Starting phenix.real_space_refine
on Wed Mar  4 13:00:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dgi_27423/03_2026/8dgi_27423.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dgi_27423/03_2026/8dgi_27423.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.94
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dgi_27423/03_2026/8dgi_27423.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dgi_27423/03_2026/8dgi_27423.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dgi_27423/03_2026/8dgi_27423.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dgi_27423/03_2026/8dgi_27423.cif"
  }
  resolution = 3.94
  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=   0.008
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      74      5.16       5
     C    8608      2.51       5
     N    2384      2.21       5
     O    2514      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13580
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 12733
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1582, 12733
          Classifications: {'peptide': 1582}
          Link IDs: {'PTRANS': 96, 'TRANS': 1485}
          Chain breaks: 9
    Chain: "N"
      Number of atoms: 847
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 847
          Classifications: {'peptide': 108}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 105}
  Time building chain proxies: 2.91, per 1000 atoms: 0.21
  Number of scatterers: 13580
  At special positions: 0
  Unit cell: (153.12, 134.85, 135.72, 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      74     16.00
     O    2514      8.00
     N    2384      7.00
     C    8608      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: 1.06
  Conformation dependent library (CDL) restraints added in 590.2 milliseconds
  

  3336 Ramachandran restraints generated.
    1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3222

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 10 sheets defined
      51.0% alpha, 9.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 31
      removed outlier: 3.774A  pdb=" N   ARG A  31 " --> pdb=" O   THR A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 39 through 61
      removed outlier: 3.823A  pdb=" N   LYS A  43 " --> pdb=" O   HIS A  39 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ARG A  56 " --> pdb=" O   GLN A  52 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   ARG A  57 " --> pdb=" O   GLU A  53 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   ARG A  60 " --> pdb=" O   ARG A  56 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   HIS A  61 " --> pdb=" O   ARG A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 88
    Processing helix  chain 'A' and resid 117 through 127
    Processing helix  chain 'A' and resid 131 through 135
      removed outlier: 3.737A  pdb=" N   VAL A 135 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 160
      Proline residue:  A 154  - end of helix
      removed outlier: 3.593A  pdb=" N   HIS A 159 " --> pdb=" O   LEU A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 168
      removed outlier: 3.535A  pdb=" N   ARG A 168 " --> pdb=" O   PRO A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 181
    Processing helix  chain 'A' and resid 184 through 200
    Processing helix  chain 'A' and resid 207 through 215
    Processing helix  chain 'A' and resid 232 through 252
    Processing helix  chain 'A' and resid 255 through 260
    Processing helix  chain 'A' and resid 267 through 272
      removed outlier: 4.004A  pdb=" N   ASP A 271 " --> pdb=" O   ASP A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 293
    Processing helix  chain 'A' and resid 294 through 316
      removed outlier: 4.114A  pdb=" N   LYS A 311 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   THR A 316 " --> pdb=" O   LEU A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 346
      removed outlier: 3.515A  pdb=" N   TYR A 322 " --> pdb=" O   HIS A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 361
      removed outlier: 3.508A  pdb=" N   TYR A 360 " --> pdb=" O   THR A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 374
    Processing helix  chain 'A' and resid 501 through 517
    Processing helix  chain 'A' and resid 540 through 560
      removed outlier: 3.855A  pdb=" N   MET A 560 " --> pdb=" O   LYS A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 569 through 573
    Processing helix  chain 'A' and resid 592 through 603
      removed outlier: 3.857A  pdb=" N   ALA A 603 " --> pdb=" O   CYS A 599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 763 through 783
    Processing helix  chain 'A' and resid 791 through 802
    Processing helix  chain 'A' and resid 824 through 835
    Processing helix  chain 'A' and resid 884 through 904
    Processing helix  chain 'A' and resid 921 through 929
      removed outlier: 5.266A  pdb=" N   GLU A 926 " --> pdb=" O   PRO A 923 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   CYS A 927 " --> pdb=" O   ASP A 924 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1045 through 1062
    Processing helix  chain 'A' and resid 1098 through 1108
    Processing helix  chain 'A' and resid 1117 through 1123
    Processing helix  chain 'A' and resid 1171 through 1180
    Processing helix  chain 'A' and resid 1204 through 1208
    Processing helix  chain 'A' and resid 1223 through 1231
    Processing helix  chain 'A' and resid 1238 through 1240
      No H-bonds generated for 'chain 'A' and resid 1238 through 1240'
    Processing helix  chain 'A' and resid 1248 through 1256
    Processing helix  chain 'A' and resid 1261 through 1268
      removed outlier: 3.566A  pdb=" N   ILE A1265 " --> pdb=" O   ILE A1261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1269 through 1283
    Processing helix  chain 'A' and resid 1519 through 1535
      removed outlier: 4.240A  pdb=" N   THR A1535 " --> pdb=" O   ILE A1531 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1537 through 1547
      removed outlier: 3.612A  pdb=" N   GLN A1541 " --> pdb=" O   ALA A1537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1562 through 1579
      removed outlier: 3.516A  pdb=" N   ARG A1566 " --> pdb=" O   PRO A1562 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   SER A1570 " --> pdb=" O   ARG A1566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1608 through 1616
    Processing helix  chain 'A' and resid 1620 through 1629
      removed outlier: 3.722A  pdb=" N   LEU A1624 " --> pdb=" O   ASN A1620 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1635 through 1650
    Processing helix  chain 'A' and resid 1665 through 1669
      removed outlier: 4.481A  pdb=" N   ASN A1668 " --> pdb=" O   ASP A1665 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1722 through 1731
      removed outlier: 4.027A  pdb=" N   ILE A1726 " --> pdb=" O   SER A1722 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1741 through 1764
      removed outlier: 3.674A  pdb=" N   THR A1746 " --> pdb=" O   GLU A1742 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   ILE A1747 " --> pdb=" O   ARG A1743 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   SER A1750 " --> pdb=" O   THR A1746 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LYS A1753 " --> pdb=" O   ASP A1749 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   TYR A1754 " --> pdb=" O   SER A1750 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   THR A1758 " --> pdb=" O   TYR A1754 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   TYR A1759 " --> pdb=" O   ALA A1755 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   TYR A1764 " --> pdb=" O   LEU A1760 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1768 through 1780
      removed outlier: 3.939A  pdb=" N   LEU A1772 " --> pdb=" O   HIS A1768 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   HIS A1774 " --> pdb=" O   GLY A1770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1781 through 1792
      removed outlier: 3.806A  pdb=" N   LYS A1792 " --> pdb=" O   LEU A1788 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1899 through 1914
      removed outlier: 3.504A  pdb=" N   ILE A1903 " --> pdb=" O   PRO A1899 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ALA A1904 " --> pdb=" O   ASP A1900 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   ALA A1909 " --> pdb=" O   ASP A1905 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ILE A1911 " --> pdb=" O   VAL A1907 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1920 through 1931
      removed outlier: 3.581A  pdb=" N   MET A1927 " --> pdb=" O   ALA A1923 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1981 through 1990
      removed outlier: 4.340A  pdb=" N   LEU A1990 " --> pdb=" O   LEU A1986 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1992 through 2001
      removed outlier: 3.600A  pdb=" N   PHE A1996 " --> pdb=" O   GLY A1992 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2007 through 2014
    Processing helix  chain 'A' and resid 2030 through 2050
      removed outlier: 3.750A  pdb=" N   LEU A2034 " --> pdb=" O   ARG A2030 " (cutoff:3.500A)
      removed outlier: 4.670A  pdb=" N   ALA A2037 " --> pdb=" O   PHE A2033 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   ASP A2050 " --> pdb=" O   HIS A2046 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2055 through 2067
    Processing helix  chain 'A' and resid 2068 through 2079
      removed outlier: 3.934A  pdb=" N   PHE A2072 " --> pdb=" O   ASN A2068 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2091 through 2107
    Processing helix  chain 'A' and resid 2110 through 2121
      removed outlier: 5.117A  pdb=" N   SER A2118 " --> pdb=" O   TYR A2114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2132 through 2149
      removed outlier: 3.941A  pdb=" N   PHE A2138 " --> pdb=" O   LEU A2134 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   ALA A2142 " --> pdb=" O   PHE A2138 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLY A2143 " --> pdb=" O   GLU A2139 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   SER A2149 " --> pdb=" O   ILE A2145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2152 through 2172
      removed outlier: 3.567A  pdb=" N   VAL A2156 " --> pdb=" O   SER A2152 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   ASN A2162 " --> pdb=" O   HIS A2158 " (cutoff:3.500A)
      removed outlier: 5.043A  pdb=" N   MET A2163 " --> pdb=" O   VAL A2159 " (cutoff:3.500A)
      Proline residue:  A2166  - end of helix
    Processing helix  chain 'A' and resid 2178 through 2187
    Processing helix  chain 'A' and resid 2223 through 2240
    Processing helix  chain 'N' and resid 359 through 372
    Processing helix  chain 'N' and resid 376 through 385
    Processing helix  chain 'N' and resid 394 through 405
    Processing helix  chain 'N' and resid 443 through 463
    Processing sheet with id=AA1, first strand: chain 'A' and resid 137 through 140
      removed outlier: 5.435A  pdb=" N   ILE A  34 " --> pdb=" O   GLU A 204 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 68
      removed outlier: 6.438A  pdb=" N   SER A  65 " --> pdb=" O   SER A 114 " (cutoff:3.500A)
      removed outlier: 7.382A  pdb=" N   LEU A 116 " --> pdb=" O   SER A  65 " (cutoff:3.500A)
      removed outlier: 5.580A  pdb=" N   TYR A  67 " --> pdb=" O   LEU A 116 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 527 through 529
      removed outlier: 6.771A  pdb=" N   GLN A 528 " --> pdb=" O   ILE A 567 " (cutoff:3.500A)
      removed outlier: 8.142A  pdb=" N   VAL A1585 " --> pdb=" O   GLU A 221 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   ILE A 223 " --> pdb=" O   VAL A1585 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 847 through 855
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1022 through 1026
      removed outlier: 3.942A  pdb=" N   PHE A1022 " --> pdb=" O   VAL A1033 " (cutoff:3.500A)
      removed outlier: 5.874A  pdb=" N   LYS A1032 " --> pdb=" O   LEU A 983 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   LEU A 983 " --> pdb=" O   LYS A1032 " (cutoff:3.500A)
      removed outlier: 7.303A  pdb=" N   SER A1034 " --> pdb=" O   LEU A 981 " (cutoff:3.500A)
      removed outlier: 5.258A  pdb=" N   LEU A 981 " --> pdb=" O   SER A1034 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   GLU A1036 " --> pdb=" O   ILE A 979 " (cutoff:3.500A)
      removed outlier: 5.663A  pdb=" N   ILE A 979 " --> pdb=" O   GLU A1036 " (cutoff:3.500A)
      removed outlier: 4.813A  pdb=" N   PHE A1008 " --> pdb=" O   ILE A 979 " (cutoff:3.500A)
      removed outlier: 8.495A  pdb=" N   LEU A 981 " --> pdb=" O   GLN A1006 " (cutoff:3.500A)
      removed outlier: 10.060A  pdb=" N   GLN A1006 " --> pdb=" O   LEU A 981 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1236 through 1237
      removed outlier: 7.273A  pdb=" N   LEU A1191 " --> pdb=" O   ILE A1154 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   ILE A1154 " --> pdb=" O   LEU A1191 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   ASP A1193 " --> pdb=" O   ALA A1152 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1937 through 1940
    Processing sheet with id=AA8, first strand: chain 'A' and resid 2191 through 2193
    Processing sheet with id=AA9, first strand: chain 'A' and resid 2191 through 2193
    Processing sheet with id=AB1, first strand: chain 'N' and resid 409 through 414
      removed outlier: 4.551A  pdb=" N   GLN N 424 " --> pdb=" O   ILE N 414 " (cutoff:3.500A)

    640 hydrogen bonds defined for protein.
    1839 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.94

  Time building geometry restraints manager: 1.44 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4471
        1.34 -     1.46: 2789
        1.46 -     1.58: 6516
        1.58 -     1.70: 3
        1.70 -     1.82: 100
  Bond restraints: 13879
  Sorted by residual:
  bond pdb=" C   GLU A 922 "
       pdb=" N   PRO A 923 "
    ideal  model  delta    sigma   weight residual
    1.336  1.376 -0.040 1.08e-02 8.57e+03 1.36e+01
  bond pdb=" C   LYS A2083 "
       pdb=" N   PHE A2084 "
    ideal  model  delta    sigma   weight residual
    1.332  1.374 -0.041 1.40e-02 5.10e+03 8.64e+00
  bond pdb=" C   VAL A2175 "
       pdb=" N   PRO A2176 "
    ideal  model  delta    sigma   weight residual
    1.334  1.401 -0.067 2.34e-02 1.83e+03 8.22e+00
  bond pdb=" N   ASP A  90 "
       pdb=" CA  ASP A  90 "
    ideal  model  delta    sigma   weight residual
    1.463  1.434  0.029 1.23e-02 6.61e+03 5.65e+00
  bond pdb=" C   VAL A2130 "
       pdb=" N   PRO A2131 "
    ideal  model  delta    sigma   weight residual
    1.334  1.386 -0.052 2.34e-02 1.83e+03 4.89e+00
  ... (remaining 13874 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.42: 18426
        3.42 -     6.83: 305
        6.83 -    10.25: 67
       10.25 -    13.66: 13
       13.66 -    17.08: 5
  Bond angle restraints: 18816
  Sorted by residual:
  angle pdb=" N   ARG A2030 "
        pdb=" CA  ARG A2030 "
        pdb=" C   ARG A2030 "
      ideal   model   delta    sigma   weight residual
     114.75  106.58    8.17 1.26e+00 6.30e-01 4.20e+01
  angle pdb=" CA  ARG A1566 "
        pdb=" CB  ARG A1566 "
        pdb=" CG  ARG A1566 "
      ideal   model   delta    sigma   weight residual
     114.10  125.30  -11.20 2.00e+00 2.50e-01 3.14e+01
  angle pdb=" N   PRO A 256 "
        pdb=" CD  PRO A 256 "
        pdb=" CG  PRO A 256 "
      ideal   model   delta    sigma   weight residual
     103.20   95.23    7.97 1.50e+00 4.44e-01 2.82e+01
  angle pdb=" CA  PRO A 256 "
        pdb=" N   PRO A 256 "
        pdb=" CD  PRO A 256 "
      ideal   model   delta    sigma   weight residual
     112.00  104.70    7.30 1.40e+00 5.10e-01 2.72e+01
  angle pdb=" CA  GLN N 406 "
        pdb=" CB  GLN N 406 "
        pdb=" CG  GLN N 406 "
      ideal   model   delta    sigma   weight residual
     114.10  124.32  -10.22 2.00e+00 2.50e-01 2.61e+01
  ... (remaining 18811 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.22: 7380
       18.22 -    36.45: 888
       36.45 -    54.67: 160
       54.67 -    72.90: 30
       72.90 -    91.12: 11
  Dihedral angle restraints: 8469
    sinusoidal: 3504
      harmonic: 4965
  Sorted by residual:
  dihedral pdb=" CA  THR A1205 "
           pdb=" C   THR A1205 "
           pdb=" N   PRO A1206 "
           pdb=" CA  PRO A1206 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -133.56  -46.44     0      5.00e+00 4.00e-02 8.63e+01
  dihedral pdb=" CA  LEU A2116 "
           pdb=" C   LEU A2116 "
           pdb=" N   LEU A2117 "
           pdb=" CA  LEU A2117 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.49   31.51     0      5.00e+00 4.00e-02 3.97e+01
  dihedral pdb=" CA  ILE A2110 "
           pdb=" C   ILE A2110 "
           pdb=" N   SER A2111 "
           pdb=" CA  SER A2111 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.47  -28.53     0      5.00e+00 4.00e-02 3.26e+01
  ... (remaining 8466 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 1750
       0.069 -    0.139: 292
       0.139 -    0.208: 45
       0.208 -    0.278: 7
       0.278 -    0.347: 4
  Chirality restraints: 2098
  Sorted by residual:
  chirality pdb=" CB  VAL A 554 "
            pdb=" CA  VAL A 554 "
            pdb=" CG1 VAL A 554 "
            pdb=" CG2 VAL A 554 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.28   -0.35 2.00e-01 2.50e+01 3.01e+00
  chirality pdb=" CA  MET A 161 "
            pdb=" N   MET A 161 "
            pdb=" C   MET A 161 "
            pdb=" CB  MET A 161 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.30 2.00e-01 2.50e+01 2.18e+00
  chirality pdb=" CA  TYR A2041 "
            pdb=" N   TYR A2041 "
            pdb=" C   TYR A2041 "
            pdb=" CB  TYR A2041 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.16e+00
  ... (remaining 2095 not shown)

  Planarity restraints: 2448
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A2041 "    0.039 2.00e-02 2.50e+03   2.30e-02 1.06e+01
        pdb=" CG  TYR A2041 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 TYR A2041 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD2 TYR A2041 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE1 TYR A2041 "    0.022 2.00e-02 2.50e+03
        pdb=" CE2 TYR A2041 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A2041 "    0.007 2.00e-02 2.50e+03
        pdb=" OH  TYR A2041 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 532 "   -0.016 2.00e-02 2.50e+03   3.11e-02 9.69e+00
        pdb=" C   ASP A 532 "    0.054 2.00e-02 2.50e+03
        pdb=" O   ASP A 532 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   ARG A 533 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU N 432 "    0.051 5.00e-02 4.00e+02   7.76e-02 9.65e+00
        pdb=" N   PRO N 433 "   -0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO N 433 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO N 433 "    0.038 5.00e-02 4.00e+02
  ... (remaining 2445 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 3153
        2.79 -     3.32: 12530
        3.32 -     3.85: 23811
        3.85 -     4.37: 26896
        4.37 -     4.90: 43684
  Nonbonded interactions: 110074
  Sorted by model distance:
  nonbonded pdb=" OG  SER A1750 "
            pdb=" OD2 ASP A2040 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" O   ASP A2040 "
            pdb=" OG1 THR A2044 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" OE1 GLU A 221 "
            pdb=" OH  TYR A 596 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   PRO A 868 "
            pdb=" OG  SER A 871 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" OH  TYR A2002 "
            pdb=" OD1 ASP A2148 "
     model   vdw
     2.306 3.040
  ... (remaining 110069 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     14.110
  Find NCS groups from input model:        0.060
  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:             0.010
  Load rotamer database and sin/cos tables:1.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5162
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.094  13879  Z= 0.255
  Angle     :  1.162  17.078  18816  Z= 0.605
  Chirality :  0.055   0.347   2098
  Planarity :  0.009   0.087   2448
  Dihedral  : 15.934  91.123   5247
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  5.88 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 21.65 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.25 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.03 %
    Twisted General : 0.06 %

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 (0.18), residues: 1668
  helix: -1.62 (0.15), residues: 791
  sheet: -0.16 (0.38), residues: 189
  loop : -1.68 (0.22), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A1566 
 TYR   0.039   0.002   TYR A2041 
 PHE   0.037   0.003   PHE A2072 
 TRP   0.021   0.002   TRP A1968 
 HIS   0.015   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 (13879)
  covalent geometry    : angle       1.16164 (18816)
  hydrogen bonds       : bond        0.15975 (  638)
  hydrogen bonds       : angle       7.42394 ( 1839)

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

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

  3336 Ramachandran restraints generated.
    1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3336 Ramachandran restraints generated.
    1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 132
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 LYS cc_start: 0.8179 (tmtt) cc_final: 0.7832 (tptp)
  outliers start: 10
  outliers final: 3
  residues processed: 137
  average time/residue: 0.1136
  time to fit residues: 22.7089
Evaluate side-chains
  121 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 118
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ARG
Chi-restraints excluded: chain A residue  841 PHE
Chi-restraints excluded: chain A residue 2054 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    0.0020
   chunk 130 optimal weight:    8.9990
   chunk 124 optimal weight:   30.0000
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    0.0570
   chunk 149 optimal weight:    2.9990
   overall best weight:    0.7108

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

Flipped N/Q/H residues before XYZ refinement:
A 548 HIS
A 773 GLN
A 895 GLN
A1668 ASN
A1774 HIS
** A2012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2029 GLN
A2054 HIS
N 389 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5181 r_free = 0.5181 target = 0.196131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4961 r_free = 0.4961 target = 0.176515 restraints weight = 38408.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4935 r_free = 0.4935 target = 0.176953 restraints weight = 38508.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4950 r_free = 0.4950 target = 0.178302 restraints weight = 30397.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4953 r_free = 0.4953 target = 0.178694 restraints weight = 22811.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4954 r_free = 0.4954 target = 0.178796 restraints weight = 21400.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.4984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4794
moved from start:          0.1154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  13879  Z= 0.138
  Angle     :  0.680  10.387  18816  Z= 0.343
  Chirality :  0.043   0.164   2098
  Planarity :  0.006   0.069   2448
  Dihedral  :  5.549  43.282   1864
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.16 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 18.25 %
    Favored  : 79.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.03 %
    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: -1.09 (0.20), residues: 1668
  helix: -0.31 (0.17), residues: 803
  sheet: -0.16 (0.38), residues: 193
  loop : -1.28 (0.24), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  60 
 TYR   0.030   0.001   TYR A2041 
 PHE   0.022   0.001   PHE A2085 
 TRP   0.010   0.001   TRP A 848 
 HIS   0.009   0.001   HIS A2087 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (13879)
  covalent geometry    : angle       0.68018 (18816)
  hydrogen bonds       : bond        0.04205 (  638)
  hydrogen bonds       : angle       5.26710 ( 1839)

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

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

  3336 Ramachandran restraints generated.
    1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3336 Ramachandran restraints generated.
    1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 127
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 LEU cc_start: 0.5368 (OUTLIER) cc_final: 0.4851 (pp)
REVERT: A  286 LEU cc_start: 0.4598 (mt) cc_final: 0.4242 (mt)
REVERT: A 1137 MET cc_start: 0.2001 (OUTLIER) cc_final: 0.1492 (mmp)
  outliers start: 40
  outliers final: 15
  residues processed: 158
  average time/residue: 0.1122
  time to fit residues: 26.0059
Evaluate side-chains
  128 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 PHE
Chi-restraints excluded: chain A residue   90 ASP
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  201 CYS
Chi-restraints excluded: chain A residue 1137 MET
Chi-restraints excluded: chain A residue 1261 ILE
Chi-restraints excluded: chain A residue 1747 ILE
Chi-restraints excluded: chain A residue 1768 HIS
Chi-restraints excluded: chain A residue 1973 SER
Chi-restraints excluded: chain A residue 2028 TYR
Chi-restraints excluded: chain A residue 2046 HIS
Chi-restraints excluded: chain A residue 2069 ASN
Chi-restraints excluded: chain A residue 2070 THR
Chi-restraints excluded: chain A residue 2089 SER
Chi-restraints excluded: chain A residue 2100 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 119 optimal weight:    4.9990
   chunk 11 optimal weight:    9.9990
   chunk 17 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 112 optimal weight:    0.7980
   chunk 153 optimal weight:    0.9980
   chunk 88 optimal weight:    0.8980
   chunk 30 optimal weight:    8.9990
   chunk 72 optimal weight:   10.0000
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 548 HIS
A1067 GLN
** A1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2054 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5169 r_free = 0.5169 target = 0.195174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4944 r_free = 0.4944 target = 0.175502 restraints weight = 38719.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4910 r_free = 0.4910 target = 0.175412 restraints weight = 39977.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4930 r_free = 0.4930 target = 0.176957 restraints weight = 34323.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4933 r_free = 0.4933 target = 0.177378 restraints weight = 23084.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4935 r_free = 0.4935 target = 0.177558 restraints weight = 21544.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.4967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4851
moved from start:          0.1658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13879  Z= 0.136
  Angle     :  0.656  11.232  18816  Z= 0.324
  Chirality :  0.043   0.194   2098
  Planarity :  0.005   0.067   2448
  Dihedral  :  5.110  44.468   1856
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.94 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 17.32 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.03 %
    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: -0.58 (0.21), residues: 1668
  helix:  0.20 (0.18), residues: 806
  sheet: -0.32 (0.40), residues: 181
  loop : -1.01 (0.25), residues: 681

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1566 
 TYR   0.021   0.001   TYR A2028 
 PHE   0.022   0.001   PHE A2085 
 TRP   0.010   0.001   TRP A 848 
 HIS   0.008   0.001   HIS A2087 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (13879)
  covalent geometry    : angle       0.65632 (18816)
  hydrogen bonds       : bond        0.03776 (  638)
  hydrogen bonds       : angle       4.91701 ( 1839)

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

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

  3336 Ramachandran restraints generated.
    1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3336 Ramachandran restraints generated.
    1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 121
  time to evaluate  : 0.508 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 LEU cc_start: 0.5507 (OUTLIER) cc_final: 0.4946 (pp)
REVERT: A  286 LEU cc_start: 0.4776 (mt) cc_final: 0.4340 (mt)
REVERT: A  572 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6539 (tt)
REVERT: A 1137 MET cc_start: 0.1698 (OUTLIER) cc_final: 0.1186 (mmp)
REVERT: A 1173 LYS cc_start: 0.5404 (OUTLIER) cc_final: 0.4988 (mmmt)
REVERT: A 1543 GLN cc_start: 0.6491 (OUTLIER) cc_final: 0.6235 (tm-30)
REVERT: A 1632 ARG cc_start: 0.6903 (mpt180) cc_final: 0.6651 (mpt180)
REVERT: A 1749 ASP cc_start: 0.7546 (t0) cc_final: 0.7162 (t0)
REVERT: A 1975 LEU cc_start: 0.4993 (tp) cc_final: 0.4492 (mt)
REVERT: A 2020 THR cc_start: 0.6393 (OUTLIER) cc_final: 0.5865 (p)
  outliers start: 60
  outliers final: 33
  residues processed: 169
  average time/residue: 0.1101
  time to fit residues: 27.5270
Evaluate side-chains
  150 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 111
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   77 GLU
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue   89 THR
Chi-restraints excluded: chain A residue   90 ASP
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  297 CYS
Chi-restraints excluded: chain A residue  521 ASP
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  764 THR
Chi-restraints excluded: chain A residue  768 VAL
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue 1137 MET
Chi-restraints excluded: chain A residue 1173 LYS
Chi-restraints excluded: chain A residue 1261 ILE
Chi-restraints excluded: chain A residue 1268 LEU
Chi-restraints excluded: chain A residue 1282 LEU
Chi-restraints excluded: chain A residue 1543 GLN
Chi-restraints excluded: chain A residue 1747 ILE
Chi-restraints excluded: chain A residue 1768 HIS
Chi-restraints excluded: chain A residue 1769 GLU
Chi-restraints excluded: chain A residue 1780 VAL
Chi-restraints excluded: chain A residue 1917 GLU
Chi-restraints excluded: chain A residue 1927 MET
Chi-restraints excluded: chain A residue 1973 SER
Chi-restraints excluded: chain A residue 2020 THR
Chi-restraints excluded: chain A residue 2028 TYR
Chi-restraints excluded: chain A residue 2046 HIS
Chi-restraints excluded: chain A residue 2069 ASN
Chi-restraints excluded: chain A residue 2070 THR
Chi-restraints excluded: chain A residue 2089 SER
Chi-restraints excluded: chain A residue 2100 VAL
Chi-restraints excluded: chain A residue 2158 HIS
Chi-restraints excluded: chain N residue  392 ILE
Chi-restraints excluded: chain N residue  462 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   chunk 167 optimal weight:   10.0000
   chunk 129 optimal weight:   10.0000
   chunk 89 optimal weight:   20.0000
   chunk 28 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 132 optimal weight:    0.7980
   chunk 141 optimal weight:    1.9990
   chunk 108 optimal weight:    3.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
A 548 HIS
** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1559 GLN
** A1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5127 r_free = 0.5127 target = 0.191619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4874 r_free = 0.4874 target = 0.169039 restraints weight = 37430.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4817 r_free = 0.4817 target = 0.168006 restraints weight = 34177.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4831 r_free = 0.4831 target = 0.169124 restraints weight = 31005.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4841 r_free = 0.4841 target = 0.170081 restraints weight = 22246.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4845 r_free = 0.4845 target = 0.170389 restraints weight = 18883.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.4899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5078
moved from start:          0.2175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13879  Z= 0.149
  Angle     :  0.658  11.476  18816  Z= 0.327
  Chirality :  0.043   0.192   2098
  Planarity :  0.005   0.066   2448
  Dihedral  :  5.057  44.405   1856
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 14.35
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.24 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 18.25 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.03 %
    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: -0.44 (0.21), residues: 1668
  helix:  0.40 (0.18), residues: 813
  sheet: -0.43 (0.39), residues: 181
  loop : -1.00 (0.25), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 594 
 TYR   0.023   0.001   TYR A2028 
 PHE   0.023   0.002   PHE A2138 
 TRP   0.012   0.001   TRP A 848 
 HIS   0.008   0.001   HIS A2087 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (13879)
  covalent geometry    : angle       0.65799 (18816)
  hydrogen bonds       : bond        0.03698 (  638)
  hydrogen bonds       : angle       4.84787 ( 1839)

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

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

  3336 Ramachandran restraints generated.
    1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3336 Ramachandran restraints generated.
    1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 119
  time to evaluate  : 0.617 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 LEU cc_start: 0.5567 (OUTLIER) cc_final: 0.5082 (pp)
REVERT: A  286 LEU cc_start: 0.4978 (mt) cc_final: 0.4551 (mt)
REVERT: A  572 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6763 (tt)
REVERT: A  609 TYR cc_start: 0.6919 (m-80) cc_final: 0.6703 (m-10)
REVERT: A  994 ARG cc_start: -0.3709 (OUTLIER) cc_final: -0.4436 (mpt180)
REVERT: A 1137 MET cc_start: 0.1585 (mmp) cc_final: 0.0919 (mmm)
REVERT: A 1149 PHE cc_start: 0.7370 (m-80) cc_final: 0.7013 (m-80)
REVERT: A 1633 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7104 (pp20)
REVERT: A 1749 ASP cc_start: 0.7567 (t0) cc_final: 0.7209 (t0)
REVERT: A 2020 THR cc_start: 0.6744 (OUTLIER) cc_final: 0.5427 (t)
REVERT: A 2041 TYR cc_start: 0.5523 (t80) cc_final: 0.5189 (t80)
  outliers start: 61
  outliers final: 36
  residues processed: 170
  average time/residue: 0.1104
  time to fit residues: 28.2028
Evaluate side-chains
  149 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 108
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   77 GLU
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue   89 THR
Chi-restraints excluded: chain A residue   90 ASP
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  297 CYS
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  764 THR
Chi-restraints excluded: chain A residue  768 VAL
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  994 ARG
Chi-restraints excluded: chain A residue 1088 VAL
Chi-restraints excluded: chain A residue 1192 LEU
Chi-restraints excluded: chain A residue 1238 VAL
Chi-restraints excluded: chain A residue 1261 ILE
Chi-restraints excluded: chain A residue 1282 LEU
Chi-restraints excluded: chain A residue 1633 GLU
Chi-restraints excluded: chain A residue 1747 ILE
Chi-restraints excluded: chain A residue 1762 ILE
Chi-restraints excluded: chain A residue 1768 HIS
Chi-restraints excluded: chain A residue 1769 GLU
Chi-restraints excluded: chain A residue 1780 VAL
Chi-restraints excluded: chain A residue 1927 MET
Chi-restraints excluded: chain A residue 1973 SER
Chi-restraints excluded: chain A residue 2020 THR
Chi-restraints excluded: chain A residue 2028 TYR
Chi-restraints excluded: chain A residue 2046 HIS
Chi-restraints excluded: chain A residue 2069 ASN
Chi-restraints excluded: chain A residue 2070 THR
Chi-restraints excluded: chain A residue 2089 SER
Chi-restraints excluded: chain A residue 2100 VAL
Chi-restraints excluded: chain A residue 2158 HIS
Chi-restraints excluded: chain N residue  392 ILE
Chi-restraints excluded: chain N residue  462 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 75 optimal weight:   30.0000
   chunk 3 optimal weight:    0.9980
   chunk 111 optimal weight:    0.7980
   chunk 96 optimal weight:    9.9990
   chunk 54 optimal weight:    7.9990
   chunk 81 optimal weight:    8.9990
   chunk 99 optimal weight:    0.8980
   chunk 97 optimal weight:    2.9990
   chunk 157 optimal weight:    0.9980
   chunk 69 optimal weight:    0.1980
   chunk 161 optimal weight:    5.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 548 HIS
** A1196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1766 ASN
** A2012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5154 r_free = 0.5154 target = 0.193786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4925 r_free = 0.4925 target = 0.174234 restraints weight = 38443.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4904 r_free = 0.4904 target = 0.174081 restraints weight = 40223.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4919 r_free = 0.4919 target = 0.175717 restraints weight = 34432.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4920 r_free = 0.4920 target = 0.175886 restraints weight = 24472.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4921 r_free = 0.4921 target = 0.176122 restraints weight = 24864.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.4950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4896
moved from start:          0.2374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13879  Z= 0.132
  Angle     :  0.655  12.578  18816  Z= 0.322
  Chirality :  0.043   0.377   2098
  Planarity :  0.004   0.065   2448
  Dihedral  :  4.940  44.818   1856
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.12 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 19.25 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.03 %
    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: -0.29 (0.21), residues: 1668
  helix:  0.51 (0.18), residues: 813
  sheet: -0.52 (0.39), residues: 180
  loop : -0.87 (0.25), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1566 
 TYR   0.018   0.001   TYR A2028 
 PHE   0.022   0.001   PHE A2138 
 TRP   0.008   0.001   TRP A1139 
 HIS   0.007   0.001   HIS A2087 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (13879)
  covalent geometry    : angle       0.65520 (18816)
  hydrogen bonds       : bond        0.03492 (  638)
  hydrogen bonds       : angle       4.72271 ( 1839)

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

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

  3336 Ramachandran restraints generated.
    1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3336 Ramachandran restraints generated.
    1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 117
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 LEU cc_start: 0.5804 (OUTLIER) cc_final: 0.5283 (pp)
REVERT: A  286 LEU cc_start: 0.4923 (mt) cc_final: 0.4439 (mt)
REVERT: A  572 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6693 (tt)
REVERT: A  994 ARG cc_start: -0.3663 (OUTLIER) cc_final: -0.4002 (mtt90)
REVERT: A 1137 MET cc_start: 0.2328 (OUTLIER) cc_final: 0.1783 (mmp)
REVERT: A 1633 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7288 (pp20)
REVERT: A 1749 ASP cc_start: 0.7515 (t0) cc_final: 0.7241 (t0)
REVERT: A 2020 THR cc_start: 0.6535 (OUTLIER) cc_final: 0.5337 (t)
  outliers start: 50
  outliers final: 30
  residues processed: 158
  average time/residue: 0.1065
  time to fit residues: 25.2171
Evaluate side-chains
  143 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 107
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   77 GLU
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue   89 THR
Chi-restraints excluded: chain A residue   90 ASP
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  297 CYS
Chi-restraints excluded: chain A residue  303 HIS
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  764 THR
Chi-restraints excluded: chain A residue  768 VAL
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  994 ARG
Chi-restraints excluded: chain A residue 1137 MET
Chi-restraints excluded: chain A residue 1192 LEU
Chi-restraints excluded: chain A residue 1261 ILE
Chi-restraints excluded: chain A residue 1282 LEU
Chi-restraints excluded: chain A residue 1633 GLU
Chi-restraints excluded: chain A residue 1747 ILE
Chi-restraints excluded: chain A residue 1768 HIS
Chi-restraints excluded: chain A residue 1769 GLU
Chi-restraints excluded: chain A residue 1927 MET
Chi-restraints excluded: chain A residue 1968 TRP
Chi-restraints excluded: chain A residue 1973 SER
Chi-restraints excluded: chain A residue 2020 THR
Chi-restraints excluded: chain A residue 2028 TYR
Chi-restraints excluded: chain A residue 2046 HIS
Chi-restraints excluded: chain A residue 2070 THR
Chi-restraints excluded: chain A residue 2100 VAL
Chi-restraints excluded: chain A residue 2158 HIS
Chi-restraints excluded: chain N residue  392 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 146 optimal weight:    0.9980
   chunk 45 optimal weight:    0.5980
   chunk 105 optimal weight:    7.9990
   chunk 138 optimal weight:    0.9990
   chunk 118 optimal weight:    1.9990
   chunk 89 optimal weight:    9.9990
   chunk 104 optimal weight:    0.9990
   chunk 65 optimal weight:    7.9990
   chunk 162 optimal weight:    0.0030
   chunk 32 optimal weight:    4.9990
   overall best weight:    0.7194

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

Flipped N/Q/H residues before XYZ refinement:
A 548 HIS
** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 875 HIS
A1782 ASN
** A1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5137 r_free = 0.5137 target = 0.192520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4879 r_free = 0.4879 target = 0.169669 restraints weight = 37477.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4846 r_free = 0.4846 target = 0.169942 restraints weight = 28186.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4864 r_free = 0.4864 target = 0.171596 restraints weight = 22743.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4869 r_free = 0.4869 target = 0.172007 restraints weight = 17288.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4870 r_free = 0.4870 target = 0.172121 restraints weight = 16068.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.4920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5016
moved from start:          0.2606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13879  Z= 0.126
  Angle     :  0.648  13.180  18816  Z= 0.317
  Chirality :  0.042   0.168   2098
  Planarity :  0.004   0.064   2448
  Dihedral  :  4.845  44.637   1856
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.12 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 19.25 %
    Favored  : 77.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.03 %
    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: -0.18 (0.21), residues: 1668
  helix:  0.67 (0.18), residues: 808
  sheet: -0.55 (0.39), residues: 175
  loop : -0.86 (0.25), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1286 
 TYR   0.025   0.001   TYR A1542 
 PHE   0.019   0.001   PHE A1552 
 TRP   0.010   0.001   TRP A1929 
 HIS   0.007   0.001   HIS A2087 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (13879)
  covalent geometry    : angle       0.64829 (18816)
  hydrogen bonds       : bond        0.03338 (  638)
  hydrogen bonds       : angle       4.62959 ( 1839)

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

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

  3336 Ramachandran restraints generated.
    1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3336 Ramachandran restraints generated.
    1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 118
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 LEU cc_start: 0.5636 (OUTLIER) cc_final: 0.5054 (pp)
REVERT: A  524 PHE cc_start: 0.5767 (p90) cc_final: 0.5559 (p90)
REVERT: A  873 LEU cc_start: 0.4996 (OUTLIER) cc_final: 0.4543 (mp)
REVERT: A  930 LEU cc_start: 0.3551 (OUTLIER) cc_final: 0.1923 (mp)
REVERT: A  994 ARG cc_start: -0.3733 (OUTLIER) cc_final: -0.4226 (mpt180)
REVERT: A 1137 MET cc_start: 0.2309 (OUTLIER) cc_final: 0.1608 (mmm)
REVERT: A 1633 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7339 (pp20)
REVERT: A 1749 ASP cc_start: 0.7547 (t0) cc_final: 0.7314 (t0)
REVERT: A 2020 THR cc_start: 0.6744 (OUTLIER) cc_final: 0.5504 (t)
REVERT: A 2153 LEU cc_start: 0.3035 (OUTLIER) cc_final: 0.2415 (mp)
REVERT: A 2177 LYS cc_start: 0.4621 (OUTLIER) cc_final: 0.1562 (mmmt)
  outliers start: 53
  outliers final: 34
  residues processed: 164
  average time/residue: 0.1001
  time to fit residues: 24.7338
Evaluate side-chains
  147 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 104
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue   77 GLU
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue   89 THR
Chi-restraints excluded: chain A residue   90 ASP
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  297 CYS
Chi-restraints excluded: chain A residue  303 HIS
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  764 THR
Chi-restraints excluded: chain A residue  768 VAL
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  930 LEU
Chi-restraints excluded: chain A residue  994 ARG
Chi-restraints excluded: chain A residue 1088 VAL
Chi-restraints excluded: chain A residue 1137 MET
Chi-restraints excluded: chain A residue 1192 LEU
Chi-restraints excluded: chain A residue 1261 ILE
Chi-restraints excluded: chain A residue 1282 LEU
Chi-restraints excluded: chain A residue 1633 GLU
Chi-restraints excluded: chain A residue 1747 ILE
Chi-restraints excluded: chain A residue 1768 HIS
Chi-restraints excluded: chain A residue 1769 GLU
Chi-restraints excluded: chain A residue 1780 VAL
Chi-restraints excluded: chain A residue 1927 MET
Chi-restraints excluded: chain A residue 1968 TRP
Chi-restraints excluded: chain A residue 1973 SER
Chi-restraints excluded: chain A residue 2020 THR
Chi-restraints excluded: chain A residue 2028 TYR
Chi-restraints excluded: chain A residue 2046 HIS
Chi-restraints excluded: chain A residue 2070 THR
Chi-restraints excluded: chain A residue 2089 SER
Chi-restraints excluded: chain A residue 2100 VAL
Chi-restraints excluded: chain A residue 2134 LEU
Chi-restraints excluded: chain A residue 2153 LEU
Chi-restraints excluded: chain A residue 2158 HIS
Chi-restraints excluded: chain A residue 2177 LYS
Chi-restraints excluded: chain N residue  392 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 120 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 101 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 108 optimal weight:    0.6980
   chunk 157 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 143 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 548 HIS
** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1196 HIS
** A1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 454 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5155 r_free = 0.5155 target = 0.194012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4928 r_free = 0.4928 target = 0.174380 restraints weight = 38263.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4901 r_free = 0.4901 target = 0.174239 restraints weight = 39853.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4918 r_free = 0.4918 target = 0.175643 restraints weight = 33366.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4928 r_free = 0.4928 target = 0.176855 restraints weight = 24007.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4930 r_free = 0.4930 target = 0.177046 restraints weight = 21537.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.4960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4891
moved from start:          0.2790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13879  Z= 0.129
  Angle     :  0.652  13.385  18816  Z= 0.318
  Chirality :  0.043   0.172   2098
  Planarity :  0.004   0.062   2448
  Dihedral  :  4.793  44.904   1856
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.88 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 19.72 %
    Favored  : 76.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.03 %
    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: -0.15 (0.21), residues: 1668
  helix:  0.70 (0.18), residues: 805
  sheet: -0.55 (0.39), residues: 175
  loop : -0.86 (0.25), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1566 
 TYR   0.028   0.001   TYR A 863 
 PHE   0.016   0.001   PHE A2085 
 TRP   0.012   0.001   TRP A1139 
 HIS   0.007   0.001   HIS A2087 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (13879)
  covalent geometry    : angle       0.65168 (18816)
  hydrogen bonds       : bond        0.03398 (  638)
  hydrogen bonds       : angle       4.61036 ( 1839)

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

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

  3336 Ramachandran restraints generated.
    1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3336 Ramachandran restraints generated.
    1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 120
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 LEU cc_start: 0.5621 (OUTLIER) cc_final: 0.5090 (pp)
REVERT: A  873 LEU cc_start: 0.5016 (OUTLIER) cc_final: 0.4568 (mp)
REVERT: A  930 LEU cc_start: 0.3532 (OUTLIER) cc_final: 0.1894 (mp)
REVERT: A  994 ARG cc_start: -0.3750 (OUTLIER) cc_final: -0.4266 (mpt180)
REVERT: A 1137 MET cc_start: 0.2614 (OUTLIER) cc_final: 0.1951 (mmm)
REVERT: A 1633 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7334 (pp20)
REVERT: A 2020 THR cc_start: 0.6671 (OUTLIER) cc_final: 0.5429 (t)
REVERT: A 2153 LEU cc_start: 0.3072 (OUTLIER) cc_final: 0.2436 (mp)
REVERT: A 2177 LYS cc_start: 0.4682 (OUTLIER) cc_final: 0.1637 (mmmt)
  outliers start: 52
  outliers final: 38
  residues processed: 164
  average time/residue: 0.0994
  time to fit residues: 24.9260
Evaluate side-chains
  155 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 108
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   45 PHE
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue   77 GLU
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue   89 THR
Chi-restraints excluded: chain A residue   90 ASP
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  293 MET
Chi-restraints excluded: chain A residue  297 CYS
Chi-restraints excluded: chain A residue  303 HIS
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain A residue  764 THR
Chi-restraints excluded: chain A residue  768 VAL
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  863 TYR
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  930 LEU
Chi-restraints excluded: chain A residue  994 ARG
Chi-restraints excluded: chain A residue 1088 VAL
Chi-restraints excluded: chain A residue 1137 MET
Chi-restraints excluded: chain A residue 1192 LEU
Chi-restraints excluded: chain A residue 1261 ILE
Chi-restraints excluded: chain A residue 1282 LEU
Chi-restraints excluded: chain A residue 1633 GLU
Chi-restraints excluded: chain A residue 1747 ILE
Chi-restraints excluded: chain A residue 1768 HIS
Chi-restraints excluded: chain A residue 1769 GLU
Chi-restraints excluded: chain A residue 1780 VAL
Chi-restraints excluded: chain A residue 1927 MET
Chi-restraints excluded: chain A residue 1968 TRP
Chi-restraints excluded: chain A residue 1973 SER
Chi-restraints excluded: chain A residue 2020 THR
Chi-restraints excluded: chain A residue 2028 TYR
Chi-restraints excluded: chain A residue 2046 HIS
Chi-restraints excluded: chain A residue 2070 THR
Chi-restraints excluded: chain A residue 2100 VAL
Chi-restraints excluded: chain A residue 2134 LEU
Chi-restraints excluded: chain A residue 2153 LEU
Chi-restraints excluded: chain A residue 2158 HIS
Chi-restraints excluded: chain A residue 2177 LYS
Chi-restraints excluded: chain N residue  392 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 15 optimal weight:    0.0020
   chunk 12 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 167 optimal weight:    0.9980
   chunk 9 optimal weight:    8.9990
   chunk 162 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 101 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 100 optimal weight:    0.9990
   overall best weight:    0.7190

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

Flipped N/Q/H residues before XYZ refinement:
A 548 HIS
** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1559 GLN
** A1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5136 r_free = 0.5136 target = 0.192494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4875 r_free = 0.4875 target = 0.169233 restraints weight = 37087.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4841 r_free = 0.4841 target = 0.169210 restraints weight = 29525.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4857 r_free = 0.4857 target = 0.170846 restraints weight = 22885.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4862 r_free = 0.4862 target = 0.171396 restraints weight = 18066.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4863 r_free = 0.4863 target = 0.171495 restraints weight = 16518.179|
|-----------------------------------------------------------------------------|
r_work (final): 0.4916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5039
moved from start:          0.2997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13879  Z= 0.126
  Angle     :  0.650  13.649  18816  Z= 0.315
  Chirality :  0.043   0.220   2098
  Planarity :  0.004   0.061   2448
  Dihedral  :  4.745  44.732   1856
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.06 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 20.19 %
    Favored  : 76.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.03 %
    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: -0.14 (0.21), residues: 1668
  helix:  0.72 (0.18), residues: 806
  sheet: -0.57 (0.39), residues: 175
  loop : -0.84 (0.25), residues: 687

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1566 
 TYR   0.023   0.001   TYR N 458 
 PHE   0.018   0.001   PHE A2085 
 TRP   0.008   0.001   TRP A1139 
 HIS   0.007   0.001   HIS A2087 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (13879)
  covalent geometry    : angle       0.64983 (18816)
  hydrogen bonds       : bond        0.03326 (  638)
  hydrogen bonds       : angle       4.59261 ( 1839)

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

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

  3336 Ramachandran restraints generated.
    1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3336 Ramachandran restraints generated.
    1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 119
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 MET cc_start: 0.6545 (pmm) cc_final: 0.6257 (pmm)
REVERT: A  178 LEU cc_start: 0.5559 (OUTLIER) cc_final: 0.5033 (pp)
REVERT: A  873 LEU cc_start: 0.5140 (OUTLIER) cc_final: 0.4666 (mp)
REVERT: A  930 LEU cc_start: 0.3648 (OUTLIER) cc_final: 0.2513 (mp)
REVERT: A  994 ARG cc_start: -0.3782 (OUTLIER) cc_final: -0.4246 (mpt180)
REVERT: A 1137 MET cc_start: 0.2541 (OUTLIER) cc_final: 0.1877 (mmm)
REVERT: A 1633 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7282 (pp20)
REVERT: A 1749 ASP cc_start: 0.7529 (t0) cc_final: 0.6985 (t0)
REVERT: A 2041 TYR cc_start: 0.5692 (t80) cc_final: 0.5329 (t80)
  outliers start: 50
  outliers final: 38
  residues processed: 160
  average time/residue: 0.0996
  time to fit residues: 24.2662
Evaluate side-chains
  157 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 113
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue   77 GLU
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue   89 THR
Chi-restraints excluded: chain A residue   90 ASP
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  293 MET
Chi-restraints excluded: chain A residue  297 CYS
Chi-restraints excluded: chain A residue  303 HIS
Chi-restraints excluded: chain A residue  563 CYS
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain A residue  768 VAL
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  863 TYR
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  930 LEU
Chi-restraints excluded: chain A residue  994 ARG
Chi-restraints excluded: chain A residue 1081 CYS
Chi-restraints excluded: chain A residue 1088 VAL
Chi-restraints excluded: chain A residue 1137 MET
Chi-restraints excluded: chain A residue 1192 LEU
Chi-restraints excluded: chain A residue 1261 ILE
Chi-restraints excluded: chain A residue 1282 LEU
Chi-restraints excluded: chain A residue 1633 GLU
Chi-restraints excluded: chain A residue 1747 ILE
Chi-restraints excluded: chain A residue 1768 HIS
Chi-restraints excluded: chain A residue 1769 GLU
Chi-restraints excluded: chain A residue 1780 VAL
Chi-restraints excluded: chain A residue 1896 HIS
Chi-restraints excluded: chain A residue 1927 MET
Chi-restraints excluded: chain A residue 1968 TRP
Chi-restraints excluded: chain A residue 1973 SER
Chi-restraints excluded: chain A residue 2020 THR
Chi-restraints excluded: chain A residue 2046 HIS
Chi-restraints excluded: chain A residue 2070 THR
Chi-restraints excluded: chain A residue 2100 VAL
Chi-restraints excluded: chain A residue 2134 LEU
Chi-restraints excluded: chain A residue 2158 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 24 optimal weight:    0.0020
   chunk 8 optimal weight:    0.7980
   chunk 151 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 79 optimal weight:    7.9990
   chunk 46 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 145 optimal weight:    0.0670
   chunk 100 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 167 optimal weight:    0.8980
   overall best weight:    0.5326

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 548 HIS
** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 862 GLN
** A1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5151 r_free = 0.5151 target = 0.193814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4910 r_free = 0.4910 target = 0.171346 restraints weight = 37668.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4853 r_free = 0.4853 target = 0.171252 restraints weight = 34218.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4871 r_free = 0.4871 target = 0.172567 restraints weight = 27052.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4878 r_free = 0.4878 target = 0.173120 restraints weight = 20478.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4881 r_free = 0.4881 target = 0.173477 restraints weight = 17553.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.4934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5011
moved from start:          0.3153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13879  Z= 0.117
  Angle     :  0.643  13.706  18816  Z= 0.311
  Chirality :  0.043   0.261   2098
  Planarity :  0.004   0.061   2448
  Dihedral  :  4.653  44.814   1856
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.70 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 20.39 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.03 %
    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: -0.02 (0.21), residues: 1668
  helix:  0.82 (0.19), residues: 806
  sheet: -0.44 (0.38), residues: 184
  loop : -0.83 (0.25), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1566 
 TYR   0.020   0.001   TYR N 458 
 PHE   0.016   0.001   PHE A2085 
 TRP   0.008   0.001   TRP A1139 
 HIS   0.008   0.001   HIS A2087 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (13879)
  covalent geometry    : angle       0.64275 (18816)
  hydrogen bonds       : bond        0.03202 (  638)
  hydrogen bonds       : angle       4.49912 ( 1839)

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

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

  3336 Ramachandran restraints generated.
    1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3336 Ramachandran restraints generated.
    1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 120
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 LEU cc_start: 0.5486 (OUTLIER) cc_final: 0.4990 (pp)
REVERT: A  873 LEU cc_start: 0.4873 (OUTLIER) cc_final: 0.4471 (mp)
REVERT: A  930 LEU cc_start: 0.3542 (OUTLIER) cc_final: 0.2449 (mp)
REVERT: A  994 ARG cc_start: -0.3703 (OUTLIER) cc_final: -0.4155 (mpt180)
REVERT: A 1137 MET cc_start: 0.2544 (OUTLIER) cc_final: 0.1206 (mmm)
REVERT: A 1633 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7309 (pp20)
REVERT: A 1749 ASP cc_start: 0.7368 (t0) cc_final: 0.6650 (t0)
REVERT: A 2020 THR cc_start: 0.6756 (OUTLIER) cc_final: 0.5458 (t)
REVERT: A 2088 LEU cc_start: 0.3769 (OUTLIER) cc_final: 0.3249 (tt)
  outliers start: 44
  outliers final: 32
  residues processed: 157
  average time/residue: 0.0960
  time to fit residues: 23.2687
Evaluate side-chains
  151 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 111
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   45 PHE
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue   77 GLU
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue   89 THR
Chi-restraints excluded: chain A residue   90 ASP
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  297 CYS
Chi-restraints excluded: chain A residue  303 HIS
Chi-restraints excluded: chain A residue  768 VAL
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  863 TYR
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  930 LEU
Chi-restraints excluded: chain A residue  994 ARG
Chi-restraints excluded: chain A residue 1081 CYS
Chi-restraints excluded: chain A residue 1088 VAL
Chi-restraints excluded: chain A residue 1137 MET
Chi-restraints excluded: chain A residue 1192 LEU
Chi-restraints excluded: chain A residue 1261 ILE
Chi-restraints excluded: chain A residue 1282 LEU
Chi-restraints excluded: chain A residue 1633 GLU
Chi-restraints excluded: chain A residue 1747 ILE
Chi-restraints excluded: chain A residue 1768 HIS
Chi-restraints excluded: chain A residue 1769 GLU
Chi-restraints excluded: chain A residue 1927 MET
Chi-restraints excluded: chain A residue 1968 TRP
Chi-restraints excluded: chain A residue 1973 SER
Chi-restraints excluded: chain A residue 2020 THR
Chi-restraints excluded: chain A residue 2028 TYR
Chi-restraints excluded: chain A residue 2046 HIS
Chi-restraints excluded: chain A residue 2070 THR
Chi-restraints excluded: chain A residue 2088 LEU
Chi-restraints excluded: chain A residue 2100 VAL
Chi-restraints excluded: chain A residue 2134 LEU
Chi-restraints excluded: chain A residue 2158 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 115 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 157 optimal weight:    5.9990
   chunk 158 optimal weight:    9.9990
   chunk 155 optimal weight:    0.7980
   chunk 65 optimal weight:    0.5980
   chunk 77 optimal weight:    0.2980
   chunk 24 optimal weight:    0.4980
   chunk 126 optimal weight:    0.2980
   chunk 61 optimal weight:    0.5980
   chunk 135 optimal weight:    0.8980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 548 HIS
** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2012 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 = 0.5154 r_free = 0.5154 target = 0.194048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4910 r_free = 0.4910 target = 0.171597 restraints weight = 37409.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4872 r_free = 0.4872 target = 0.172613 restraints weight = 33551.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4888 r_free = 0.4888 target = 0.173704 restraints weight = 25261.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4895 r_free = 0.4895 target = 0.174259 restraints weight = 19179.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4897 r_free = 0.4897 target = 0.174426 restraints weight = 16639.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.4951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4958
moved from start:          0.3261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13879  Z= 0.116
  Angle     :  0.653  13.852  18816  Z= 0.315
  Chirality :  0.043   0.280   2098
  Planarity :  0.004   0.061   2448
  Dihedral  :  4.620  44.670   1856
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.76 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 20.59 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.03 %
    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: -0.02 (0.21), residues: 1668
  helix:  0.84 (0.19), residues: 804
  sheet: -0.49 (0.38), residues: 184
  loop : -0.83 (0.25), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A1566 
 TYR   0.021   0.001   TYR N 458 
 PHE   0.016   0.001   PHE A2085 
 TRP   0.007   0.001   TRP A1139 
 HIS   0.008   0.001   HIS A2087 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (13879)
  covalent geometry    : angle       0.65279 (18816)
  hydrogen bonds       : bond        0.03198 (  638)
  hydrogen bonds       : angle       4.50688 ( 1839)

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

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

  3336 Ramachandran restraints generated.
    1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3336 Ramachandran restraints generated.
    1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 118
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 MET cc_start: 0.6442 (pmm) cc_final: 0.6146 (pmm)
REVERT: A  178 LEU cc_start: 0.5526 (OUTLIER) cc_final: 0.5025 (pp)
REVERT: A  873 LEU cc_start: 0.4886 (OUTLIER) cc_final: 0.4408 (mp)
REVERT: A  994 ARG cc_start: -0.3625 (OUTLIER) cc_final: -0.4104 (mpt180)
REVERT: A 1137 MET cc_start: 0.2546 (OUTLIER) cc_final: 0.1296 (mmm)
REVERT: A 1609 MET cc_start: 0.6047 (mmp) cc_final: 0.5778 (mmp)
REVERT: A 1633 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7311 (pp20)
REVERT: A 1749 ASP cc_start: 0.7289 (t0) cc_final: 0.6769 (t0)
REVERT: A 2020 THR cc_start: 0.6713 (OUTLIER) cc_final: 0.5421 (t)
REVERT: A 2088 LEU cc_start: 0.3753 (OUTLIER) cc_final: 0.3228 (tt)
REVERT: A 2182 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8037 (mm-30)
  outliers start: 42
  outliers final: 32
  residues processed: 154
  average time/residue: 0.0958
  time to fit residues: 22.5839
Evaluate side-chains
  152 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 113
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   45 PHE
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue   77 GLU
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue   89 THR
Chi-restraints excluded: chain A residue   90 ASP
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  297 CYS
Chi-restraints excluded: chain A residue  303 HIS
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  863 TYR
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  994 ARG
Chi-restraints excluded: chain A residue 1081 CYS
Chi-restraints excluded: chain A residue 1088 VAL
Chi-restraints excluded: chain A residue 1137 MET
Chi-restraints excluded: chain A residue 1192 LEU
Chi-restraints excluded: chain A residue 1261 ILE
Chi-restraints excluded: chain A residue 1282 LEU
Chi-restraints excluded: chain A residue 1633 GLU
Chi-restraints excluded: chain A residue 1747 ILE
Chi-restraints excluded: chain A residue 1768 HIS
Chi-restraints excluded: chain A residue 1769 GLU
Chi-restraints excluded: chain A residue 1896 HIS
Chi-restraints excluded: chain A residue 1927 MET
Chi-restraints excluded: chain A residue 1968 TRP
Chi-restraints excluded: chain A residue 1973 SER
Chi-restraints excluded: chain A residue 2020 THR
Chi-restraints excluded: chain A residue 2028 TYR
Chi-restraints excluded: chain A residue 2046 HIS
Chi-restraints excluded: chain A residue 2070 THR
Chi-restraints excluded: chain A residue 2088 LEU
Chi-restraints excluded: chain A residue 2100 VAL
Chi-restraints excluded: chain A residue 2134 LEU
Chi-restraints excluded: chain A residue 2158 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 115 optimal weight:    0.9980
   chunk 112 optimal weight:    0.0040
   chunk 155 optimal weight:    0.4980
   chunk 135 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0020
   chunk 160 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.4000

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 334 GLN
A 548 HIS
** A1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5160 r_free = 0.5160 target = 0.194622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4919 r_free = 0.4919 target = 0.172222 restraints weight = 38164.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4879 r_free = 0.4879 target = 0.172952 restraints weight = 29854.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4895 r_free = 0.4895 target = 0.174144 restraints weight = 24547.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4902 r_free = 0.4902 target = 0.174699 restraints weight = 18029.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4903 r_free = 0.4903 target = 0.174811 restraints weight = 15946.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.4955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4947
moved from start:          0.3370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13879  Z= 0.117
  Angle     :  0.667  14.478  18816  Z= 0.321
  Chirality :  0.043   0.282   2098
  Planarity :  0.005   0.084   2448
  Dihedral  :  4.607  44.776   1856
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.76 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 20.99 %
    Favored  : 76.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.03 %
    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:  0.02 (0.21), residues: 1668
  helix:  0.86 (0.19), residues: 805
  sheet: -0.53 (0.38), residues: 183
  loop : -0.77 (0.25), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  60 
 TYR   0.025   0.001   TYR N 458 
 PHE   0.016   0.001   PHE A2085 
 TRP   0.008   0.001   TRP A1139 
 HIS   0.008   0.001   HIS A2087 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (13879)
  covalent geometry    : angle       0.66746 (18816)
  hydrogen bonds       : bond        0.03271 (  638)
  hydrogen bonds       : angle       4.47874 ( 1839)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1980.65 seconds
wall clock time: 35 minutes 12.92 seconds (2112.92 seconds total)