Starting phenix.real_space_refine on Tue Jul 29 11:45:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kvf_23049/07_2025/7kvf_23049.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kvf_23049/07_2025/7kvf_23049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kvf_23049/07_2025/7kvf_23049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kvf_23049/07_2025/7kvf_23049.map" model { file = "/net/cci-nas-00/data/ceres_data/7kvf_23049/07_2025/7kvf_23049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kvf_23049/07_2025/7kvf_23049.cif" } resolution = 3.6 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= 0.047 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: 6.92, per 1000 atoms: 0.62 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: 2.58 Conformation dependent library (CDL) restraints added in 1.6 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: 1.42 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: 4.40 Time building geometry restraints manager: 3.16 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 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: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 29.830 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: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 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 185 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 178 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 343 MET cc_start: -0.0768 (tpt) cc_final: -0.2784 (tmm) REVERT: B 491 LEU cc_start: 0.5908 (mt) cc_final: 0.5376 (mt) REVERT: B 613 LEU cc_start: 0.8120 (tp) cc_final: 0.7800 (tt) REVERT: B 619 ARG cc_start: 0.8250 (ptt90) cc_final: 0.7877 (tpp-160) outliers start: 7 outliers final: 2 residues processed: 184 average time/residue: 0.2720 time to fit residues: 70.0238 Evaluate side-chains 122 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 120 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1750 GLU Chi-restraints excluded: chain B residue 2061 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN ** B 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 GLN B 134 HIS B 182 GLN B 222 HIS B 307 ASN B 315 GLN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 HIS B 556 ASN B 562 ASN B 583 HIS B 609 HIS B 639 ASN ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1643 HIS B1645 HIS B1670 ASN B1713 HIS ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1828 GLN B1830 GLN B2002 ASN B2031 GLN B2046 ASN B2093 GLN B2128 HIS B2162 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.078952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.060589 restraints weight = 61284.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.061982 restraints weight = 44930.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.062572 restraints weight = 36319.681| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 11442 Z= 0.204 Angle : 0.755 10.709 15502 Z= 0.390 Chirality : 0.047 0.200 1627 Planarity : 0.006 0.093 1999 Dihedral : 6.532 44.826 1515 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.21 % Favored : 86.79 % Rotamer: Outliers : 2.86 % Allowed : 14.78 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -5.11 (0.18), residues: 1370 helix: -3.29 (0.50), residues: 59 sheet: -2.89 (0.25), residues: 362 loop : -3.89 (0.16), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B2064 HIS 0.006 0.001 HIS B 242 PHE 0.013 0.002 PHE B1872 TYR 0.013 0.002 TYR B1903 ARG 0.007 0.001 ARG B2072 Details of bonding type rmsd hydrogen bonds : bond 0.04452 ( 150) hydrogen bonds : angle 8.38247 ( 384) SS BOND : bond 0.00880 ( 6) SS BOND : angle 1.81736 ( 12) covalent geometry : bond 0.00443 (11436) covalent geometry : angle 0.75405 (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 162 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 270 MET cc_start: 0.7689 (ppp) cc_final: 0.7293 (ppp) REVERT: B 343 MET cc_start: 0.0038 (tpt) cc_final: -0.1057 (tpt) REVERT: B 491 LEU cc_start: 0.7689 (mt) cc_final: 0.7010 (mt) REVERT: B 592 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8455 (pm20) REVERT: B 605 TYR cc_start: 0.8991 (t80) cc_final: 0.8755 (t80) REVERT: B 613 LEU cc_start: 0.8771 (tp) cc_final: 0.8410 (tt) REVERT: B 1700 TRP cc_start: 0.7889 (OUTLIER) cc_final: 0.7528 (m-90) REVERT: B 1716 LEU cc_start: 0.8964 (mt) cc_final: 0.8509 (mp) REVERT: B 1868 MET cc_start: 0.4569 (mtt) cc_final: 0.4038 (mtt) REVERT: B 1881 MET cc_start: 0.8709 (ppp) cc_final: 0.8126 (ppp) REVERT: B 2120 MET cc_start: 0.6745 (ptp) cc_final: 0.6350 (pmm) outliers start: 35 outliers final: 17 residues processed: 153 average time/residue: 0.2499 time to fit residues: 55.2070 Evaluate side-chains 120 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 229 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 505 ARG Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 1654 GLU Chi-restraints excluded: chain B residue 1700 TRP Chi-restraints excluded: chain B residue 1814 VAL Chi-restraints excluded: chain B residue 1843 THR Chi-restraints excluded: chain B residue 1876 ASP Chi-restraints excluded: chain B residue 1901 LEU Chi-restraints excluded: chain B residue 1920 TRP Chi-restraints excluded: chain B residue 2095 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 8 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 69 optimal weight: 0.0020 chunk 85 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 overall best weight: 3.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 HIS B 244 ASN ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN ** B 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1819 GLN B1863 ASN B1986 ASN B2031 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.074351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.056984 restraints weight = 65614.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.058264 restraints weight = 47284.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.059173 restraints weight = 37991.584| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 11442 Z= 0.268 Angle : 0.811 10.391 15502 Z= 0.423 Chirality : 0.048 0.176 1627 Planarity : 0.006 0.098 1999 Dihedral : 6.540 28.511 1508 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 15.62 % Favored : 84.31 % Rotamer: Outliers : 3.51 % Allowed : 19.76 % 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 (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: -4.98 (0.19), residues: 1370 helix: -3.14 (0.49), residues: 72 sheet: -2.90 (0.24), residues: 392 loop : -3.75 (0.17), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B1700 HIS 0.008 0.001 HIS B 134 PHE 0.017 0.002 PHE B1748 TYR 0.016 0.002 TYR B2139 ARG 0.006 0.001 ARG B1606 Details of bonding type rmsd hydrogen bonds : bond 0.04797 ( 150) hydrogen bonds : angle 8.40962 ( 384) SS BOND : bond 0.00561 ( 6) SS BOND : angle 1.56622 ( 12) covalent geometry : bond 0.00578 (11436) covalent geometry : angle 0.81053 (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 144 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 101 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 TYR cc_start: 0.7744 (OUTLIER) cc_final: 0.5638 (p90) REVERT: B 289 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8824 (mm-40) REVERT: B 343 MET cc_start: -0.0076 (tpt) cc_final: -0.1311 (tpt) REVERT: B 357 ASN cc_start: 0.7131 (OUTLIER) cc_final: 0.6931 (p0) REVERT: B 491 LEU cc_start: 0.7958 (mt) cc_final: 0.7258 (mt) REVERT: B 523 PHE cc_start: 0.8986 (m-80) cc_final: 0.8749 (m-80) REVERT: B 590 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8338 (pm20) REVERT: B 613 LEU cc_start: 0.8671 (tp) cc_final: 0.8240 (tt) REVERT: B 1700 TRP cc_start: 0.8075 (OUTLIER) cc_final: 0.7479 (m-90) REVERT: B 1738 MET cc_start: 0.8428 (ttm) cc_final: 0.8226 (ttt) REVERT: B 1761 ARG cc_start: 0.8739 (mmm160) cc_final: 0.8389 (mmp80) REVERT: B 1793 TYR cc_start: 0.7972 (m-80) cc_final: 0.7767 (m-80) REVERT: B 1812 HIS cc_start: 0.8794 (OUTLIER) cc_final: 0.8254 (m90) REVERT: B 1868 MET cc_start: 0.4625 (mtt) cc_final: 0.4003 (mtt) outliers start: 43 outliers final: 28 residues processed: 135 average time/residue: 0.2643 time to fit residues: 52.2488 Evaluate side-chains 126 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 90 ARG 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 224 HIS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 1654 GLU Chi-restraints excluded: chain B residue 1657 THR Chi-restraints excluded: chain B residue 1700 TRP Chi-restraints excluded: chain B residue 1787 LEU Chi-restraints excluded: chain B residue 1812 HIS Chi-restraints excluded: chain B residue 1814 VAL Chi-restraints excluded: chain B residue 1843 THR Chi-restraints excluded: chain B residue 1901 LEU Chi-restraints excluded: chain B residue 1935 ILE Chi-restraints excluded: chain B residue 1956 TYR Chi-restraints excluded: chain B residue 1988 MET Chi-restraints excluded: chain B residue 2095 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 0 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 75 optimal weight: 0.3980 chunk 87 optimal weight: 10.0000 chunk 34 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 HIS B 556 ASN B 597 HIS B 699 GLN ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.076878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.059117 restraints weight = 64024.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.060482 restraints weight = 45990.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.061108 restraints weight = 36800.955| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11442 Z= 0.149 Angle : 0.703 11.265 15502 Z= 0.355 Chirality : 0.046 0.175 1627 Planarity : 0.005 0.093 1999 Dihedral : 5.975 26.649 1508 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.92 % Favored : 87.08 % Rotamer: Outliers : 3.18 % Allowed : 21.88 % 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 (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: -4.48 (0.20), residues: 1370 helix: -3.19 (0.54), residues: 66 sheet: -2.41 (0.25), residues: 375 loop : -3.44 (0.17), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1700 HIS 0.004 0.001 HIS B 134 PHE 0.013 0.001 PHE B1979 TYR 0.013 0.001 TYR B 17 ARG 0.004 0.000 ARG B 90 Details of bonding type rmsd hydrogen bonds : bond 0.03506 ( 150) hydrogen bonds : angle 7.47491 ( 384) SS BOND : bond 0.00284 ( 6) SS BOND : angle 1.44633 ( 12) covalent geometry : bond 0.00326 (11436) covalent geometry : angle 0.70181 (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 146 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 107 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 289 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8846 (mm-40) REVERT: B 292 MET cc_start: 0.8139 (ppp) cc_final: 0.7900 (ppp) REVERT: B 343 MET cc_start: 0.0246 (tpt) cc_final: -0.1009 (tpt) REVERT: B 357 ASN cc_start: 0.7029 (OUTLIER) cc_final: 0.6789 (p0) REVERT: B 420 HIS cc_start: 0.6584 (OUTLIER) cc_final: 0.6273 (m170) REVERT: B 491 LEU cc_start: 0.7861 (mt) cc_final: 0.7264 (mt) REVERT: B 523 PHE cc_start: 0.9030 (m-80) cc_final: 0.8742 (m-80) REVERT: B 613 LEU cc_start: 0.8520 (tp) cc_final: 0.8154 (tt) REVERT: B 1700 TRP cc_start: 0.7895 (OUTLIER) cc_final: 0.7364 (m-90) REVERT: B 1716 LEU cc_start: 0.9098 (mt) cc_final: 0.8883 (mp) REVERT: B 1793 TYR cc_start: 0.7793 (m-80) cc_final: 0.7565 (m-80) REVERT: B 1868 MET cc_start: 0.4409 (mtt) cc_final: 0.4121 (mtt) REVERT: B 1883 MET cc_start: 0.8876 (mmm) cc_final: 0.8577 (mpp) REVERT: B 1939 MET cc_start: 0.8888 (pmm) cc_final: 0.8685 (pmm) REVERT: B 1973 GLN cc_start: 0.9102 (mt0) cc_final: 0.8811 (mp10) outliers start: 39 outliers final: 16 residues processed: 138 average time/residue: 0.2826 time to fit residues: 56.2712 Evaluate side-chains 119 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 1654 GLU Chi-restraints excluded: chain B residue 1700 TRP Chi-restraints excluded: chain B residue 1787 LEU Chi-restraints excluded: chain B residue 1901 LEU Chi-restraints excluded: chain B residue 1956 TYR 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: 1.9990 chunk 76 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN ** B 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.075038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.058526 restraints weight = 63934.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.059736 restraints weight = 46766.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.060313 restraints weight = 37747.609| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11442 Z= 0.221 Angle : 0.751 11.608 15502 Z= 0.383 Chirality : 0.047 0.217 1627 Planarity : 0.005 0.098 1999 Dihedral : 6.142 26.980 1508 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 15.40 % Favored : 84.53 % Rotamer: Outliers : 3.92 % Allowed : 21.96 % 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 (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: -4.42 (0.20), residues: 1370 helix: -3.39 (0.47), residues: 66 sheet: -2.44 (0.25), residues: 396 loop : -3.33 (0.18), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B1700 HIS 0.007 0.001 HIS B 134 PHE 0.014 0.002 PHE B 538 TYR 0.013 0.002 TYR B 209 ARG 0.005 0.001 ARG B 90 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 150) hydrogen bonds : angle 7.66428 ( 384) SS BOND : bond 0.00506 ( 6) SS BOND : angle 1.84419 ( 12) covalent geometry : bond 0.00479 (11436) covalent geometry : angle 0.75001 (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 140 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 92 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 289 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8831 (mm-40) REVERT: B 343 MET cc_start: 0.0547 (tpt) cc_final: -0.0608 (tpt) REVERT: B 491 LEU cc_start: 0.8030 (mt) cc_final: 0.7423 (mt) REVERT: B 523 PHE cc_start: 0.9055 (m-80) cc_final: 0.8765 (m-80) REVERT: B 590 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8124 (pm20) REVERT: B 613 LEU cc_start: 0.8733 (tp) cc_final: 0.8330 (tt) REVERT: B 1700 TRP cc_start: 0.7880 (OUTLIER) cc_final: 0.7338 (m-90) REVERT: B 1738 MET cc_start: 0.8185 (ttt) cc_final: 0.7915 (ttt) REVERT: B 1792 MET cc_start: 0.8737 (mtm) cc_final: 0.8467 (mtp) REVERT: B 1793 TYR cc_start: 0.7967 (m-80) cc_final: 0.7720 (m-80) REVERT: B 1868 MET cc_start: 0.4148 (mtt) cc_final: 0.3872 (mtt) REVERT: B 1883 MET cc_start: 0.8868 (mmm) cc_final: 0.8486 (mpp) REVERT: B 1956 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.7383 (p90) outliers start: 48 outliers final: 32 residues processed: 135 average time/residue: 0.2104 time to fit residues: 42.6948 Evaluate side-chains 127 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 90 ARG 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 229 LEU Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 494 LEU 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 579 THR Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 1654 GLU Chi-restraints excluded: chain B residue 1657 THR Chi-restraints excluded: chain B residue 1700 TRP Chi-restraints excluded: chain B residue 1787 LEU Chi-restraints excluded: chain B residue 1814 VAL Chi-restraints excluded: chain B residue 1849 SER Chi-restraints excluded: chain B residue 1901 LEU Chi-restraints excluded: chain B residue 1956 TYR Chi-restraints excluded: chain B residue 2013 ILE Chi-restraints excluded: chain B residue 2095 LEU Chi-restraints excluded: chain B residue 2193 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 122 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 121 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 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 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2165 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 = 0.3976 r_free = 0.3976 target = 0.072431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.056257 restraints weight = 65890.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.057407 restraints weight = 48814.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.057973 restraints weight = 39243.818| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.5493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 11442 Z= 0.288 Angle : 0.826 12.750 15502 Z= 0.426 Chirality : 0.048 0.194 1627 Planarity : 0.006 0.101 1999 Dihedral : 6.586 30.141 1508 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 24.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 15.91 % Favored : 84.01 % Rotamer: Outliers : 4.65 % Allowed : 21.71 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.47 (0.20), residues: 1370 helix: -3.49 (0.44), residues: 66 sheet: -2.42 (0.27), residues: 355 loop : -3.39 (0.17), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B1563 HIS 0.009 0.002 HIS B 228 PHE 0.015 0.002 PHE B2004 TYR 0.015 0.002 TYR B2021 ARG 0.006 0.001 ARG B 90 Details of bonding type rmsd hydrogen bonds : bond 0.04539 ( 150) hydrogen bonds : angle 8.09357 ( 384) SS BOND : bond 0.00519 ( 6) SS BOND : angle 1.72716 ( 12) covalent geometry : bond 0.00619 (11436) covalent geometry : angle 0.82488 (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 146 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 89 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 TYR cc_start: 0.7944 (OUTLIER) cc_final: 0.5659 (p90) REVERT: B 163 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9067 (pp) REVERT: B 289 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8476 (mp10) REVERT: B 343 MET cc_start: 0.0736 (tpt) cc_final: -0.0615 (tpt) REVERT: B 590 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8235 (pm20) REVERT: B 613 LEU cc_start: 0.8686 (tp) cc_final: 0.8327 (tt) REVERT: B 618 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7592 (mtt) REVERT: B 1700 TRP cc_start: 0.7979 (OUTLIER) cc_final: 0.7199 (m-90) REVERT: B 1738 MET cc_start: 0.8154 (ttt) cc_final: 0.7711 (ttt) REVERT: B 1793 TYR cc_start: 0.8160 (m-80) cc_final: 0.7920 (m-80) REVERT: B 1868 MET cc_start: 0.3946 (mtt) cc_final: 0.3613 (mtt) REVERT: B 1883 MET cc_start: 0.8922 (mmm) cc_final: 0.8471 (mpp) REVERT: B 1956 TYR cc_start: 0.8394 (OUTLIER) cc_final: 0.7537 (p90) outliers start: 57 outliers final: 35 residues processed: 137 average time/residue: 0.2105 time to fit residues: 43.3724 Evaluate side-chains 127 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 85 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 163 LEU 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 229 LEU Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 495 LEU 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 618 MET Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 1654 GLU Chi-restraints excluded: chain B residue 1657 THR Chi-restraints excluded: chain B residue 1700 TRP Chi-restraints excluded: chain B residue 1744 LEU Chi-restraints excluded: chain B residue 1787 LEU Chi-restraints excluded: chain B residue 1798 VAL Chi-restraints excluded: chain B residue 1814 VAL Chi-restraints excluded: chain B residue 1849 SER Chi-restraints excluded: chain B residue 1935 ILE Chi-restraints excluded: chain B residue 1939 MET Chi-restraints excluded: chain B residue 1956 TYR Chi-restraints excluded: chain B residue 2013 ILE Chi-restraints excluded: chain B residue 2095 LEU Chi-restraints excluded: chain B residue 2171 ARG Chi-restraints excluded: chain B residue 2193 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 94 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 3 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 HIS ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4027 r_free = 0.4027 target = 0.074612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.058284 restraints weight = 64171.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.059689 restraints weight = 45777.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.060648 restraints weight = 36410.780| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.5505 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= 0.161 Angle : 0.727 11.312 15502 Z= 0.367 Chirality : 0.047 0.177 1627 Planarity : 0.005 0.094 1999 Dihedral : 6.075 26.882 1508 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.80 % Favored : 86.20 % Rotamer: Outliers : 3.02 % Allowed : 24.82 % Favored : 72.16 % 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: -4.19 (0.20), residues: 1370 helix: -3.36 (0.48), residues: 66 sheet: -2.23 (0.27), residues: 352 loop : -3.18 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B1700 HIS 0.005 0.001 HIS B 134 PHE 0.009 0.001 PHE B 105 TYR 0.012 0.001 TYR B 209 ARG 0.004 0.000 ARG B 90 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 150) hydrogen bonds : angle 7.40754 ( 384) SS BOND : bond 0.00385 ( 6) SS BOND : angle 1.49264 ( 12) covalent geometry : bond 0.00353 (11436) covalent geometry : angle 0.72627 (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 129 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 92 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 203 MET cc_start: 0.7874 (ppp) cc_final: 0.7301 (ppp) REVERT: B 289 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.8796 (mm-40) REVERT: B 343 MET cc_start: 0.0027 (tpt) cc_final: -0.1443 (tpt) REVERT: B 491 LEU cc_start: 0.8232 (mt) cc_final: 0.7715 (mt) REVERT: B 558 MET cc_start: 0.7727 (mpp) cc_final: 0.7484 (mpp) REVERT: B 613 LEU cc_start: 0.8775 (tp) cc_final: 0.8513 (tp) REVERT: B 1691 GLU cc_start: 0.6524 (OUTLIER) cc_final: 0.5316 (mt-10) REVERT: B 1700 TRP cc_start: 0.7791 (OUTLIER) cc_final: 0.7133 (m-90) REVERT: B 1703 TYR cc_start: 0.6114 (p90) cc_final: 0.5838 (p90) REVERT: B 1716 LEU cc_start: 0.9174 (mt) cc_final: 0.8888 (mp) REVERT: B 1746 MET cc_start: 0.7534 (tmm) cc_final: 0.7299 (tmm) REVERT: B 1793 TYR cc_start: 0.7919 (m-80) cc_final: 0.7647 (m-80) REVERT: B 1883 MET cc_start: 0.8949 (mmm) cc_final: 0.8631 (mpp) REVERT: B 1939 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8566 (pmm) REVERT: B 1956 TYR cc_start: 0.8388 (OUTLIER) cc_final: 0.7357 (p90) outliers start: 37 outliers final: 25 residues processed: 126 average time/residue: 0.2093 time to fit residues: 40.5118 Evaluate side-chains 117 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 ARG 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 256 SER Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 1550 ASN Chi-restraints excluded: chain B residue 1654 GLU Chi-restraints excluded: chain B residue 1657 THR Chi-restraints excluded: chain B residue 1691 GLU Chi-restraints excluded: chain B residue 1700 TRP Chi-restraints excluded: chain B residue 1787 LEU Chi-restraints excluded: chain B residue 1849 SER Chi-restraints excluded: chain B residue 1939 MET Chi-restraints excluded: chain B residue 1956 TYR Chi-restraints excluded: chain B residue 2013 ILE Chi-restraints excluded: chain B residue 2171 ARG Chi-restraints excluded: chain B residue 2193 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 82 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.073454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.057535 restraints weight = 65449.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.058756 restraints weight = 47036.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.059646 restraints weight = 37739.497| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.5731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11442 Z= 0.202 Angle : 0.757 11.794 15502 Z= 0.383 Chirality : 0.047 0.190 1627 Planarity : 0.005 0.097 1999 Dihedral : 6.107 25.595 1508 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.40 % Favored : 84.60 % Rotamer: Outliers : 3.35 % Allowed : 24.57 % Favored : 72.08 % 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: -4.16 (0.20), residues: 1370 helix: -3.35 (0.48), residues: 66 sheet: -2.21 (0.27), residues: 350 loop : -3.16 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B1700 HIS 0.007 0.001 HIS B 597 PHE 0.011 0.001 PHE B2004 TYR 0.011 0.002 TYR B2139 ARG 0.005 0.001 ARG B 90 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 150) hydrogen bonds : angle 7.52848 ( 384) SS BOND : bond 0.00439 ( 6) SS BOND : angle 1.42333 ( 12) covalent geometry : bond 0.00442 (11436) covalent geometry : angle 0.75632 (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 127 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 86 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 203 MET cc_start: 0.7877 (ppp) cc_final: 0.7443 (ppp) REVERT: B 289 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8778 (mm-40) REVERT: B 343 MET cc_start: -0.0049 (tpt) cc_final: -0.1500 (tpt) REVERT: B 491 LEU cc_start: 0.8042 (mt) cc_final: 0.7484 (mt) REVERT: B 558 MET cc_start: 0.7807 (mpp) cc_final: 0.7528 (mpp) REVERT: B 613 LEU cc_start: 0.8807 (tp) cc_final: 0.8424 (tt) REVERT: B 618 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7405 (mtt) REVERT: B 638 MET cc_start: 0.8318 (ppp) cc_final: 0.8015 (ppp) REVERT: B 1691 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.5224 (mp0) REVERT: B 1700 TRP cc_start: 0.7789 (OUTLIER) cc_final: 0.7129 (m-90) REVERT: B 1793 TYR cc_start: 0.7908 (m-80) cc_final: 0.7620 (m-80) REVERT: B 1883 MET cc_start: 0.8926 (mmm) cc_final: 0.8661 (mpp) REVERT: B 1939 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8576 (pmm) REVERT: B 1956 TYR cc_start: 0.8420 (OUTLIER) cc_final: 0.7360 (p90) outliers start: 41 outliers final: 30 residues processed: 123 average time/residue: 0.2153 time to fit residues: 40.3355 Evaluate side-chains 121 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 85 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 ARG 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 252 HIS Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 1550 ASN Chi-restraints excluded: chain B residue 1654 GLU Chi-restraints excluded: chain B residue 1657 THR Chi-restraints excluded: chain B residue 1691 GLU Chi-restraints excluded: chain B residue 1700 TRP Chi-restraints excluded: chain B residue 1787 LEU Chi-restraints excluded: chain B residue 1814 VAL Chi-restraints excluded: chain B residue 1849 SER Chi-restraints excluded: chain B residue 1939 MET Chi-restraints excluded: chain B residue 1956 TYR Chi-restraints excluded: chain B residue 2013 ILE Chi-restraints excluded: chain B residue 2171 ARG Chi-restraints excluded: chain B residue 2193 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 104 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.073405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.057565 restraints weight = 64552.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.058813 restraints weight = 47516.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.059707 restraints weight = 37650.987| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.5883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11442 Z= 0.189 Angle : 0.757 11.598 15502 Z= 0.382 Chirality : 0.047 0.172 1627 Planarity : 0.005 0.096 1999 Dihedral : 6.089 25.542 1508 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.11 % Favored : 84.89 % Rotamer: Outliers : 3.84 % Allowed : 24.49 % Favored : 71.67 % 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: -4.14 (0.20), residues: 1370 helix: -3.36 (0.47), residues: 66 sheet: -2.25 (0.26), residues: 377 loop : -3.11 (0.18), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 457 HIS 0.006 0.001 HIS B 134 PHE 0.010 0.001 PHE B2004 TYR 0.012 0.002 TYR B 209 ARG 0.005 0.000 ARG B 90 Details of bonding type rmsd hydrogen bonds : bond 0.03747 ( 150) hydrogen bonds : angle 7.42812 ( 384) SS BOND : bond 0.00405 ( 6) SS BOND : angle 1.42718 ( 12) covalent geometry : bond 0.00413 (11436) covalent geometry : angle 0.75600 (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 135 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 88 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 203 MET cc_start: 0.7885 (ppp) cc_final: 0.7458 (ppp) REVERT: B 289 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8785 (mm-40) REVERT: B 343 MET cc_start: 0.0120 (tpt) cc_final: -0.1283 (tpt) REVERT: B 491 LEU cc_start: 0.8078 (mt) cc_final: 0.7510 (mt) REVERT: B 613 LEU cc_start: 0.8811 (tp) cc_final: 0.8536 (tt) REVERT: B 618 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7371 (mtt) REVERT: B 621 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6822 (tt0) REVERT: B 638 MET cc_start: 0.8408 (ppp) cc_final: 0.7728 (ppp) REVERT: B 1691 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.5228 (mp0) REVERT: B 1700 TRP cc_start: 0.7781 (OUTLIER) cc_final: 0.7089 (m-90) REVERT: B 1703 TYR cc_start: 0.5935 (p90) cc_final: 0.5713 (p90) REVERT: B 1792 MET cc_start: 0.8764 (mtm) cc_final: 0.8552 (mtp) REVERT: B 1793 TYR cc_start: 0.7802 (m-80) cc_final: 0.7496 (m-80) REVERT: B 1939 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8564 (pmm) REVERT: B 1956 TYR cc_start: 0.8447 (OUTLIER) cc_final: 0.7430 (p90) outliers start: 47 outliers final: 34 residues processed: 129 average time/residue: 0.2059 time to fit residues: 40.5335 Evaluate side-chains 126 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 85 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 90 ARG 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 256 SER Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 1550 ASN Chi-restraints excluded: chain B residue 1654 GLU Chi-restraints excluded: chain B residue 1657 THR Chi-restraints excluded: chain B residue 1691 GLU Chi-restraints excluded: chain B residue 1700 TRP Chi-restraints excluded: chain B residue 1738 MET Chi-restraints excluded: chain B residue 1787 LEU Chi-restraints excluded: chain B residue 1798 VAL Chi-restraints excluded: chain B residue 1814 VAL Chi-restraints excluded: chain B residue 1849 SER Chi-restraints excluded: chain B residue 1935 ILE Chi-restraints excluded: chain B residue 1939 MET Chi-restraints excluded: chain B residue 1956 TYR Chi-restraints excluded: chain B residue 2013 ILE Chi-restraints excluded: chain B residue 2171 ARG Chi-restraints excluded: chain B residue 2193 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 0.0000 chunk 10 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 110 optimal weight: 30.0000 chunk 104 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.075745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.059932 restraints weight = 64100.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.061195 restraints weight = 45318.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.062089 restraints weight = 35877.451| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.5952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11442 Z= 0.128 Angle : 0.728 11.531 15502 Z= 0.360 Chirality : 0.047 0.173 1627 Planarity : 0.005 0.091 1999 Dihedral : 5.679 25.486 1508 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.07 % Favored : 86.93 % Rotamer: Outliers : 2.61 % Allowed : 25.63 % Favored : 71.76 % 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: -3.95 (0.21), residues: 1370 helix: -3.38 (0.45), residues: 73 sheet: -2.13 (0.27), residues: 368 loop : -2.95 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 333 HIS 0.004 0.001 HIS B 134 PHE 0.017 0.001 PHE B 576 TYR 0.011 0.001 TYR B 363 ARG 0.003 0.000 ARG B 90 Details of bonding type rmsd hydrogen bonds : bond 0.03300 ( 150) hydrogen bonds : angle 6.96483 ( 384) SS BOND : bond 0.00341 ( 6) SS BOND : angle 1.25786 ( 12) covalent geometry : bond 0.00288 (11436) covalent geometry : angle 0.72782 (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 124 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 203 MET cc_start: 0.7830 (ppp) cc_final: 0.7462 (ppp) REVERT: B 289 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8858 (mm-40) REVERT: B 343 MET cc_start: -0.0086 (tpt) cc_final: -0.1536 (tpt) REVERT: B 491 LEU cc_start: 0.7951 (mt) cc_final: 0.7460 (mt) REVERT: B 613 LEU cc_start: 0.8810 (tp) cc_final: 0.8564 (tp) REVERT: B 627 MET cc_start: 0.6170 (ptt) cc_final: 0.5769 (ptt) REVERT: B 638 MET cc_start: 0.8454 (ppp) cc_final: 0.7666 (ppp) REVERT: B 1703 TYR cc_start: 0.5959 (p90) cc_final: 0.5696 (p90) REVERT: B 1716 LEU cc_start: 0.9122 (mt) cc_final: 0.8869 (mp) REVERT: B 1792 MET cc_start: 0.8708 (mtm) cc_final: 0.8470 (mtp) REVERT: B 1793 TYR cc_start: 0.7589 (m-80) cc_final: 0.7256 (m-80) REVERT: B 1844 LEU cc_start: 0.8418 (mt) cc_final: 0.8218 (mm) REVERT: B 1883 MET cc_start: 0.9010 (mmm) cc_final: 0.8701 (mpp) REVERT: B 1939 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8545 (pmm) REVERT: B 1956 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.7347 (p90) outliers start: 32 outliers final: 25 residues processed: 119 average time/residue: 0.2158 time to fit residues: 38.8562 Evaluate side-chains 116 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 256 SER Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 1657 THR Chi-restraints excluded: chain B residue 1738 MET Chi-restraints excluded: chain B residue 1787 LEU Chi-restraints excluded: chain B residue 1837 LEU Chi-restraints excluded: chain B residue 1849 SER Chi-restraints excluded: chain B residue 1939 MET Chi-restraints excluded: chain B residue 1956 TYR Chi-restraints excluded: chain B residue 2013 ILE Chi-restraints excluded: chain B residue 2171 ARG Chi-restraints excluded: chain B residue 2193 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 100 optimal weight: 0.0570 chunk 102 optimal weight: 0.9990 chunk 76 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 26 optimal weight: 0.0170 chunk 136 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 86 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 699 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.078514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.062550 restraints weight = 64452.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.063995 restraints weight = 45222.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.065014 restraints weight = 35500.411| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.6059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11442 Z= 0.113 Angle : 0.722 11.516 15502 Z= 0.353 Chirality : 0.047 0.172 1627 Planarity : 0.005 0.086 1999 Dihedral : 5.295 27.095 1508 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.97 % Favored : 88.03 % Rotamer: Outliers : 1.96 % Allowed : 26.53 % Favored : 71.51 % 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: -3.55 (0.21), residues: 1370 helix: -3.25 (0.48), residues: 67 sheet: -1.69 (0.28), residues: 345 loop : -2.74 (0.19), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 333 HIS 0.002 0.001 HIS B 85 PHE 0.009 0.001 PHE B 576 TYR 0.024 0.001 TYR B2021 ARG 0.012 0.000 ARG B1687 Details of bonding type rmsd hydrogen bonds : bond 0.03104 ( 150) hydrogen bonds : angle 6.51534 ( 384) SS BOND : bond 0.00317 ( 6) SS BOND : angle 1.09469 ( 12) covalent geometry : bond 0.00256 (11436) covalent geometry : angle 0.72176 (15490) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3975.28 seconds wall clock time: 71 minutes 54.89 seconds (4314.89 seconds total)