Starting phenix.real_space_refine on Wed Sep 25 21:46:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kvf_23049/09_2024/7kvf_23049.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kvf_23049/09_2024/7kvf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kvf_23049/09_2024/7kvf_23049.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kvf_23049/09_2024/7kvf_23049.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kvf_23049/09_2024/7kvf_23049.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kvf_23049/09_2024/7kvf_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-5461/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: 5.95, per 1000 atoms: 0.53 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: 2.13 Conformation dependent library (CDL) restraints added in 1.3 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: 1.49 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: 3.84 Time building geometry restraints manager: 2.59 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 25.180 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.440 ------------------------------------------------------------------------------- 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 11436 Z= 0.319 Angle : 0.817 12.087 15490 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 *********************** 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 fitting. rotamer outliers: 7 poor density : 178 time to evaluate : 1.220 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: 0.2545 time to fit residues: 65.0848 Evaluate side-chains 122 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 120 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 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 11436 Z= 0.292 Angle : 0.754 10.709 15490 Z= 0.389 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 *********************** 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 fitting. rotamer outliers: 35 poor density : 127 time to evaluate : 1.329 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: 0.7284 (ppp) cc_final: 0.6959 (ppp) REVERT: B 343 MET cc_start: -0.0709 (tpt) cc_final: -0.1907 (tpt) REVERT: B 443 MET cc_start: 0.1096 (ptp) cc_final: 0.0859 (ptp) REVERT: B 491 LEU cc_start: 0.6184 (mt) cc_final: 0.5747 (mt) REVERT: B 613 LEU cc_start: 0.8249 (tp) cc_final: 0.7982 (tt) REVERT: B 1700 TRP cc_start: 0.7989 (OUTLIER) cc_final: 0.7639 (m-90) REVERT: B 1716 LEU cc_start: 0.8031 (mt) cc_final: 0.7654 (mp) REVERT: B 1868 MET cc_start: 0.5536 (mtt) cc_final: 0.4910 (mtt) outliers start: 35 outliers final: 17 residues processed: 153 average time/residue: 0.2610 time to fit residues: 57.7623 Evaluate side-chains 119 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 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 69 optimal weight: 0.0020 chunk 38 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 overall best weight: 2.3594 ------------------------------------------------------------------------------- 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 242 HIS B 244 ASN ** B 350 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** B1819 GLN B1986 ASN B2031 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11436 Z= 0.259 Angle : 0.721 10.990 15490 Z= 0.369 Chirality : 0.046 0.176 1627 Planarity : 0.005 0.093 1999 Dihedral : 6.013 28.052 1508 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.09 % Favored : 85.91 % Rotamer: Outliers : 3.27 % Allowed : 18.53 % Favored : 78.20 % 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: -4.85 (0.19), residues: 1370 helix: -3.20 (0.50), residues: 66 sheet: -2.72 (0.24), residues: 394 loop : -3.70 (0.17), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B1700 HIS 0.005 0.001 HIS B 134 PHE 0.021 0.001 PHE B1748 TYR 0.014 0.002 TYR B 209 ARG 0.003 0.001 ARG B1799 *********************** 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 143 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 103 time to evaluate : 1.185 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 343 MET cc_start: -0.1102 (tpt) cc_final: -0.2402 (tpt) REVERT: B 357 ASN cc_start: 0.6762 (OUTLIER) cc_final: 0.6365 (p0) REVERT: B 491 LEU cc_start: 0.6184 (mt) cc_final: 0.5748 (mt) REVERT: B 613 LEU cc_start: 0.8257 (tp) cc_final: 0.7925 (tt) REVERT: B 1700 TRP cc_start: 0.7910 (OUTLIER) cc_final: 0.7470 (m-90) REVERT: B 1716 LEU cc_start: 0.8082 (mt) cc_final: 0.7797 (mp) REVERT: B 1868 MET cc_start: 0.5566 (mtt) cc_final: 0.4998 (mtt) REVERT: B 2184 ILE cc_start: 0.6764 (mm) cc_final: 0.6541 (mm) outliers start: 40 outliers final: 22 residues processed: 135 average time/residue: 0.2211 time to fit residues: 44.0981 Evaluate side-chains 115 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 91 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 265 SER 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 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 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 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 123 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 64 optimal weight: 0.0270 chunk 13 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 125 optimal weight: 0.6980 chunk 132 optimal weight: 0.4980 chunk 65 optimal weight: 0.4980 chunk 118 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 GLN ** 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 379 HIS B 556 ASN ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1570 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11436 Z= 0.166 Angle : 0.674 11.687 15490 Z= 0.336 Chirality : 0.046 0.211 1627 Planarity : 0.005 0.088 1999 Dihedral : 5.504 26.134 1508 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.61 % Favored : 88.39 % Rotamer: Outliers : 1.88 % Allowed : 20.00 % Favored : 78.12 % 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: -4.39 (0.20), residues: 1370 helix: -3.50 (0.49), residues: 59 sheet: -2.28 (0.26), residues: 385 loop : -3.38 (0.17), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1700 HIS 0.004 0.001 HIS B 597 PHE 0.012 0.001 PHE B 462 TYR 0.012 0.001 TYR B 477 ARG 0.004 0.000 ARG B 90 *********************** 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 142 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 1.146 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 251 ASN cc_start: 0.8338 (t0) cc_final: 0.7892 (t0) REVERT: B 292 MET cc_start: 0.7350 (ppp) cc_final: 0.7083 (ppp) REVERT: B 343 MET cc_start: -0.1024 (tpt) cc_final: -0.2334 (tpt) REVERT: B 491 LEU cc_start: 0.5917 (mt) cc_final: 0.5530 (mt) REVERT: B 613 LEU cc_start: 0.8161 (tp) cc_final: 0.7882 (tt) REVERT: B 1716 LEU cc_start: 0.7951 (mt) cc_final: 0.7565 (mp) REVERT: B 1868 MET cc_start: 0.5245 (mtt) cc_final: 0.4813 (mtt) outliers start: 23 outliers final: 12 residues processed: 138 average time/residue: 0.2233 time to fit residues: 45.1553 Evaluate side-chains 112 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 ARG 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 256 SER Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 1787 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 110 optimal weight: 0.0970 chunk 75 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 98 optimal weight: 0.0050 chunk 54 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 GLN ** 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 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2046 ASN ** B2132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11436 Z= 0.216 Angle : 0.682 11.619 15490 Z= 0.345 Chirality : 0.045 0.169 1627 Planarity : 0.005 0.091 1999 Dihedral : 5.473 26.611 1508 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.43 % Favored : 86.57 % Rotamer: Outliers : 2.86 % Allowed : 20.65 % Favored : 76.49 % 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: -4.27 (0.20), residues: 1370 helix: -3.17 (0.49), residues: 73 sheet: -2.26 (0.26), residues: 377 loop : -3.27 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1563 HIS 0.004 0.001 HIS B 134 PHE 0.012 0.001 PHE B1748 TYR 0.024 0.001 TYR B2021 ARG 0.007 0.000 ARG B 90 *********************** 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 137 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 102 time to evaluate : 1.350 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 343 MET cc_start: -0.1213 (tpt) cc_final: -0.2479 (tpt) REVERT: B 491 LEU cc_start: 0.6142 (mt) cc_final: 0.5743 (mt) REVERT: B 613 LEU cc_start: 0.8150 (tp) cc_final: 0.7844 (tt) REVERT: B 618 MET cc_start: 0.7619 (mtt) cc_final: 0.7405 (mtt) REVERT: B 1700 TRP cc_start: 0.7917 (OUTLIER) cc_final: 0.7507 (m-90) REVERT: B 1716 LEU cc_start: 0.8033 (mt) cc_final: 0.7667 (mp) REVERT: B 1868 MET cc_start: 0.5232 (mtt) cc_final: 0.4885 (mtt) REVERT: B 1881 MET cc_start: 0.7501 (ppp) cc_final: 0.7208 (ppp) outliers start: 35 outliers final: 22 residues processed: 132 average time/residue: 0.2304 time to fit residues: 44.7485 Evaluate side-chains 118 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 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 560 THR Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 678 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 1956 TYR 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 44 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 11 optimal weight: 0.0870 chunk 43 optimal weight: 20.0000 chunk 69 optimal weight: 7.9990 overall best weight: 3.5964 ------------------------------------------------------------------------------- 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 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 ** B 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1863 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 11436 Z= 0.360 Angle : 0.780 11.920 15490 Z= 0.403 Chirality : 0.047 0.240 1627 Planarity : 0.006 0.101 1999 Dihedral : 6.133 28.770 1508 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 21.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 14.96 % Favored : 84.96 % Rotamer: Outliers : 3.76 % Allowed : 21.55 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.35 (0.20), residues: 1370 helix: -3.24 (0.48), residues: 66 sheet: -2.34 (0.25), residues: 395 loop : -3.32 (0.18), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B1563 HIS 0.007 0.001 HIS B 134 PHE 0.014 0.002 PHE B1777 TYR 0.014 0.002 TYR B2139 ARG 0.009 0.001 ARG B 90 *********************** 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 134 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 88 time to evaluate : 1.390 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 343 MET cc_start: -0.0099 (tpt) cc_final: -0.1568 (tpt) REVERT: B 357 ASN cc_start: 0.6890 (OUTLIER) cc_final: 0.6532 (p0) REVERT: B 613 LEU cc_start: 0.8265 (tp) cc_final: 0.7914 (tt) REVERT: B 618 MET cc_start: 0.7598 (mtt) cc_final: 0.7388 (mtt) REVERT: B 1700 TRP cc_start: 0.8168 (OUTLIER) cc_final: 0.7556 (m-90) REVERT: B 1868 MET cc_start: 0.5228 (mtt) cc_final: 0.4759 (mtt) REVERT: B 1881 MET cc_start: 0.7626 (ppp) cc_final: 0.7424 (ppp) REVERT: B 1956 TYR cc_start: 0.7396 (OUTLIER) cc_final: 0.6448 (p90) outliers start: 46 outliers final: 34 residues processed: 124 average time/residue: 0.2337 time to fit residues: 42.4664 Evaluate side-chains 122 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 85 time to evaluate : 1.251 ------------------------------------------------------------------------------- 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 256 SER Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 284 THR 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 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 572 LEU Chi-restraints excluded: chain B residue 596 ILE 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 1849 SER Chi-restraints excluded: chain B residue 1920 TRP 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 2095 LEU 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 127 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 96 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 142 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** B 556 ASN ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11436 Z= 0.180 Angle : 0.686 10.831 15490 Z= 0.344 Chirality : 0.046 0.176 1627 Planarity : 0.005 0.092 1999 Dihedral : 5.563 26.335 1508 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.63 % Favored : 87.37 % Rotamer: Outliers : 2.45 % Allowed : 23.02 % Favored : 74.53 % 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: -4.10 (0.21), residues: 1370 helix: -2.95 (0.51), residues: 73 sheet: -2.14 (0.27), residues: 378 loop : -3.16 (0.18), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 333 HIS 0.003 0.001 HIS B 134 PHE 0.009 0.001 PHE B1979 TYR 0.013 0.001 TYR B 144 ARG 0.005 0.000 ARG B 90 *********************** 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 123 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 93 time to evaluate : 1.267 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 203 MET cc_start: 0.7263 (ppp) cc_final: 0.6820 (ppp) REVERT: B 343 MET cc_start: -0.0964 (tpt) cc_final: -0.2404 (tpt) REVERT: B 357 ASN cc_start: 0.6671 (OUTLIER) cc_final: 0.6245 (p0) REVERT: B 491 LEU cc_start: 0.6441 (mt) cc_final: 0.6115 (mt) REVERT: B 613 LEU cc_start: 0.8055 (tp) cc_final: 0.7783 (tt) REVERT: B 618 MET cc_start: 0.7446 (mtt) cc_final: 0.7174 (mtt) REVERT: B 1716 LEU cc_start: 0.7967 (mt) cc_final: 0.7736 (mp) REVERT: B 1868 MET cc_start: 0.5092 (mtt) cc_final: 0.4844 (mtt) REVERT: B 1956 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.6388 (p90) outliers start: 30 outliers final: 21 residues processed: 120 average time/residue: 0.2450 time to fit residues: 43.5675 Evaluate side-chains 111 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 88 time to evaluate : 1.339 ------------------------------------------------------------------------------- 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 357 ASN Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 560 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 678 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 1956 TYR 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 52 optimal weight: 5.9990 chunk 78 optimal weight: 0.0470 chunk 39 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 83 optimal weight: 0.0470 chunk 89 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 GLN ** 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 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11436 Z= 0.159 Angle : 0.669 11.159 15490 Z= 0.329 Chirality : 0.046 0.171 1627 Planarity : 0.005 0.087 1999 Dihedral : 5.110 25.224 1508 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 2.04 % Allowed : 24.24 % Favored : 73.71 % 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: -3.71 (0.21), residues: 1370 helix: -2.44 (0.61), residues: 59 sheet: -1.76 (0.28), residues: 364 loop : -2.96 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1834 HIS 0.003 0.000 HIS B 134 PHE 0.010 0.001 PHE B1979 TYR 0.011 0.001 TYR B 363 ARG 0.004 0.000 ARG B 90 *********************** 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 129 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 104 time to evaluate : 1.196 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 343 MET cc_start: -0.1199 (tpt) cc_final: -0.2701 (tpt) REVERT: B 491 LEU cc_start: 0.6002 (mt) cc_final: 0.5688 (mt) REVERT: B 618 MET cc_start: 0.7309 (mtt) cc_final: 0.6997 (mtt) REVERT: B 1716 LEU cc_start: 0.7851 (mt) cc_final: 0.7537 (mp) REVERT: B 1881 MET cc_start: 0.7641 (ppp) cc_final: 0.7362 (ppp) REVERT: B 1956 TYR cc_start: 0.7396 (OUTLIER) cc_final: 0.6141 (p90) REVERT: B 1979 PHE cc_start: 0.5506 (t80) cc_final: 0.5290 (t80) outliers start: 25 outliers final: 17 residues processed: 124 average time/residue: 0.2338 time to fit residues: 42.8011 Evaluate side-chains 114 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 ARG 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 284 THR Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 560 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 1654 GLU Chi-restraints excluded: chain B residue 1657 THR Chi-restraints excluded: chain B residue 1787 LEU Chi-restraints excluded: chain B residue 1956 TYR 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 115 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 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** ** B2132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 11436 Z= 0.342 Angle : 0.799 13.599 15490 Z= 0.403 Chirality : 0.047 0.169 1627 Planarity : 0.006 0.097 1999 Dihedral : 5.809 26.396 1508 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 21.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.04 % Favored : 84.96 % Rotamer: Outliers : 2.29 % Allowed : 25.39 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.98 (0.21), residues: 1370 helix: -3.14 (0.49), residues: 67 sheet: -1.98 (0.27), residues: 373 loop : -3.10 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B1920 HIS 0.008 0.001 HIS B 420 PHE 0.015 0.002 PHE B1979 TYR 0.017 0.002 TYR B2021 ARG 0.009 0.001 ARG B 90 *********************** 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 116 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 88 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 343 MET cc_start: -0.0736 (tpt) cc_final: -0.2198 (tpt) REVERT: B 491 LEU cc_start: 0.6391 (mt) cc_final: 0.6022 (mt) REVERT: B 618 MET cc_start: 0.7668 (mtt) cc_final: 0.7393 (mtt) REVERT: B 1700 TRP cc_start: 0.7979 (OUTLIER) cc_final: 0.7385 (m-90) REVERT: B 1881 MET cc_start: 0.7780 (ppp) cc_final: 0.7543 (ppp) REVERT: B 1956 TYR cc_start: 0.7429 (OUTLIER) cc_final: 0.6506 (p90) outliers start: 28 outliers final: 22 residues processed: 113 average time/residue: 0.2359 time to fit residues: 40.2153 Evaluate side-chains 109 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 85 time to evaluate : 1.286 ------------------------------------------------------------------------------- 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 256 SER Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 363 TYR 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 596 ILE 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 1943 VAL Chi-restraints excluded: chain B residue 1956 TYR 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 130 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 136 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.5692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11436 Z= 0.286 Angle : 0.781 12.836 15490 Z= 0.391 Chirality : 0.047 0.174 1627 Planarity : 0.006 0.095 1999 Dihedral : 5.818 25.678 1508 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.01 % Favored : 85.99 % Rotamer: Outliers : 2.04 % Allowed : 25.71 % Favored : 72.24 % 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: -3.99 (0.21), residues: 1370 helix: -2.98 (0.49), residues: 74 sheet: -1.99 (0.27), residues: 365 loop : -3.11 (0.18), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1563 HIS 0.005 0.001 HIS B 134 PHE 0.012 0.001 PHE B1979 TYR 0.012 0.002 TYR B 204 ARG 0.008 0.001 ARG B 90 ********************** 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 111 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 86 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 343 MET cc_start: -0.1177 (tpt) cc_final: -0.2742 (tpt) REVERT: B 491 LEU cc_start: 0.6359 (mt) cc_final: 0.6016 (mt) REVERT: B 618 MET cc_start: 0.7614 (mtt) cc_final: 0.7342 (mtt) REVERT: B 1700 TRP cc_start: 0.7915 (OUTLIER) cc_final: 0.7632 (m-10) REVERT: B 1716 LEU cc_start: 0.8202 (mt) cc_final: 0.7862 (mp) REVERT: B 1881 MET cc_start: 0.7745 (ppp) cc_final: 0.7415 (ppp) REVERT: B 1883 MET cc_start: 0.7340 (mpp) cc_final: 0.7113 (mpp) REVERT: B 1956 TYR cc_start: 0.7496 (OUTLIER) cc_final: 0.6356 (p90) outliers start: 25 outliers final: 22 residues processed: 110 average time/residue: 0.2228 time to fit residues: 36.3716 Evaluate side-chains 108 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 1.234 ------------------------------------------------------------------------------- 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 284 THR Chi-restraints excluded: chain B residue 363 TYR 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 560 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 678 THR 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 1943 VAL Chi-restraints excluded: chain B residue 1956 TYR Chi-restraints excluded: chain B residue 2132 GLN 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: 2.9990 chunk 33 optimal weight: 8.9990 chunk 100 optimal weight: 0.2980 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 108 optimal weight: 0.1980 chunk 45 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** ** B2132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.077471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.061354 restraints weight = 63312.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.062704 restraints weight = 45025.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.063658 restraints weight = 35808.035| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11436 Z= 0.188 Angle : 0.731 12.408 15490 Z= 0.360 Chirality : 0.047 0.173 1627 Planarity : 0.005 0.089 1999 Dihedral : 5.414 24.822 1508 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.26 % Favored : 87.74 % Rotamer: Outliers : 1.71 % Allowed : 26.20 % 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: -3.72 (0.21), residues: 1370 helix: -2.88 (0.51), residues: 67 sheet: -1.75 (0.28), residues: 353 loop : -2.93 (0.18), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 457 HIS 0.003 0.001 HIS B 134 PHE 0.013 0.001 PHE B1979 TYR 0.010 0.001 TYR B 363 ARG 0.005 0.000 ARG B 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2250.70 seconds wall clock time: 41 minutes 32.55 seconds (2492.55 seconds total)