O GLN A1951 " (cutoff:3.500A) Processing helix chain 'A' and resid 1963 through 1992 removed outlier: 4.056A pdb=" N ALA A1990 " --> pdb=" O ARG A1986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1996 through 2019 Proline residue: A2016 - end of helix Processing helix chain 'B' and resid 15 through 25 Processing helix chain 'B' and resid 62 through 72 removed outlier: 3.643A pdb=" N ASP B 65 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG B 66 " --> pdb=" O ASP B 63 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG B 68 " --> pdb=" O ASP B 65 " (cutoff:3.500A) Proline residue: B 69 - end of helix removed outlier: 3.647A pdb=" N TYR B 72 " --> pdb=" O PRO B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 105 removed outlier: 3.887A pdb=" N PHE B 90 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 94 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N TYR B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) Proline residue: B 99 - end of helix Processing helix chain 'B' and resid 116 through 122 removed outlier: 4.230A pdb=" N ASP B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 132 removed outlier: 4.562A pdb=" N LYS B 128 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS B 132 " --> pdb=" O LYS B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 removed outlier: 3.784A pdb=" N MET B 145 " --> pdb=" O GLN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 177 removed outlier: 3.893A pdb=" N ILE B 173 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 86 Processing sheet with id=AA2, first strand: chain 'A' and resid 261 through 265 Processing sheet with id=AA3, first strand: chain 'A' and resid 296 through 298 removed outlier: 3.697A pdb=" N PHE A 278 " --> pdb=" O GLU A 343 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU A 343 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A 341 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU A 338 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ALA A 398 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ILE A 340 " --> pdb=" O TRP A 396 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TRP A 396 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU A 342 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA5, first strand: chain 'A' and resid 510 through 511 removed outlier: 4.095A pdb=" N CYS A 510 " --> pdb=" O ILE A 518 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 619 through 622 removed outlier: 6.857A pdb=" N SER A 708 " --> pdb=" O HIS A 556 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 570 through 577 removed outlier: 3.502A pdb=" N GLN A 575 " --> pdb=" O LEU A 634 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 634 " --> pdb=" O GLN A 575 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 570 through 577 removed outlier: 3.502A pdb=" N GLN A 575 " --> pdb=" O LEU A 634 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 634 " --> pdb=" O GLN A 575 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 589 through 590 removed outlier: 3.762A pdb=" N ILE A 589 " --> pdb=" O THR A 599 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 741 through 742 Processing sheet with id=AB2, first strand: chain 'A' and resid 792 through 793 Processing sheet with id=AB3, first strand: chain 'A' and resid 1799 through 1801 removed outlier: 5.732A pdb=" N GLU A1768 " --> pdb=" O VAL A1891 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR A1849 " --> pdb=" O TYR A1828 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1799 through 1801 removed outlier: 5.732A pdb=" N GLU A1768 " --> pdb=" O VAL A1891 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 41 through 45 removed outlier: 7.082A pdb=" N CYS B 6 " --> pdb=" O TRP B 56 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LYS B 5 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU B 79 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL B 7 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N CYS B 81 " --> pdb=" O VAL B 7 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 9 " --> pdb=" O CYS B 81 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS B 153 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 155 " --> pdb=" O LEU B 112 " (cutoff:3.500A) 781 hydrogen bonds defined for protein. 2223 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.64 Time building geometry restraints manager: 1.91 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: 4887 1.34 - 1.46: 2918 1.46 - 1.58: 7298 1.58 - 1.70: 0 1.70 - 1.82: 99 Bond restraints: 15202 Sorted by residual: bond pdb=" CA GLN A 128 " pdb=" C GLN A 128 " ideal model delta sigma weight residual 1.522 1.467 0.055 1.38e-02 5.25e+03 1.61e+01 bond pdb=" CA ASN A1653 " pdb=" C ASN A1653 " ideal model delta sigma weight residual 1.522 1.477 0.045 1.72e-02 3.38e+03 6.74e+00 bond pdb=" CB LEU A1142 " pdb=" CG LEU A1142 " ideal model delta sigma weight residual 1.530 1.481 0.049 2.00e-02 2.50e+03 6.10e+00 bond pdb=" CB VAL A1391 " pdb=" CG2 VAL A1391 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.84e+00 bond pdb=" C SER A1592 " pdb=" N PRO A1593 " ideal model delta sigma weight residual 1.336 1.311 0.025 1.20e-02 6.94e+03 4.18e+00 ... (remaining 15197 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 20240 2.89 - 5.78: 344 5.78 - 8.67: 41 8.67 - 11.56: 5 11.56 - 14.44: 2 Bond angle restraints: 20632 Sorted by residual: angle pdb=" CA LEU A1533 " pdb=" CB LEU A1533 " pdb=" CG LEU A1533 " ideal model delta sigma weight residual 116.30 130.74 -14.44 3.50e+00 8.16e-02 1.70e+01 angle pdb=" CA ARG A1465 " pdb=" CB ARG A1465 " pdb=" CG ARG A1465 " ideal model delta sigma weight residual 114.10 105.85 8.25 2.00e+00 2.50e-01 1.70e+01 angle pdb=" CG LYS B 153 " pdb=" CD LYS B 153 " pdb=" CE LYS B 153 " ideal model delta sigma weight residual 111.30 119.75 -8.45 2.30e+00 1.89e-01 1.35e+01 angle pdb=" N VAL B 36 " pdb=" CA VAL B 36 " pdb=" C VAL B 36 " ideal model delta sigma weight residual 112.98 108.43 4.55 1.25e+00 6.40e-01 1.33e+01 angle pdb=" CA LEU A 965 " pdb=" CB LEU A 965 " pdb=" CG LEU A 965 " ideal model delta sigma weight residual 116.30 103.98 12.32 3.50e+00 8.16e-02 1.24e+01 ... (remaining 20627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 8254 17.79 - 35.59: 828 35.59 - 53.38: 131 53.38 - 71.17: 17 71.17 - 88.96: 7 Dihedral angle restraints: 9237 sinusoidal: 3764 harmonic: 5473 Sorted by residual: dihedral pdb=" CA PHE A1452 " pdb=" C PHE A1452 " pdb=" N GLU A1453 " pdb=" CA GLU A1453 " ideal model delta harmonic sigma weight residual 180.00 -152.78 -27.22 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA ARG A 466 " pdb=" C ARG A 466 " pdb=" N LEU A 467 " pdb=" CA LEU A 467 " ideal model delta harmonic sigma weight residual -180.00 -155.33 -24.67 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA PHE A 560 " pdb=" C PHE A 560 " pdb=" N SER A 561 " pdb=" CA SER A 561 " ideal model delta harmonic sigma weight residual 180.00 156.48 23.52 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 9234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1443 0.040 - 0.080: 632 0.080 - 0.121: 197 0.121 - 0.161: 48 0.161 - 0.201: 9 Chirality restraints: 2329 Sorted by residual: chirality pdb=" CB VAL B 36 " pdb=" CA VAL B 36 " pdb=" CG1 VAL B 36 " pdb=" CG2 VAL B 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CG LEU A1258 " pdb=" CB LEU A1258 " pdb=" CD1 LEU A1258 " pdb=" CD2 LEU A1258 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" CA GLN A 128 " pdb=" N GLN A 128 " pdb=" C GLN A 128 " pdb=" CB GLN A 128 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.66e-01 ... (remaining 2326 not shown) Planarity restraints: 2672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 105 " -0.042 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO B 106 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 106 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 106 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A1939 " -0.040 5.00e-02 4.00e+02 5.98e-02 5.71e+00 pdb=" N PRO A1940 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A1940 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A1940 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1694 " -0.022 2.00e-02 2.50e+03 1.79e-02 5.58e+00 pdb=" CG PHE A1694 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE A1694 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A1694 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A1694 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A1694 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A1694 " -0.004 2.00e-02 2.50e+03 ... (remaining 2669 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 233 2.51 - 3.11: 13043 3.11 - 3.71: 24759 3.71 - 4.30: 33780 4.30 - 4.90: 52951 Nonbonded interactions: 124766 Sorted by model distance: nonbonded pdb=" O ILE A1650 " pdb=" OH TYR A1845 " model vdw 1.917 3.040 nonbonded pdb=" O SER A1512 " pdb=" OG1 THR A1516 " model vdw 2.006 3.040 nonbonded pdb=" O GLY A1111 " pdb=" OG1 THR A1115 " model vdw 2.025 3.040 nonbonded pdb=" O LEU A1916 " pdb=" OG1 THR A1920 " model vdw 2.045 3.040 nonbonded pdb=" O PHE A1789 " pdb=" NH1 ARG A1793 " model vdw 2.062 3.120 ... (remaining 124761 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: 0.880 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.260 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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 0.073 15202 Z= 0.394 Angle : 0.958 14.445 20632 Z= 0.509 Chirality : 0.050 0.201 2329 Planarity : 0.006 0.064 2672 Dihedral : 14.047 88.964 5679 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 31.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -2.29 (0.18), residues: 1847 helix: -1.26 (0.16), residues: 890 sheet: -1.86 (0.33), residues: 207 loop : -1.54 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG A1965 TYR 0.028 0.003 TYR A1790 PHE 0.041 0.003 PHE A1694 TRP 0.034 0.003 TRP B 56 HIS 0.011 0.002 HIS B 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00831 / 0.39 (15202) covalent geometry : angle 0.95812 / 0.51 (20632) hydrogen bonds : bond 0.18689 / 11.99 ( 752) hydrogen bonds : angle 7.93053 / 5.45 ( 2223) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8344 (pmm) cc_final: 0.8077 (pmm) REVERT: A 392 MET cc_start: 0.8916 (mpp) cc_final: 0.8686 (mpp) REVERT: A 633 LEU cc_start: 0.9280 (mt) cc_final: 0.8785 (tt) REVERT: A 1555 MET cc_start: 0.8880 (mpp) cc_final: 0.8168 (mpp) REVERT: A 1744 TRP cc_start: 0.6195 (m-90) cc_final: 0.5879 (m100) REVERT: A 1932 MET cc_start: 0.8468 (ppp) cc_final: 0.8178 (ppp) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1051 time to fit residues: 23.9704 Evaluate side-chains 110 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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: 0.2980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 462 GLN ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1557 ASN A1559 HIS A1602 ASN A1648 GLN ** A1653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1709 ASN A1931 GLN A1988 ASN B 61 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.074937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.051762 restraints weight = 70380.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.053535 restraints weight = 44821.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.054688 restraints weight = 33738.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.055470 restraints weight = 28027.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.055977 restraints weight = 24758.547| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15202 Z= 0.138 Angle : 0.658 7.554 20632 Z= 0.338 Chirality : 0.043 0.190 2329 Planarity : 0.005 0.057 2672 Dihedral : 5.617 23.237 2034 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.25 % Allowed : 5.16 % Favored : 94.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -1.01 (0.19), residues: 1847 helix: 0.12 (0.17), residues: 906 sheet: -1.47 (0.34), residues: 206 loop : -1.31 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1465 TYR 0.015 0.002 TYR A1021 PHE 0.028 0.002 PHE A1694 TRP 0.022 0.002 TRP B 56 HIS 0.008 0.001 HIS A1435 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (15202) covalent geometry : angle 0.65790 / 0.34 (20632) hydrogen bonds : bond 0.04491 / 2.98 ( 752) hydrogen bonds : angle 5.56083 / 3.89 ( 2223) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 188 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8176 (pmm) cc_final: 0.7910 (pmm) REVERT: A 292 ILE cc_start: 0.9035 (pt) cc_final: 0.8819 (mp) REVERT: A 392 MET cc_start: 0.8681 (mpp) cc_final: 0.8397 (mpp) REVERT: A 1270 GLN cc_start: 0.8977 (pp30) cc_final: 0.8564 (tm-30) REVERT: A 1518 GLN cc_start: 0.7910 (mp10) cc_final: 0.7518 (mp10) REVERT: A 1555 MET cc_start: 0.9063 (mpp) cc_final: 0.8532 (mpp) REVERT: A 1847 LEU cc_start: 0.9163 (mt) cc_final: 0.8875 (mt) REVERT: A 1929 MET cc_start: 0.9482 (mpp) cc_final: 0.9224 (mpp) REVERT: A 1932 MET cc_start: 0.8354 (ppp) cc_final: 0.8145 (ppp) REVERT: B 20 LEU cc_start: 0.9297 (mm) cc_final: 0.9021 (mm) REVERT: B 40 TYR cc_start: 0.7702 (m-80) cc_final: 0.7378 (m-80) outliers start: 4 outliers final: 1 residues processed: 191 average time/residue: 0.1037 time to fit residues: 31.7322 Evaluate side-chains 132 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 18 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 2 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 23 optimal weight: 30.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 ASN ** A1550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.072774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.050033 restraints weight = 73598.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.051611 restraints weight = 49221.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.052628 restraints weight = 38032.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.053292 restraints weight = 32182.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.053761 restraints weight = 28793.968| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15202 Z= 0.240 Angle : 0.711 8.792 20632 Z= 0.360 Chirality : 0.044 0.198 2329 Planarity : 0.006 0.057 2672 Dihedral : 5.618 25.632 2034 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.06 % Allowed : 4.48 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.93 (0.19), residues: 1847 helix: 0.14 (0.17), residues: 905 sheet: -1.46 (0.33), residues: 206 loop : -1.19 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A2009 TYR 0.018 0.002 TYR A1289 PHE 0.019 0.002 PHE A 590 TRP 0.011 0.001 TRP A 120 HIS 0.010 0.002 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.24 (15202) covalent geometry : angle 0.71058 / 0.36 (20632) hydrogen bonds : bond 0.04624 / 3.04 ( 752) hydrogen bonds : angle 5.58569 / 3.91 ( 2223) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8163 (pmm) cc_final: 0.7843 (pmm) REVERT: A 292 ILE cc_start: 0.8934 (pt) cc_final: 0.8675 (mp) REVERT: A 392 MET cc_start: 0.8810 (mpp) cc_final: 0.8609 (mpp) REVERT: A 1270 GLN cc_start: 0.8978 (pp30) cc_final: 0.8656 (tm-30) REVERT: A 1504 MET cc_start: 0.7635 (ptm) cc_final: 0.7143 (ptp) REVERT: A 1847 LEU cc_start: 0.9233 (mt) cc_final: 0.9002 (mt) REVERT: A 1929 MET cc_start: 0.9525 (mpp) cc_final: 0.9274 (mpp) REVERT: A 1932 MET cc_start: 0.8305 (ppp) cc_final: 0.8015 (ppp) REVERT: B 16 LYS cc_start: 0.8563 (mttt) cc_final: 0.8228 (mttt) REVERT: B 20 LEU cc_start: 0.9300 (mm) cc_final: 0.8978 (mm) REVERT: B 40 TYR cc_start: 0.7975 (m-80) cc_final: 0.7499 (m-80) REVERT: B 78 PHE cc_start: 0.8327 (m-10) cc_final: 0.8071 (m-80) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.1030 time to fit residues: 27.2254 Evaluate side-chains 118 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 34 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 15 optimal weight: 0.4980 chunk 74 optimal weight: 0.7980 chunk 174 optimal weight: 0.0670 chunk 143 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 overall best weight: 1.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 639 HIS ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 ASN A1550 GLN A1602 ASN A1653 ASN A1880 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.075026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.051749 restraints weight = 70995.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.053518 restraints weight = 45301.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.054692 restraints weight = 34084.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.055449 restraints weight = 28286.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.055957 restraints weight = 25016.909| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15202 Z= 0.126 Angle : 0.615 7.605 20632 Z= 0.310 Chirality : 0.042 0.184 2329 Planarity : 0.005 0.055 2672 Dihedral : 5.142 23.064 2034 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.06 % Allowed : 3.62 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.39 (0.20), residues: 1847 helix: 0.64 (0.17), residues: 904 sheet: -1.15 (0.33), residues: 211 loop : -1.03 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1465 TYR 0.015 0.001 TYR A1751 PHE 0.021 0.001 PHE A 590 TRP 0.014 0.001 TRP A 658 HIS 0.006 0.001 HIS A1893 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (15202) covalent geometry : angle 0.61453 / 0.31 (20632) hydrogen bonds : bond 0.03924 / 2.62 ( 752) hydrogen bonds : angle 5.12984 / 3.60 ( 2223) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8208 (pmm) cc_final: 0.7914 (pmm) REVERT: A 392 MET cc_start: 0.8664 (mpp) cc_final: 0.8417 (mpp) REVERT: A 633 LEU cc_start: 0.9200 (tp) cc_final: 0.8926 (tp) REVERT: A 1096 MET cc_start: 0.8599 (ttm) cc_final: 0.8056 (mtt) REVERT: A 1270 GLN cc_start: 0.8975 (pp30) cc_final: 0.8675 (tm-30) REVERT: A 1491 GLN cc_start: 0.8649 (pp30) cc_final: 0.8108 (pp30) REVERT: A 1504 MET cc_start: 0.7679 (ptm) cc_final: 0.7198 (ptm) REVERT: A 1566 VAL cc_start: 0.9077 (t) cc_final: 0.8740 (t) REVERT: A 1847 LEU cc_start: 0.9191 (mt) cc_final: 0.8945 (mt) REVERT: B 20 LEU cc_start: 0.9293 (mm) cc_final: 0.9063 (tp) REVERT: B 40 TYR cc_start: 0.7600 (m-80) cc_final: 0.7361 (m-80) REVERT: B 41 SER cc_start: 0.8004 (p) cc_final: 0.7800 (t) REVERT: B 78 PHE cc_start: 0.8292 (m-10) cc_final: 0.8051 (m-80) outliers start: 1 outliers final: 1 residues processed: 188 average time/residue: 0.1060 time to fit residues: 31.5071 Evaluate side-chains 135 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 152 optimal weight: 0.9990 chunk 154 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 163 optimal weight: 8.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** A1435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 ASN A1602 ASN ** A1717 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.074804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.051775 restraints weight = 72469.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.053359 restraints weight = 48474.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.054427 restraints weight = 37530.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.055130 restraints weight = 31746.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.055553 restraints weight = 28355.744| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15202 Z= 0.143 Angle : 0.627 8.894 20632 Z= 0.317 Chirality : 0.042 0.241 2329 Planarity : 0.005 0.054 2672 Dihedral : 5.010 21.530 2034 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.28 (0.20), residues: 1847 helix: 0.73 (0.17), residues: 907 sheet: -1.06 (0.33), residues: 201 loop : -0.99 (0.24), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1965 TYR 0.015 0.001 TYR A1999 PHE 0.017 0.001 PHE A 590 TRP 0.043 0.002 TRP B 56 HIS 0.006 0.001 HIS A1571 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (15202) covalent geometry : angle 0.62722 / 0.32 (20632) hydrogen bonds : bond 0.03874 / 2.58 ( 752) hydrogen bonds : angle 5.07159 / 3.55 ( 2223) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 MET cc_start: 0.8646 (mpp) cc_final: 0.8393 (mpp) REVERT: A 1270 GLN cc_start: 0.8988 (pp30) cc_final: 0.8667 (tm-30) REVERT: A 1504 MET cc_start: 0.7676 (ptm) cc_final: 0.7180 (ptm) REVERT: A 1555 MET cc_start: 0.8968 (mpp) cc_final: 0.8445 (mpp) REVERT: A 1570 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7727 (tm-30) REVERT: A 1847 LEU cc_start: 0.9221 (mt) cc_final: 0.9020 (mt) REVERT: B 78 PHE cc_start: 0.8267 (m-80) cc_final: 0.7992 (m-80) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1058 time to fit residues: 29.6355 Evaluate side-chains 133 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 34 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 70 optimal weight: 20.0000 chunk 122 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 ASN ** A1602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1717 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1760 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.073865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.050895 restraints weight = 73056.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.052439 restraints weight = 48858.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.053455 restraints weight = 37991.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.054121 restraints weight = 32256.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.054485 restraints weight = 28928.705| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15202 Z= 0.190 Angle : 0.651 9.700 20632 Z= 0.329 Chirality : 0.043 0.195 2329 Planarity : 0.005 0.056 2672 Dihedral : 5.055 20.965 2034 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 1847 helix: 0.63 (0.17), residues: 910 sheet: -1.07 (0.34), residues: 189 loop : -0.98 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1965 TYR 0.013 0.002 TYR A1999 PHE 0.017 0.002 PHE A 590 TRP 0.021 0.001 TRP B 56 HIS 0.008 0.001 HIS A1571 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (15202) covalent geometry : angle 0.65116 / 0.33 (20632) hydrogen bonds : bond 0.03995 / 2.66 ( 752) hydrogen bonds : angle 5.09882 / 3.57 ( 2223) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8168 (pmm) cc_final: 0.7754 (pmm) REVERT: A 392 MET cc_start: 0.8909 (mpp) cc_final: 0.8648 (mpp) REVERT: A 479 MET cc_start: 0.8412 (mtm) cc_final: 0.8210 (mtt) REVERT: A 1012 PHE cc_start: 0.8470 (t80) cc_final: 0.8184 (t80) REVERT: A 1270 GLN cc_start: 0.9014 (pp30) cc_final: 0.8762 (tm-30) REVERT: A 1465 ARG cc_start: 0.8083 (mtt180) cc_final: 0.7879 (mtp180) REVERT: A 1504 MET cc_start: 0.7680 (ptm) cc_final: 0.7216 (ptm) REVERT: A 1570 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7752 (tm-30) REVERT: A 1929 MET cc_start: 0.9258 (mpp) cc_final: 0.8867 (mpp) REVERT: A 1932 MET cc_start: 0.8473 (ppp) cc_final: 0.8145 (ppp) REVERT: B 2 GLN cc_start: 0.6920 (pm20) cc_final: 0.6591 (pm20) REVERT: B 78 PHE cc_start: 0.8225 (m-80) cc_final: 0.7918 (m-80) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1083 time to fit residues: 29.2243 Evaluate side-chains 132 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 ASN ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 ASN A1602 ASN ** A1717 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1760 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.075152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.051940 restraints weight = 71017.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.053657 restraints weight = 45738.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.054827 restraints weight = 34498.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.055586 restraints weight = 28630.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.056105 restraints weight = 25328.624| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15202 Z= 0.128 Angle : 0.628 10.240 20632 Z= 0.313 Chirality : 0.042 0.176 2329 Planarity : 0.005 0.054 2672 Dihedral : 4.863 24.464 2034 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.13 (0.20), residues: 1847 helix: 0.83 (0.17), residues: 912 sheet: -0.79 (0.34), residues: 198 loop : -0.97 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A1965 TYR 0.018 0.001 TYR B 23 PHE 0.017 0.001 PHE A 590 TRP 0.014 0.001 TRP B 56 HIS 0.006 0.001 HIS A1607 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (15202) covalent geometry : angle 0.62808 / 0.31 (20632) hydrogen bonds : bond 0.03762 / 2.52 ( 752) hydrogen bonds : angle 4.90001 / 3.44 ( 2223) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 392 MET cc_start: 0.8649 (mpp) cc_final: 0.8354 (mpp) REVERT: A 479 MET cc_start: 0.8455 (mtm) cc_final: 0.8255 (mtt) REVERT: A 551 LEU cc_start: 0.9476 (tp) cc_final: 0.9231 (tt) REVERT: A 1012 PHE cc_start: 0.8536 (t80) cc_final: 0.8148 (t80) REVERT: A 1258 LEU cc_start: 0.9276 (mt) cc_final: 0.9068 (mt) REVERT: A 1270 GLN cc_start: 0.8991 (pp30) cc_final: 0.8584 (tm-30) REVERT: A 1504 MET cc_start: 0.7668 (ptm) cc_final: 0.7225 (ptm) REVERT: A 1555 MET cc_start: 0.8976 (mpp) cc_final: 0.8491 (mpp) REVERT: A 1570 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7911 (tm-30) REVERT: A 2003 LEU cc_start: 0.8117 (mt) cc_final: 0.7836 (mt) REVERT: B 2 GLN cc_start: 0.6866 (pm20) cc_final: 0.6530 (pm20) REVERT: B 41 SER cc_start: 0.7936 (p) cc_final: 0.7677 (t) REVERT: B 78 PHE cc_start: 0.8189 (m-80) cc_final: 0.7819 (m-80) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1068 time to fit residues: 31.8226 Evaluate side-chains 137 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 14 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 144 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 909 HIS ** A1435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 ASN ** A1602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1893 HIS B 61 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.073769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.050776 restraints weight = 72659.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.052433 restraints weight = 46815.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.053533 restraints weight = 35479.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.054216 restraints weight = 29668.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.054731 restraints weight = 26385.296| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15202 Z= 0.192 Angle : 0.678 10.117 20632 Z= 0.342 Chirality : 0.044 0.290 2329 Planarity : 0.005 0.056 2672 Dihedral : 5.010 21.632 2034 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.24 (0.20), residues: 1847 helix: 0.70 (0.17), residues: 912 sheet: -0.89 (0.34), residues: 199 loop : -0.94 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1465 TYR 0.016 0.002 TYR B 23 PHE 0.017 0.002 PHE A1752 TRP 0.010 0.001 TRP A1259 HIS 0.010 0.001 HIS A1571 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (15202) covalent geometry : angle 0.67833 / 0.34 (20632) hydrogen bonds : bond 0.04026 / 2.66 ( 752) hydrogen bonds : angle 5.08985 / 3.55 ( 2223) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 392 MET cc_start: 0.8694 (mpp) cc_final: 0.8406 (mpp) REVERT: A 479 MET cc_start: 0.8410 (mtm) cc_final: 0.8192 (mtt) REVERT: A 614 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8267 (tt0) REVERT: A 1504 MET cc_start: 0.7814 (ptm) cc_final: 0.7345 (ptm) REVERT: A 1555 MET cc_start: 0.8989 (mpp) cc_final: 0.8569 (mpp) REVERT: A 1570 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7864 (tm-30) REVERT: A 1847 LEU cc_start: 0.9210 (mt) cc_final: 0.8963 (mt) REVERT: A 1929 MET cc_start: 0.9236 (mpp) cc_final: 0.8814 (mpp) REVERT: A 1932 MET cc_start: 0.8483 (ppp) cc_final: 0.8104 (ppp) REVERT: B 72 TYR cc_start: 0.7528 (p90) cc_final: 0.7325 (p90) REVERT: B 78 PHE cc_start: 0.8268 (m-80) cc_final: 0.7921 (m-80) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1051 time to fit residues: 27.8711 Evaluate side-chains 126 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 52 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 159 optimal weight: 0.1980 chunk 136 optimal weight: 0.9990 chunk 14 optimal weight: 0.0060 chunk 93 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 984 HIS ** A1435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 ASN A1602 ASN A1648 GLN A1717 HIS A1893 HIS B 61 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.076036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.052783 restraints weight = 70593.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.054546 restraints weight = 45269.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.055720 restraints weight = 34110.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.056521 restraints weight = 28292.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.057047 restraints weight = 24883.956| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15202 Z= 0.120 Angle : 0.642 8.372 20632 Z= 0.319 Chirality : 0.042 0.270 2329 Planarity : 0.005 0.053 2672 Dihedral : 4.764 20.100 2034 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.02 (0.20), residues: 1847 helix: 0.85 (0.17), residues: 916 sheet: -0.59 (0.34), residues: 199 loop : -0.88 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1894 TYR 0.023 0.001 TYR B 23 PHE 0.015 0.001 PHE A 590 TRP 0.018 0.001 TRP A1259 HIS 0.017 0.001 HIS A1893 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (15202) covalent geometry : angle 0.64158 / 0.32 (20632) hydrogen bonds : bond 0.03649 / 2.45 ( 752) hydrogen bonds : angle 4.88294 / 3.41 ( 2223) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 MET cc_start: 0.8671 (mpp) cc_final: 0.8360 (mpp) REVERT: A 614 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8105 (tt0) REVERT: A 1012 PHE cc_start: 0.8519 (t80) cc_final: 0.8157 (t80) REVERT: A 1491 GLN cc_start: 0.8666 (pp30) cc_final: 0.8093 (pp30) REVERT: A 1504 MET cc_start: 0.7695 (ptm) cc_final: 0.7315 (ptm) REVERT: A 1518 GLN cc_start: 0.7413 (mp10) cc_final: 0.7211 (mp10) REVERT: A 1570 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7884 (tm-30) REVERT: A 1772 LYS cc_start: 0.8605 (tmtt) cc_final: 0.8250 (tmtt) REVERT: A 1847 LEU cc_start: 0.9224 (mt) cc_final: 0.8927 (mt) REVERT: A 1932 MET cc_start: 0.8332 (ppp) cc_final: 0.8068 (tmm) REVERT: A 2003 LEU cc_start: 0.8262 (mt) cc_final: 0.7997 (mt) REVERT: B 72 TYR cc_start: 0.7445 (p90) cc_final: 0.7217 (p90) REVERT: B 78 PHE cc_start: 0.8372 (m-80) cc_final: 0.8041 (m-80) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1063 time to fit residues: 30.9829 Evaluate side-chains 137 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 176 optimal weight: 5.9990 chunk 153 optimal weight: 8.9990 chunk 175 optimal weight: 6.9990 chunk 85 optimal weight: 0.4980 chunk 74 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 122 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 110 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 GLN A 915 GLN ** A1435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 ASN ** A1602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.076451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.053464 restraints weight = 71857.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.055063 restraints weight = 48299.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.056118 restraints weight = 37590.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.056818 restraints weight = 31824.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.057204 restraints weight = 28432.113| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 15202 Z= 0.122 Angle : 0.649 12.336 20632 Z= 0.320 Chirality : 0.042 0.268 2329 Planarity : 0.005 0.054 2672 Dihedral : 4.625 19.685 2034 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.06 % Allowed : 0.31 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.06 (0.20), residues: 1847 helix: 0.89 (0.17), residues: 916 sheet: -0.56 (0.35), residues: 206 loop : -0.79 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1965 TYR 0.018 0.001 TYR B 23 PHE 0.014 0.001 PHE A1752 TRP 0.015 0.001 TRP A1259 HIS 0.011 0.001 HIS A1893 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (15202) covalent geometry : angle 0.64907 / 0.32 (20632) hydrogen bonds : bond 0.03618 / 2.43 ( 752) hydrogen bonds : angle 4.83726 / 3.37 ( 2223) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: -0.3826 (mmp) cc_final: -0.4136 (mmt) REVERT: A 392 MET cc_start: 0.8636 (mpp) cc_final: 0.8303 (mpp) REVERT: A 550 LEU cc_start: 0.9047 (mt) cc_final: 0.8782 (mt) REVERT: A 614 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8094 (tt0) REVERT: A 1570 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7825 (tm-30) REVERT: A 1772 LYS cc_start: 0.8629 (tmtt) cc_final: 0.8265 (tmtt) REVERT: A 1847 LEU cc_start: 0.9158 (mt) cc_final: 0.8925 (mt) REVERT: A 1909 MET cc_start: 0.8164 (ptt) cc_final: 0.7881 (ptt) REVERT: A 1932 MET cc_start: 0.8356 (ppp) cc_final: 0.8093 (tmm) REVERT: A 2003 LEU cc_start: 0.8223 (mt) cc_final: 0.7956 (mt) REVERT: B 72 TYR cc_start: 0.7370 (p90) cc_final: 0.7163 (p90) REVERT: B 78 PHE cc_start: 0.8350 (m-80) cc_final: 0.8003 (m-80) REVERT: B 112 LEU cc_start: 0.9342 (tp) cc_final: 0.9119 (tp) outliers start: 1 outliers final: 1 residues processed: 187 average time/residue: 0.1137 time to fit residues: 33.0951 Evaluate side-chains 136 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 18 optimal weight: 8.9990 chunk 126 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 179 optimal weight: 0.3980 chunk 160 optimal weight: 0.9980 chunk 170 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 171 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 GLN A 915 GLN A1435 HIS A1492 ASN A1518 GLN ** A1602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1880 HIS B 61 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.073315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.050243 restraints weight = 73694.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.051833 restraints weight = 48559.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.052885 restraints weight = 37333.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.053596 restraints weight = 31434.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.054044 restraints weight = 28059.213| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 15202 Z= 0.223 Angle : 0.721 9.207 20632 Z= 0.360 Chirality : 0.044 0.275 2329 Planarity : 0.005 0.057 2672 Dihedral : 4.968 22.060 2034 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.08 (0.20), residues: 1847 helix: 0.76 (0.17), residues: 908 sheet: -0.58 (0.34), residues: 198 loop : -0.83 (0.24), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1965 TYR 0.018 0.002 TYR A1535 PHE 0.019 0.002 PHE A1432 TRP 0.007 0.001 TRP A1259 HIS 0.008 0.002 HIS A1571 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.22 (15202) covalent geometry : angle 0.72051 / 0.36 (20632) hydrogen bonds : bond 0.04035 / 2.65 ( 752) hydrogen bonds : angle 5.14250 / 3.58 ( 2223) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2631.75 seconds wall clock time: 46 minutes 29.19 seconds (2789.19 seconds total)