Starting phenix.real_space_refine on Tue Jul 29 11:45:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kve_23048/07_2025/7kve_23048.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kve_23048/07_2025/7kve_23048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kve_23048/07_2025/7kve_23048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kve_23048/07_2025/7kve_23048.map" model { file = "/net/cci-nas-00/data/ceres_data/7kve_23048/07_2025/7kve_23048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kve_23048/07_2025/7kve_23048.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.067 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 55 5.16 5 C 7074 2.51 5 N 1905 2.21 5 O 2108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11142 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 11142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1374, 11142 Classifications: {'peptide': 1374} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 66, 'TRANS': 1305} Chain breaks: 1 Time building chain proxies: 6.97, per 1000 atoms: 0.63 Number of scatterers: 11142 At special positions: 0 Unit cell: (100.1, 106.7, 141.9, 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 55 16.00 O 2108 8.00 N 1905 7.00 C 7074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 165 " distance=2.04 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 472 " - pdb=" SG CYS B 498 " distance=2.03 Simple disulfide: pdb=" SG CYS B1697 " - pdb=" SG CYS B1723 " distance=2.03 Simple disulfide: pdb=" SG CYS B1879 " - pdb=" SG CYS B2033 " distance=2.04 Simple disulfide: pdb=" SG CYS B2038 " - pdb=" SG CYS B2193 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.4 seconds 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2588 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 21 sheets defined 6.8% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'B' and resid 23 through 28 removed outlier: 4.475A pdb=" N LEU B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.904A pdb=" N LYS B 46 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 344 through 352 removed outlier: 3.948A pdb=" N ARG B 348 " --> pdb=" O ASP B 344 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 490 Processing helix chain 'B' and resid 526 through 528 No H-bonds generated for 'chain 'B' and resid 526 through 528' Processing helix chain 'B' and resid 549 through 556 removed outlier: 3.779A pdb=" N ASN B 556 " --> pdb=" O PHE B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 1608 through 1612 removed outlier: 4.352A pdb=" N HIS B1612 " --> pdb=" O TYR B1609 " (cutoff:3.500A) Processing helix chain 'B' and resid 1650 through 1654 removed outlier: 3.612A pdb=" N GLU B1654 " --> pdb=" O LYS B1651 " (cutoff:3.500A) Processing helix chain 'B' and resid 1665 through 1669 removed outlier: 3.606A pdb=" N GLU B1668 " --> pdb=" O TRP B1665 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASP B1669 " --> pdb=" O PHE B1666 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1665 through 1669' Processing helix chain 'B' and resid 1685 through 1689 Processing helix chain 'B' and resid 1707 through 1713 removed outlier: 3.863A pdb=" N ILE B1712 " --> pdb=" O PRO B1708 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS B1713 " --> pdb=" O GLU B1709 " (cutoff:3.500A) Processing helix chain 'B' and resid 1768 through 1772 removed outlier: 4.038A pdb=" N LYS B1772 " --> pdb=" O SER B1769 " (cutoff:3.500A) Processing helix chain 'B' and resid 1860 through 1865 removed outlier: 3.833A pdb=" N ARG B1865 " --> pdb=" O GLY B1861 " (cutoff:3.500A) Processing helix chain 'B' and resid 1891 through 1893 No H-bonds generated for 'chain 'B' and resid 1891 through 1893' Processing helix chain 'B' and resid 1905 through 1909 Processing helix chain 'B' and resid 2050 through 2052 No H-bonds generated for 'chain 'B' and resid 2050 through 2052' Processing sheet with id=AA1, first strand: chain 'B' and resid 36 through 40 removed outlier: 3.670A pdb=" N GLN B 11 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ARG B 4 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N HIS B 73 " --> pdb=" O ARG B 4 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N PHE B 6 " --> pdb=" O HIS B 73 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 70 " --> pdb=" O TRP B 124 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 62 through 64 removed outlier: 6.768A pdb=" N LEU B 62 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 75 through 76 removed outlier: 3.519A pdb=" N ASN B 76 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG B 118 " --> pdb=" O ASN B 76 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 185 through 189 removed outlier: 6.339A pdb=" N LEU B 185 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N MET B 232 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N PHE B 187 " --> pdb=" O MET B 232 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET B 270 " --> pdb=" O ILE B 225 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 268 " --> pdb=" O TRP B 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 217 through 219 removed outlier: 3.521A pdb=" N ILE B 217 " --> pdb=" O TYR B 295 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 370 through 371 removed outlier: 4.167A pdb=" N PHE B 325 " --> pdb=" O TYR B 371 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N TYR B 324 " --> pdb=" O VAL B 406 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LYS B 408 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ILE B 326 " --> pdb=" O LYS B 408 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE B 407 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 394 through 397 Processing sheet with id=AA8, first strand: chain 'B' and resid 515 through 520 removed outlier: 3.695A pdb=" N CYS B 585 " --> pdb=" O ALA B 518 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 522 through 524 Processing sheet with id=AB1, first strand: chain 'B' and resid 612 through 615 removed outlier: 3.815A pdb=" N LEU B 613 " --> pdb=" O ILE B 596 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 594 " --> pdb=" O LEU B 615 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1550 through 1554 removed outlier: 5.491A pdb=" N ASN B1550 " --> pdb=" O VAL B1627 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N GLN B1629 " --> pdb=" O ASN B1550 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ARG B1552 " --> pdb=" O GLN B1629 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ARG B1631 " --> pdb=" O ARG B1552 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TYR B1554 " --> pdb=" O ARG B1631 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1556 through 1563 removed outlier: 3.907A pdb=" N ALA B1557 " --> pdb=" O ARG B1593 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B1593 " --> pdb=" O ALA B1557 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1697 through 1698 Processing sheet with id=AB5, first strand: chain 'B' and resid 1701 through 1703 Processing sheet with id=AB6, first strand: chain 'B' and resid 1776 through 1780 removed outlier: 3.513A pdb=" N MET B1746 " --> pdb=" O ALA B1779 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1791 through 1792 Processing sheet with id=AB8, first strand: chain 'B' and resid 1834 through 1836 Processing sheet with id=AB9, first strand: chain 'B' and resid 1881 through 1882 removed outlier: 6.390A pdb=" N GLN B2031 " --> pdb=" O THR B1946 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL B1943 " --> pdb=" O ALA B2010 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N GLY B1947 " --> pdb=" O PRO B2006 " (cutoff:3.500A) removed outlier: 11.882A pdb=" N GLN B1949 " --> pdb=" O PHE B2004 " (cutoff:3.500A) removed outlier: 12.332A pdb=" N PHE B2004 " --> pdb=" O GLN B1949 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1895 through 1897 removed outlier: 6.746A pdb=" N GLU B1964 " --> pdb=" O THR B2018 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA B2020 " --> pdb=" O THR B1962 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N THR B1962 " --> pdb=" O ALA B2020 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 2040 through 2041 removed outlier: 3.788A pdb=" N THR B2040 " --> pdb=" O GLY B2192 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY B2192 " --> pdb=" O THR B2040 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLU B2189 " --> pdb=" O ILE B2108 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ILE B2108 " --> pdb=" O GLU B2189 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE B2191 " --> pdb=" O THR B2106 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ARG B2171 " --> pdb=" O LEU B2099 " (cutoff:3.500A) removed outlier: 10.342A pdb=" N LYS B2101 " --> pdb=" O ILE B2169 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N ILE B2169 " --> pdb=" O LYS B2101 " (cutoff:3.500A) removed outlier: 9.659A pdb=" N LYS B2103 " --> pdb=" O PRO B2167 " (cutoff:3.500A) removed outlier: 10.470A pdb=" N ILE B2105 " --> pdb=" O ASN B2165 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ASN B2165 " --> pdb=" O ILE B2105 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ALA B2107 " --> pdb=" O PHE B2163 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N PHE B2163 " --> pdb=" O ALA B2107 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE B2109 " --> pdb=" O LYS B2161 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LYS B2161 " --> pdb=" O ILE B2109 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER B2124 " --> pdb=" O LYS B2178 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP B2180 " --> pdb=" O VAL B2122 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL B2122 " --> pdb=" O TRP B2180 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET B2120 " --> pdb=" O CYS B2113 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N CYS B2113 " --> pdb=" O MET B2120 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 2054 through 2056 removed outlier: 6.999A pdb=" N ARG B2171 " --> pdb=" O LEU B2099 " (cutoff:3.500A) removed outlier: 10.342A pdb=" N LYS B2101 " --> pdb=" O ILE B2169 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N ILE B2169 " --> pdb=" O LYS B2101 " (cutoff:3.500A) removed outlier: 9.659A pdb=" N LYS B2103 " --> pdb=" O PRO B2167 " (cutoff:3.500A) removed outlier: 10.470A pdb=" N ILE B2105 " --> pdb=" O ASN B2165 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ASN B2165 " --> pdb=" O ILE B2105 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ALA B2107 " --> pdb=" O PHE B2163 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N PHE B2163 " --> pdb=" O ALA B2107 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE B2109 " --> pdb=" O LYS B2161 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LYS B2161 " --> pdb=" O ILE B2109 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER B2124 " --> pdb=" O LYS B2178 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP B2180 " --> pdb=" O VAL B2122 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL B2122 " --> pdb=" O TRP B2180 " (cutoff:3.500A) 160 hydrogen bonds defined for protein. 384 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.79 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1844 1.29 - 1.42: 3119 1.42 - 1.56: 6380 1.56 - 1.70: 1 1.70 - 1.83: 92 Bond restraints: 11436 Sorted by residual: bond pdb=" C VAL B 654 " pdb=" O VAL B 654 " ideal model delta sigma weight residual 1.231 1.153 0.078 1.29e-02 6.01e+03 3.63e+01 bond pdb=" C CYS B 656 " pdb=" O CYS B 656 " ideal model delta sigma weight residual 1.235 1.188 0.047 1.26e-02 6.30e+03 1.38e+01 bond pdb=" C ASP B 653 " pdb=" N VAL B 654 " ideal model delta sigma weight residual 1.331 1.290 0.041 1.20e-02 6.94e+03 1.19e+01 bond pdb=" C ASN B 541 " pdb=" N PRO B 542 " ideal model delta sigma weight residual 1.331 1.359 -0.027 7.90e-03 1.60e+04 1.18e+01 bond pdb=" CA VAL B 654 " pdb=" C VAL B 654 " ideal model delta sigma weight residual 1.526 1.477 0.049 1.43e-02 4.89e+03 1.16e+01 ... (remaining 11431 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 15170 2.42 - 4.84: 283 4.84 - 7.25: 25 7.25 - 9.67: 9 9.67 - 12.09: 3 Bond angle restraints: 15490 Sorted by residual: angle pdb=" N VAL B 654 " pdb=" CA VAL B 654 " pdb=" CB VAL B 654 " ideal model delta sigma weight residual 112.60 100.51 12.09 1.29e+00 6.01e-01 8.78e+01 angle pdb=" N PHE B2059 " pdb=" CA PHE B2059 " pdb=" C PHE B2059 " ideal model delta sigma weight residual 112.72 103.01 9.71 1.36e+00 5.41e-01 5.10e+01 angle pdb=" N VAL B1706 " pdb=" CA VAL B1706 " pdb=" C VAL B1706 " ideal model delta sigma weight residual 112.12 107.30 4.82 8.40e-01 1.42e+00 3.29e+01 angle pdb=" N ASP B 401 " pdb=" CA ASP B 401 " pdb=" C ASP B 401 " ideal model delta sigma weight residual 112.57 106.64 5.93 1.13e+00 7.83e-01 2.75e+01 angle pdb=" C ASN B2036 " pdb=" N GLY B2037 " pdb=" CA GLY B2037 " ideal model delta sigma weight residual 121.51 129.34 -7.83 1.52e+00 4.33e-01 2.65e+01 ... (remaining 15485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6070 17.94 - 35.88: 666 35.88 - 53.82: 92 53.82 - 71.76: 20 71.76 - 89.70: 8 Dihedral angle restraints: 6856 sinusoidal: 2828 harmonic: 4028 Sorted by residual: dihedral pdb=" CB CYS B 139 " pdb=" SG CYS B 139 " pdb=" SG CYS B 165 " pdb=" CB CYS B 165 " ideal model delta sinusoidal sigma weight residual 93.00 20.33 72.67 1 1.00e+01 1.00e-02 6.74e+01 dihedral pdb=" N VAL B 654 " pdb=" C VAL B 654 " pdb=" CA VAL B 654 " pdb=" CB VAL B 654 " ideal model delta harmonic sigma weight residual 123.40 108.17 15.23 0 2.50e+00 1.60e-01 3.71e+01 dihedral pdb=" CA ARG B 90 " pdb=" C ARG B 90 " pdb=" N TYR B 91 " pdb=" CA TYR B 91 " ideal model delta harmonic sigma weight residual -180.00 -155.50 -24.50 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 6853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1519 0.100 - 0.199: 101 0.199 - 0.299: 3 0.299 - 0.398: 3 0.398 - 0.498: 1 Chirality restraints: 1627 Sorted by residual: chirality pdb=" CB VAL B 654 " pdb=" CA VAL B 654 " pdb=" CG1 VAL B 654 " pdb=" CG2 VAL B 654 " both_signs ideal model delta sigma weight residual False -2.63 -2.13 -0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" CA ASP B 660 " pdb=" N ASP B 660 " pdb=" C ASP B 660 " pdb=" CB ASP B 660 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA VAL B 654 " pdb=" N VAL B 654 " pdb=" C VAL B 654 " pdb=" CB VAL B 654 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 1624 not shown) Planarity restraints: 1999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B2033 " -0.021 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C CYS B2033 " 0.071 2.00e-02 2.50e+03 pdb=" O CYS B2033 " -0.026 2.00e-02 2.50e+03 pdb=" N GLU B2034 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 669 " 0.060 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO B 670 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 670 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 670 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B2023 " -0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO B2024 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B2024 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B2024 " -0.028 5.00e-02 4.00e+02 ... (remaining 1996 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1223 2.74 - 3.28: 11124 3.28 - 3.82: 17231 3.82 - 4.36: 20716 4.36 - 4.90: 36116 Nonbonded interactions: 86410 Sorted by model distance: nonbonded pdb=" OD1 ASP B 191 " pdb=" OG SER B 193 " model vdw 2.204 3.040 nonbonded pdb=" OH TYR B1609 " pdb=" OD2 ASP B2005 " model vdw 2.204 3.040 nonbonded pdb=" O SER B 349 " pdb=" NE2 GLN B 358 " model vdw 2.204 3.120 nonbonded pdb=" OH TYR B1554 " pdb=" O ARG B1621 " model vdw 2.212 3.040 nonbonded pdb=" OH TYR B 605 " pdb=" OE2 GLU B 621 " model vdw 2.214 3.040 ... (remaining 86405 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.270 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 11442 Z= 0.257 Angle : 0.818 12.087 15502 Z= 0.482 Chirality : 0.053 0.498 1627 Planarity : 0.005 0.091 1999 Dihedral : 14.673 89.697 4250 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.36 % Allowed : 18.25 % Favored : 81.39 % Rotamer: Outliers : 0.57 % Allowed : 8.65 % Favored : 90.78 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.88 (0.17), residues: 1370 helix: -4.25 (0.41), residues: 45 sheet: -3.39 (0.23), residues: 373 loop : -4.44 (0.14), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B1700 HIS 0.005 0.001 HIS B 242 PHE 0.016 0.001 PHE B2071 TYR 0.021 0.002 TYR B 363 ARG 0.008 0.001 ARG B 90 Details of bonding type rmsd hydrogen bonds : bond 0.29500 ( 150) hydrogen bonds : angle 12.46977 ( 384) SS BOND : bond 0.00789 ( 6) SS BOND : angle 1.65774 ( 12) covalent geometry : bond 0.00477 (11436) covalent geometry : angle 0.81660 (15490) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 153 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 136 ASP cc_start: 0.7739 (m-30) cc_final: 0.7530 (m-30) REVERT: B 244 ASN cc_start: 0.8815 (m-40) cc_final: 0.8450 (m110) REVERT: B 424 PHE cc_start: 0.6930 (m-80) cc_final: 0.6696 (m-80) REVERT: B 445 ARG cc_start: 0.6960 (pmt170) cc_final: 0.6568 (ptt-90) REVERT: B 610 GLU cc_start: 0.7053 (mp0) cc_final: 0.6436 (mp0) REVERT: B 621 GLU cc_start: 0.6896 (tt0) cc_final: 0.6687 (tt0) REVERT: B 650 LYS cc_start: 0.7591 (mptt) cc_final: 0.7251 (mmtm) REVERT: B 1703 TYR cc_start: 0.6750 (p90) cc_final: 0.6523 (p90) REVERT: B 1738 MET cc_start: 0.7127 (ttt) cc_final: 0.6684 (ttt) REVERT: B 1776 GLU cc_start: 0.7933 (tt0) cc_final: 0.7723 (tt0) REVERT: B 1868 MET cc_start: 0.7417 (mtt) cc_final: 0.7128 (mtt) REVERT: B 1878 ASP cc_start: 0.8013 (m-30) cc_final: 0.7598 (p0) outliers start: 7 outliers final: 1 residues processed: 158 average time/residue: 0.2743 time to fit residues: 60.2823 Evaluate side-chains 120 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2036 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.0070 chunk 103 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 55 optimal weight: 0.0370 chunk 107 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 65 optimal weight: 0.0060 chunk 79 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 overall best weight: 0.3694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 134 HIS B 182 GLN B 252 HIS B 307 ASN B 315 GLN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN B 562 ASN B 583 HIS B 597 HIS B 609 HIS B 639 ASN B 700 ASN ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1643 HIS B1645 HIS B1713 HIS B1778 HIS ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1819 GLN B1936 GLN B2002 ASN B2003 GLN B2162 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.143462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.123309 restraints weight = 25204.966| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 3.65 r_work: 0.3820 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11442 Z= 0.121 Angle : 0.651 9.834 15502 Z= 0.337 Chirality : 0.047 0.169 1627 Planarity : 0.005 0.088 1999 Dihedral : 5.835 29.709 1510 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.97 % Favored : 88.03 % Rotamer: Outliers : 1.55 % Allowed : 13.80 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.99 (0.18), residues: 1370 helix: -3.24 (0.61), residues: 45 sheet: -2.67 (0.26), residues: 350 loop : -3.87 (0.15), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B2180 HIS 0.004 0.001 HIS B 252 PHE 0.016 0.001 PHE B2172 TYR 0.026 0.001 TYR B1903 ARG 0.004 0.000 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.03942 ( 150) hydrogen bonds : angle 7.73478 ( 384) SS BOND : bond 0.00460 ( 6) SS BOND : angle 1.37740 ( 12) covalent geometry : bond 0.00256 (11436) covalent geometry : angle 0.65019 (15490) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 445 ARG cc_start: 0.7259 (pmt170) cc_final: 0.6902 (ptt-90) REVERT: B 610 GLU cc_start: 0.8071 (mp0) cc_final: 0.7868 (mm-30) REVERT: B 1638 ARG cc_start: 0.7679 (ptm-80) cc_final: 0.7324 (mtp-110) REVERT: B 1703 TYR cc_start: 0.6986 (p90) cc_final: 0.6755 (p90) REVERT: B 1738 MET cc_start: 0.7377 (ttt) cc_final: 0.6913 (ttt) REVERT: B 1850 LYS cc_start: 0.7928 (mtpp) cc_final: 0.7263 (mttp) REVERT: B 1868 MET cc_start: 0.7221 (mtt) cc_final: 0.6935 (mtt) REVERT: B 1878 ASP cc_start: 0.8113 (m-30) cc_final: 0.7366 (t0) REVERT: B 2044 MET cc_start: 0.6452 (mmm) cc_final: 0.5998 (mmm) REVERT: B 2067 TYR cc_start: 0.3786 (p90) cc_final: 0.3414 (p90) REVERT: B 2172 PHE cc_start: 0.6874 (m-80) cc_final: 0.6534 (m-10) outliers start: 19 outliers final: 10 residues processed: 149 average time/residue: 0.2701 time to fit residues: 58.3949 Evaluate side-chains 128 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 1798 VAL Chi-restraints excluded: chain B residue 1843 THR Chi-restraints excluded: chain B residue 1920 TRP Chi-restraints excluded: chain B residue 2015 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 8 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 25 optimal weight: 0.0060 chunk 47 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1670 ASN B1781 ASN B2036 ASN B2128 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.140189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.120429 restraints weight = 25794.804| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 3.64 r_work: 0.3769 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11442 Z= 0.156 Angle : 0.665 10.949 15502 Z= 0.341 Chirality : 0.047 0.150 1627 Planarity : 0.005 0.091 1999 Dihedral : 5.923 32.276 1508 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.60 % Favored : 85.40 % Rotamer: Outliers : 2.37 % Allowed : 15.84 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.79 (0.19), residues: 1370 helix: -3.31 (0.53), residues: 52 sheet: -2.53 (0.26), residues: 368 loop : -3.72 (0.16), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B2084 HIS 0.003 0.001 HIS B 242 PHE 0.014 0.001 PHE B1568 TYR 0.021 0.002 TYR B1903 ARG 0.003 0.000 ARG B 90 Details of bonding type rmsd hydrogen bonds : bond 0.03792 ( 150) hydrogen bonds : angle 7.19423 ( 384) SS BOND : bond 0.00370 ( 6) SS BOND : angle 1.34818 ( 12) covalent geometry : bond 0.00356 (11436) covalent geometry : angle 0.66393 (15490) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 1.403 Fit side-chains REVERT: B 390 ILE cc_start: 0.5120 (OUTLIER) cc_final: 0.4889 (tt) REVERT: B 445 ARG cc_start: 0.7264 (pmt170) cc_final: 0.6923 (ptt-90) REVERT: B 621 GLU cc_start: 0.7616 (tt0) cc_final: 0.7144 (tt0) REVERT: B 1700 TRP cc_start: 0.7637 (OUTLIER) cc_final: 0.7431 (m-10) REVERT: B 1703 TYR cc_start: 0.7191 (p90) cc_final: 0.6960 (p90) REVERT: B 1738 MET cc_start: 0.7381 (ttt) cc_final: 0.6949 (ttt) REVERT: B 1850 LYS cc_start: 0.7874 (mtpp) cc_final: 0.7160 (mttp) REVERT: B 1868 MET cc_start: 0.7238 (mtt) cc_final: 0.6967 (mtt) outliers start: 29 outliers final: 19 residues processed: 144 average time/residue: 0.2653 time to fit residues: 57.7489 Evaluate side-chains 129 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 1559 GLU Chi-restraints excluded: chain B residue 1700 TRP Chi-restraints excluded: chain B residue 1744 LEU Chi-restraints excluded: chain B residue 1798 VAL Chi-restraints excluded: chain B residue 1843 THR Chi-restraints excluded: chain B residue 1856 LEU Chi-restraints excluded: chain B residue 1920 TRP Chi-restraints excluded: chain B residue 2009 VAL Chi-restraints excluded: chain B residue 2015 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 0 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 20 optimal weight: 0.0470 chunk 75 optimal weight: 0.8980 chunk 87 optimal weight: 0.0570 chunk 34 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 HIS B 289 GLN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1781 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.143255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.123325 restraints weight = 25677.119| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 3.66 r_work: 0.3805 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11442 Z= 0.109 Angle : 0.611 10.154 15502 Z= 0.313 Chirality : 0.045 0.193 1627 Planarity : 0.005 0.089 1999 Dihedral : 5.518 28.137 1508 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.61 % Favored : 88.39 % Rotamer: Outliers : 2.45 % Allowed : 18.20 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (0.20), residues: 1370 helix: -3.27 (0.54), residues: 52 sheet: -2.26 (0.26), residues: 382 loop : -3.50 (0.17), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1700 HIS 0.002 0.000 HIS B 242 PHE 0.021 0.001 PHE B 552 TYR 0.021 0.001 TYR B 418 ARG 0.001 0.000 ARG B1687 Details of bonding type rmsd hydrogen bonds : bond 0.03134 ( 150) hydrogen bonds : angle 6.57629 ( 384) SS BOND : bond 0.00479 ( 6) SS BOND : angle 1.12080 ( 12) covalent geometry : bond 0.00248 (11436) covalent geometry : angle 0.61047 (15490) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 1.405 Fit side-chains revert: symmetry clash REVERT: B 93 LYS cc_start: 0.7781 (mmtt) cc_final: 0.7562 (tppt) REVERT: B 390 ILE cc_start: 0.5048 (OUTLIER) cc_final: 0.4837 (tt) REVERT: B 398 GLN cc_start: 0.5627 (tp40) cc_final: 0.5089 (tp40) REVERT: B 445 ARG cc_start: 0.7168 (pmt170) cc_final: 0.6846 (ptt-90) REVERT: B 484 MET cc_start: 0.8419 (mmt) cc_final: 0.8188 (mmm) REVERT: B 594 LEU cc_start: 0.8581 (mt) cc_final: 0.8366 (mt) REVERT: B 621 GLU cc_start: 0.7553 (tt0) cc_final: 0.7214 (tt0) REVERT: B 1638 ARG cc_start: 0.7685 (ptm-80) cc_final: 0.7283 (mtp-110) REVERT: B 1700 TRP cc_start: 0.7535 (OUTLIER) cc_final: 0.5693 (m-10) REVERT: B 1703 TYR cc_start: 0.7197 (p90) cc_final: 0.6907 (p90) REVERT: B 1738 MET cc_start: 0.7287 (ttt) cc_final: 0.6910 (ttt) REVERT: B 1746 MET cc_start: 0.8274 (ttp) cc_final: 0.8044 (ttt) REVERT: B 1850 LYS cc_start: 0.8009 (mtpp) cc_final: 0.7397 (mttp) REVERT: B 1868 MET cc_start: 0.7203 (mtt) cc_final: 0.6914 (mtt) REVERT: B 1883 MET cc_start: 0.8873 (mmm) cc_final: 0.8294 (mpp) REVERT: B 2067 TYR cc_start: 0.3843 (p90) cc_final: 0.3639 (p90) outliers start: 30 outliers final: 16 residues processed: 152 average time/residue: 0.2570 time to fit residues: 60.5872 Evaluate side-chains 136 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 1559 GLU Chi-restraints excluded: chain B residue 1700 TRP Chi-restraints excluded: chain B residue 1783 MET Chi-restraints excluded: chain B residue 1798 VAL Chi-restraints excluded: chain B residue 1843 THR Chi-restraints excluded: chain B residue 1920 TRP Chi-restraints excluded: chain B residue 2009 VAL Chi-restraints excluded: chain B residue 2015 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 43 optimal weight: 0.0470 chunk 36 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 overall best weight: 2.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 ASN ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1781 ASN ** B2132 GLN ** 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 = 0.4129 r_free = 0.4129 target = 0.137864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.118310 restraints weight = 25916.102| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 3.64 r_work: 0.3734 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11442 Z= 0.207 Angle : 0.710 13.119 15502 Z= 0.365 Chirality : 0.048 0.208 1627 Planarity : 0.006 0.094 1999 Dihedral : 6.139 34.743 1508 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.69 % Favored : 84.31 % Rotamer: Outliers : 3.27 % Allowed : 19.43 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.53 (0.20), residues: 1370 helix: -3.41 (0.53), residues: 52 sheet: -2.25 (0.26), residues: 373 loop : -3.56 (0.17), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B1700 HIS 0.003 0.001 HIS B 351 PHE 0.030 0.002 PHE B 552 TYR 0.017 0.002 TYR B1966 ARG 0.007 0.000 ARG B 648 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 150) hydrogen bonds : angle 6.86103 ( 384) SS BOND : bond 0.00484 ( 6) SS BOND : angle 1.40718 ( 12) covalent geometry : bond 0.00476 (11436) covalent geometry : angle 0.70880 (15490) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 1.230 Fit side-chains revert: symmetry clash REVERT: B 323 GLU cc_start: 0.7353 (pt0) cc_final: 0.7144 (pt0) REVERT: B 390 ILE cc_start: 0.5100 (OUTLIER) cc_final: 0.4859 (tt) REVERT: B 418 TYR cc_start: 0.8568 (t80) cc_final: 0.8365 (t80) REVERT: B 445 ARG cc_start: 0.7145 (pmt170) cc_final: 0.6796 (ptt-90) REVERT: B 590 GLN cc_start: 0.6791 (OUTLIER) cc_final: 0.6376 (pm20) REVERT: B 605 TYR cc_start: 0.8586 (t80) cc_final: 0.8383 (t80) REVERT: B 621 GLU cc_start: 0.7660 (tt0) cc_final: 0.7313 (tt0) REVERT: B 627 MET cc_start: 0.7094 (mmp) cc_final: 0.6817 (mmp) REVERT: B 1700 TRP cc_start: 0.7778 (OUTLIER) cc_final: 0.7409 (m-10) REVERT: B 1703 TYR cc_start: 0.7267 (p90) cc_final: 0.7042 (p90) REVERT: B 1738 MET cc_start: 0.7437 (ttt) cc_final: 0.7027 (ttt) REVERT: B 1850 LYS cc_start: 0.7899 (mtpp) cc_final: 0.7176 (mttp) REVERT: B 1868 MET cc_start: 0.7525 (mtt) cc_final: 0.7254 (mtt) REVERT: B 2067 TYR cc_start: 0.4215 (p90) cc_final: 0.4007 (p90) outliers start: 40 outliers final: 26 residues processed: 142 average time/residue: 0.2255 time to fit residues: 47.6923 Evaluate side-chains 130 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 1559 GLU Chi-restraints excluded: chain B residue 1700 TRP Chi-restraints excluded: chain B residue 1746 MET Chi-restraints excluded: chain B residue 1798 VAL Chi-restraints excluded: chain B residue 1843 THR Chi-restraints excluded: chain B residue 1856 LEU Chi-restraints excluded: chain B residue 1920 TRP Chi-restraints excluded: chain B residue 2009 VAL Chi-restraints excluded: chain B residue 2015 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 122 optimal weight: 0.0060 chunk 95 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 70 optimal weight: 0.1980 chunk 121 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 78 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 398 GLN B 700 ASN ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1781 ASN B1869 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.138207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.118689 restraints weight = 26296.484| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 3.62 r_work: 0.3731 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11442 Z= 0.183 Angle : 0.678 9.587 15502 Z= 0.351 Chirality : 0.047 0.194 1627 Planarity : 0.005 0.094 1999 Dihedral : 6.096 35.210 1508 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.89 % Favored : 85.11 % Rotamer: Outliers : 3.35 % Allowed : 20.73 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.44 (0.20), residues: 1370 helix: -3.05 (0.54), residues: 58 sheet: -2.20 (0.26), residues: 394 loop : -3.52 (0.17), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B1700 HIS 0.004 0.001 HIS B 682 PHE 0.018 0.001 PHE B 552 TYR 0.017 0.002 TYR B1903 ARG 0.002 0.000 ARG B1606 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 150) hydrogen bonds : angle 6.74669 ( 384) SS BOND : bond 0.00450 ( 6) SS BOND : angle 1.31451 ( 12) covalent geometry : bond 0.00420 (11436) covalent geometry : angle 0.67742 (15490) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 111 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 363 TYR cc_start: 0.4638 (OUTLIER) cc_final: 0.3237 (t80) REVERT: B 390 ILE cc_start: 0.5091 (OUTLIER) cc_final: 0.4859 (tt) REVERT: B 445 ARG cc_start: 0.7096 (pmt170) cc_final: 0.6744 (ptt-90) REVERT: B 590 GLN cc_start: 0.6876 (OUTLIER) cc_final: 0.6500 (pm20) REVERT: B 605 TYR cc_start: 0.8545 (t80) cc_final: 0.8276 (t80) REVERT: B 621 GLU cc_start: 0.7532 (tt0) cc_final: 0.7076 (tt0) REVERT: B 627 MET cc_start: 0.7061 (mmp) cc_final: 0.6782 (mmp) REVERT: B 1700 TRP cc_start: 0.7747 (OUTLIER) cc_final: 0.7319 (m-10) REVERT: B 1703 TYR cc_start: 0.7238 (p90) cc_final: 0.7012 (p90) REVERT: B 1738 MET cc_start: 0.7356 (ttt) cc_final: 0.6963 (ttt) REVERT: B 1850 LYS cc_start: 0.7943 (mtpp) cc_final: 0.7285 (mttp) REVERT: B 1868 MET cc_start: 0.7681 (mtt) cc_final: 0.7391 (mtt) outliers start: 41 outliers final: 27 residues processed: 146 average time/residue: 0.2174 time to fit residues: 47.6172 Evaluate side-chains 137 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 1559 GLU Chi-restraints excluded: chain B residue 1700 TRP Chi-restraints excluded: chain B residue 1746 MET Chi-restraints excluded: chain B residue 1747 THR Chi-restraints excluded: chain B residue 1798 VAL Chi-restraints excluded: chain B residue 1843 THR Chi-restraints excluded: chain B residue 1856 LEU Chi-restraints excluded: chain B residue 1920 TRP Chi-restraints excluded: chain B residue 2009 VAL Chi-restraints excluded: chain B residue 2015 ILE Chi-restraints excluded: chain B residue 2173 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 94 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 92 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 700 ASN ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1781 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.141212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.121541 restraints weight = 25966.810| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 3.66 r_work: 0.3778 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 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 0.041 11442 Z= 0.118 Angle : 0.628 9.781 15502 Z= 0.322 Chirality : 0.046 0.182 1627 Planarity : 0.005 0.089 1999 Dihedral : 5.667 30.939 1508 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.28 % Favored : 86.72 % Rotamer: Outliers : 3.59 % Allowed : 21.06 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.22 (0.20), residues: 1370 helix: -3.23 (0.52), residues: 52 sheet: -2.00 (0.27), residues: 375 loop : -3.36 (0.17), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1700 HIS 0.002 0.000 HIS B 682 PHE 0.019 0.001 PHE B 552 TYR 0.018 0.001 TYR B1903 ARG 0.003 0.000 ARG B 648 Details of bonding type rmsd hydrogen bonds : bond 0.03021 ( 150) hydrogen bonds : angle 6.34389 ( 384) SS BOND : bond 0.00354 ( 6) SS BOND : angle 1.11480 ( 12) covalent geometry : bond 0.00273 (11436) covalent geometry : angle 0.62793 (15490) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 116 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 363 TYR cc_start: 0.4486 (OUTLIER) cc_final: 0.3221 (t80) REVERT: B 445 ARG cc_start: 0.7454 (pmt170) cc_final: 0.7109 (ptt-90) REVERT: B 505 ARG cc_start: 0.6992 (ptt-90) cc_final: 0.6038 (tpp80) REVERT: B 621 GLU cc_start: 0.7461 (tt0) cc_final: 0.6917 (tt0) REVERT: B 638 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.6564 (mtp) REVERT: B 1638 ARG cc_start: 0.7827 (ptm-80) cc_final: 0.7174 (mtp-110) REVERT: B 1700 TRP cc_start: 0.7618 (OUTLIER) cc_final: 0.5833 (m-10) REVERT: B 1703 TYR cc_start: 0.7192 (p90) cc_final: 0.6857 (p90) REVERT: B 1738 MET cc_start: 0.7300 (ttt) cc_final: 0.6900 (ttt) REVERT: B 1850 LYS cc_start: 0.8008 (mtpp) cc_final: 0.7438 (mttp) REVERT: B 1868 MET cc_start: 0.7509 (mtt) cc_final: 0.7214 (mtt) REVERT: B 1883 MET cc_start: 0.8780 (mmm) cc_final: 0.8418 (mpp) outliers start: 44 outliers final: 25 residues processed: 155 average time/residue: 0.2029 time to fit residues: 47.7980 Evaluate side-chains 137 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 1559 GLU Chi-restraints excluded: chain B residue 1700 TRP Chi-restraints excluded: chain B residue 1746 MET Chi-restraints excluded: chain B residue 1747 THR Chi-restraints excluded: chain B residue 1798 VAL Chi-restraints excluded: chain B residue 1843 THR Chi-restraints excluded: chain B residue 1856 LEU Chi-restraints excluded: chain B residue 1920 TRP Chi-restraints excluded: chain B residue 2015 ILE Chi-restraints excluded: chain B residue 2026 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 82 optimal weight: 0.0770 chunk 88 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 129 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 133 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 700 ASN ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1729 HIS B1781 ASN B1894 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.139174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.119589 restraints weight = 26014.936| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 3.65 r_work: 0.3743 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11442 Z= 0.159 Angle : 0.667 9.636 15502 Z= 0.343 Chirality : 0.047 0.174 1627 Planarity : 0.005 0.092 1999 Dihedral : 5.836 31.901 1508 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.53 % Favored : 85.47 % Rotamer: Outliers : 3.51 % Allowed : 21.80 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.20 (0.20), residues: 1370 helix: -3.17 (0.53), residues: 52 sheet: -1.93 (0.27), residues: 380 loop : -3.39 (0.17), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1700 HIS 0.003 0.001 HIS B 682 PHE 0.022 0.001 PHE B 552 TYR 0.033 0.002 TYR B 418 ARG 0.002 0.000 ARG B 648 Details of bonding type rmsd hydrogen bonds : bond 0.03271 ( 150) hydrogen bonds : angle 6.38018 ( 384) SS BOND : bond 0.00471 ( 6) SS BOND : angle 1.24188 ( 12) covalent geometry : bond 0.00369 (11436) covalent geometry : angle 0.66601 (15490) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 113 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 352 LEU cc_start: 0.1204 (OUTLIER) cc_final: 0.0897 (tp) REVERT: B 363 TYR cc_start: 0.4552 (OUTLIER) cc_final: 0.3361 (t80) REVERT: B 445 ARG cc_start: 0.7434 (pmt170) cc_final: 0.7072 (ptt-90) REVERT: B 505 ARG cc_start: 0.6964 (ptt-90) cc_final: 0.6061 (tpp80) REVERT: B 605 TYR cc_start: 0.8512 (t80) cc_final: 0.8198 (t80) REVERT: B 621 GLU cc_start: 0.7500 (tt0) cc_final: 0.7281 (tt0) REVERT: B 638 MET cc_start: 0.6997 (OUTLIER) cc_final: 0.6751 (mtp) REVERT: B 1700 TRP cc_start: 0.7685 (OUTLIER) cc_final: 0.5858 (m-10) REVERT: B 1703 TYR cc_start: 0.7234 (p90) cc_final: 0.6966 (p90) REVERT: B 1738 MET cc_start: 0.7355 (ttt) cc_final: 0.6935 (ttt) REVERT: B 1850 LYS cc_start: 0.7868 (mtpp) cc_final: 0.7238 (mttp) REVERT: B 1868 MET cc_start: 0.7577 (mtt) cc_final: 0.7253 (mtt) outliers start: 43 outliers final: 34 residues processed: 151 average time/residue: 0.1959 time to fit residues: 44.9504 Evaluate side-chains 150 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 1550 ASN Chi-restraints excluded: chain B residue 1559 GLU Chi-restraints excluded: chain B residue 1700 TRP Chi-restraints excluded: chain B residue 1744 LEU Chi-restraints excluded: chain B residue 1746 MET Chi-restraints excluded: chain B residue 1747 THR Chi-restraints excluded: chain B residue 1798 VAL Chi-restraints excluded: chain B residue 1843 THR Chi-restraints excluded: chain B residue 1856 LEU Chi-restraints excluded: chain B residue 1920 TRP Chi-restraints excluded: chain B residue 1959 SER Chi-restraints excluded: chain B residue 2015 ILE Chi-restraints excluded: chain B residue 2026 LEU Chi-restraints excluded: chain B residue 2173 ILE Chi-restraints excluded: chain B residue 2186 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 104 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 125 optimal weight: 0.0170 chunk 30 optimal weight: 1.9990 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 700 ASN ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1781 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.141349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.121571 restraints weight = 25941.877| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 3.66 r_work: 0.3779 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11442 Z= 0.122 Angle : 0.634 9.820 15502 Z= 0.325 Chirality : 0.046 0.176 1627 Planarity : 0.005 0.089 1999 Dihedral : 5.579 29.045 1508 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.07 % Favored : 86.93 % Rotamer: Outliers : 3.18 % Allowed : 22.45 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.20), residues: 1370 helix: -3.09 (0.53), residues: 52 sheet: -1.87 (0.27), residues: 373 loop : -3.27 (0.17), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1700 HIS 0.003 0.001 HIS B 228 PHE 0.024 0.001 PHE B 552 TYR 0.017 0.001 TYR B1903 ARG 0.002 0.000 ARG B 90 Details of bonding type rmsd hydrogen bonds : bond 0.03001 ( 150) hydrogen bonds : angle 6.14505 ( 384) SS BOND : bond 0.00369 ( 6) SS BOND : angle 1.13852 ( 12) covalent geometry : bond 0.00285 (11436) covalent geometry : angle 0.63372 (15490) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 352 LEU cc_start: 0.1269 (OUTLIER) cc_final: 0.0903 (tp) REVERT: B 363 TYR cc_start: 0.4510 (OUTLIER) cc_final: 0.3382 (t80) REVERT: B 424 PHE cc_start: 0.7034 (m-80) cc_final: 0.6829 (m-80) REVERT: B 445 ARG cc_start: 0.7451 (pmt170) cc_final: 0.7108 (ptt-90) REVERT: B 505 ARG cc_start: 0.6989 (ptt-90) cc_final: 0.6076 (tpp80) REVERT: B 605 TYR cc_start: 0.8481 (t80) cc_final: 0.8176 (t80) REVERT: B 621 GLU cc_start: 0.7441 (tt0) cc_final: 0.7201 (tt0) REVERT: B 634 MET cc_start: 0.7789 (mmm) cc_final: 0.7502 (mmm) REVERT: B 638 MET cc_start: 0.6869 (OUTLIER) cc_final: 0.6486 (mtp) REVERT: B 1638 ARG cc_start: 0.7839 (ptm-80) cc_final: 0.7110 (mtm110) REVERT: B 1700 TRP cc_start: 0.7603 (OUTLIER) cc_final: 0.5825 (m-10) REVERT: B 1703 TYR cc_start: 0.7207 (p90) cc_final: 0.6877 (p90) REVERT: B 1738 MET cc_start: 0.7326 (ttt) cc_final: 0.6902 (ttt) REVERT: B 1827 LYS cc_start: 0.7649 (tppt) cc_final: 0.7132 (mmtm) REVERT: B 1850 LYS cc_start: 0.8005 (mtpp) cc_final: 0.7411 (mttp) REVERT: B 1868 MET cc_start: 0.7418 (mtt) cc_final: 0.7099 (mtt) REVERT: B 1883 MET cc_start: 0.8798 (mmm) cc_final: 0.8354 (mpp) outliers start: 39 outliers final: 32 residues processed: 154 average time/residue: 0.2225 time to fit residues: 51.4928 Evaluate side-chains 148 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 1550 ASN Chi-restraints excluded: chain B residue 1559 GLU Chi-restraints excluded: chain B residue 1700 TRP Chi-restraints excluded: chain B residue 1746 MET Chi-restraints excluded: chain B residue 1747 THR Chi-restraints excluded: chain B residue 1781 ASN Chi-restraints excluded: chain B residue 1798 VAL Chi-restraints excluded: chain B residue 1843 THR Chi-restraints excluded: chain B residue 1856 LEU Chi-restraints excluded: chain B residue 1920 TRP Chi-restraints excluded: chain B residue 1959 SER Chi-restraints excluded: chain B residue 2015 ILE Chi-restraints excluded: chain B residue 2026 LEU Chi-restraints excluded: chain B residue 2173 ILE Chi-restraints excluded: chain B residue 2186 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 133 optimal weight: 0.4980 chunk 112 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 ASN ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1781 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.140244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.120497 restraints weight = 26078.983| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 3.66 r_work: 0.3756 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11442 Z= 0.148 Angle : 0.659 9.772 15502 Z= 0.338 Chirality : 0.046 0.172 1627 Planarity : 0.005 0.090 1999 Dihedral : 5.679 29.780 1508 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.16 % Favored : 85.84 % Rotamer: Outliers : 3.10 % Allowed : 22.86 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.20), residues: 1370 helix: -3.09 (0.54), residues: 52 sheet: -1.78 (0.27), residues: 365 loop : -3.29 (0.18), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1700 HIS 0.003 0.001 HIS B 228 PHE 0.025 0.001 PHE B 552 TYR 0.016 0.001 TYR B1903 ARG 0.006 0.000 ARG B 648 Details of bonding type rmsd hydrogen bonds : bond 0.03124 ( 150) hydrogen bonds : angle 6.23849 ( 384) SS BOND : bond 0.00414 ( 6) SS BOND : angle 1.20339 ( 12) covalent geometry : bond 0.00343 (11436) covalent geometry : angle 0.65799 (15490) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 111 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 352 LEU cc_start: 0.1130 (OUTLIER) cc_final: 0.0510 (tp) REVERT: B 363 TYR cc_start: 0.4525 (OUTLIER) cc_final: 0.3331 (t80) REVERT: B 424 PHE cc_start: 0.6990 (m-80) cc_final: 0.6747 (m-80) REVERT: B 445 ARG cc_start: 0.7543 (pmt170) cc_final: 0.7188 (ptt-90) REVERT: B 505 ARG cc_start: 0.7057 (ptt-90) cc_final: 0.6092 (mmp80) REVERT: B 605 TYR cc_start: 0.8493 (t80) cc_final: 0.8176 (t80) REVERT: B 621 GLU cc_start: 0.7515 (tt0) cc_final: 0.7235 (tt0) REVERT: B 638 MET cc_start: 0.6896 (OUTLIER) cc_final: 0.6544 (mtp) REVERT: B 1638 ARG cc_start: 0.7916 (ptm-80) cc_final: 0.7134 (mtp-110) REVERT: B 1700 TRP cc_start: 0.7633 (OUTLIER) cc_final: 0.5833 (m-10) REVERT: B 1703 TYR cc_start: 0.7234 (p90) cc_final: 0.6997 (p90) REVERT: B 1738 MET cc_start: 0.7370 (ttt) cc_final: 0.6945 (ttt) REVERT: B 1850 LYS cc_start: 0.8007 (mtpp) cc_final: 0.7399 (mttp) REVERT: B 1868 MET cc_start: 0.7558 (mtt) cc_final: 0.7242 (mtt) REVERT: B 1883 MET cc_start: 0.8833 (mmm) cc_final: 0.8430 (mpp) outliers start: 38 outliers final: 32 residues processed: 144 average time/residue: 0.2574 time to fit residues: 55.4468 Evaluate side-chains 146 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 1550 ASN Chi-restraints excluded: chain B residue 1559 GLU Chi-restraints excluded: chain B residue 1700 TRP Chi-restraints excluded: chain B residue 1746 MET Chi-restraints excluded: chain B residue 1747 THR Chi-restraints excluded: chain B residue 1781 ASN Chi-restraints excluded: chain B residue 1798 VAL Chi-restraints excluded: chain B residue 1843 THR Chi-restraints excluded: chain B residue 1856 LEU Chi-restraints excluded: chain B residue 1920 TRP Chi-restraints excluded: chain B residue 1959 SER Chi-restraints excluded: chain B residue 2015 ILE Chi-restraints excluded: chain B residue 2026 LEU Chi-restraints excluded: chain B residue 2173 ILE Chi-restraints excluded: chain B residue 2186 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 100 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 700 ASN ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1781 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.139657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.119913 restraints weight = 26096.112| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 3.66 r_work: 0.3748 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11442 Z= 0.160 Angle : 0.670 9.724 15502 Z= 0.344 Chirality : 0.047 0.174 1627 Planarity : 0.005 0.091 1999 Dihedral : 5.764 30.769 1508 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.09 % Favored : 85.91 % Rotamer: Outliers : 3.43 % Allowed : 22.69 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.20), residues: 1370 helix: -3.10 (0.54), residues: 52 sheet: -1.79 (0.27), residues: 370 loop : -3.30 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1700 HIS 0.003 0.001 HIS B 228 PHE 0.042 0.002 PHE B 552 TYR 0.016 0.001 TYR B1903 ARG 0.005 0.000 ARG B 648 Details of bonding type rmsd hydrogen bonds : bond 0.03159 ( 150) hydrogen bonds : angle 6.31540 ( 384) SS BOND : bond 0.00433 ( 6) SS BOND : angle 1.22828 ( 12) covalent geometry : bond 0.00371 (11436) covalent geometry : angle 0.66937 (15490) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5983.92 seconds wall clock time: 108 minutes 15.72 seconds (6495.72 seconds total)