Starting phenix.real_space_refine on Wed Mar 4 05:52:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kve_23048/03_2026/7kve_23048.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kve_23048/03_2026/7kve_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 { model { file = "/net/cci-nas-00/data/ceres_data/7kve_23048/03_2026/7kve_23048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kve_23048/03_2026/7kve_23048.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kve_23048/03_2026/7kve_23048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kve_23048/03_2026/7kve_23048.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.067 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.12, per 1000 atoms: 0.19 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: 0.59 Conformation dependent library (CDL) restraints added in 365.5 milliseconds 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: 0.47 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: 2.29 Time building geometry restraints manager: 0.83 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: 1.710 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.410 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.810 ------------------------------------------------------------------------------- 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 : 17.14 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.008 0.001 ARG B 90 TYR 0.021 0.002 TYR B 363 PHE 0.016 0.001 PHE B2071 TRP 0.025 0.002 TRP B1700 HIS 0.005 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00477 (11436) covalent geometry : angle 0.81660 (15490) SS BOND : bond 0.00789 ( 6) SS BOND : angle 1.65774 ( 12) hydrogen bonds : bond 0.29500 ( 150) hydrogen bonds : angle 12.46977 ( 384) *********************** 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 : 0.304 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: 0.6437 (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: 0.1227 time to fit residues: 26.5951 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 : 0.407 ------------------------------------------------------------------------------- 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 98 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 B1670 ASN B1713 HIS B1778 HIS B1781 ASN B1819 GLN B1828 GLN B1830 GLN B1936 GLN B2002 ASN B2003 GLN B2093 GLN B2128 HIS B2162 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.137162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.117454 restraints weight = 26001.255| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 3.61 r_work: 0.3728 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11442 Z= 0.220 Angle : 0.745 9.649 15502 Z= 0.390 Chirality : 0.049 0.160 1627 Planarity : 0.006 0.095 1999 Dihedral : 6.620 36.284 1510 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.20 % Favored : 83.80 % Rotamer: Outliers : 2.37 % Allowed : 14.69 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.28 (0.18), residues: 1370 helix: -3.49 (0.51), residues: 49 sheet: -2.94 (0.25), residues: 375 loop : -4.04 (0.15), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 90 TYR 0.029 0.002 TYR B1903 PHE 0.020 0.002 PHE B2071 TRP 0.020 0.002 TRP B1700 HIS 0.006 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00500 (11436) covalent geometry : angle 0.74409 (15490) SS BOND : bond 0.00536 ( 6) SS BOND : angle 1.57941 ( 12) hydrogen bonds : bond 0.04606 ( 150) hydrogen bonds : angle 8.16315 ( 384) *********************** 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 151 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: B 244 ASN cc_start: 0.8861 (m-40) cc_final: 0.8577 (m110) REVERT: B 424 PHE cc_start: 0.6870 (m-80) cc_final: 0.6642 (m-80) REVERT: B 445 ARG cc_start: 0.7300 (pmt170) cc_final: 0.6915 (ptt-90) REVERT: B 610 GLU cc_start: 0.8152 (mp0) cc_final: 0.7762 (mm-30) REVERT: B 621 GLU cc_start: 0.7582 (tt0) cc_final: 0.7216 (tt0) REVERT: B 1703 TYR cc_start: 0.7089 (p90) cc_final: 0.6875 (p90) REVERT: B 1738 MET cc_start: 0.7554 (ttt) cc_final: 0.7118 (ttt) REVERT: B 1850 LYS cc_start: 0.7828 (mtpp) cc_final: 0.7131 (mttp) REVERT: B 1868 MET cc_start: 0.7510 (mtt) cc_final: 0.7257 (mtt) REVERT: B 2044 MET cc_start: 0.6458 (mmm) cc_final: 0.5980 (mmm) outliers start: 29 outliers final: 16 residues processed: 147 average time/residue: 0.1025 time to fit residues: 21.8364 Evaluate side-chains 123 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 561 ILE Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 1559 GLU 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 106 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 80 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 289 GLN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN B1570 GLN B1781 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.136665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.117229 restraints weight = 26210.653| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 3.62 r_work: 0.3710 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11442 Z= 0.207 Angle : 0.725 10.681 15502 Z= 0.376 Chirality : 0.048 0.170 1627 Planarity : 0.006 0.095 1999 Dihedral : 6.552 37.044 1508 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.50 % Favored : 83.50 % Rotamer: Outliers : 3.27 % Allowed : 18.37 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.02 (0.19), residues: 1370 helix: -3.29 (0.55), residues: 50 sheet: -2.67 (0.26), residues: 372 loop : -3.91 (0.16), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 608 TYR 0.024 0.002 TYR B1903 PHE 0.018 0.002 PHE B2071 TRP 0.014 0.002 TRP B1563 HIS 0.004 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00471 (11436) covalent geometry : angle 0.72395 (15490) SS BOND : bond 0.00481 ( 6) SS BOND : angle 1.47575 ( 12) hydrogen bonds : bond 0.03981 ( 150) hydrogen bonds : angle 7.50752 ( 384) *********************** 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 154 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 114 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: B 244 ASN cc_start: 0.8784 (m-40) cc_final: 0.8466 (m110) REVERT: B 424 PHE cc_start: 0.6918 (m-80) cc_final: 0.6646 (m-80) REVERT: B 445 ARG cc_start: 0.7119 (pmt170) cc_final: 0.6742 (ptt-90) REVERT: B 590 GLN cc_start: 0.6922 (OUTLIER) cc_final: 0.6554 (pm20) REVERT: B 621 GLU cc_start: 0.7586 (tt0) cc_final: 0.7124 (tt0) REVERT: B 1700 TRP cc_start: 0.7890 (OUTLIER) cc_final: 0.7626 (m-10) REVERT: B 1703 TYR cc_start: 0.7088 (p90) cc_final: 0.6860 (p90) REVERT: B 1738 MET cc_start: 0.7529 (ttt) cc_final: 0.7079 (ttt) REVERT: B 1850 LYS cc_start: 0.7951 (mtpp) cc_final: 0.7243 (mttp) REVERT: B 1868 MET cc_start: 0.7628 (mtt) cc_final: 0.7329 (mtt) REVERT: B 2044 MET cc_start: 0.6622 (mmm) cc_final: 0.6235 (mmm) outliers start: 40 outliers final: 23 residues processed: 148 average time/residue: 0.0875 time to fit residues: 19.5106 Evaluate side-chains 133 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 417 ILE Chi-restraints excluded: chain B residue 519 VAL 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 615 LEU Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 678 THR 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 1814 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 Chi-restraints excluded: chain B residue 2026 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 89 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1781 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.138997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.119379 restraints weight = 26381.249| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 3.65 r_work: 0.3749 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.1980 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= 0.143 Angle : 0.661 9.707 15502 Z= 0.341 Chirality : 0.047 0.171 1627 Planarity : 0.005 0.092 1999 Dihedral : 6.122 34.081 1508 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.31 % Favored : 85.69 % Rotamer: Outliers : 2.94 % Allowed : 20.33 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.76 (0.19), residues: 1370 helix: -3.25 (0.58), residues: 51 sheet: -2.37 (0.26), residues: 379 loop : -3.77 (0.16), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 90 TYR 0.023 0.001 TYR B1903 PHE 0.023 0.001 PHE B 552 TRP 0.012 0.001 TRP B1700 HIS 0.004 0.001 HIS B1815 Details of bonding type rmsd covalent geometry : bond 0.00325 (11436) covalent geometry : angle 0.65994 (15490) SS BOND : bond 0.00272 ( 6) SS BOND : angle 1.31099 ( 12) hydrogen bonds : bond 0.03288 ( 150) hydrogen bonds : angle 6.93586 ( 384) *********************** 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 152 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 445 ARG cc_start: 0.7121 (pmt170) cc_final: 0.6758 (ptt-90) REVERT: B 621 GLU cc_start: 0.7583 (tt0) cc_final: 0.7194 (tt0) REVERT: B 648 ARG cc_start: 0.8940 (mtm180) cc_final: 0.8684 (mtm110) REVERT: B 1700 TRP cc_start: 0.7689 (OUTLIER) cc_final: 0.5857 (m-10) REVERT: B 1703 TYR cc_start: 0.7182 (p90) cc_final: 0.6880 (p90) REVERT: B 1738 MET cc_start: 0.7464 (ttt) cc_final: 0.7050 (ttt) REVERT: B 1850 LYS cc_start: 0.7925 (mtpp) cc_final: 0.7242 (mttp) REVERT: B 1868 MET cc_start: 0.7487 (mtt) cc_final: 0.7189 (mtt) outliers start: 36 outliers final: 22 residues processed: 143 average time/residue: 0.0951 time to fit residues: 20.3004 Evaluate side-chains 129 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 279 ILE 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 630 VAL Chi-restraints excluded: chain B residue 634 MET 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 1814 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 2009 VAL Chi-restraints excluded: chain B residue 2015 ILE Chi-restraints excluded: chain B residue 2173 ILE Chi-restraints excluded: chain B residue 2186 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 96 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 85 optimal weight: 0.0570 chunk 2 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 38 optimal weight: 0.0770 chunk 25 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.1660 ------------------------------------------------------------------------------- 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 B1729 HIS B1781 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.139015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.119526 restraints weight = 25949.047| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 3.63 r_work: 0.3745 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11442 Z= 0.144 Angle : 0.659 9.129 15502 Z= 0.338 Chirality : 0.046 0.174 1627 Planarity : 0.005 0.092 1999 Dihedral : 5.974 32.557 1508 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.82 % Favored : 85.18 % Rotamer: Outliers : 4.57 % Allowed : 20.49 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.60 (0.19), residues: 1370 helix: -3.16 (0.58), residues: 51 sheet: -2.24 (0.26), residues: 376 loop : -3.67 (0.16), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 485 TYR 0.020 0.001 TYR B1903 PHE 0.015 0.001 PHE B 187 TRP 0.012 0.001 TRP B1563 HIS 0.003 0.001 HIS B 682 Details of bonding type rmsd covalent geometry : bond 0.00331 (11436) covalent geometry : angle 0.65839 (15490) SS BOND : bond 0.00350 ( 6) SS BOND : angle 1.19764 ( 12) hydrogen bonds : bond 0.03187 ( 150) hydrogen bonds : angle 6.70535 ( 384) *********************** 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 175 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 119 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 203 MET cc_start: 0.6515 (tpp) cc_final: 0.6183 (mmt) REVERT: B 352 LEU cc_start: 0.1202 (OUTLIER) cc_final: 0.0664 (tp) REVERT: B 363 TYR cc_start: 0.4593 (OUTLIER) cc_final: 0.3358 (t80) REVERT: B 418 TYR cc_start: 0.8631 (t80) cc_final: 0.8422 (t80) REVERT: B 445 ARG cc_start: 0.7110 (pmt170) cc_final: 0.6759 (ptt-90) REVERT: B 590 GLN cc_start: 0.6791 (OUTLIER) cc_final: 0.6393 (pm20) REVERT: B 605 TYR cc_start: 0.8570 (t80) cc_final: 0.8330 (t80) REVERT: B 621 GLU cc_start: 0.7584 (tt0) cc_final: 0.7277 (tt0) REVERT: B 627 MET cc_start: 0.7124 (mmp) cc_final: 0.6863 (mmp) REVERT: B 648 ARG cc_start: 0.8892 (mtm180) cc_final: 0.8679 (mtm110) REVERT: B 702 LEU cc_start: -0.1515 (OUTLIER) cc_final: -0.1777 (tt) REVERT: B 1700 TRP cc_start: 0.7705 (OUTLIER) cc_final: 0.5910 (m-10) REVERT: B 1703 TYR cc_start: 0.7176 (p90) cc_final: 0.6834 (p90) REVERT: B 1738 MET cc_start: 0.7520 (ttt) cc_final: 0.7127 (ttt) REVERT: B 1850 LYS cc_start: 0.7919 (mtpp) cc_final: 0.7241 (mttp) REVERT: B 1868 MET cc_start: 0.7518 (mtt) cc_final: 0.7203 (mtt) outliers start: 56 outliers final: 31 residues processed: 166 average time/residue: 0.0860 time to fit residues: 21.9373 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 : 0.502 ------------------------------------------------------------------------------- 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 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 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 590 GLN Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 702 LEU 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 1959 SER Chi-restraints excluded: chain B residue 2009 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 2 optimal weight: 1.9990 chunk 81 optimal weight: 0.4980 chunk 117 optimal weight: 1.9990 chunk 94 optimal weight: 0.0060 chunk 133 optimal weight: 0.0370 chunk 6 optimal weight: 3.9990 chunk 31 optimal weight: 0.0370 chunk 132 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 0.0570 chunk 45 optimal weight: 1.9990 overall best weight: 0.1270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 HIS B 350 GLN B 379 HIS B 700 ASN B1781 ASN B2036 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.145384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.125441 restraints weight = 25953.625| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 3.71 r_work: 0.3840 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11442 Z= 0.103 Angle : 0.604 9.533 15502 Z= 0.308 Chirality : 0.045 0.175 1627 Planarity : 0.005 0.086 1999 Dihedral : 5.286 25.177 1508 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.39 % Favored : 88.61 % Rotamer: Outliers : 2.78 % Allowed : 21.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.27 (0.20), residues: 1370 helix: -2.89 (0.57), residues: 57 sheet: -2.05 (0.26), residues: 382 loop : -3.42 (0.17), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 485 TYR 0.026 0.001 TYR B 477 PHE 0.017 0.001 PHE B1568 TRP 0.014 0.001 TRP B1834 HIS 0.002 0.000 HIS B 379 Details of bonding type rmsd covalent geometry : bond 0.00229 (11436) covalent geometry : angle 0.60376 (15490) SS BOND : bond 0.00243 ( 6) SS BOND : angle 0.96430 ( 12) hydrogen bonds : bond 0.02809 ( 150) hydrogen bonds : angle 6.01705 ( 384) *********************** 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 163 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 134 HIS cc_start: 0.5883 (t70) cc_final: 0.5065 (t-90) REVERT: B 203 MET cc_start: 0.6258 (tpp) cc_final: 0.5938 (mmp) REVERT: B 292 MET cc_start: 0.7570 (ptp) cc_final: 0.7346 (ptp) REVERT: B 363 TYR cc_start: 0.4317 (OUTLIER) cc_final: 0.3223 (t80) REVERT: B 445 ARG cc_start: 0.7166 (pmt170) cc_final: 0.6855 (ptt-90) REVERT: B 621 GLU cc_start: 0.7520 (tt0) cc_final: 0.7157 (tt0) REVERT: B 1638 ARG cc_start: 0.7485 (ptm-80) cc_final: 0.6884 (mtm110) REVERT: B 1700 TRP cc_start: 0.7454 (OUTLIER) cc_final: 0.5745 (m-10) REVERT: B 1703 TYR cc_start: 0.6963 (p90) cc_final: 0.6575 (p90) REVERT: B 1738 MET cc_start: 0.7468 (ttt) cc_final: 0.7023 (ttt) REVERT: B 1850 LYS cc_start: 0.7976 (mtpp) cc_final: 0.7424 (mttp) REVERT: B 1868 MET cc_start: 0.7284 (mtt) cc_final: 0.7031 (mtt) REVERT: B 1878 ASP cc_start: 0.8283 (m-30) cc_final: 0.7684 (p0) REVERT: B 1883 MET cc_start: 0.8754 (mmm) cc_final: 0.8292 (mpp) REVERT: B 2044 MET cc_start: 0.6366 (mmm) cc_final: 0.5824 (mmm) REVERT: B 2145 MET cc_start: 0.2317 (mpp) cc_final: 0.2110 (mmm) outliers start: 34 outliers final: 19 residues processed: 155 average time/residue: 0.0941 time to fit residues: 21.5819 Evaluate side-chains 137 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 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 420 HIS Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 1550 ASN Chi-restraints excluded: chain B residue 1700 TRP 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 2063 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 125 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 20 optimal weight: 0.0870 chunk 108 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 70 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 ASN ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1894 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.140716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.121087 restraints weight = 26065.448| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 3.68 r_work: 0.3765 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11442 Z= 0.144 Angle : 0.641 9.294 15502 Z= 0.329 Chirality : 0.046 0.188 1627 Planarity : 0.005 0.089 1999 Dihedral : 5.580 27.556 1508 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.58 % Favored : 86.42 % Rotamer: Outliers : 3.27 % Allowed : 22.61 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.27 (0.20), residues: 1370 helix: -3.13 (0.53), residues: 51 sheet: -1.98 (0.27), residues: 366 loop : -3.42 (0.17), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 648 TYR 0.026 0.002 TYR B 418 PHE 0.013 0.001 PHE B 552 TRP 0.017 0.001 TRP B2084 HIS 0.003 0.001 HIS B1812 Details of bonding type rmsd covalent geometry : bond 0.00333 (11436) covalent geometry : angle 0.64037 (15490) SS BOND : bond 0.00458 ( 6) SS BOND : angle 1.16606 ( 12) hydrogen bonds : bond 0.03194 ( 150) hydrogen bonds : angle 6.10345 ( 384) *********************** 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 156 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 0.444 Fit side-chains REVERT: B 134 HIS cc_start: 0.6078 (t70) cc_final: 0.5301 (t70) REVERT: B 352 LEU cc_start: 0.1306 (OUTLIER) cc_final: 0.0963 (tp) REVERT: B 363 TYR cc_start: 0.4559 (OUTLIER) cc_final: 0.3536 (t80) REVERT: B 445 ARG cc_start: 0.7155 (pmt170) cc_final: 0.6822 (ptt-90) REVERT: B 505 ARG cc_start: 0.7019 (ptt-90) cc_final: 0.6119 (tpp80) REVERT: B 605 TYR cc_start: 0.8487 (t80) cc_final: 0.8194 (t80) REVERT: B 702 LEU cc_start: -0.1679 (OUTLIER) cc_final: -0.1909 (tt) REVERT: B 1700 TRP cc_start: 0.7727 (OUTLIER) cc_final: 0.5980 (m-10) REVERT: B 1703 TYR cc_start: 0.7069 (p90) cc_final: 0.6727 (p90) REVERT: B 1738 MET cc_start: 0.7626 (ttt) cc_final: 0.7212 (ttt) REVERT: B 1850 LYS cc_start: 0.7995 (mtpp) cc_final: 0.7421 (mttp) REVERT: B 1868 MET cc_start: 0.7190 (mtt) cc_final: 0.6923 (mtt) REVERT: B 1883 MET cc_start: 0.8770 (mmm) cc_final: 0.8356 (mpp) REVERT: B 2067 TYR cc_start: 0.3736 (p90) cc_final: 0.3418 (p90) outliers start: 40 outliers final: 28 residues processed: 150 average time/residue: 0.0960 time to fit residues: 21.8053 Evaluate side-chains 145 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 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 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 678 THR Chi-restraints excluded: chain B residue 702 LEU 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 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 1946 THR Chi-restraints excluded: chain B residue 1959 SER Chi-restraints excluded: chain B residue 2015 ILE Chi-restraints excluded: chain B residue 2173 ILE Chi-restraints excluded: chain B residue 2186 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 89 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 133 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 536 ASN ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1812 HIS B1828 GLN B1830 GLN B1863 ASN ** B2132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2165 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.131947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.113183 restraints weight = 26805.802| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 3.54 r_work: 0.3650 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.100 11442 Z= 0.389 Angle : 0.907 9.296 15502 Z= 0.476 Chirality : 0.054 0.176 1627 Planarity : 0.007 0.104 1999 Dihedral : 7.364 43.557 1508 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.22 % Allowed : 19.93 % Favored : 79.85 % Rotamer: Outliers : 3.84 % Allowed : 23.18 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.76 (0.19), residues: 1370 helix: -3.22 (0.53), residues: 48 sheet: -2.38 (0.26), residues: 397 loop : -3.78 (0.16), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 648 TYR 0.027 0.003 TYR B 204 PHE 0.024 0.003 PHE B2071 TRP 0.024 0.003 TRP B1563 HIS 0.007 0.002 HIS B 351 Details of bonding type rmsd covalent geometry : bond 0.00890 (11436) covalent geometry : angle 0.90579 (15490) SS BOND : bond 0.00885 ( 6) SS BOND : angle 1.95795 ( 12) hydrogen bonds : bond 0.04727 ( 150) hydrogen bonds : angle 7.37790 ( 384) *********************** 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 153 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 106 time to evaluate : 0.412 Fit side-chains REVERT: B 352 LEU cc_start: 0.1646 (OUTLIER) cc_final: 0.1415 (tp) REVERT: B 621 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7269 (tp30) REVERT: B 702 LEU cc_start: -0.1430 (OUTLIER) cc_final: -0.1730 (tt) REVERT: B 1700 TRP cc_start: 0.7998 (OUTLIER) cc_final: 0.7131 (m-10) REVERT: B 1738 MET cc_start: 0.7844 (ttt) cc_final: 0.7441 (ttt) REVERT: B 1850 LYS cc_start: 0.7935 (mtpp) cc_final: 0.7259 (mttp) REVERT: B 1868 MET cc_start: 0.7925 (mtt) cc_final: 0.7667 (mtt) outliers start: 47 outliers final: 37 residues processed: 147 average time/residue: 0.0839 time to fit residues: 19.1918 Evaluate side-chains 139 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 98 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 143 ILE 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 519 VAL Chi-restraints excluded: chain B residue 531 LEU 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 592 GLU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 702 LEU 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 1747 THR Chi-restraints excluded: chain B residue 1798 VAL Chi-restraints excluded: chain B residue 1843 THR Chi-restraints excluded: chain B residue 1885 LEU Chi-restraints excluded: chain B residue 1920 TRP Chi-restraints excluded: chain B residue 1946 THR 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 2165 ASN 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 125 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 398 GLN ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1869 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.139880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.120543 restraints weight = 26106.575| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 3.59 r_work: 0.3764 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 11442 Z= 0.132 Angle : 0.685 11.949 15502 Z= 0.351 Chirality : 0.047 0.231 1627 Planarity : 0.005 0.090 1999 Dihedral : 6.177 36.543 1508 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.70 % Favored : 87.30 % Rotamer: Outliers : 2.86 % Allowed : 24.41 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.40 (0.20), residues: 1370 helix: -3.17 (0.53), residues: 51 sheet: -2.05 (0.27), residues: 382 loop : -3.55 (0.17), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 648 TYR 0.020 0.001 TYR B1903 PHE 0.013 0.001 PHE B2164 TRP 0.013 0.001 TRP B1700 HIS 0.003 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00308 (11436) covalent geometry : angle 0.68217 (15490) SS BOND : bond 0.00453 ( 6) SS BOND : angle 2.34026 ( 12) hydrogen bonds : bond 0.03342 ( 150) hydrogen bonds : angle 6.40152 ( 384) *********************** 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 150 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: B 352 LEU cc_start: 0.1178 (OUTLIER) cc_final: 0.0747 (tp) REVERT: B 363 TYR cc_start: 0.4481 (OUTLIER) cc_final: 0.3401 (t80) REVERT: B 410 MET cc_start: 0.7666 (mtm) cc_final: 0.7361 (mtm) REVERT: B 445 ARG cc_start: 0.7190 (pmt170) cc_final: 0.6847 (ptt-90) REVERT: B 619 ARG cc_start: 0.8171 (ptt90) cc_final: 0.7800 (ptp90) REVERT: B 702 LEU cc_start: -0.1599 (OUTLIER) cc_final: -0.1847 (tt) REVERT: B 1638 ARG cc_start: 0.7875 (ptm-80) cc_final: 0.7545 (ptm-80) REVERT: B 1700 TRP cc_start: 0.7656 (OUTLIER) cc_final: 0.5973 (m-10) REVERT: B 1703 TYR cc_start: 0.7148 (p90) cc_final: 0.6876 (p90) REVERT: B 1738 MET cc_start: 0.7620 (ttt) cc_final: 0.7172 (ttt) REVERT: B 1850 LYS cc_start: 0.8030 (mtpp) cc_final: 0.7378 (mttp) REVERT: B 1868 MET cc_start: 0.7457 (mtt) cc_final: 0.7124 (mtt) outliers start: 35 outliers final: 26 residues processed: 148 average time/residue: 0.0989 time to fit residues: 21.4288 Evaluate side-chains 141 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 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 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 592 GLU 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 702 LEU Chi-restraints excluded: chain B residue 1550 ASN Chi-restraints excluded: chain B residue 1559 GLU Chi-restraints excluded: chain B residue 1657 THR Chi-restraints excluded: chain B residue 1700 TRP 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 1946 THR Chi-restraints excluded: chain B residue 1959 SER Chi-restraints excluded: chain B residue 2015 ILE Chi-restraints excluded: chain B residue 2165 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 85 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 66 optimal weight: 0.1980 chunk 34 optimal weight: 0.1980 chunk 105 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 ASN ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.142426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.122818 restraints weight = 26364.658| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 3.67 r_work: 0.3799 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11442 Z= 0.113 Angle : 0.652 12.985 15502 Z= 0.330 Chirality : 0.046 0.165 1627 Planarity : 0.005 0.088 1999 Dihedral : 5.589 27.325 1508 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.87 % Favored : 86.13 % Rotamer: Outliers : 2.45 % Allowed : 24.73 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.16 (0.20), residues: 1370 helix: -3.09 (0.54), residues: 52 sheet: -1.84 (0.28), residues: 351 loop : -3.36 (0.17), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 400 TYR 0.037 0.001 TYR B 418 PHE 0.021 0.001 PHE B1568 TRP 0.016 0.001 TRP B1934 HIS 0.003 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00260 (11436) covalent geometry : angle 0.65058 (15490) SS BOND : bond 0.00754 ( 6) SS BOND : angle 1.56303 ( 12) hydrogen bonds : bond 0.02939 ( 150) hydrogen bonds : angle 5.96477 ( 384) ********************** 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 151 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: B 270 MET cc_start: 0.8679 (ppp) cc_final: 0.6892 (ppp) REVERT: B 352 LEU cc_start: 0.1104 (OUTLIER) cc_final: 0.0590 (tp) REVERT: B 363 TYR cc_start: 0.4370 (OUTLIER) cc_final: 0.3448 (t80) REVERT: B 445 ARG cc_start: 0.7551 (pmt170) cc_final: 0.7211 (ptt-90) REVERT: B 678 THR cc_start: 0.7561 (OUTLIER) cc_final: 0.7324 (p) REVERT: B 1638 ARG cc_start: 0.7760 (ptm-80) cc_final: 0.7099 (mtm110) REVERT: B 1700 TRP cc_start: 0.7474 (OUTLIER) cc_final: 0.5790 (m-10) REVERT: B 1703 TYR cc_start: 0.7100 (p90) cc_final: 0.6731 (p90) REVERT: B 1738 MET cc_start: 0.7528 (ttt) cc_final: 0.7020 (ttt) REVERT: B 1827 LYS cc_start: 0.7687 (tppt) cc_final: 0.7342 (tptt) REVERT: B 1846 MET cc_start: 0.8667 (mmm) cc_final: 0.8100 (mmm) REVERT: B 1850 LYS cc_start: 0.8134 (mtpp) cc_final: 0.7443 (mttp) REVERT: B 1868 MET cc_start: 0.7321 (mtt) cc_final: 0.6966 (mtt) outliers start: 30 outliers final: 22 residues processed: 150 average time/residue: 0.0928 time to fit residues: 21.1205 Evaluate side-chains 139 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 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 352 LEU Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 592 GLU 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 1550 ASN Chi-restraints excluded: chain B residue 1559 GLU Chi-restraints excluded: chain B residue 1700 TRP Chi-restraints excluded: chain B residue 1798 VAL Chi-restraints excluded: chain B residue 1843 THR Chi-restraints excluded: chain B residue 1885 LEU Chi-restraints excluded: chain B residue 1920 TRP Chi-restraints excluded: chain B residue 1946 THR Chi-restraints excluded: chain B residue 1959 SER Chi-restraints excluded: chain B residue 2015 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 23 optimal weight: 5.9990 chunk 17 optimal weight: 0.0170 chunk 104 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 639 ASN ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1809 GLN ** B1819 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 = 0.4167 r_free = 0.4167 target = 0.141299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.121813 restraints weight = 26243.377| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 3.62 r_work: 0.3781 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2936 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= 0.131 Angle : 0.660 12.555 15502 Z= 0.336 Chirality : 0.046 0.162 1627 Planarity : 0.005 0.089 1999 Dihedral : 5.649 27.498 1508 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.99 % Favored : 87.01 % Rotamer: Outliers : 2.94 % Allowed : 24.73 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.06 (0.20), residues: 1370 helix: -3.11 (0.54), residues: 52 sheet: -1.63 (0.29), residues: 354 loop : -3.35 (0.17), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 648 TYR 0.018 0.001 TYR B1903 PHE 0.009 0.001 PHE B 187 TRP 0.014 0.001 TRP B1934 HIS 0.003 0.001 HIS B1817 Details of bonding type rmsd covalent geometry : bond 0.00304 (11436) covalent geometry : angle 0.65872 (15490) SS BOND : bond 0.00655 ( 6) SS BOND : angle 1.62114 ( 12) hydrogen bonds : bond 0.03109 ( 150) hydrogen bonds : angle 5.93344 ( 384) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2486.27 seconds wall clock time: 43 minutes 31.50 seconds (2611.50 seconds total)