Starting phenix.real_space_refine
on Thu Jul 31 20:20:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dgi_27423/07_2025/8dgi_27423.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dgi_27423/07_2025/8dgi_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_27423/07_2025/8dgi_27423.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dgi_27423/07_2025/8dgi_27423.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dgi_27423/07_2025/8dgi_27423.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dgi_27423/07_2025/8dgi_27423.cif"
  }
  resolution = 3.94
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.008
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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.39, per 1000 atoms: 0.62
  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: 2.99
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  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: 1.76
  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: 4.86

  Time building geometry restraints manager: 3.60 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:             3.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.550
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     32.840
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.840
-------------------------------------------------------------------------------
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 : 8.89
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.021   0.002   TRP A1968 
 HIS   0.015   0.001   HIS A  87 
 PHE   0.037   0.003   PHE A2072 
 TYR   0.039   0.002   TYR A2041 
 ARG   0.016   0.001   ARG A1566 

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

*********************** 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  : 1.465 
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: 0.2836
  time to fit residues: 57.1103
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  : 1.484 
-------------------------------------------------------------------------------
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 141 optimal weight:    0.0870
   chunk 127 optimal weight:    0.6980
   chunk 70 optimal weight:   20.0000
   chunk 43 optimal weight:    0.8980
   chunk 85 optimal weight:   40.0000
   chunk 68 optimal weight:    0.9990
   chunk 131 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 80 optimal weight:   20.0000
   chunk 98 optimal weight:    3.9990
   chunk 152 optimal weight:    7.9990
   overall best weight:    1.1362

-------------------------------------------------------------------------------
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
** A1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1774 HIS
** A2012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2029 GLN
A2054 HIS
N 389 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5159 r_free = 0.5159 target = 0.194306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4940 r_free = 0.4940 target = 0.175176 restraints weight = 38285.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4905 r_free = 0.4905 target = 0.174692 restraints weight = 41099.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4921 r_free = 0.4921 target = 0.176082 restraints weight = 33970.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.4949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4857
moved from start:          0.1212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13879  Z= 0.157
  Angle     :  0.705  11.013  18816  Z= 0.356
  Chirality :  0.043   0.168   2098
  Planarity :  0.006   0.069   2448
  Dihedral  :  5.663  43.418   1864
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.28 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 18.65 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.03 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.18 (0.20), residues: 1668
  helix: -0.40 (0.17), residues: 805
  sheet: -0.21 (0.38), residues: 193
  loop : -1.29 (0.24), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 848 
 HIS   0.009   0.001   HIS A2087 
 PHE   0.023   0.002   PHE A2085 
 TYR   0.032   0.002   TYR A2041 
 ARG   0.005   0.000   ARG A 170 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04355 (  638)
  hydrogen bonds       : angle       5.37715 ( 1839)
  covalent geometry    : bond        0.00342 (13879)
  covalent geometry    : angle       0.70533 (18816)

*********************** 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
  172 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 127
  time to evaluate  : 1.423 
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: 0.5394 (OUTLIER) cc_final: 0.4824 (pp)
REVERT: A  286 LEU cc_start: 0.4687 (mt) cc_final: 0.4299 (mt)
REVERT: A 1137 MET cc_start: 0.2029 (OUTLIER) cc_final: 0.1531 (mmp)
REVERT: A 1975 LEU cc_start: 0.4998 (tp) cc_final: 0.4505 (mt)
REVERT: A 2138 PHE cc_start: 0.4371 (t80) cc_final: 0.3553 (t80)
  outliers start: 45
  outliers final: 22
  residues processed: 162
  average time/residue: 0.2845
  time to fit residues: 67.0635
Evaluate side-chains
  138 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 114
  time to evaluate  : 1.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   81 ILE
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  612 ILE
Chi-restraints excluded: chain A residue  768 VAL
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 1780 VAL
Chi-restraints excluded: chain A residue 1973 SER
Chi-restraints excluded: chain A residue 2028 TYR
Chi-restraints excluded: chain A residue 2034 LEU
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 N residue  392 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 164 optimal weight:    0.9980
   chunk 29 optimal weight:    6.9990
   chunk 91 optimal weight:    0.0270
   chunk 113 optimal weight:    8.9990
   chunk 51 optimal weight:    4.9990
   chunk 154 optimal weight:    0.4980
   chunk 131 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 73 optimal weight:   20.0000
   chunk 94 optimal weight:    4.9990
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.6238

-------------------------------------------------------------------------------
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 548 HIS
A1067 GLN
** A1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1668 ASN
** A2012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2054 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5175 r_free = 0.5175 target = 0.195566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4950 r_free = 0.4950 target = 0.175653 restraints weight = 38351.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4928 r_free = 0.4928 target = 0.176492 restraints weight = 38276.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4944 r_free = 0.4944 target = 0.177890 restraints weight = 29905.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.4973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4826
moved from start:          0.1645

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= 0.128
  Angle     :  0.651  11.193  18816  Z= 0.320
  Chirality :  0.043   0.183   2098
  Planarity :  0.005   0.065   2448
  Dihedral  :  5.119  44.280   1856
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 12.69
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.70 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 18.32 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.03 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.21), residues: 1668
  helix:  0.19 (0.18), residues: 806
  sheet: -0.29 (0.38), residues: 187
  loop : -1.03 (0.25), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1139 
 HIS   0.009   0.001   HIS A2087 
 PHE   0.019   0.001   PHE A  45 
 TYR   0.017   0.001   TYR A2028 
 ARG   0.005   0.000   ARG A 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03694 (  638)
  hydrogen bonds       : angle       4.92425 ( 1839)
  covalent geometry    : bond        0.00276 (13879)
  covalent geometry    : angle       0.65052 (18816)

*********************** 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
  171 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 121
  time to evaluate  : 1.409 
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: 0.5340 (OUTLIER) cc_final: 0.4788 (pp)
REVERT: A  286 LEU cc_start: 0.4688 (mt) cc_final: 0.4289 (mt)
REVERT: A  572 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6444 (tt)
REVERT: A 1137 MET cc_start: 0.1855 (OUTLIER) cc_final: 0.1364 (mmp)
REVERT: A 1543 GLN cc_start: 0.6478 (OUTLIER) cc_final: 0.6239 (tm-30)
REVERT: A 1749 ASP cc_start: 0.7437 (t0) cc_final: 0.7008 (t0)
REVERT: A 1975 LEU cc_start: 0.4983 (tp) cc_final: 0.4475 (mt)
REVERT: A 2020 THR cc_start: 0.6470 (OUTLIER) cc_final: 0.5954 (p)
  outliers start: 50
  outliers final: 27
  residues processed: 160
  average time/residue: 0.2600
  time to fit residues: 62.2078
Evaluate side-chains
  140 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 108
  time to evaluate  : 1.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ARG
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  293 MET
Chi-restraints excluded: chain A residue  297 CYS
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  782 LEU
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 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 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 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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 89 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 100 optimal weight:    3.9990
   chunk 77 optimal weight:    7.9990
   chunk 20 optimal weight:    0.6980
   chunk 98 optimal weight:   10.0000
   chunk 34 optimal weight:    1.9990
   chunk 31 optimal weight:   10.0000
   chunk 51 optimal weight:    5.9990
   chunk 123 optimal weight:    5.9990
   chunk 13 optimal weight:    0.8980
   overall best weight:    2.5186

-------------------------------------------------------------------------------
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 875 HIS
** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1533 GLN
A1559 GLN
A1656 ASN
A1766 ASN
** A1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2093 ASN
A2103 GLN
** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5070 r_free = 0.5070 target = 0.186705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4814 r_free = 0.4814 target = 0.166100 restraints weight = 37883.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4773 r_free = 0.4773 target = 0.164729 restraints weight = 50441.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4789 r_free = 0.4789 target = 0.166113 restraints weight = 41186.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.4817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5279
moved from start:          0.2849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.079  13879  Z= 0.275
  Angle     :  0.852  12.360  18816  Z= 0.430
  Chirality :  0.048   0.196   2098
  Planarity :  0.006   0.069   2448
  Dihedral  :  5.809  45.171   1856
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 22.25
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.97 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  5.80 %
    Allowed  : 17.85 %
    Favored  : 76.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.03 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.20), residues: 1668
  helix: -0.21 (0.18), residues: 801
  sheet: -0.85 (0.39), residues: 176
  loop : -1.15 (0.24), residues: 691

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 848 
 HIS   0.012   0.002   HIS A  87 
 PHE   0.030   0.003   PHE A1996 
 TYR   0.047   0.003   TYR A2028 
 ARG   0.016   0.001   ARG A1264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04859 (  638)
  hydrogen bonds       : angle       5.50770 ( 1839)
  covalent geometry    : bond        0.00621 (13879)
  covalent geometry    : angle       0.85183 (18816)

*********************** 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
  207 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 87
    poor density    : 120
  time to evaluate  : 1.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 LEU cc_start: 0.5980 (OUTLIER) cc_final: 0.5537 (pp)
REVERT: A  873 LEU cc_start: 0.5853 (OUTLIER) cc_final: 0.5353 (mp)
REVERT: A  994 ARG cc_start: -0.3482 (OUTLIER) cc_final: -0.3859 (mpt90)
REVERT: A 1137 MET cc_start: 0.2117 (OUTLIER) cc_final: 0.1424 (mmm)
REVERT: A 1749 ASP cc_start: 0.7719 (t0) cc_final: 0.7457 (t0)
REVERT: A 2034 LEU cc_start: 0.4700 (OUTLIER) cc_final: 0.4417 (tp)
REVERT: A 2041 TYR cc_start: 0.6098 (t80) cc_final: 0.5888 (t80)
REVERT: A 2088 LEU cc_start: 0.4851 (OUTLIER) cc_final: 0.4102 (tt)
REVERT: A 2094 ASP cc_start: 0.5093 (OUTLIER) cc_final: 0.4568 (p0)
  outliers start: 87
  outliers final: 50
  residues processed: 193
  average time/residue: 0.2520
  time to fit residues: 72.9289
Evaluate side-chains
  162 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 105
  time to evaluate  : 1.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ASP
Chi-restraints excluded: chain A residue   22 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  213 LEU
Chi-restraints excluded: chain A residue  297 CYS
Chi-restraints excluded: chain A residue  303 HIS
Chi-restraints excluded: chain A residue  304 HIS
Chi-restraints excluded: chain A residue  521 ASP
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  560 MET
Chi-restraints excluded: chain A residue  563 CYS
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  611 VAL
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  782 LEU
Chi-restraints excluded: chain A residue  871 SER
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  994 ARG
Chi-restraints excluded: chain A residue 1041 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 1238 VAL
Chi-restraints excluded: chain A residue 1261 ILE
Chi-restraints excluded: chain A residue 1282 LEU
Chi-restraints excluded: chain A residue 1747 ILE
Chi-restraints excluded: chain A residue 1762 ILE
Chi-restraints excluded: chain A residue 1769 GLU
Chi-restraints excluded: chain A residue 1774 HIS
Chi-restraints excluded: chain A residue 1780 VAL
Chi-restraints excluded: chain A residue 1896 HIS
Chi-restraints excluded: chain A residue 1917 GLU
Chi-restraints excluded: chain A residue 2015 THR
Chi-restraints excluded: chain A residue 2020 THR
Chi-restraints excluded: chain A residue 2028 TYR
Chi-restraints excluded: chain A residue 2034 LEU
Chi-restraints excluded: chain A residue 2043 ILE
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 2071 ILE
Chi-restraints excluded: chain A residue 2088 LEU
Chi-restraints excluded: chain A residue 2089 SER
Chi-restraints excluded: chain A residue 2094 ASP
Chi-restraints excluded: chain A residue 2100 VAL
Chi-restraints excluded: chain A residue 2113 GLU
Chi-restraints excluded: chain A residue 2134 LEU
Chi-restraints excluded: chain A residue 2175 VAL
Chi-restraints excluded: chain N residue  392 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 75 optimal weight:   20.0000
   chunk 110 optimal weight:    4.9990
   chunk 126 optimal weight:    1.9990
   chunk 157 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 158 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 152 optimal weight:    0.0980
   chunk 99 optimal weight:    0.8980
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1536 ASN
** 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 = 0.5116 r_free = 0.5116 target = 0.190468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4881 r_free = 0.4881 target = 0.170693 restraints weight = 37918.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4847 r_free = 0.4847 target = 0.170004 restraints weight = 43610.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4866 r_free = 0.4866 target = 0.171700 restraints weight = 42622.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.4895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5068
moved from start:          0.2914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  13879  Z= 0.161
  Angle     :  0.708  12.028  18816  Z= 0.349
  Chirality :  0.044   0.195   2098
  Planarity :  0.005   0.067   2448
  Dihedral  :  5.389  44.983   1856
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 16.90
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.59 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 19.92 %
    Favored  : 76.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.03 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.21), residues: 1668
  helix:  0.13 (0.18), residues: 802
  sheet: -0.90 (0.38), residues: 178
  loop : -1.08 (0.25), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1139 
 HIS   0.008   0.001   HIS A2087 
 PHE   0.021   0.002   PHE A2138 
 TYR   0.024   0.002   TYR A2028 
 ARG   0.003   0.000   ARG A 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03811 (  638)
  hydrogen bonds       : angle       5.08194 ( 1839)
  covalent geometry    : bond        0.00360 (13879)
  covalent geometry    : angle       0.70751 (18816)

*********************** 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
  169 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 113
  time to evaluate  : 1.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 LEU cc_start: 0.6090 (OUTLIER) cc_final: 0.5521 (pp)
REVERT: A  286 LEU cc_start: 0.5278 (mt) cc_final: 0.4904 (mt)
REVERT: A  873 LEU cc_start: 0.5599 (OUTLIER) cc_final: 0.5139 (mp)
REVERT: A  994 ARG cc_start: -0.3564 (OUTLIER) cc_final: -0.4161 (mpt180)
REVERT: A 1137 MET cc_start: 0.2154 (mmp) cc_final: 0.0478 (mmp)
REVERT: A 1633 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7200 (pp20)
REVERT: A 1749 ASP cc_start: 0.7640 (t0) cc_final: 0.7340 (t0)
REVERT: A 2041 TYR cc_start: 0.5884 (t80) cc_final: 0.5523 (t80)
  outliers start: 56
  outliers final: 35
  residues processed: 165
  average time/residue: 0.2552
  time to fit residues: 63.5514
Evaluate side-chains
  146 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 107
  time to evaluate  : 1.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  297 CYS
Chi-restraints excluded: chain A residue  303 HIS
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  783 SER
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  821 ASP
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 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 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 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 2113 GLU
Chi-restraints excluded: chain A residue 2153 LEU
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 11 optimal weight:    8.9990
   chunk 114 optimal weight:    9.9990
   chunk 127 optimal weight:    0.8980
   chunk 92 optimal weight:   10.0000
   chunk 117 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 132 optimal weight:    0.0980
   chunk 156 optimal weight:   10.0000
   chunk 73 optimal weight:   10.0000
   chunk 138 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A1671 HIS
A1782 ASN
** 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5142 r_free = 0.5142 target = 0.192749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4911 r_free = 0.4911 target = 0.172957 restraints weight = 38339.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4885 r_free = 0.4885 target = 0.172987 restraints weight = 42943.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4895 r_free = 0.4895 target = 0.174076 restraints weight = 36361.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.4923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4990
moved from start:          0.3013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13879  Z= 0.130
  Angle     :  0.671  12.894  18816  Z= 0.327
  Chirality :  0.043   0.172   2098
  Planarity :  0.005   0.066   2448
  Dihedral  :  5.084  44.597   1856
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 14.80
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.47 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 20.05 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.21), residues: 1668
  helix:  0.35 (0.18), residues: 805
  sheet: -0.80 (0.38), residues: 180
  loop : -1.00 (0.25), residues: 683

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1139 
 HIS   0.009   0.001   HIS A2087 
 PHE   0.019   0.001   PHE A2138 
 TYR   0.024   0.001   TYR N 458 
 ARG   0.005   0.000   ARG A1566 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03435 (  638)
  hydrogen bonds       : angle       4.83838 ( 1839)
  covalent geometry    : bond        0.00288 (13879)
  covalent geometry    : angle       0.67101 (18816)

*********************** 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
  174 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 119
  time to evaluate  : 1.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 LEU cc_start: 0.6019 (OUTLIER) cc_final: 0.5523 (pp)
REVERT: A  286 LEU cc_start: 0.5007 (mt) cc_final: 0.4565 (mt)
REVERT: A  873 LEU cc_start: 0.5379 (OUTLIER) cc_final: 0.4961 (mp)
REVERT: A  994 ARG cc_start: -0.3589 (OUTLIER) cc_final: -0.4259 (mpt180)
REVERT: A 1137 MET cc_start: 0.2533 (OUTLIER) cc_final: 0.1779 (mmp)
REVERT: A 1633 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7236 (pp20)
REVERT: A 1749 ASP cc_start: 0.7508 (t0) cc_final: 0.7276 (t0)
REVERT: A 1917 GLU cc_start: 0.4737 (OUTLIER) cc_final: 0.4401 (pm20)
REVERT: A 2088 LEU cc_start: 0.4083 (mt) cc_final: 0.3633 (tt)
REVERT: A 2153 LEU cc_start: 0.2833 (OUTLIER) cc_final: 0.2172 (mt)
  outliers start: 55
  outliers final: 33
  residues processed: 165
  average time/residue: 0.2378
  time to fit residues: 59.6693
Evaluate side-chains
  147 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 107
  time to evaluate  : 1.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue   77 GLU
Chi-restraints excluded: chain A residue   83 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  297 CYS
Chi-restraints excluded: chain A residue  303 HIS
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  783 SER
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  821 ASP
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  878 VAL
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 1917 GLU
Chi-restraints excluded: chain A residue 1927 MET
Chi-restraints excluded: chain A residue 1968 TRP
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 2153 LEU
Chi-restraints excluded: chain A residue 2158 HIS
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 56 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0370
   chunk 11 optimal weight:    8.9990
   chunk 99 optimal weight:    0.9980
   chunk 113 optimal weight:    0.0060
   chunk 103 optimal weight:    2.9990
   chunk 94 optimal weight:    8.9990
   chunk 26 optimal weight:    7.9990
   chunk 142 optimal weight:    4.9990
   chunk 82 optimal weight:    0.0020
   chunk 121 optimal weight:    6.9990
   overall best weight:    0.3882

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A1656 ASN
** A1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2093 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5157 r_free = 0.5157 target = 0.194139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4940 r_free = 0.4940 target = 0.175044 restraints weight = 38196.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4909 r_free = 0.4909 target = 0.175091 restraints weight = 38926.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4927 r_free = 0.4927 target = 0.176556 restraints weight = 31075.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.4955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4931
moved from start:          0.3089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13879  Z= 0.122
  Angle     :  0.672  13.197  18816  Z= 0.327
  Chirality :  0.044   0.350   2098
  Planarity :  0.005   0.064   2448
  Dihedral  :  4.964  44.652   1856
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.06 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 20.39 %
    Favored  : 76.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.03 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.21), residues: 1668
  helix:  0.48 (0.18), residues: 807
  sheet: -0.73 (0.38), residues: 178
  loop : -0.93 (0.25), residues: 683

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1139 
 HIS   0.010   0.001   HIS A2087 
 PHE   0.029   0.001   PHE A  45 
 TYR   0.026   0.001   TYR A1542 
 ARG   0.006   0.000   ARG A 594 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03269 (  638)
  hydrogen bonds       : angle       4.70198 ( 1839)
  covalent geometry    : bond        0.00269 (13879)
  covalent geometry    : angle       0.67153 (18816)

*********************** 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: 54
    poor density    : 118
  time to evaluate  : 1.572 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 LEU cc_start: 0.6120 (OUTLIER) cc_final: 0.5616 (pp)
REVERT: A  286 LEU cc_start: 0.5040 (mt) cc_final: 0.4544 (mt)
REVERT: A  873 LEU cc_start: 0.5055 (OUTLIER) cc_final: 0.4745 (mp)
REVERT: A  994 ARG cc_start: -0.3858 (OUTLIER) cc_final: -0.4458 (mpt180)
REVERT: A 1137 MET cc_start: 0.2496 (mmp) cc_final: 0.0749 (mmp)
REVERT: A 1149 PHE cc_start: 0.5617 (m-80) cc_final: 0.5374 (t80)
REVERT: A 1277 GLN cc_start: 0.7228 (OUTLIER) cc_final: 0.6609 (mp10)
REVERT: A 1633 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7217 (pp20)
REVERT: A 1975 LEU cc_start: 0.6371 (tp) cc_final: 0.6140 (tt)
REVERT: A 2153 LEU cc_start: 0.2760 (OUTLIER) cc_final: 0.1969 (mp)
  outliers start: 54
  outliers final: 35
  residues processed: 164
  average time/residue: 0.2439
  time to fit residues: 61.7940
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  : 1.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  297 CYS
Chi-restraints excluded: chain A residue  303 HIS
Chi-restraints excluded: chain A residue  564 ASN
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  869 ILE
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  878 VAL
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 1261 ILE
Chi-restraints excluded: chain A residue 1277 GLN
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 2020 THR
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 N residue  392 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 64 optimal weight:    0.2980
   chunk 38 optimal weight:    2.9990
   chunk 139 optimal weight:    0.7980
   chunk 82 optimal weight:    0.2980
   chunk 91 optimal weight:    9.9990
   chunk 151 optimal weight:    6.9990
   chunk 124 optimal weight:    0.2980
   chunk 5 optimal weight:    0.8980
   chunk 66 optimal weight:   10.0000
   chunk 14 optimal weight:    1.9990
   chunk 153 optimal weight:    8.9990
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A1960 ASN
** 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 = 0.5156 r_free = 0.5156 target = 0.194043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4937 r_free = 0.4937 target = 0.175143 restraints weight = 38631.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4915 r_free = 0.4915 target = 0.175398 restraints weight = 38632.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4931 r_free = 0.4931 target = 0.176789 restraints weight = 32236.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.4958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4911
moved from start:          0.3245

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= 0.122
  Angle     :  0.663  13.220  18816  Z= 0.322
  Chirality :  0.043   0.196   2098
  Planarity :  0.004   0.062   2448
  Dihedral  :  4.839  44.604   1856
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 13.95
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.24 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 20.45 %
    Favored  : 76.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.03 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.21), residues: 1668
  helix:  0.58 (0.19), residues: 808
  sheet: -0.70 (0.38), residues: 178
  loop : -0.91 (0.25), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1139 
 HIS   0.009   0.001   HIS A2087 
 PHE   0.027   0.002   PHE A 841 
 TYR   0.027   0.001   TYR A1542 
 ARG   0.010   0.000   ARG A 594 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03309 (  638)
  hydrogen bonds       : angle       4.63150 ( 1839)
  covalent geometry    : bond        0.00269 (13879)
  covalent geometry    : angle       0.66275 (18816)

*********************** 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
  174 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 123
  time to evaluate  : 1.616 
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: A  178 LEU cc_start: 0.5937 (OUTLIER) cc_final: 0.5433 (pp)
REVERT: A  286 LEU cc_start: 0.5015 (mt) cc_final: 0.4516 (mt)
REVERT: A  873 LEU cc_start: 0.5183 (OUTLIER) cc_final: 0.4867 (mp)
REVERT: A  994 ARG cc_start: -0.3797 (OUTLIER) cc_final: -0.4570 (mpt180)
REVERT: A 1137 MET cc_start: 0.2765 (OUTLIER) cc_final: 0.0914 (mmp)
REVERT: A 1277 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6537 (mp10)
REVERT: A 1633 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7213 (pp20)
REVERT: A 1749 ASP cc_start: 0.7519 (t0) cc_final: 0.7020 (t0)
REVERT: A 2153 LEU cc_start: 0.2809 (OUTLIER) cc_final: 0.2043 (mp)
  outliers start: 51
  outliers final: 37
  residues processed: 165
  average time/residue: 0.2628
  time to fit residues: 65.6581
Evaluate side-chains
  161 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 117
  time to evaluate  : 1.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   87 HIS
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  564 ASN
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  821 ASP
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  878 VAL
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 1277 GLN
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 2020 THR
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 114 optimal weight:    2.9990
   chunk 80 optimal weight:   20.0000
   chunk 3 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   chunk 88 optimal weight:   10.0000
   chunk 63 optimal weight:    0.0980
   chunk 96 optimal weight:   10.0000
   chunk 42 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 167 optimal weight:    0.9980
   chunk 121 optimal weight:    4.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5132 r_free = 0.5132 target = 0.191978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4902 r_free = 0.4902 target = 0.173202 restraints weight = 38072.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4873 r_free = 0.4873 target = 0.172080 restraints weight = 50262.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4885 r_free = 0.4885 target = 0.173301 restraints weight = 36794.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.4912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5019
moved from start:          0.3509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  13879  Z= 0.146
  Angle     :  0.701  13.903  18816  Z= 0.340
  Chirality :  0.044   0.268   2098
  Planarity :  0.005   0.065   2448
  Dihedral  :  4.907  44.944   1856
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 14.94
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.24 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 20.59 %
    Favored  : 76.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.03 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.21), residues: 1668
  helix:  0.53 (0.18), residues: 806
  sheet: -0.77 (0.38), residues: 178
  loop : -0.96 (0.25), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 848 
 HIS   0.008   0.001   HIS A  87 
 PHE   0.029   0.002   PHE A 841 
 TYR   0.022   0.002   TYR A2028 
 ARG   0.009   0.000   ARG A 594 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03472 (  638)
  hydrogen bonds       : angle       4.68421 ( 1839)
  covalent geometry    : bond        0.00329 (13879)
  covalent geometry    : angle       0.70068 (18816)

*********************** 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
  171 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 120
  time to evaluate  : 1.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 MET cc_start: 0.6450 (pmm) cc_final: 0.6172 (pmm)
REVERT: A  178 LEU cc_start: 0.5972 (OUTLIER) cc_final: 0.5560 (pp)
REVERT: A  873 LEU cc_start: 0.5711 (OUTLIER) cc_final: 0.5198 (mp)
REVERT: A  994 ARG cc_start: -0.3895 (OUTLIER) cc_final: -0.4744 (mpt180)
REVERT: A 1137 MET cc_start: 0.2812 (mmp) cc_final: 0.0909 (mmp)
REVERT: A 1149 PHE cc_start: 0.5286 (m-80) cc_final: 0.5012 (t80)
REVERT: A 1277 GLN cc_start: 0.7178 (OUTLIER) cc_final: 0.6632 (mp10)
REVERT: A 1633 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7242 (pp20)
REVERT: A 1749 ASP cc_start: 0.7554 (t0) cc_final: 0.7142 (t0)
REVERT: A 2041 TYR cc_start: 0.5921 (t80) cc_final: 0.5483 (t80)
REVERT: A 2153 LEU cc_start: 0.3070 (OUTLIER) cc_final: 0.2509 (mp)
  outliers start: 51
  outliers final: 41
  residues processed: 162
  average time/residue: 0.2352
  time to fit residues: 57.9851
Evaluate side-chains
  158 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 111
  time to evaluate  : 1.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  564 ASN
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain A residue  763 THR
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  821 ASP
Chi-restraints excluded: chain A residue  869 ILE
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  878 VAL
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 1192 LEU
Chi-restraints excluded: chain A residue 1261 ILE
Chi-restraints excluded: chain A residue 1277 GLN
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 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 2205 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 69 optimal weight:    0.2980
   chunk 1 optimal weight:    0.3980
   chunk 110 optimal weight:    7.9990
   chunk 130 optimal weight:   20.0000
   chunk 96 optimal weight:   10.0000
   chunk 105 optimal weight:    8.9990
   chunk 85 optimal weight:   30.0000
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 122 optimal weight:    7.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2093 ASN
** A2104 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 = 0.5089 r_free = 0.5089 target = 0.188124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4816 r_free = 0.4816 target = 0.164764 restraints weight = 36316.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4793 r_free = 0.4793 target = 0.165781 restraints weight = 28610.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4808 r_free = 0.4808 target = 0.167028 restraints weight = 23276.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.4867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5174
moved from start:          0.3846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  13879  Z= 0.165
  Angle     :  0.728  13.961  18816  Z= 0.355
  Chirality :  0.045   0.280   2098
  Planarity :  0.005   0.064   2448
  Dihedral  :  5.077  45.075   1856
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 16.23
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.43 %
    Favored  : 92.51 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 20.79 %
    Favored  : 75.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.03 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.21), residues: 1668
  helix:  0.41 (0.18), residues: 806
  sheet: -0.94 (0.39), residues: 178
  loop : -1.00 (0.25), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 848 
 HIS   0.011   0.001   HIS A  87 
 PHE   0.023   0.002   PHE A2085 
 TYR   0.029   0.002   TYR A2028 
 ARG   0.008   0.000   ARG A 594 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03741 (  638)
  hydrogen bonds       : angle       4.82885 ( 1839)
  covalent geometry    : bond        0.00372 (13879)
  covalent geometry    : angle       0.72754 (18816)

********************** 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
  179 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 125
  time to evaluate  : 1.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 LEU cc_start: 0.5995 (OUTLIER) cc_final: 0.5694 (pp)
REVERT: A  873 LEU cc_start: 0.5947 (OUTLIER) cc_final: 0.5458 (mp)
REVERT: A  994 ARG cc_start: -0.4090 (OUTLIER) cc_final: -0.4792 (mpt180)
REVERT: A 1137 MET cc_start: 0.2670 (mmp) cc_final: 0.0920 (mmp)
REVERT: A 1149 PHE cc_start: 0.5747 (m-80) cc_final: 0.5293 (t80)
REVERT: A 1633 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7188 (pp20)
REVERT: A 1749 ASP cc_start: 0.7589 (t0) cc_final: 0.7199 (t0)
REVERT: A 2041 TYR cc_start: 0.6135 (t80) cc_final: 0.5614 (t80)
REVERT: A 2153 LEU cc_start: 0.3282 (OUTLIER) cc_final: 0.2838 (mp)
REVERT: A 2182 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8168 (mm-30)
  outliers start: 54
  outliers final: 44
  residues processed: 169
  average time/residue: 0.2602
  time to fit residues: 65.7777
Evaluate side-chains
  166 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 117
  time to evaluate  : 1.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   87 HIS
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  564 ASN
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain A residue  763 THR
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  821 ASP
Chi-restraints excluded: chain A residue  869 ILE
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  878 VAL
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 1192 LEU
Chi-restraints excluded: chain A residue 1261 ILE
Chi-restraints excluded: chain A residue 1277 GLN
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 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 2205 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 92 optimal weight:    0.9990
   chunk 112 optimal weight:    0.7980
   chunk 141 optimal weight:    0.8980
   chunk 123 optimal weight:    2.9990
   chunk 122 optimal weight:    0.9980
   chunk 116 optimal weight:    2.9990
   chunk 146 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 113 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 162 optimal weight:    1.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5130 r_free = 0.5130 target = 0.191834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4903 r_free = 0.4903 target = 0.172657 restraints weight = 38171.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4870 r_free = 0.4870 target = 0.171961 restraints weight = 44849.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4890 r_free = 0.4890 target = 0.173682 restraints weight = 37547.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.4917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5011
moved from start:          0.3974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13879  Z= 0.143
  Angle     :  0.717  14.027  18816  Z= 0.348
  Chirality :  0.044   0.274   2098
  Planarity :  0.005   0.064   2448
  Dihedral  :  5.008  44.949   1856
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 15.57
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.29 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 20.92 %
    Favored  : 75.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.03 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.21), residues: 1668
  helix:  0.46 (0.18), residues: 805
  sheet: -0.96 (0.39), residues: 177
  loop : -0.99 (0.25), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 848 
 HIS   0.010   0.001   HIS A  87 
 PHE   0.045   0.002   PHE A 841 
 TYR   0.025   0.002   TYR N 394 
 ARG   0.008   0.000   ARG A  60 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03536 (  638)
  hydrogen bonds       : angle       4.75582 ( 1839)
  covalent geometry    : bond        0.00321 (13879)
  covalent geometry    : angle       0.71711 (18816)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4133.54 seconds
wall clock time: 72 minutes 46.60 seconds (4366.60 seconds total)