Starting phenix.real_space_refine
on Fri Jul  3 14:16:46 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/9yqq_73344/07_2026/9yqq_73344_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9yqq_73344/07_2026/9yqq_73344.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9yqq_73344/07_2026/9yqq_73344.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9yqq_73344/07_2026/9yqq_73344.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9yqq_73344/07_2026/9yqq_73344_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9yqq_73344/07_2026/9yqq_73344_neut.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.035
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      79      5.16       5
     C    8865      2.51       5
     N    2326      2.21       5
     O    2569      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 13839
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 13839
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1739, 13839
          Classifications: {'peptide': 1739}
          Link IDs: {'PCIS': 3, 'PTRANS': 71, 'TRANS': 1664}
          Chain breaks: 10
  Time building chain proxies: 2.69, per 1000 atoms: 0.19
  Number of scatterers: 13839
  At special positions: 0
  Unit cell: (140.976, 119.616, 175.152, 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      79     16.00
     O    2569      8.00
     N    2326      7.00
     C    8865      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  Conformation dependent library (CDL) restraints added in 628.4 milliseconds
  

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3332

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 27 sheets defined
      14.1% alpha, 40.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1682 through 1688
    Processing helix  chain 'A' and resid 1708 through 1713
    Processing helix  chain 'A' and resid 1872 through 1886
      removed outlier: 3.557A  pdb=" N   LEU A1886 " --> pdb=" O   LEU A1882 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2053 through 2068
    Processing helix  chain 'A' and resid 2162 through 2167
      removed outlier: 4.022A  pdb=" N   GLY A2167 " --> pdb=" O   ARG A2163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2205 through 2219
      removed outlier: 3.507A  pdb=" N   LEU A2219 " --> pdb=" O   ILE A2215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2392 through 2411
    Processing helix  chain 'A' and resid 2582 through 2587
      removed outlier: 3.973A  pdb=" N   ARG A2587 " --> pdb=" O   LEU A2583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2596 through 2600
    Processing helix  chain 'A' and resid 2611 through 2615
      removed outlier: 3.685A  pdb=" N   GLU A2614 " --> pdb=" O   TRP A2611 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LEU A2615 " --> pdb=" O   LYS A2612 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 2611 through 2615'
    Processing helix  chain 'A' and resid 3067 through 3074
    Processing helix  chain 'A' and resid 3131 through 3149
    Processing helix  chain 'A' and resid 3228 through 3233
    Processing helix  chain 'A' and resid 3274 through 3285
    Processing helix  chain 'A' and resid 3290 through 3295
      removed outlier: 3.716A  pdb=" N   ARG A3295 " --> pdb=" O   GLU A3291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3300 through 3309
    Processing helix  chain 'A' and resid 3311 through 3315
      removed outlier: 3.620A  pdb=" N   THR A3314 " --> pdb=" O   LEU A3311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3361 through 3369
      removed outlier: 4.239A  pdb=" N   LEU A3365 " --> pdb=" O   VAL A3361 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   LYS A3366 " --> pdb=" O   ASN A3362 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   GLY A3369 " --> pdb=" O   LEU A3365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3393 through 3417
      removed outlier: 3.627A  pdb=" N   GLN A3408 " --> pdb=" O   HIS A3404 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   VAL A3415 " --> pdb=" O   LYS A3411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3613 through 3624
    Processing helix  chain 'A' and resid 3715 through 3729
    Processing helix  chain 'A' and resid 3730 through 3746
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1602 through 1611
      removed outlier: 6.520A  pdb=" N   ALA A1607 " --> pdb=" O   HIS A1625 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   HIS A1625 " --> pdb=" O   ALA A1607 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   ASN A1609 " --> pdb=" O   LYS A1623 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   LYS A1623 " --> pdb=" O   ASN A1609 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   PHE A1611 " --> pdb=" O   ASP A1621 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   ASP A1621 " --> pdb=" O   PHE A1611 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   MET A1627 " --> pdb=" O   LEU A1644 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   LEU A1644 " --> pdb=" O   MET A1627 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   ALA A1629 " --> pdb=" O   ALA A1642 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   ALA A1642 " --> pdb=" O   ALA A1629 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ALA A1642 " --> pdb=" O   PHE A1672 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1662 through 1664
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1764 through 1768
      removed outlier: 3.576A  pdb=" N   ASP A1780 " --> pdb=" O   LYS A1815 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLY A1782 " --> pdb=" O   GLN A1813 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   GLN A1813 " --> pdb=" O   GLY A1782 " (cutoff:3.500A)
      removed outlier: 5.923A  pdb=" N   VAL A1836 " --> pdb=" O   GLN A1813 " (cutoff:3.500A)
      removed outlier: 5.147A  pdb=" N   LYS A1815 " --> pdb=" O   LYS A1834 " (cutoff:3.500A)
      removed outlier: 7.181A  pdb=" N   LYS A1834 " --> pdb=" O   LYS A1815 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   SER A1817 " --> pdb=" O   ILE A1832 " (cutoff:3.500A)
      removed outlier: 6.049A  pdb=" N   ILE A1832 " --> pdb=" O   SER A1817 " (cutoff:3.500A)
      removed outlier: 5.811A  pdb=" N   THR A1819 " --> pdb=" O   ILE A1830 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   ILE A1830 " --> pdb=" O   THR A1819 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ASP A2042 " --> pdb=" O   SER A2031 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   SER A2039 " --> pdb=" O   THR A2104 " (cutoff:3.500A)
      removed outlier: 8.164A  pdb=" N   LYS A2106 " --> pdb=" O   SER A2039 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   ILE A2041 " --> pdb=" O   LYS A2106 " (cutoff:3.500A)
      removed outlier: 8.442A  pdb=" N   MET A2108 " --> pdb=" O   ILE A2041 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   ALA A2043 " --> pdb=" O   MET A2108 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   CYS A2134 " --> pdb=" O   ILE A2109 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   GLN A2133 " --> pdb=" O   ASP A2153 " (cutoff:3.500A)
      removed outlier: 5.522A  pdb=" N   ASP A2153 " --> pdb=" O   GLN A2133 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   ASN A2135 " --> pdb=" O   VAL A2151 " (cutoff:3.500A)
      removed outlier: 5.787A  pdb=" N   VAL A2151 " --> pdb=" O   ASN A2135 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   SER A2137 " --> pdb=" O   ALA A2149 " (cutoff:3.500A)
      removed outlier: 5.164A  pdb=" N   ALA A2149 " --> pdb=" O   SER A2137 " (cutoff:3.500A)
      removed outlier: 7.481A  pdb=" N   SER A2139 " --> pdb=" O   MET A2147 " (cutoff:3.500A)
      removed outlier: 5.748A  pdb=" N   MET A2147 " --> pdb=" O   SER A2139 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   VAL A2156 " --> pdb=" O   VAL A2173 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1787 through 1792
      removed outlier: 5.923A  pdb=" N   VAL A1836 " --> pdb=" O   GLN A1813 " (cutoff:3.500A)
      removed outlier: 5.147A  pdb=" N   LYS A1815 " --> pdb=" O   LYS A1834 " (cutoff:3.500A)
      removed outlier: 7.181A  pdb=" N   LYS A1834 " --> pdb=" O   LYS A1815 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   SER A1817 " --> pdb=" O   ILE A1832 " (cutoff:3.500A)
      removed outlier: 6.049A  pdb=" N   ILE A1832 " --> pdb=" O   SER A1817 " (cutoff:3.500A)
      removed outlier: 5.811A  pdb=" N   THR A1819 " --> pdb=" O   ILE A1830 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   ILE A1830 " --> pdb=" O   THR A1819 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ASP A2042 " --> pdb=" O   SER A2031 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   SER A2039 " --> pdb=" O   THR A2104 " (cutoff:3.500A)
      removed outlier: 8.164A  pdb=" N   LYS A2106 " --> pdb=" O   SER A2039 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   ILE A2041 " --> pdb=" O   LYS A2106 " (cutoff:3.500A)
      removed outlier: 8.442A  pdb=" N   MET A2108 " --> pdb=" O   ILE A2041 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   ALA A2043 " --> pdb=" O   MET A2108 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   CYS A2134 " --> pdb=" O   ILE A2109 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   GLN A2133 " --> pdb=" O   ASP A2153 " (cutoff:3.500A)
      removed outlier: 5.522A  pdb=" N   ASP A2153 " --> pdb=" O   GLN A2133 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   ASN A2135 " --> pdb=" O   VAL A2151 " (cutoff:3.500A)
      removed outlier: 5.787A  pdb=" N   VAL A2151 " --> pdb=" O   ASN A2135 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   SER A2137 " --> pdb=" O   ALA A2149 " (cutoff:3.500A)
      removed outlier: 5.164A  pdb=" N   ALA A2149 " --> pdb=" O   SER A2137 " (cutoff:3.500A)
      removed outlier: 7.481A  pdb=" N   SER A2139 " --> pdb=" O   MET A2147 " (cutoff:3.500A)
      removed outlier: 5.748A  pdb=" N   MET A2147 " --> pdb=" O   SER A2139 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1868 through 1871
      removed outlier: 6.611A  pdb=" N   VAL A1868 " --> pdb=" O   ILE A1948 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   TYR A1950 " --> pdb=" O   VAL A1868 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   LEU A1870 " --> pdb=" O   TYR A1950 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   ILE A1947 " --> pdb=" O   GLU A1971 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   GLU A1971 " --> pdb=" O   ILE A1947 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   LEU A1949 " --> pdb=" O   LEU A1969 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 2195 through 2197
      removed outlier: 6.663A  pdb=" N   ILE A2195 " --> pdb=" O   VAL A2279 " (cutoff:3.500A)
      removed outlier: 8.028A  pdb=" N   GLU A2281 " --> pdb=" O   ILE A2195 " (cutoff:3.500A)
      removed outlier: 8.960A  pdb=" N   VAL A2197 " --> pdb=" O   GLU A2281 " (cutoff:3.500A)
      removed outlier: 7.743A  pdb=" N   ILE A2283 " --> pdb=" O   VAL A2197 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   SER A2282 " --> pdb=" O   SER A2303 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   SER A2303 " --> pdb=" O   SER A2282 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   GLN A2284 " --> pdb=" O   ALA A2301 " (cutoff:3.500A)
      removed outlier: 6.000A  pdb=" N   ALA A2301 " --> pdb=" O   GLN A2284 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   THR A2286 " --> pdb=" O   LEU A2299 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   LEU A2299 " --> pdb=" O   THR A2286 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   GLU A2288 " --> pdb=" O   PRO A2297 " (cutoff:3.500A)
      removed outlier: 7.680A  pdb=" N   LEU A2298 " --> pdb=" O   TYR A2329 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 2200 through 2204
      removed outlier: 3.960A  pdb=" N   SER A2282 " --> pdb=" O   SER A2303 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   SER A2303 " --> pdb=" O   SER A2282 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   GLN A2284 " --> pdb=" O   ALA A2301 " (cutoff:3.500A)
      removed outlier: 6.000A  pdb=" N   ALA A2301 " --> pdb=" O   GLN A2284 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   THR A2286 " --> pdb=" O   LEU A2299 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   LEU A2299 " --> pdb=" O   THR A2286 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   GLU A2288 " --> pdb=" O   PRO A2297 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LYS A2304 " --> pdb=" O   THR A2323 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   THR A2323 " --> pdb=" O   LYS A2304 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   SER A2306 " --> pdb=" O   ASP A2321 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   ALA A2320 " --> pdb=" O   LEU A2353 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   VAL A2322 " --> pdb=" O   LEU A2351 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 2342 through 2343
      removed outlier: 3.857A  pdb=" N   ARG A2347 " --> pdb=" O   VAL A2343 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 2442 through 2444
      removed outlier: 6.183A  pdb=" N   THR A2425 " --> pdb=" O   ILE A2539 " (cutoff:3.500A)
      removed outlier: 7.765A  pdb=" N   LEU A2541 " --> pdb=" O   THR A2425 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   LYS A2427 " --> pdb=" O   LEU A2541 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 2454 through 2456
    Processing sheet with id=AB2, first strand: chain 'A' and resid 2578 through 2580
      removed outlier: 6.766A  pdb=" N   GLN A2546 " --> pdb=" O   ILE A2664 " (cutoff:3.500A)
      removed outlier: 7.931A  pdb=" N   LEU A2666 " --> pdb=" O   GLN A2546 " (cutoff:3.500A)
      removed outlier: 7.456A  pdb=" N   LYS A2548 " --> pdb=" O   LEU A2666 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 2567 through 2573
      removed outlier: 5.456A  pdb=" N   ARG A2569 " --> pdb=" O   LYS A2559 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   LYS A2559 " --> pdb=" O   ARG A2569 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   GLY A2571 " --> pdb=" O   ILE A2557 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 2698 through 2700
      removed outlier: 6.419A  pdb=" N   THR A2671 " --> pdb=" O   LEU A2766 " (cutoff:3.500A)
      removed outlier: 7.658A  pdb=" N   VAL A2768 " --> pdb=" O   THR A2671 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   ARG A2673 " --> pdb=" O   VAL A2768 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   VAL A2751 " --> pdb=" O   PHE A2741 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 2691 through 2693
      removed outlier: 3.521A  pdb=" N   GLU A2709 " --> pdb=" O   ILE A2729 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   LYS A2717 " --> pdb=" O   LYS A2721 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   LYS A2721 " --> pdb=" O   LYS A2717 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 2801 through 2803
      removed outlier: 3.776A  pdb=" N   LEU A2868 " --> pdb=" O   ILE A2775 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 2790 through 2793
      removed outlier: 3.654A  pdb=" N   LEU A2782 " --> pdb=" O   HIS A2793 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 2905 through 2908
      removed outlier: 6.713A  pdb=" N   THR A2873 " --> pdb=" O   ILE A2965 " (cutoff:3.500A)
      removed outlier: 8.142A  pdb=" N   PHE A2967 " --> pdb=" O   THR A2873 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   ALA A2875 " --> pdb=" O   PHE A2967 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   SER A2968 " --> pdb=" O   LEU A2953 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   LEU A2953 " --> pdb=" O   SER A2968 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 2899 through 2900
      removed outlier: 3.902A  pdb=" N   ILE A2887 " --> pdb=" O   LYS A2917 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   LYS A2917 " --> pdb=" O   ILE A2887 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 3006 through 3008
      removed outlier: 3.778A  pdb=" N   LEU A3062 " --> pdb=" O   LEU A2978 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLN A3059 " --> pdb=" O   ASP A3056 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLY A3037 " --> pdb=" O   SER A3053 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'A' and resid 3000 through 3001
    Processing sheet with id=AC3, first strand: chain 'A' and resid 3094 through 3095
      removed outlier: 3.824A  pdb=" N   THR A3113 " --> pdb=" O   TRP A3206 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   TRP A3206 " --> pdb=" O   THR A3113 " (cutoff:3.500A)
      removed outlier: 5.900A  pdb=" N   ASN A3211 " --> pdb=" O   VAL A3220 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   VAL A3220 " --> pdb=" O   ASN A3211 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'A' and resid 3128 through 3129
      removed outlier: 6.505A  pdb=" N   PHE A3160 " --> pdb=" O   LEU A3156 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'A' and resid 3188 through 3190
      removed outlier: 3.982A  pdb=" N   GLN A3188 " --> pdb=" O   ARG A3203 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   ARG A3201 " --> pdb=" O   GLU A3190 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   ARG A3248 " --> pdb=" O   PHE A3258 " (cutoff:3.500A)
      removed outlier: 5.402A  pdb=" N   PHE A3258 " --> pdb=" O   ARG A3248 " (cutoff:3.500A)
      removed outlier: 8.674A  pdb=" N   HIS A3329 " --> pdb=" O   LYS A3259 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   PHE A3261 " --> pdb=" O   HIS A3329 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'A' and resid 3188 through 3190
      removed outlier: 3.982A  pdb=" N   GLN A3188 " --> pdb=" O   ARG A3203 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   ARG A3201 " --> pdb=" O   GLU A3190 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   ARG A3248 " --> pdb=" O   PHE A3258 " (cutoff:3.500A)
      removed outlier: 5.402A  pdb=" N   PHE A3258 " --> pdb=" O   ARG A3248 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   PHE A3324 " --> pdb=" O   PHE A3258 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   TYR A3260 " --> pdb=" O   PHE A3324 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   GLN A3390 " --> pdb=" O   PHE A3325 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'A' and resid 3271 through 3273
      removed outlier: 7.404A  pdb=" N   LEU A3339 " --> pdb=" O   ASP A3376 " (cutoff:3.500A)
      removed outlier: 5.404A  pdb=" N   ASP A3376 " --> pdb=" O   LEU A3339 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'A' and resid 3632 through 3637
      removed outlier: 3.794A  pdb=" N   ARG A3652 " --> pdb=" O   THR A3649 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   LYS A3657 " --> pdb=" O   VAL A3667 " (cutoff:3.500A)
      removed outlier: 5.401A  pdb=" N   VAL A3667 " --> pdb=" O   LYS A3657 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'A' and resid 3681 through 3682

    563 hydrogen bonds defined for protein.
    1500 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: 3.98

  Time building geometry restraints manager: 1.32 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.19 -     1.32: 2288
        1.32 -     1.44: 3583
        1.44 -     1.56: 8118
        1.56 -     1.69: 0
        1.69 -     1.81: 128
  Bond restraints: 14117
  Sorted by residual:
  bond pdb=" C   MET A1756 "
       pdb=" O   MET A1756 "
    ideal  model  delta    sigma   weight residual
    1.235  1.191  0.044 1.20e-02 6.94e+03 1.34e+01
  bond pdb=" N   MET A1627 "
       pdb=" CA  MET A1627 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.23e-02 6.61e+03 6.72e+00
  bond pdb=" N   VAL A2430 "
       pdb=" CA  VAL A2430 "
    ideal  model  delta    sigma   weight residual
    1.462  1.491 -0.029 1.17e-02 7.31e+03 6.06e+00
  bond pdb=" N   PHE A2447 "
       pdb=" CA  PHE A2447 "
    ideal  model  delta    sigma   weight residual
    1.463  1.487 -0.024 1.11e-02 8.12e+03 4.77e+00
  bond pdb=" N   LEU A1783 "
       pdb=" CA  LEU A1783 "
    ideal  model  delta    sigma   weight residual
    1.459  1.483 -0.024 1.22e-02 6.72e+03 3.78e+00
  ... (remaining 14112 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 18696
        1.75 -     3.49: 365
        3.49 -     5.24: 43
        5.24 -     6.98: 4
        6.98 -     8.73: 2
  Bond angle restraints: 19110
  Sorted by residual:
  angle pdb=" CA  ILE A1624 "
        pdb=" C   ILE A1624 "
        pdb=" O   ILE A1624 "
      ideal   model   delta    sigma   weight residual
     121.67  116.60    5.07 1.05e+00 9.07e-01 2.33e+01
  angle pdb=" CA  MET A1866 "
        pdb=" C   MET A1866 "
        pdb=" O   MET A1866 "
      ideal   model   delta    sigma   weight residual
     121.56  116.54    5.02 1.21e+00 6.83e-01 1.72e+01
  angle pdb=" CA  MET A1756 "
        pdb=" C   MET A1756 "
        pdb=" O   MET A1756 "
      ideal   model   delta    sigma   weight residual
     120.81  116.40    4.41 1.15e+00 7.56e-01 1.47e+01
  angle pdb=" CA  MET A1866 "
        pdb=" C   MET A1866 "
        pdb=" N   GLN A1867 "
      ideal   model   delta    sigma   weight residual
     115.27  120.69   -5.42 1.47e+00 4.63e-01 1.36e+01
  angle pdb=" N   VAL A2430 "
        pdb=" CA  VAL A2430 "
        pdb=" C   VAL A2430 "
      ideal   model   delta    sigma   weight residual
     113.07  108.46    4.61 1.36e+00 5.41e-01 1.15e+01
  ... (remaining 19105 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 7363
       17.84 -    35.67: 921
       35.67 -    53.51: 233
       53.51 -    71.34: 52
       71.34 -    89.18: 24
  Dihedral angle restraints: 8593
    sinusoidal: 3484
      harmonic: 5109
  Sorted by residual:
  dihedral pdb=" CA  ASN A3685 "
           pdb=" C   ASN A3685 "
           pdb=" N   VAL A3686 "
           pdb=" CA  VAL A3686 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.43  -19.57     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  ARG A2542 "
           pdb=" C   ARG A2542 "
           pdb=" N   SER A2543 "
           pdb=" CA  SER A2543 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.15   17.85     0      5.00e+00 4.00e-02 1.27e+01
  dihedral pdb=" CA  SER A3093 "
           pdb=" C   SER A3093 "
           pdb=" N   LEU A3094 "
           pdb=" CA  LEU A3094 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.18   17.82     0      5.00e+00 4.00e-02 1.27e+01
  ... (remaining 8590 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1829
       0.056 -    0.112: 285
       0.112 -    0.167: 87
       0.167 -    0.223: 2
       0.223 -    0.279: 1
  Chirality restraints: 2204
  Sorted by residual:
  chirality pdb=" CA  MET A1866 "
            pdb=" N   MET A1866 "
            pdb=" C   MET A1866 "
            pdb=" CB  MET A1866 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.95e+00
  chirality pdb=" CA  LEU A1783 "
            pdb=" N   LEU A1783 "
            pdb=" C   LEU A1783 "
            pdb=" CB  LEU A1783 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CA  ILE A1624 "
            pdb=" N   ILE A1624 "
            pdb=" C   ILE A1624 "
            pdb=" CB  ILE A1624 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.07e+00
  ... (remaining 2201 not shown)

  Planarity restraints: 2418
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A1783 "   -0.014 2.00e-02 2.50e+03   2.84e-02 8.09e+00
        pdb=" C   LEU A1783 "    0.049 2.00e-02 2.50e+03
        pdb=" O   LEU A1783 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   ILE A1784 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A1866 "    0.014 2.00e-02 2.50e+03   2.77e-02 7.65e+00
        pdb=" C   MET A1866 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   MET A1866 "    0.017 2.00e-02 2.50e+03
        pdb=" N   GLN A1867 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A1756 "   -0.013 2.00e-02 2.50e+03   2.64e-02 6.94e+00
        pdb=" C   MET A1756 "    0.046 2.00e-02 2.50e+03
        pdb=" O   MET A1756 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ASP A1757 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 2415 not shown)

  Histogram of nonbonded interaction distances:
        2.40 -     2.90: 5599
        2.90 -     3.40: 13226
        3.40 -     3.90: 22155
        3.90 -     4.40: 25053
        4.40 -     4.90: 43518
  Nonbonded interactions: 109551
  Sorted by model distance:
  nonbonded pdb=" OG  SER A2823 "
            pdb=" O   PRO A2843 "
     model   vdw
     2.398 3.040
  nonbonded pdb=" O   ALA A3725 "
            pdb=" OD1 ASP A3728 "
     model   vdw
     2.400 3.040
  nonbonded pdb=" OE1 GLN A2937 "
            pdb=" O   VAL A2956 "
     model   vdw
     2.407 3.040
  nonbonded pdb=" O   SER A2139 "
            pdb=" OG  SER A2139 "
     model   vdw
     2.407 3.040
  nonbonded pdb=" OG  SER A2303 "
            pdb=" O   THR A2323 "
     model   vdw
     2.408 3.040
  ... (remaining 109546 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.420
  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:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     14.120
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5847
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      :  0.003   0.044  14117  Z= 0.146
  Angle     :  0.596   8.726  19110  Z= 0.328
  Chirality :  0.047   0.279   2204
  Planarity :  0.004   0.047   2418
  Dihedral  : 17.375  89.179   5261
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.86 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  : 26.88 %
    Favored  : 73.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.25 (0.20), residues: 1717
  helix:  1.07 (0.38), residues: 195
  sheet: -1.75 (0.19), residues: 705
  loop : -1.80 (0.21), residues: 817

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A2342 
 TYR   0.013   0.001   TYR A3205 
 PHE   0.013   0.001   PHE A3222 
 TRP   0.010   0.001   TRP A2312 
 HIS   0.007   0.001   HIS A1625 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.15 (14117)
  covalent geometry    : angle       0.59625 /  0.33 (19110)
  hydrogen bonds       : bond        0.09161 /  5.99 (  492)
  hydrogen bonds       : angle       7.65032 /  5.16 ( 1500)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 182
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 182
  average time/residue: 0.0806
  time to fit residues: 24.1902
Evaluate side-chains
  161 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 160
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1790 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    0.8980
   chunk 77 optimal weight:    0.0070
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    0.6980
   chunk 149 optimal weight:    0.9990
   overall best weight:    0.6998

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A2845 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4604 r_free = 0.4604 target = 0.221432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4546 r_free = 0.4546 target = 0.212777 restraints weight = 13646.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.211999 restraints weight = 18747.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.210597 restraints weight = 19647.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.210024 restraints weight = 20398.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.209235 restraints weight = 19822.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.4515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5928
moved from start:          0.0783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  14117  Z= 0.183
  Angle     :  0.628   9.744  19110  Z= 0.327
  Chirality :  0.047   0.178   2204
  Planarity :  0.004   0.049   2418
  Dihedral  :  5.032  57.483   1850
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.79 %
    Favored  : 91.09 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 26.69 %
    Favored  : 70.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.19 (0.20), residues: 1717
  helix:  1.04 (0.37), residues: 193
  sheet: -1.66 (0.19), residues: 714
  loop : -1.79 (0.21), residues: 810

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2864 
 TYR   0.019   0.002   TYR A3205 
 PHE   0.021   0.002   PHE A3222 
 TRP   0.028   0.002   TRP A3119 
 HIS   0.006   0.001   HIS A1625 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00416 /  0.18 (14117)
  covalent geometry    : angle       0.62801 /  0.33 (19110)
  hydrogen bonds       : bond        0.03507 /  2.38 (  492)
  hydrogen bonds       : angle       6.53185 /  4.41 ( 1500)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 176
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2105 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7642 (tp)
REVERT: A 2383 SER cc_start: 0.8435 (OUTLIER) cc_final: 0.7352 (m)
REVERT: A 2963 THR cc_start: 0.6280 (t) cc_final: 0.5945 (p)
REVERT: A 2982 HIS cc_start: 0.6335 (OUTLIER) cc_final: 0.5167 (t-90)
REVERT: A 3222 PHE cc_start: 0.6582 (OUTLIER) cc_final: 0.6239 (t80)
  outliers start: 48
  outliers final: 22
  residues processed: 213
  average time/residue: 0.0918
  time to fit residues: 31.2949
Evaluate side-chains
  190 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 164
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1689 MET
Chi-restraints excluded: chain A residue 1941 HIS
Chi-restraints excluded: chain A residue 2044 VAL
Chi-restraints excluded: chain A residue 2105 LEU
Chi-restraints excluded: chain A residue 2135 ASN
Chi-restraints excluded: chain A residue 2137 SER
Chi-restraints excluded: chain A residue 2172 THR
Chi-restraints excluded: chain A residue 2188 SER
Chi-restraints excluded: chain A residue 2383 SER
Chi-restraints excluded: chain A residue 2500 VAL
Chi-restraints excluded: chain A residue 2526 VAL
Chi-restraints excluded: chain A residue 2553 ILE
Chi-restraints excluded: chain A residue 2609 ILE
Chi-restraints excluded: chain A residue 2624 MET
Chi-restraints excluded: chain A residue 2626 GLN
Chi-restraints excluded: chain A residue 2629 SER
Chi-restraints excluded: chain A residue 2705 ARG
Chi-restraints excluded: chain A residue 2775 ILE
Chi-restraints excluded: chain A residue 2842 CYS
Chi-restraints excluded: chain A residue 2884 VAL
Chi-restraints excluded: chain A residue 2938 ASP
Chi-restraints excluded: chain A residue 2982 HIS
Chi-restraints excluded: chain A residue 3017 THR
Chi-restraints excluded: chain A residue 3222 PHE
Chi-restraints excluded: chain A residue 3417 VAL
Chi-restraints excluded: chain A residue 3647 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 120 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 144 optimal weight:    1.9990
   chunk 147 optimal weight:    0.2980
   chunk 118 optimal weight:    0.9980
   chunk 5 optimal weight:    9.9990
   chunk 47 optimal weight:    0.3980
   chunk 66 optimal weight:    0.6980
   chunk 121 optimal weight:    0.6980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A2284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2809 ASN
** A2992 GLN ** 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 = 0.4620 r_free = 0.4620 target = 0.223313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4561 r_free = 0.4561 target = 0.214547 restraints weight = 13730.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.213880 restraints weight = 18801.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.212605 restraints weight = 19119.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.212255 restraints weight = 19898.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.211787 restraints weight = 16821.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.4537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5902
moved from start:          0.0937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14117  Z= 0.154
  Angle     :  0.597   8.468  19110  Z= 0.310
  Chirality :  0.046   0.164   2204
  Planarity :  0.004   0.045   2418
  Dihedral  :  4.776  21.792   1848
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.92 %
    Favored  : 91.96 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 27.07 %
    Favored  : 69.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.16 (0.20), residues: 1717
  helix:  1.07 (0.37), residues: 193
  sheet: -1.66 (0.19), residues: 721
  loop : -1.74 (0.22), residues: 803

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2574 
 TYR   0.017   0.001   TYR A3085 
 PHE   0.020   0.002   PHE A3222 
 TRP   0.015   0.001   TRP A2186 
 HIS   0.006   0.001   HIS A1625 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.15 (14117)
  covalent geometry    : angle       0.59726 /  0.31 (19110)
  hydrogen bonds       : bond        0.03333 /  2.25 (  492)
  hydrogen bonds       : angle       6.31723 /  4.27 ( 1500)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 173
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2105 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7360 (tp)
REVERT: A 2383 SER cc_start: 0.8386 (OUTLIER) cc_final: 0.7323 (m)
REVERT: A 2543 SER cc_start: 0.7788 (OUTLIER) cc_final: 0.7585 (p)
REVERT: A 2963 THR cc_start: 0.6187 (t) cc_final: 0.5854 (p)
REVERT: A 2982 HIS cc_start: 0.6275 (OUTLIER) cc_final: 0.5118 (t-90)
REVERT: A 3201 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6801 (mtp180)
  outliers start: 54
  outliers final: 32
  residues processed: 218
  average time/residue: 0.0870
  time to fit residues: 30.2975
Evaluate side-chains
  201 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 164
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1610 VAL
Chi-restraints excluded: chain A residue 1631 ILE
Chi-restraints excluded: chain A residue 1689 MET
Chi-restraints excluded: chain A residue 1766 ILE
Chi-restraints excluded: chain A residue 1767 ILE
Chi-restraints excluded: chain A residue 1790 PHE
Chi-restraints excluded: chain A residue 1941 HIS
Chi-restraints excluded: chain A residue 2028 ILE
Chi-restraints excluded: chain A residue 2064 PHE
Chi-restraints excluded: chain A residue 2105 LEU
Chi-restraints excluded: chain A residue 2135 ASN
Chi-restraints excluded: chain A residue 2172 THR
Chi-restraints excluded: chain A residue 2188 SER
Chi-restraints excluded: chain A residue 2300 LEU
Chi-restraints excluded: chain A residue 2383 SER
Chi-restraints excluded: chain A residue 2426 VAL
Chi-restraints excluded: chain A residue 2500 VAL
Chi-restraints excluded: chain A residue 2526 VAL
Chi-restraints excluded: chain A residue 2543 SER
Chi-restraints excluded: chain A residue 2583 LEU
Chi-restraints excluded: chain A residue 2609 ILE
Chi-restraints excluded: chain A residue 2629 SER
Chi-restraints excluded: chain A residue 2754 SER
Chi-restraints excluded: chain A residue 2775 ILE
Chi-restraints excluded: chain A residue 2822 THR
Chi-restraints excluded: chain A residue 2842 CYS
Chi-restraints excluded: chain A residue 2938 ASP
Chi-restraints excluded: chain A residue 2961 HIS
Chi-restraints excluded: chain A residue 2979 ILE
Chi-restraints excluded: chain A residue 2982 HIS
Chi-restraints excluded: chain A residue 3020 LEU
Chi-restraints excluded: chain A residue 3070 LEU
Chi-restraints excluded: chain A residue 3114 SER
Chi-restraints excluded: chain A residue 3201 ARG
Chi-restraints excluded: chain A residue 3417 VAL
Chi-restraints excluded: chain A residue 3620 LEU
Chi-restraints excluded: chain A residue 3647 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 120 optimal weight:    2.9990
   chunk 107 optimal weight:    3.9990
   chunk 169 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 128 optimal weight:    0.4980
   chunk 140 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 149 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9980
   chunk 119 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A2284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3705 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4599 r_free = 0.4599 target = 0.220619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.211737 restraints weight = 13791.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.210906 restraints weight = 19446.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.209940 restraints weight = 19390.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.209521 restraints weight = 19511.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.209008 restraints weight = 17451.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.4512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5940
moved from start:          0.1179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14117  Z= 0.196
  Angle     :  0.634   8.405  19110  Z= 0.330
  Chirality :  0.047   0.186   2204
  Planarity :  0.004   0.046   2418
  Dihedral  :  4.952  23.750   1848
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  9.32 %
    Favored  : 90.62 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 26.43 %
    Favored  : 69.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.21 (0.20), residues: 1717
  helix:  0.94 (0.36), residues: 193
  sheet: -1.65 (0.19), residues: 711
  loop : -1.80 (0.21), residues: 813

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A2705 
 TYR   0.020   0.002   TYR A3085 
 PHE   0.022   0.002   PHE A3222 
 TRP   0.018   0.001   TRP A2186 
 HIS   0.006   0.001   HIS A1625 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00449 /  0.20 (14117)
  covalent geometry    : angle       0.63428 /  0.33 (19110)
  hydrogen bonds       : bond        0.03504 /  2.39 (  492)
  hydrogen bonds       : angle       6.38261 /  4.30 ( 1500)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 173
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
REVERT: A 2105 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7002 (tt)
REVERT: A 2383 SER cc_start: 0.8483 (OUTLIER) cc_final: 0.8258 (t)
REVERT: A 2963 THR cc_start: 0.6232 (t) cc_final: 0.5874 (p)
REVERT: A 2982 HIS cc_start: 0.6154 (OUTLIER) cc_final: 0.4931 (t-90)
REVERT: A 3222 PHE cc_start: 0.6522 (OUTLIER) cc_final: 0.6165 (t80)
  outliers start: 70
  outliers final: 46
  residues processed: 226
  average time/residue: 0.0805
  time to fit residues: 29.3138
Evaluate side-chains
  217 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 167
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1610 VAL
Chi-restraints excluded: chain A residue 1631 ILE
Chi-restraints excluded: chain A residue 1689 MET
Chi-restraints excluded: chain A residue 1766 ILE
Chi-restraints excluded: chain A residue 1767 ILE
Chi-restraints excluded: chain A residue 1790 PHE
Chi-restraints excluded: chain A residue 1941 HIS
Chi-restraints excluded: chain A residue 2028 ILE
Chi-restraints excluded: chain A residue 2044 VAL
Chi-restraints excluded: chain A residue 2064 PHE
Chi-restraints excluded: chain A residue 2105 LEU
Chi-restraints excluded: chain A residue 2135 ASN
Chi-restraints excluded: chain A residue 2137 SER
Chi-restraints excluded: chain A residue 2172 THR
Chi-restraints excluded: chain A residue 2181 MET
Chi-restraints excluded: chain A residue 2188 SER
Chi-restraints excluded: chain A residue 2300 LEU
Chi-restraints excluded: chain A residue 2383 SER
Chi-restraints excluded: chain A residue 2426 VAL
Chi-restraints excluded: chain A residue 2430 VAL
Chi-restraints excluded: chain A residue 2500 VAL
Chi-restraints excluded: chain A residue 2526 VAL
Chi-restraints excluded: chain A residue 2583 LEU
Chi-restraints excluded: chain A residue 2609 ILE
Chi-restraints excluded: chain A residue 2626 GLN
Chi-restraints excluded: chain A residue 2629 SER
Chi-restraints excluded: chain A residue 2665 HIS
Chi-restraints excluded: chain A residue 2671 THR
Chi-restraints excluded: chain A residue 2754 SER
Chi-restraints excluded: chain A residue 2775 ILE
Chi-restraints excluded: chain A residue 2822 THR
Chi-restraints excluded: chain A residue 2842 CYS
Chi-restraints excluded: chain A residue 2851 VAL
Chi-restraints excluded: chain A residue 2858 SER
Chi-restraints excluded: chain A residue 2884 VAL
Chi-restraints excluded: chain A residue 2938 ASP
Chi-restraints excluded: chain A residue 2961 HIS
Chi-restraints excluded: chain A residue 2979 ILE
Chi-restraints excluded: chain A residue 2982 HIS
Chi-restraints excluded: chain A residue 3000 VAL
Chi-restraints excluded: chain A residue 3017 THR
Chi-restraints excluded: chain A residue 3020 LEU
Chi-restraints excluded: chain A residue 3070 LEU
Chi-restraints excluded: chain A residue 3114 SER
Chi-restraints excluded: chain A residue 3222 PHE
Chi-restraints excluded: chain A residue 3255 VAL
Chi-restraints excluded: chain A residue 3416 LEU
Chi-restraints excluded: chain A residue 3417 VAL
Chi-restraints excluded: chain A residue 3620 LEU
Chi-restraints excluded: chain A residue 3647 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 119 optimal weight:    0.0870
   chunk 33 optimal weight:    2.9990
   chunk 128 optimal weight:    0.9990
   chunk 167 optimal weight:    0.0030
   chunk 77 optimal weight:    0.7980
   chunk 145 optimal weight:    0.9980
   chunk 159 optimal weight:    0.0170
   chunk 122 optimal weight:    1.9990
   chunk 147 optimal weight:    0.4980
   overall best weight:    0.2806

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A2284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2992 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 = 0.4642 r_free = 0.4642 target = 0.226230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.217603 restraints weight = 13530.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4576 r_free = 0.4576 target = 0.216910 restraints weight = 17705.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4565 r_free = 0.4565 target = 0.215770 restraints weight = 18185.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4561 r_free = 0.4561 target = 0.215383 restraints weight = 19821.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4556 r_free = 0.4556 target = 0.214814 restraints weight = 17088.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.4560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5837
moved from start:          0.1273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  14117  Z= 0.111
  Angle     :  0.571   7.441  19110  Z= 0.294
  Chirality :  0.046   0.168   2204
  Planarity :  0.004   0.045   2418
  Dihedral  :  4.609  18.522   1848
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.94 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 27.71 %
    Favored  : 68.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.03 (0.20), residues: 1717
  helix:  1.03 (0.37), residues: 197
  sheet: -1.55 (0.19), residues: 714
  loop : -1.67 (0.22), residues: 806

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A2510 
 TYR   0.014   0.001   TYR A3085 
 PHE   0.015   0.001   PHE A3222 
 TRP   0.022   0.001   TRP A2186 
 HIS   0.006   0.001   HIS A1625 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00244 /  0.11 (14117)
  covalent geometry    : angle       0.57124 /  0.29 (19110)
  hydrogen bonds       : bond        0.03029 /  2.03 (  492)
  hydrogen bonds       : angle       5.98215 /  4.04 ( 1500)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 173
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2105 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.6779 (tp)
REVERT: A 2982 HIS cc_start: 0.6103 (OUTLIER) cc_final: 0.4945 (t-90)
REVERT: A 3171 MET cc_start: 0.2531 (ppp) cc_final: 0.2027 (ppp)
  outliers start: 56
  outliers final: 38
  residues processed: 219
  average time/residue: 0.0838
  time to fit residues: 29.3222
Evaluate side-chains
  207 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 167
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1610 VAL
Chi-restraints excluded: chain A residue 1631 ILE
Chi-restraints excluded: chain A residue 1689 MET
Chi-restraints excluded: chain A residue 1698 PHE
Chi-restraints excluded: chain A residue 1712 PHE
Chi-restraints excluded: chain A residue 1766 ILE
Chi-restraints excluded: chain A residue 1767 ILE
Chi-restraints excluded: chain A residue 1783 LEU
Chi-restraints excluded: chain A residue 1790 PHE
Chi-restraints excluded: chain A residue 1941 HIS
Chi-restraints excluded: chain A residue 1980 SER
Chi-restraints excluded: chain A residue 2064 PHE
Chi-restraints excluded: chain A residue 2105 LEU
Chi-restraints excluded: chain A residue 2120 LEU
Chi-restraints excluded: chain A residue 2135 ASN
Chi-restraints excluded: chain A residue 2137 SER
Chi-restraints excluded: chain A residue 2172 THR
Chi-restraints excluded: chain A residue 2181 MET
Chi-restraints excluded: chain A residue 2300 LEU
Chi-restraints excluded: chain A residue 2383 SER
Chi-restraints excluded: chain A residue 2426 VAL
Chi-restraints excluded: chain A residue 2500 VAL
Chi-restraints excluded: chain A residue 2583 LEU
Chi-restraints excluded: chain A residue 2626 GLN
Chi-restraints excluded: chain A residue 2665 HIS
Chi-restraints excluded: chain A residue 2760 ILE
Chi-restraints excluded: chain A residue 2822 THR
Chi-restraints excluded: chain A residue 2880 LEU
Chi-restraints excluded: chain A residue 2958 THR
Chi-restraints excluded: chain A residue 2961 HIS
Chi-restraints excluded: chain A residue 2982 HIS
Chi-restraints excluded: chain A residue 3000 VAL
Chi-restraints excluded: chain A residue 3020 LEU
Chi-restraints excluded: chain A residue 3070 LEU
Chi-restraints excluded: chain A residue 3114 SER
Chi-restraints excluded: chain A residue 3361 VAL
Chi-restraints excluded: chain A residue 3416 LEU
Chi-restraints excluded: chain A residue 3417 VAL
Chi-restraints excluded: chain A residue 3620 LEU
Chi-restraints excluded: chain A residue 3647 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 120 optimal weight:    1.9990
   chunk 155 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   chunk 165 optimal weight:   10.0000
   chunk 130 optimal weight:    0.9990
   chunk 151 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 94 optimal weight:    1.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2135 ASN
A2361 GLN
** A2385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3404 HIS ** 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 = 0.4571 r_free = 0.4571 target = 0.216834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.208110 restraints weight = 13849.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.207604 restraints weight = 20531.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.206213 restraints weight = 20374.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.205549 restraints weight = 21815.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.205019 restraints weight = 18165.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.4481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6011
moved from start:          0.1532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  14117  Z= 0.266
  Angle     :  0.718   8.616  19110  Z= 0.374
  Chirality :  0.049   0.241   2204
  Planarity :  0.005   0.050   2418
  Dihedral  :  5.241  23.387   1848
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 13.86
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 10.54 %
    Favored  : 89.40 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 27.39 %
    Favored  : 67.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.31 (0.20), residues: 1717
  helix:  0.81 (0.37), residues: 193
  sheet: -1.69 (0.20), residues: 667
  loop : -1.89 (0.21), residues: 857

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A2763 
 TYR   0.024   0.002   TYR A3385 
 PHE   0.028   0.003   PHE A1670 
 TRP   0.023   0.002   TRP A2186 
 HIS   0.012   0.001   HIS A3404 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00614 /  0.27 (14117)
  covalent geometry    : angle       0.71825 /  0.37 (19110)
  hydrogen bonds       : bond        0.03925 /  2.71 (  492)
  hydrogen bonds       : angle       6.60788 /  4.44 ( 1500)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 170
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2048 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7724 (tp)
REVERT: A 2105 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7153 (tt)
REVERT: A 2383 SER cc_start: 0.8646 (OUTLIER) cc_final: 0.8355 (t)
REVERT: A 2793 HIS cc_start: 0.6834 (OUTLIER) cc_final: 0.6245 (t-90)
REVERT: A 2820 ILE cc_start: 0.6716 (OUTLIER) cc_final: 0.6406 (tp)
REVERT: A 2982 HIS cc_start: 0.6138 (OUTLIER) cc_final: 0.4881 (t-90)
REVERT: A 3171 MET cc_start: 0.2522 (ppp) cc_final: 0.1998 (ppp)
  outliers start: 73
  outliers final: 54
  residues processed: 228
  average time/residue: 0.0768
  time to fit residues: 28.3287
Evaluate side-chains
  226 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 166
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1610 VAL
Chi-restraints excluded: chain A residue 1630 SER
Chi-restraints excluded: chain A residue 1631 ILE
Chi-restraints excluded: chain A residue 1689 MET
Chi-restraints excluded: chain A residue 1766 ILE
Chi-restraints excluded: chain A residue 1767 ILE
Chi-restraints excluded: chain A residue 1803 VAL
Chi-restraints excluded: chain A residue 1941 HIS
Chi-restraints excluded: chain A residue 1980 SER
Chi-restraints excluded: chain A residue 1994 LYS
Chi-restraints excluded: chain A residue 2044 VAL
Chi-restraints excluded: chain A residue 2048 LEU
Chi-restraints excluded: chain A residue 2064 PHE
Chi-restraints excluded: chain A residue 2105 LEU
Chi-restraints excluded: chain A residue 2120 LEU
Chi-restraints excluded: chain A residue 2137 SER
Chi-restraints excluded: chain A residue 2172 THR
Chi-restraints excluded: chain A residue 2181 MET
Chi-restraints excluded: chain A residue 2300 LEU
Chi-restraints excluded: chain A residue 2383 SER
Chi-restraints excluded: chain A residue 2426 VAL
Chi-restraints excluded: chain A residue 2432 VAL
Chi-restraints excluded: chain A residue 2453 ILE
Chi-restraints excluded: chain A residue 2492 ILE
Chi-restraints excluded: chain A residue 2526 VAL
Chi-restraints excluded: chain A residue 2583 LEU
Chi-restraints excluded: chain A residue 2609 ILE
Chi-restraints excluded: chain A residue 2623 CYS
Chi-restraints excluded: chain A residue 2624 MET
Chi-restraints excluded: chain A residue 2626 GLN
Chi-restraints excluded: chain A residue 2629 SER
Chi-restraints excluded: chain A residue 2638 ILE
Chi-restraints excluded: chain A residue 2671 THR
Chi-restraints excluded: chain A residue 2704 SER
Chi-restraints excluded: chain A residue 2754 SER
Chi-restraints excluded: chain A residue 2775 ILE
Chi-restraints excluded: chain A residue 2793 HIS
Chi-restraints excluded: chain A residue 2820 ILE
Chi-restraints excluded: chain A residue 2822 THR
Chi-restraints excluded: chain A residue 2842 CYS
Chi-restraints excluded: chain A residue 2851 VAL
Chi-restraints excluded: chain A residue 2858 SER
Chi-restraints excluded: chain A residue 2884 VAL
Chi-restraints excluded: chain A residue 2938 ASP
Chi-restraints excluded: chain A residue 2958 THR
Chi-restraints excluded: chain A residue 2961 HIS
Chi-restraints excluded: chain A residue 2979 ILE
Chi-restraints excluded: chain A residue 2982 HIS
Chi-restraints excluded: chain A residue 3000 VAL
Chi-restraints excluded: chain A residue 3020 LEU
Chi-restraints excluded: chain A residue 3070 LEU
Chi-restraints excluded: chain A residue 3114 SER
Chi-restraints excluded: chain A residue 3221 VAL
Chi-restraints excluded: chain A residue 3255 VAL
Chi-restraints excluded: chain A residue 3361 VAL
Chi-restraints excluded: chain A residue 3416 LEU
Chi-restraints excluded: chain A residue 3417 VAL
Chi-restraints excluded: chain A residue 3620 LEU
Chi-restraints excluded: chain A residue 3631 THR
Chi-restraints excluded: chain A residue 3647 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 168 optimal weight:    8.9990
   chunk 52 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 150 optimal weight:    0.8980
   chunk 113 optimal weight:    0.9990
   chunk 166 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 34 optimal weight:    0.2980
   chunk 144 optimal weight:    0.7980
   chunk 155 optimal weight:    0.5980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A2284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3327 HIS ** 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 = 0.4598 r_free = 0.4598 target = 0.220545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.211930 restraints weight = 13822.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.211576 restraints weight = 19069.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.210458 restraints weight = 15862.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.209809 restraints weight = 17806.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.209197 restraints weight = 16986.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.4512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5943
moved from start:          0.1526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14117  Z= 0.181
  Angle     :  0.645   7.651  19110  Z= 0.335
  Chirality :  0.048   0.180   2204
  Planarity :  0.004   0.049   2418
  Dihedral  :  5.074  24.018   1848
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.92 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 28.66 %
    Favored  : 67.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.32 (0.20), residues: 1717
  helix:  0.77 (0.37), residues: 196
  sheet: -1.72 (0.20), residues: 667
  loop : -1.89 (0.21), residues: 854

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2542 
 TYR   0.020   0.002   TYR A3085 
 PHE   0.043   0.002   PHE A3222 
 TRP   0.025   0.001   TRP A2186 
 HIS   0.006   0.001   HIS A1625 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00413 /  0.18 (14117)
  covalent geometry    : angle       0.64467 /  0.33 (19110)
  hydrogen bonds       : bond        0.03394 /  2.32 (  492)
  hydrogen bonds       : angle       6.38987 /  4.30 ( 1500)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 173
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2048 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7776 (tp)
REVERT: A 2105 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7065 (tt)
REVERT: A 2383 SER cc_start: 0.8440 (OUTLIER) cc_final: 0.7360 (m)
REVERT: A 2793 HIS cc_start: 0.6782 (OUTLIER) cc_final: 0.6150 (t-90)
REVERT: A 2820 ILE cc_start: 0.6654 (OUTLIER) cc_final: 0.6321 (tp)
REVERT: A 2963 THR cc_start: 0.6331 (t) cc_final: 0.5967 (p)
REVERT: A 2982 HIS cc_start: 0.5996 (OUTLIER) cc_final: 0.4829 (t-90)
REVERT: A 3171 MET cc_start: 0.2223 (ppp) cc_final: 0.1697 (ppp)
  outliers start: 64
  outliers final: 49
  residues processed: 221
  average time/residue: 0.0733
  time to fit residues: 26.4763
Evaluate side-chains
  223 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 168
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1610 VAL
Chi-restraints excluded: chain A residue 1630 SER
Chi-restraints excluded: chain A residue 1631 ILE
Chi-restraints excluded: chain A residue 1689 MET
Chi-restraints excluded: chain A residue 1712 PHE
Chi-restraints excluded: chain A residue 1766 ILE
Chi-restraints excluded: chain A residue 1767 ILE
Chi-restraints excluded: chain A residue 1790 PHE
Chi-restraints excluded: chain A residue 1857 MET
Chi-restraints excluded: chain A residue 1941 HIS
Chi-restraints excluded: chain A residue 1980 SER
Chi-restraints excluded: chain A residue 2048 LEU
Chi-restraints excluded: chain A residue 2064 PHE
Chi-restraints excluded: chain A residue 2105 LEU
Chi-restraints excluded: chain A residue 2120 LEU
Chi-restraints excluded: chain A residue 2135 ASN
Chi-restraints excluded: chain A residue 2137 SER
Chi-restraints excluded: chain A residue 2172 THR
Chi-restraints excluded: chain A residue 2181 MET
Chi-restraints excluded: chain A residue 2188 SER
Chi-restraints excluded: chain A residue 2300 LEU
Chi-restraints excluded: chain A residue 2383 SER
Chi-restraints excluded: chain A residue 2426 VAL
Chi-restraints excluded: chain A residue 2430 VAL
Chi-restraints excluded: chain A residue 2432 VAL
Chi-restraints excluded: chain A residue 2453 ILE
Chi-restraints excluded: chain A residue 2500 VAL
Chi-restraints excluded: chain A residue 2526 VAL
Chi-restraints excluded: chain A residue 2583 LEU
Chi-restraints excluded: chain A residue 2623 CYS
Chi-restraints excluded: chain A residue 2624 MET
Chi-restraints excluded: chain A residue 2626 GLN
Chi-restraints excluded: chain A residue 2629 SER
Chi-restraints excluded: chain A residue 2775 ILE
Chi-restraints excluded: chain A residue 2793 HIS
Chi-restraints excluded: chain A residue 2820 ILE
Chi-restraints excluded: chain A residue 2822 THR
Chi-restraints excluded: chain A residue 2851 VAL
Chi-restraints excluded: chain A residue 2880 LEU
Chi-restraints excluded: chain A residue 2933 PHE
Chi-restraints excluded: chain A residue 2958 THR
Chi-restraints excluded: chain A residue 2961 HIS
Chi-restraints excluded: chain A residue 2979 ILE
Chi-restraints excluded: chain A residue 2982 HIS
Chi-restraints excluded: chain A residue 3000 VAL
Chi-restraints excluded: chain A residue 3020 LEU
Chi-restraints excluded: chain A residue 3070 LEU
Chi-restraints excluded: chain A residue 3114 SER
Chi-restraints excluded: chain A residue 3255 VAL
Chi-restraints excluded: chain A residue 3361 VAL
Chi-restraints excluded: chain A residue 3416 LEU
Chi-restraints excluded: chain A residue 3417 VAL
Chi-restraints excluded: chain A residue 3620 LEU
Chi-restraints excluded: chain A residue 3631 THR
Chi-restraints excluded: chain A residue 3647 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 162 optimal weight:    5.9990
   chunk 61 optimal weight:    0.5980
   chunk 115 optimal weight:    2.9990
   chunk 146 optimal weight:    0.6980
   chunk 119 optimal weight:    0.3980
   chunk 143 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 77 optimal weight:    0.6980
   chunk 62 optimal weight:    0.4980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A2284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3327 HIS ** 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 = 0.4605 r_free = 0.4605 target = 0.221513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4545 r_free = 0.4545 target = 0.212558 restraints weight = 13549.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.211834 restraints weight = 19640.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.210568 restraints weight = 20087.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.210490 restraints weight = 19048.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.210392 restraints weight = 14451.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.4527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5917
moved from start:          0.1592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.080  14117  Z= 0.159
  Angle     :  0.628   7.783  19110  Z= 0.324
  Chirality :  0.047   0.210   2204
  Planarity :  0.004   0.050   2418
  Dihedral  :  4.959  23.296   1848
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.50 %
    Favored  : 91.44 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 28.85 %
    Favored  : 67.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.29 (0.20), residues: 1717
  helix:  0.86 (0.36), residues: 202
  sheet: -1.76 (0.19), residues: 698
  loop : -1.83 (0.21), residues: 817

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2542 
 TYR   0.025   0.002   TYR A2682 
 PHE   0.035   0.002   PHE A3222 
 TRP   0.017   0.001   TRP A2186 
 HIS   0.006   0.001   HIS A1625 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00367 /  0.16 (14117)
  covalent geometry    : angle       0.62793 /  0.32 (19110)
  hydrogen bonds       : bond        0.03255 /  2.21 (  492)
  hydrogen bonds       : angle       6.24477 /  4.21 ( 1500)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 172
  time to evaluate  : 0.544 
Fit side-chains
   revert: symmetry clash
REVERT: A 2048 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7768 (tp)
REVERT: A 2105 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7020 (tt)
REVERT: A 2146 MET cc_start: 0.6808 (tpp) cc_final: 0.6095 (tpp)
REVERT: A 2383 SER cc_start: 0.8396 (OUTLIER) cc_final: 0.7347 (m)
REVERT: A 2793 HIS cc_start: 0.6741 (OUTLIER) cc_final: 0.6128 (t-90)
REVERT: A 2820 ILE cc_start: 0.6672 (OUTLIER) cc_final: 0.6334 (tp)
REVERT: A 2963 THR cc_start: 0.6298 (t) cc_final: 0.5932 (p)
REVERT: A 2982 HIS cc_start: 0.6095 (OUTLIER) cc_final: 0.4916 (t-90)
REVERT: A 3054 PHE cc_start: 0.6414 (p90) cc_final: 0.6128 (p90)
REVERT: A 3171 MET cc_start: 0.2175 (ppp) cc_final: 0.1713 (ppp)
  outliers start: 65
  outliers final: 50
  residues processed: 222
  average time/residue: 0.0844
  time to fit residues: 30.4774
Evaluate side-chains
  224 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 168
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1610 VAL
Chi-restraints excluded: chain A residue 1630 SER
Chi-restraints excluded: chain A residue 1631 ILE
Chi-restraints excluded: chain A residue 1689 MET
Chi-restraints excluded: chain A residue 1712 PHE
Chi-restraints excluded: chain A residue 1766 ILE
Chi-restraints excluded: chain A residue 1767 ILE
Chi-restraints excluded: chain A residue 1790 PHE
Chi-restraints excluded: chain A residue 1941 HIS
Chi-restraints excluded: chain A residue 1980 SER
Chi-restraints excluded: chain A residue 2048 LEU
Chi-restraints excluded: chain A residue 2064 PHE
Chi-restraints excluded: chain A residue 2105 LEU
Chi-restraints excluded: chain A residue 2120 LEU
Chi-restraints excluded: chain A residue 2135 ASN
Chi-restraints excluded: chain A residue 2137 SER
Chi-restraints excluded: chain A residue 2172 THR
Chi-restraints excluded: chain A residue 2181 MET
Chi-restraints excluded: chain A residue 2188 SER
Chi-restraints excluded: chain A residue 2300 LEU
Chi-restraints excluded: chain A residue 2383 SER
Chi-restraints excluded: chain A residue 2430 VAL
Chi-restraints excluded: chain A residue 2432 VAL
Chi-restraints excluded: chain A residue 2453 ILE
Chi-restraints excluded: chain A residue 2526 VAL
Chi-restraints excluded: chain A residue 2583 LEU
Chi-restraints excluded: chain A residue 2623 CYS
Chi-restraints excluded: chain A residue 2624 MET
Chi-restraints excluded: chain A residue 2626 GLN
Chi-restraints excluded: chain A residue 2629 SER
Chi-restraints excluded: chain A residue 2754 SER
Chi-restraints excluded: chain A residue 2793 HIS
Chi-restraints excluded: chain A residue 2820 ILE
Chi-restraints excluded: chain A residue 2822 THR
Chi-restraints excluded: chain A residue 2842 CYS
Chi-restraints excluded: chain A residue 2851 VAL
Chi-restraints excluded: chain A residue 2858 SER
Chi-restraints excluded: chain A residue 2880 LEU
Chi-restraints excluded: chain A residue 2933 PHE
Chi-restraints excluded: chain A residue 2958 THR
Chi-restraints excluded: chain A residue 2961 HIS
Chi-restraints excluded: chain A residue 2979 ILE
Chi-restraints excluded: chain A residue 2982 HIS
Chi-restraints excluded: chain A residue 3000 VAL
Chi-restraints excluded: chain A residue 3020 LEU
Chi-restraints excluded: chain A residue 3070 LEU
Chi-restraints excluded: chain A residue 3114 SER
Chi-restraints excluded: chain A residue 3221 VAL
Chi-restraints excluded: chain A residue 3255 VAL
Chi-restraints excluded: chain A residue 3270 LEU
Chi-restraints excluded: chain A residue 3361 VAL
Chi-restraints excluded: chain A residue 3416 LEU
Chi-restraints excluded: chain A residue 3417 VAL
Chi-restraints excluded: chain A residue 3620 LEU
Chi-restraints excluded: chain A residue 3631 THR
Chi-restraints excluded: chain A residue 3647 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 135 optimal weight:    0.0870
   chunk 38 optimal weight:    2.9990
   chunk 88 optimal weight:    0.0020
   chunk 55 optimal weight:    0.5980
   chunk 63 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   chunk 129 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   overall best weight:    0.4566

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A2284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2992 GLN
** A3327 HIS ** 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 = 0.4619 r_free = 0.4619 target = 0.223386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4560 r_free = 0.4560 target = 0.214575 restraints weight = 13645.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4555 r_free = 0.4555 target = 0.214549 restraints weight = 18565.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.213289 restraints weight = 16199.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.212847 restraints weight = 18436.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4534 r_free = 0.4534 target = 0.212184 restraints weight = 16357.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.4535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5889
moved from start:          0.1625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  14117  Z= 0.139
  Angle     :  0.614   7.958  19110  Z= 0.316
  Chirality :  0.047   0.218   2204
  Planarity :  0.004   0.046   2418
  Dihedral  :  4.838  21.467   1848
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.40 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 29.94 %
    Favored  : 66.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.21 (0.20), residues: 1717
  helix:  0.90 (0.36), residues: 202
  sheet: -1.68 (0.20), residues: 669
  loop : -1.82 (0.21), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2510 
 TYR   0.017   0.002   TYR A3085 
 PHE   0.030   0.001   PHE A3222 
 TRP   0.013   0.001   TRP A2186 
 HIS   0.005   0.001   HIS A1625 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.14 (14117)
  covalent geometry    : angle       0.61415 /  0.32 (19110)
  hydrogen bonds       : bond        0.03115 /  2.10 (  492)
  hydrogen bonds       : angle       6.10148 /  4.11 ( 1500)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 171
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
REVERT: A 2048 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7757 (tp)
REVERT: A 2105 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7045 (tt)
REVERT: A 2128 LEU cc_start: 0.7763 (mp) cc_final: 0.7465 (mt)
REVERT: A 2383 SER cc_start: 0.8220 (OUTLIER) cc_final: 0.7273 (m)
REVERT: A 2793 HIS cc_start: 0.6680 (OUTLIER) cc_final: 0.6211 (t-90)
REVERT: A 2820 ILE cc_start: 0.6454 (OUTLIER) cc_final: 0.6062 (tp)
REVERT: A 2963 THR cc_start: 0.6504 (t) cc_final: 0.6076 (p)
REVERT: A 2982 HIS cc_start: 0.6059 (OUTLIER) cc_final: 0.4891 (t-90)
REVERT: A 3171 MET cc_start: 0.2143 (ppp) cc_final: 0.1678 (ppp)
REVERT: A 3298 LYS cc_start: 0.8090 (mttp) cc_final: 0.7842 (mttp)
  outliers start: 57
  outliers final: 44
  residues processed: 217
  average time/residue: 0.0812
  time to fit residues: 29.1042
Evaluate side-chains
  219 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 169
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1610 VAL
Chi-restraints excluded: chain A residue 1631 ILE
Chi-restraints excluded: chain A residue 1689 MET
Chi-restraints excluded: chain A residue 1766 ILE
Chi-restraints excluded: chain A residue 1767 ILE
Chi-restraints excluded: chain A residue 1790 PHE
Chi-restraints excluded: chain A residue 1941 HIS
Chi-restraints excluded: chain A residue 1980 SER
Chi-restraints excluded: chain A residue 2048 LEU
Chi-restraints excluded: chain A residue 2064 PHE
Chi-restraints excluded: chain A residue 2105 LEU
Chi-restraints excluded: chain A residue 2120 LEU
Chi-restraints excluded: chain A residue 2135 ASN
Chi-restraints excluded: chain A residue 2172 THR
Chi-restraints excluded: chain A residue 2300 LEU
Chi-restraints excluded: chain A residue 2383 SER
Chi-restraints excluded: chain A residue 2430 VAL
Chi-restraints excluded: chain A residue 2432 VAL
Chi-restraints excluded: chain A residue 2453 ILE
Chi-restraints excluded: chain A residue 2583 LEU
Chi-restraints excluded: chain A residue 2623 CYS
Chi-restraints excluded: chain A residue 2624 MET
Chi-restraints excluded: chain A residue 2626 GLN
Chi-restraints excluded: chain A residue 2629 SER
Chi-restraints excluded: chain A residue 2671 THR
Chi-restraints excluded: chain A residue 2749 THR
Chi-restraints excluded: chain A residue 2754 SER
Chi-restraints excluded: chain A residue 2760 ILE
Chi-restraints excluded: chain A residue 2793 HIS
Chi-restraints excluded: chain A residue 2820 ILE
Chi-restraints excluded: chain A residue 2822 THR
Chi-restraints excluded: chain A residue 2842 CYS
Chi-restraints excluded: chain A residue 2851 VAL
Chi-restraints excluded: chain A residue 2858 SER
Chi-restraints excluded: chain A residue 2933 PHE
Chi-restraints excluded: chain A residue 2958 THR
Chi-restraints excluded: chain A residue 2961 HIS
Chi-restraints excluded: chain A residue 2979 ILE
Chi-restraints excluded: chain A residue 2982 HIS
Chi-restraints excluded: chain A residue 3000 VAL
Chi-restraints excluded: chain A residue 3020 LEU
Chi-restraints excluded: chain A residue 3070 LEU
Chi-restraints excluded: chain A residue 3114 SER
Chi-restraints excluded: chain A residue 3255 VAL
Chi-restraints excluded: chain A residue 3361 VAL
Chi-restraints excluded: chain A residue 3416 LEU
Chi-restraints excluded: chain A residue 3417 VAL
Chi-restraints excluded: chain A residue 3620 LEU
Chi-restraints excluded: chain A residue 3631 THR
Chi-restraints excluded: chain A residue 3647 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 83 optimal weight:    0.8980
   chunk 85 optimal weight:    6.9990
   chunk 64 optimal weight:    0.7980
   chunk 116 optimal weight:    0.1980
   chunk 148 optimal weight:    0.4980
   chunk 3 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   chunk 140 optimal weight:    0.4980
   chunk 72 optimal weight:    0.9980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A2284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A3623 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4612 r_free = 0.4612 target = 0.222555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.213698 restraints weight = 13578.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.213253 restraints weight = 19543.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.212442 restraints weight = 17460.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.211930 restraints weight = 19359.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.211166 restraints weight = 17521.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.4528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5900
moved from start:          0.1717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  14117  Z= 0.149
  Angle     :  0.624   8.153  19110  Z= 0.321
  Chirality :  0.047   0.227   2204
  Planarity :  0.004   0.046   2418
  Dihedral  :  4.934  22.620   1848
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 30.13 %
    Favored  : 66.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.18 (0.20), residues: 1717
  helix:  0.87 (0.36), residues: 202
  sheet: -1.65 (0.20), residues: 694
  loop : -1.78 (0.21), residues: 821

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2542 
 TYR   0.025   0.002   TYR A2682 
 PHE   0.033   0.002   PHE A3222 
 TRP   0.012   0.001   TRP A2186 
 HIS   0.008   0.001   HIS A1625 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00343 /  0.15 (14117)
  covalent geometry    : angle       0.62369 /  0.32 (19110)
  hydrogen bonds       : bond        0.03183 /  2.15 (  492)
  hydrogen bonds       : angle       6.10450 /  4.11 ( 1500)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 174
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
REVERT: A 2048 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7768 (tp)
REVERT: A 2105 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7062 (tt)
REVERT: A 2128 LEU cc_start: 0.7777 (mp) cc_final: 0.7512 (mt)
REVERT: A 2383 SER cc_start: 0.8237 (OUTLIER) cc_final: 0.7265 (m)
REVERT: A 2793 HIS cc_start: 0.6671 (OUTLIER) cc_final: 0.6247 (t-90)
REVERT: A 2820 ILE cc_start: 0.6473 (OUTLIER) cc_final: 0.6093 (tp)
REVERT: A 2963 THR cc_start: 0.6491 (t) cc_final: 0.6060 (p)
REVERT: A 2982 HIS cc_start: 0.6068 (OUTLIER) cc_final: 0.4883 (t-90)
REVERT: A 3171 MET cc_start: 0.2145 (ppp) cc_final: 0.1663 (ppp)
REVERT: A 3298 LYS cc_start: 0.8094 (mttp) cc_final: 0.7851 (mttp)
  outliers start: 55
  outliers final: 47
  residues processed: 219
  average time/residue: 0.0812
  time to fit residues: 29.2857
Evaluate side-chains
  223 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 170
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1610 VAL
Chi-restraints excluded: chain A residue 1630 SER
Chi-restraints excluded: chain A residue 1631 ILE
Chi-restraints excluded: chain A residue 1689 MET
Chi-restraints excluded: chain A residue 1766 ILE
Chi-restraints excluded: chain A residue 1767 ILE
Chi-restraints excluded: chain A residue 1790 PHE
Chi-restraints excluded: chain A residue 1941 HIS
Chi-restraints excluded: chain A residue 1980 SER
Chi-restraints excluded: chain A residue 2028 ILE
Chi-restraints excluded: chain A residue 2048 LEU
Chi-restraints excluded: chain A residue 2064 PHE
Chi-restraints excluded: chain A residue 2105 LEU
Chi-restraints excluded: chain A residue 2120 LEU
Chi-restraints excluded: chain A residue 2135 ASN
Chi-restraints excluded: chain A residue 2172 THR
Chi-restraints excluded: chain A residue 2188 SER
Chi-restraints excluded: chain A residue 2300 LEU
Chi-restraints excluded: chain A residue 2383 SER
Chi-restraints excluded: chain A residue 2430 VAL
Chi-restraints excluded: chain A residue 2432 VAL
Chi-restraints excluded: chain A residue 2453 ILE
Chi-restraints excluded: chain A residue 2583 LEU
Chi-restraints excluded: chain A residue 2623 CYS
Chi-restraints excluded: chain A residue 2624 MET
Chi-restraints excluded: chain A residue 2626 GLN
Chi-restraints excluded: chain A residue 2629 SER
Chi-restraints excluded: chain A residue 2665 HIS
Chi-restraints excluded: chain A residue 2671 THR
Chi-restraints excluded: chain A residue 2749 THR
Chi-restraints excluded: chain A residue 2754 SER
Chi-restraints excluded: chain A residue 2793 HIS
Chi-restraints excluded: chain A residue 2820 ILE
Chi-restraints excluded: chain A residue 2822 THR
Chi-restraints excluded: chain A residue 2842 CYS
Chi-restraints excluded: chain A residue 2851 VAL
Chi-restraints excluded: chain A residue 2858 SER
Chi-restraints excluded: chain A residue 2933 PHE
Chi-restraints excluded: chain A residue 2958 THR
Chi-restraints excluded: chain A residue 2961 HIS
Chi-restraints excluded: chain A residue 2979 ILE
Chi-restraints excluded: chain A residue 2982 HIS
Chi-restraints excluded: chain A residue 3000 VAL
Chi-restraints excluded: chain A residue 3020 LEU
Chi-restraints excluded: chain A residue 3070 LEU
Chi-restraints excluded: chain A residue 3114 SER
Chi-restraints excluded: chain A residue 3255 VAL
Chi-restraints excluded: chain A residue 3361 VAL
Chi-restraints excluded: chain A residue 3416 LEU
Chi-restraints excluded: chain A residue 3417 VAL
Chi-restraints excluded: chain A residue 3620 LEU
Chi-restraints excluded: chain A residue 3631 THR
Chi-restraints excluded: chain A residue 3647 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0570
   chunk 68 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 143 optimal weight:    0.9990
   chunk 88 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 96 optimal weight:    0.9990
   chunk 82 optimal weight:    0.0970
   chunk 146 optimal weight:    0.9980
   chunk 93 optimal weight:    0.2980
   overall best weight:    0.4496

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A2284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2536 ASN
** A3327 HIS ** 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 = 0.4622 r_free = 0.4622 target = 0.223791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4566 r_free = 0.4566 target = 0.215274 restraints weight = 13575.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4556 r_free = 0.4556 target = 0.214657 restraints weight = 18546.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.212986 restraints weight = 18710.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.212552 restraints weight = 19325.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.211837 restraints weight = 17164.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.4533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5890
moved from start:          0.1787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  14117  Z= 0.136
  Angle     :  0.610   8.181  19110  Z= 0.312
  Chirality :  0.047   0.230   2204
  Planarity :  0.004   0.045   2418
  Dihedral  :  4.850  24.777   1848
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 30.06 %
    Favored  : 66.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.14 (0.20), residues: 1717
  helix:  0.92 (0.36), residues: 202
  sheet: -1.60 (0.20), residues: 670
  loop : -1.79 (0.21), residues: 845

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A3294 
 TYR   0.016   0.001   TYR A3085 
 PHE   0.029   0.001   PHE A3222 
 TRP   0.011   0.001   TRP A2186 
 HIS   0.008   0.001   HIS A1625 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.14 (14117)
  covalent geometry    : angle       0.60989 /  0.31 (19110)
  hydrogen bonds       : bond        0.03086 /  2.07 (  492)
  hydrogen bonds       : angle       6.00453 /  4.04 ( 1500)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2488.56 seconds
wall clock time: 44 minutes 0.25 seconds (2640.25 seconds total)