Starting phenix.real_space_refine
on Tue Mar  3 14:37:36 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7czb_30508/03_2026/7czb_30508.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7czb_30508/03_2026/7czb_30508.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7czb_30508/03_2026/7czb_30508.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7czb_30508/03_2026/7czb_30508.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7czb_30508/03_2026/7czb_30508.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7czb_30508/03_2026/7czb_30508.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.008 sd=   0.055
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      40      5.16       5
     C    4308      2.51       5
     N     968      2.21       5
     O     988      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 49 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6304
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1576
          Classifications: {'peptide': 194}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 11, 'TRANS': 182}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "B"
      Number of atoms: 1576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1576
          Classifications: {'peptide': 194}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 11, 'TRANS': 182}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "C"
      Number of atoms: 1576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1576
          Classifications: {'peptide': 194}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 11, 'TRANS': 182}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "D"
      Number of atoms: 1576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1576
          Classifications: {'peptide': 194}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 11, 'TRANS': 182}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 17
  Time building chain proxies: 1.58, per 1000 atoms: 0.25
  Number of scatterers: 6304
  At special positions: 0
  Unit cell: (116.1, 124.7, 70.52, 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      40     16.00
     O     988      8.00
     N     968      7.00
     C    4308      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: 0.50
  Conformation dependent library (CDL) restraints added in 303.8 milliseconds
  

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1424

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 0 sheets defined
      64.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 32
      Proline residue:  A  26  - end of helix
      removed outlier: 3.569A  pdb=" N   GLY A  32 " --> pdb=" O   VAL A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 39
    Processing helix  chain 'A' and resid 42 through 49
    Processing helix  chain 'A' and resid 57 through 61
      removed outlier: 3.924A  pdb=" N   TYR A  61 " --> pdb=" O   ALA A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 89
      removed outlier: 3.556A  pdb=" N   LEU A  73 " --> pdb=" O   GLY A  69 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   THR A  84 " --> pdb=" O   TYR A  80 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   ARG A  85 " --> pdb=" O   GLN A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 105
      removed outlier: 3.611A  pdb=" N   ASN A 105 " --> pdb=" O   MET A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 116
      removed outlier: 4.485A  pdb=" N   ILE A 111 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 136
      removed outlier: 3.549A  pdb=" N   ILE A 126 " --> pdb=" O   MET A 122 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LEU A 136 " --> pdb=" O   VAL A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 166
    Processing helix  chain 'A' and resid 170 through 188
      removed outlier: 3.683A  pdb=" N   ILE A 175 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLY A 176 " --> pdb=" O   ASN A 172 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 16 through 31
      Proline residue:  B  26  - end of helix
      removed outlier: 3.512A  pdb=" N   LEU B  31 " --> pdb=" O   LEU B  27 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 39
    Processing helix  chain 'B' and resid 43 through 48
      removed outlier: 4.452A  pdb=" N   TYR B  48 " --> pdb=" O   GLU B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 58
    Processing helix  chain 'B' and resid 70 through 90
      removed outlier: 3.833A  pdb=" N   THR B  84 " --> pdb=" O   TYR B  80 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   ARG B  85 " --> pdb=" O   GLN B  81 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   LEU B  86 " --> pdb=" O   TYR B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 116
      removed outlier: 4.277A  pdb=" N   TYR B  98 " --> pdb=" O   ARG B  94 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ASN B 105 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   TRP B 106 " --> pdb=" O   LEU B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 137
      removed outlier: 3.779A  pdb=" N   ILE B 126 " --> pdb=" O   MET B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 167
    Processing helix  chain 'B' and resid 173 through 189
      removed outlier: 3.895A  pdb=" N   HIS B 181 " --> pdb=" O   ASN B 177 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 32
      Proline residue:  C  26  - end of helix
      removed outlier: 3.578A  pdb=" N   GLY C  32 " --> pdb=" O   VAL C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 35 through 39
    Processing helix  chain 'C' and resid 42 through 49
    Processing helix  chain 'C' and resid 57 through 61
      removed outlier: 3.948A  pdb=" N   TYR C  61 " --> pdb=" O   ALA C  58 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 69 through 89
      removed outlier: 3.550A  pdb=" N   LEU C  73 " --> pdb=" O   GLY C  69 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   THR C  84 " --> pdb=" O   TYR C  80 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   ARG C  85 " --> pdb=" O   GLN C  81 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 94 through 105
      removed outlier: 3.561A  pdb=" N   TYR C  98 " --> pdb=" O   ARG C  94 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ASN C 105 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 105 through 116
      removed outlier: 4.540A  pdb=" N   ILE C 111 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 122 through 136
      removed outlier: 3.548A  pdb=" N   ILE C 126 " --> pdb=" O   MET C 122 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   LEU C 136 " --> pdb=" O   VAL C 132 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 154 through 166
    Processing helix  chain 'C' and resid 170 through 188
      removed outlier: 3.663A  pdb=" N   LEU C 174 " --> pdb=" O   VAL C 170 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   ILE C 175 " --> pdb=" O   ILE C 171 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   GLY C 176 " --> pdb=" O   ASN C 172 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 16 through 31
      Proline residue:  D  26  - end of helix
      removed outlier: 3.555A  pdb=" N   LEU D  31 " --> pdb=" O   LEU D  27 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 35 through 39
    Processing helix  chain 'D' and resid 43 through 48
      removed outlier: 4.442A  pdb=" N   TYR D  48 " --> pdb=" O   GLU D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 53 through 58
    Processing helix  chain 'D' and resid 70 through 90
      removed outlier: 3.890A  pdb=" N   THR D  84 " --> pdb=" O   TYR D  80 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   ARG D  85 " --> pdb=" O   GLN D  81 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   LEU D  86 " --> pdb=" O   TYR D  82 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 94 through 116
      removed outlier: 4.255A  pdb=" N   TYR D  98 " --> pdb=" O   ARG D  94 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ASN D 105 " --> pdb=" O   MET D 101 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   TRP D 106 " --> pdb=" O   LEU D 102 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 122 through 137
      removed outlier: 3.772A  pdb=" N   ILE D 126 " --> pdb=" O   MET D 122 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 154 through 167
    Processing helix  chain 'D' and resid 173 through 189
      removed outlier: 3.880A  pdb=" N   HIS D 181 " --> pdb=" O   ASN D 177 " (cutoff:3.500A)

    300 hydrogen bonds defined for protein.
    870 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: 0.79

  Time building geometry restraints manager: 0.64 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: 1692
        1.34 -     1.46: 1757
        1.46 -     1.58: 3013
        1.58 -     1.70: 2
        1.70 -     1.82: 72
  Bond restraints: 6536
  Sorted by residual:
  bond pdb=" CA  THR C  68 "
       pdb=" CB  THR C  68 "
    ideal  model  delta    sigma   weight residual
    1.526  1.566 -0.040 1.51e-02 4.39e+03 6.88e+00
  bond pdb=" C   ILE B 123 "
       pdb=" N   PRO B 124 "
    ideal  model  delta    sigma   weight residual
    1.336  1.363 -0.027 1.25e-02 6.40e+03 4.80e+00
  bond pdb=" C   ILE D 123 "
       pdb=" N   PRO D 124 "
    ideal  model  delta    sigma   weight residual
    1.336  1.363 -0.027 1.25e-02 6.40e+03 4.69e+00
  bond pdb=" CB  ASP C 139 "
       pdb=" CG  ASP C 139 "
    ideal  model  delta    sigma   weight residual
    1.516  1.567 -0.051 2.50e-02 1.60e+03 4.22e+00
  bond pdb=" CB  ASP A 139 "
       pdb=" CG  ASP A 139 "
    ideal  model  delta    sigma   weight residual
    1.516  1.566 -0.050 2.50e-02 1.60e+03 4.05e+00
  ... (remaining 6531 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 8550
        2.41 -     4.83: 301
        4.83 -     7.24: 47
        7.24 -     9.66: 29
        9.66 -    12.07: 1
  Bond angle restraints: 8928
  Sorted by residual:
  angle pdb=" C   ARG C 138 "
        pdb=" N   ASP C 139 "
        pdb=" CA  ASP C 139 "
      ideal   model   delta    sigma   weight residual
     121.54  133.61  -12.07 1.91e+00 2.74e-01 4.00e+01
  angle pdb=" C   ALA C  24 "
        pdb=" N   VAL C  25 "
        pdb=" CA  VAL C  25 "
      ideal   model   delta    sigma   weight residual
     120.24  123.63   -3.39 6.30e-01 2.52e+00 2.89e+01
  angle pdb=" C   ALA A  24 "
        pdb=" N   VAL A  25 "
        pdb=" CA  VAL A  25 "
      ideal   model   delta    sigma   weight residual
     120.24  123.49   -3.25 6.30e-01 2.52e+00 2.66e+01
  angle pdb=" C   ARG A 138 "
        pdb=" N   ASP A 139 "
        pdb=" CA  ASP A 139 "
      ideal   model   delta    sigma   weight residual
     125.02  134.02   -9.00 1.76e+00 3.23e-01 2.61e+01
  angle pdb=" C   ALA D 152 "
        pdb=" N   CYS D 153 "
        pdb=" CA  CYS D 153 "
      ideal   model   delta    sigma   weight residual
     121.54  129.78   -8.24 1.91e+00 2.74e-01 1.86e+01
  ... (remaining 8923 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.62: 3073
       15.62 -    31.23: 422
       31.23 -    46.85: 115
       46.85 -    62.46: 15
       62.46 -    78.08: 11
  Dihedral angle restraints: 3636
    sinusoidal: 1384
      harmonic: 2252
  Sorted by residual:
  dihedral pdb=" CA  ARG A  54 "
           pdb=" C   ARG A  54 "
           pdb=" N   PRO A  55 "
           pdb=" CA  PRO A  55 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.48   26.52     0      5.00e+00 4.00e-02 2.81e+01
  dihedral pdb=" CA  ARG C  54 "
           pdb=" C   ARG C  54 "
           pdb=" N   PRO C  55 "
           pdb=" CA  PRO C  55 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.78   25.22     0      5.00e+00 4.00e-02 2.54e+01
  dihedral pdb=" CA  MET D 118 "
           pdb=" C   MET D 118 "
           pdb=" N   GLN D 119 "
           pdb=" CA  GLN D 119 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.07  -19.93     0      5.00e+00 4.00e-02 1.59e+01
  ... (remaining 3633 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.091: 837
       0.091 -    0.183: 116
       0.183 -    0.274: 9
       0.274 -    0.365: 0
       0.365 -    0.456: 2
  Chirality restraints: 964
  Sorted by residual:
  chirality pdb=" CB  ILE C  11 "
            pdb=" CA  ILE C  11 "
            pdb=" CG1 ILE C  11 "
            pdb=" CG2 ILE C  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.19    0.46 2.00e-01 2.50e+01 5.21e+00
  chirality pdb=" CB  ILE A  11 "
            pdb=" CA  ILE A  11 "
            pdb=" CG1 ILE A  11 "
            pdb=" CG2 ILE A  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.25    0.39 2.00e-01 2.50e+01 3.89e+00
  chirality pdb=" CA  ARG C  94 "
            pdb=" N   ARG C  94 "
            pdb=" C   ARG C  94 "
            pdb=" CB  ARG C  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.47e+00
  ... (remaining 961 not shown)

  Planarity restraints: 1084
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C  54 "    0.054 5.00e-02 4.00e+02   8.16e-02 1.07e+01
        pdb=" N   PRO C  55 "   -0.141 5.00e-02 4.00e+02
        pdb=" CA  PRO C  55 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO C  55 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  54 "    0.045 5.00e-02 4.00e+02   6.83e-02 7.47e+00
        pdb=" N   PRO A  55 "   -0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO A  55 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A  55 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A  25 "    0.036 5.00e-02 4.00e+02   5.29e-02 4.48e+00
        pdb=" N   PRO A  26 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A  26 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A  26 "    0.030 5.00e-02 4.00e+02
  ... (remaining 1081 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.87: 2187
        2.87 -     3.38: 5885
        3.38 -     3.88: 9807
        3.88 -     4.39: 9919
        4.39 -     4.90: 17266
  Nonbonded interactions: 45064
  Sorted by model distance:
  nonbonded pdb=" O   ILE C 159 "
            pdb=" ND2 ASN C 163 "
     model   vdw
     2.360 3.120
  nonbonded pdb=" O   ILE A 159 "
            pdb=" ND2 ASN A 163 "
     model   vdw
     2.362 3.120
  nonbonded pdb=" O   TRP A 133 "
            pdb=" ND2 ASN A 137 "
     model   vdw
     2.375 3.120
  nonbonded pdb=" O   TRP C 133 "
            pdb=" ND2 ASN C 137 "
     model   vdw
     2.376 3.120
  nonbonded pdb=" O   TYR A 131 "
            pdb=" NE2 GLN A 135 "
     model   vdw
     2.383 3.120
  ... (remaining 45059 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.230
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.870
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
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   0.058   6536  Z= 0.249
  Angle     :  1.117  12.073   8928  Z= 0.601
  Chirality :  0.063   0.456    964
  Planarity :  0.007   0.082   1084
  Dihedral  : 15.722  78.075   2212
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.50 %
    Favored  : 87.50 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  : 11.01 %
    Favored  : 88.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.95 (0.24), residues: 768
  helix: -2.64 (0.18), residues: 430
  sheet:  None (None), residues: 0
  loop : -4.19 (0.30), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 138 
 TYR   0.016   0.002   TYR A 183 
 PHE   0.030   0.002   PHE B 188 
 TRP   0.012   0.001   TRP B 145 
 HIS   0.001   0.000   HIS A 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00515 ( 6536)
  covalent geometry    : angle       1.11735 ( 8928)
  hydrogen bonds       : bond        0.13624 (  300)
  hydrogen bonds       : angle       6.49709 (  870)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 233
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.8599 (ttp) cc_final: 0.8372 (tmm)
REVERT: A  183 TYR cc_start: 0.8821 (t80) cc_final: 0.8586 (t80)
REVERT: B   59 THR cc_start: 0.9027 (p) cc_final: 0.8813 (m)
REVERT: B  104 PHE cc_start: 0.8742 (t80) cc_final: 0.8367 (t80)
REVERT: B  123 ILE cc_start: 0.8975 (mp) cc_final: 0.8459 (mm)
REVERT: B  162 PHE cc_start: 0.7562 (m-10) cc_final: 0.7297 (m-80)
REVERT: B  185 PHE cc_start: 0.8702 (t80) cc_final: 0.8491 (t80)
REVERT: C  187 MET cc_start: 0.7799 (tmm) cc_final: 0.7245 (tmm)
REVERT: D   85 ARG cc_start: 0.8551 (mmt90) cc_final: 0.8145 (mmm-85)
REVERT: D  104 PHE cc_start: 0.8810 (t80) cc_final: 0.8352 (t80)
REVERT: D  106 TRP cc_start: 0.8995 (t60) cc_final: 0.8346 (t60)
REVERT: D  121 LEU cc_start: 0.9090 (tp) cc_final: 0.8878 (tp)
REVERT: D  123 ILE cc_start: 0.9042 (mp) cc_final: 0.8458 (mm)
  outliers start: 3
  outliers final: 0
  residues processed: 234
  average time/residue: 0.0800
  time to fit residues: 24.4021
Evaluate side-chains
  173 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    0.0040
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:   10.0000
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.5792

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

Flipped N/Q/H residues before XYZ refinement:
B  81 GLN
B 172 ASN
B 177 ASN
D 172 ASN
D 177 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.145254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.118645 restraints weight = 14448.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.121801 restraints weight = 8600.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.123883 restraints weight = 6266.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.125155 restraints weight = 5147.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.125689 restraints weight = 4553.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6536  Z= 0.128
  Angle     :  0.759   9.679   8928  Z= 0.372
  Chirality :  0.044   0.223    964
  Planarity :  0.006   0.066   1084
  Dihedral  :  5.226  20.586    864
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.81 %
    Favored  : 89.19 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 21.38 %
    Favored  : 75.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.28 (0.29), residues: 768
  helix: -1.03 (0.23), residues: 452
  sheet:  None (None), residues: 0
  loop : -3.99 (0.33), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  49 
 TYR   0.016   0.001   TYR B  77 
 PHE   0.014   0.001   PHE D 144 
 TRP   0.015   0.001   TRP B  53 
 HIS   0.001   0.000   HIS D 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6536)
  covalent geometry    : angle       0.75936 ( 8928)
  hydrogen bonds       : bond        0.04037 (  300)
  hydrogen bonds       : angle       4.79254 (  870)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 207
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 GLN cc_start: 0.9256 (tp-100) cc_final: 0.8886 (mm-40)
REVERT: A  187 MET cc_start: 0.7377 (tmm) cc_final: 0.7031 (tmm)
REVERT: B   59 THR cc_start: 0.8905 (p) cc_final: 0.8627 (m)
REVERT: B  104 PHE cc_start: 0.8717 (t80) cc_final: 0.8298 (t80)
REVERT: B  123 ILE cc_start: 0.8930 (mp) cc_final: 0.8462 (mm)
REVERT: C   81 GLN cc_start: 0.9251 (tp-100) cc_final: 0.8857 (mm-40)
REVERT: C  187 MET cc_start: 0.7759 (tmm) cc_final: 0.7029 (tmm)
REVERT: D   85 ARG cc_start: 0.8555 (mmt90) cc_final: 0.8184 (mmm-85)
REVERT: D  104 PHE cc_start: 0.8782 (t80) cc_final: 0.8396 (t80)
REVERT: D  119 GLN cc_start: 0.8726 (pm20) cc_final: 0.8472 (pm20)
REVERT: D  123 ILE cc_start: 0.8929 (mp) cc_final: 0.8454 (mm)
  outliers start: 22
  outliers final: 15
  residues processed: 212
  average time/residue: 0.0670
  time to fit residues: 18.9016
Evaluate side-chains
  195 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 180
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 TRP
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  188 PHE
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  188 PHE
Chi-restraints excluded: chain C residue   42 TRP
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  139 ASP
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  188 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 73 optimal weight:    0.7980
   chunk 69 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0010
   chunk 27 optimal weight:    0.9980
   chunk 75 optimal weight:   20.0000
   chunk 74 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0000
   chunk 12 optimal weight:    3.9990
   chunk 13 optimal weight:    7.9990
   chunk 23 optimal weight:    4.9990
   overall best weight:    0.5190

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.142487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.117016 restraints weight = 14483.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.120124 restraints weight = 8401.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.122107 restraints weight = 6010.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.123445 restraints weight = 4880.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.123855 restraints weight = 4266.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.2488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6536  Z= 0.121
  Angle     :  0.738   9.198   8928  Z= 0.356
  Chirality :  0.044   0.208    964
  Planarity :  0.005   0.067   1084
  Dihedral  :  4.841  20.413    864
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.07 %
    Favored  : 88.93 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 22.96 %
    Favored  : 72.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.43 (0.31), residues: 768
  helix: -0.34 (0.25), residues: 454
  sheet:  None (None), residues: 0
  loop : -3.66 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  49 
 TYR   0.014   0.001   TYR A  82 
 PHE   0.014   0.001   PHE B  91 
 TRP   0.012   0.001   TRP B  53 
 HIS   0.000   0.000   HIS C 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 6536)
  covalent geometry    : angle       0.73837 ( 8928)
  hydrogen bonds       : bond        0.03551 (  300)
  hydrogen bonds       : angle       4.37493 (  870)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 203
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 MET cc_start: 0.7478 (tmm) cc_final: 0.6952 (tmm)
REVERT: B   59 THR cc_start: 0.8928 (p) cc_final: 0.8620 (m)
REVERT: B  104 PHE cc_start: 0.8757 (t80) cc_final: 0.8324 (t80)
REVERT: B  187 MET cc_start: 0.7423 (tmm) cc_final: 0.6709 (tmm)
REVERT: C  187 MET cc_start: 0.7838 (tmm) cc_final: 0.7172 (tmm)
REVERT: D   85 ARG cc_start: 0.8547 (mmt90) cc_final: 0.8118 (mmm-85)
REVERT: D  104 PHE cc_start: 0.8817 (t80) cc_final: 0.8440 (t80)
  outliers start: 29
  outliers final: 16
  residues processed: 215
  average time/residue: 0.0657
  time to fit residues: 19.0798
Evaluate side-chains
  198 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 182
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 TRP
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain C residue   42 TRP
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  178 LEU
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  101 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 42 optimal weight:    5.9990
   chunk 9 optimal weight:    0.8980
   chunk 61 optimal weight:    4.9990
   chunk 51 optimal weight:    0.8980
   chunk 23 optimal weight:    4.9990
   chunk 59 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0970
   chunk 28 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9980
   overall best weight:    0.7578

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

Flipped N/Q/H residues before XYZ refinement:
D 137 ASN
D 181 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.142541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.116525 restraints weight = 14643.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.119641 restraints weight = 8646.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.121631 restraints weight = 6236.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.122630 restraints weight = 5085.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.123578 restraints weight = 4533.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.2791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6536  Z= 0.127
  Angle     :  0.750   8.391   8928  Z= 0.358
  Chirality :  0.044   0.202    964
  Planarity :  0.005   0.066   1084
  Dihedral  :  4.700  18.891    864
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.68 %
    Favored  : 89.32 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 26.89 %
    Favored  : 69.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.02 (0.32), residues: 768
  helix: -0.01 (0.25), residues: 456
  sheet:  None (None), residues: 0
  loop : -3.50 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 138 
 TYR   0.014   0.001   TYR A  82 
 PHE   0.014   0.001   PHE D  91 
 TRP   0.009   0.001   TRP A 133 
 HIS   0.001   0.000   HIS D 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6536)
  covalent geometry    : angle       0.74981 ( 8928)
  hydrogen bonds       : bond        0.03553 (  300)
  hydrogen bonds       : angle       4.22091 (  870)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 195
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8683 (tp40)
REVERT: A  187 MET cc_start: 0.7723 (tmm) cc_final: 0.7020 (tmm)
REVERT: B   59 THR cc_start: 0.8953 (p) cc_final: 0.8645 (m)
REVERT: B  103 LEU cc_start: 0.9403 (mm) cc_final: 0.9163 (mm)
REVERT: B  104 PHE cc_start: 0.8756 (t80) cc_final: 0.8327 (t80)
REVERT: B  187 MET cc_start: 0.7433 (tmm) cc_final: 0.6731 (tmm)
REVERT: C   81 GLN cc_start: 0.8885 (mm-40) cc_final: 0.8292 (tp40)
REVERT: C  178 LEU cc_start: 0.8567 (tt) cc_final: 0.8303 (pp)
REVERT: C  187 MET cc_start: 0.7853 (tmm) cc_final: 0.7057 (tmm)
REVERT: D  104 PHE cc_start: 0.8838 (t80) cc_final: 0.8510 (t80)
  outliers start: 26
  outliers final: 21
  residues processed: 207
  average time/residue: 0.0642
  time to fit residues: 17.7421
Evaluate side-chains
  201 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 180
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 PHE
Chi-restraints excluded: chain A residue   42 TRP
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain C residue   40 PHE
Chi-restraints excluded: chain C residue   42 TRP
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  123 ILE
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  101 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 62 optimal weight:    0.2980
   chunk 66 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 23 optimal weight:    0.0050
   chunk 33 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
D 181 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.143038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.116775 restraints weight = 14884.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.119939 restraints weight = 8803.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.121855 restraints weight = 6320.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.123130 restraints weight = 5162.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.123653 restraints weight = 4536.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.3033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6536  Z= 0.123
  Angle     :  0.739   9.522   8928  Z= 0.349
  Chirality :  0.044   0.200    964
  Planarity :  0.005   0.071   1084
  Dihedral  :  4.582  19.253    864
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.72 %
    Favored  : 88.28 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 27.04 %
    Favored  : 67.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.76 (0.32), residues: 768
  helix:  0.21 (0.25), residues: 456
  sheet:  None (None), residues: 0
  loop : -3.40 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  85 
 TYR   0.014   0.001   TYR C  82 
 PHE   0.014   0.001   PHE D  91 
 TRP   0.009   0.001   TRP C 133 
 HIS   0.001   0.000   HIS A 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6536)
  covalent geometry    : angle       0.73881 ( 8928)
  hydrogen bonds       : bond        0.03308 (  300)
  hydrogen bonds       : angle       4.07981 (  870)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 199
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8661 (tp40)
REVERT: A   97 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8301 (p0)
REVERT: A  187 MET cc_start: 0.7784 (tmm) cc_final: 0.6885 (tmm)
REVERT: B   59 THR cc_start: 0.8938 (p) cc_final: 0.8639 (m)
REVERT: B  103 LEU cc_start: 0.9417 (mm) cc_final: 0.9187 (mm)
REVERT: B  104 PHE cc_start: 0.8764 (t80) cc_final: 0.8332 (t80)
REVERT: B  187 MET cc_start: 0.7453 (tmm) cc_final: 0.6754 (tmm)
REVERT: C   81 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8657 (tp40)
REVERT: C  140 MET cc_start: 0.7850 (mpp) cc_final: 0.7607 (mpp)
REVERT: C  178 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8279 (pp)
REVERT: C  187 MET cc_start: 0.7877 (tmm) cc_final: 0.7096 (tmm)
REVERT: D  104 PHE cc_start: 0.8836 (t80) cc_final: 0.8519 (t80)
  outliers start: 32
  outliers final: 23
  residues processed: 213
  average time/residue: 0.0636
  time to fit residues: 18.4116
Evaluate side-chains
  210 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 185
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 PHE
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain C residue   40 PHE
Chi-restraints excluded: chain C residue   42 TRP
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  123 ILE
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  178 LEU
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   57 THR
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  101 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 53 optimal weight:    0.8980
   chunk 23 optimal weight:   10.0000
   chunk 14 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 52 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
A 137 ASN
C 135 GLN
C 137 ASN
D 181 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.141960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.115660 restraints weight = 14533.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.118664 restraints weight = 8721.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.120551 restraints weight = 6349.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.121467 restraints weight = 5214.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.122451 restraints weight = 4690.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.3213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6536  Z= 0.132
  Angle     :  0.739   8.158   8928  Z= 0.354
  Chirality :  0.045   0.198    964
  Planarity :  0.005   0.070   1084
  Dihedral  :  4.548  18.607    864
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.20 %
    Favored  : 88.80 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 27.99 %
    Favored  : 66.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.62 (0.32), residues: 768
  helix:  0.32 (0.26), residues: 458
  sheet:  None (None), residues: 0
  loop : -3.37 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 138 
 TYR   0.014   0.001   TYR A  82 
 PHE   0.018   0.001   PHE D 184 
 TRP   0.012   0.001   TRP A 133 
 HIS   0.001   0.000   HIS B 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 6536)
  covalent geometry    : angle       0.73872 ( 8928)
  hydrogen bonds       : bond        0.03603 (  300)
  hydrogen bonds       : angle       4.10448 (  870)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 188
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 GLN cc_start: 0.8901 (mm-40) cc_final: 0.8674 (tp40)
REVERT: A   97 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8274 (p0)
REVERT: A  187 MET cc_start: 0.7844 (tmm) cc_final: 0.6946 (tmm)
REVERT: B   71 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7722 (tt)
REVERT: B  103 LEU cc_start: 0.9426 (mm) cc_final: 0.9190 (mm)
REVERT: B  104 PHE cc_start: 0.8809 (t80) cc_final: 0.8381 (t80)
REVERT: C   81 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8649 (tp40)
REVERT: C  178 LEU cc_start: 0.8554 (tt) cc_final: 0.8284 (pp)
REVERT: C  187 MET cc_start: 0.7905 (tmm) cc_final: 0.7069 (tmm)
REVERT: D  104 PHE cc_start: 0.8832 (t80) cc_final: 0.8536 (t80)
  outliers start: 33
  outliers final: 25
  residues processed: 202
  average time/residue: 0.0704
  time to fit residues: 19.1656
Evaluate side-chains
  204 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 177
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 TRP
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  175 ILE
Chi-restraints excluded: chain C residue   42 TRP
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   57 THR
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  175 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 22 optimal weight:    7.9990
   chunk 14 optimal weight:    0.7980
   chunk 30 optimal weight:    0.2980
   chunk 75 optimal weight:    9.9990
   chunk 42 optimal weight:    0.4980
   chunk 2 optimal weight:    4.9990
   chunk 60 optimal weight:    0.1980
   chunk 5 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 181 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.143522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.117299 restraints weight = 14668.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.120435 restraints weight = 8672.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.122420 restraints weight = 6266.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.123414 restraints weight = 5107.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.124239 restraints weight = 4562.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6536  Z= 0.122
  Angle     :  0.738   8.860   8928  Z= 0.349
  Chirality :  0.044   0.200    964
  Planarity :  0.005   0.064   1084
  Dihedral  :  4.465  18.417    864
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.33 %
    Favored  : 88.67 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 29.25 %
    Favored  : 66.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.52 (0.33), residues: 768
  helix:  0.45 (0.26), residues: 456
  sheet:  None (None), residues: 0
  loop : -3.39 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 138 
 TYR   0.015   0.001   TYR A 183 
 PHE   0.013   0.001   PHE D  91 
 TRP   0.016   0.001   TRP C 133 
 HIS   0.001   0.000   HIS D 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6536)
  covalent geometry    : angle       0.73789 ( 8928)
  hydrogen bonds       : bond        0.03358 (  300)
  hydrogen bonds       : angle       4.04825 (  870)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 191
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8643 (tp40)
REVERT: A   97 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8326 (p0)
REVERT: A  178 LEU cc_start: 0.8576 (tt) cc_final: 0.8248 (pp)
REVERT: A  187 MET cc_start: 0.7813 (tmm) cc_final: 0.7007 (tmm)
REVERT: B    9 ARG cc_start: 0.6562 (mtt180) cc_final: 0.6167 (mtm180)
REVERT: B  103 LEU cc_start: 0.9448 (mm) cc_final: 0.9212 (mm)
REVERT: B  104 PHE cc_start: 0.8830 (t80) cc_final: 0.8404 (t80)
REVERT: C   81 GLN cc_start: 0.8832 (mm-40) cc_final: 0.8624 (tp40)
REVERT: C  178 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8236 (pp)
REVERT: C  187 MET cc_start: 0.7951 (tmm) cc_final: 0.7157 (tmm)
REVERT: D  104 PHE cc_start: 0.8841 (t80) cc_final: 0.8439 (t80)
  outliers start: 29
  outliers final: 25
  residues processed: 203
  average time/residue: 0.0669
  time to fit residues: 18.4342
Evaluate side-chains
  215 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 188
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 PHE
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  164 TYR
Chi-restraints excluded: chain B residue  175 ILE
Chi-restraints excluded: chain C residue   40 PHE
Chi-restraints excluded: chain C residue   42 TRP
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  178 LEU
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   57 THR
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  136 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 68 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0030
   chunk 30 optimal weight:    0.0020
   chunk 65 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 37 optimal weight:    8.9990
   overall best weight:    0.6800

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

Flipped N/Q/H residues before XYZ refinement:
C 172 ASN
D 181 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.143446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.117853 restraints weight = 14354.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.120907 restraints weight = 8394.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.122928 restraints weight = 6012.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.124189 restraints weight = 4872.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.124737 restraints weight = 4269.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.3514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6536  Z= 0.129
  Angle     :  0.747   9.072   8928  Z= 0.356
  Chirality :  0.044   0.201    964
  Planarity :  0.005   0.075   1084
  Dihedral  :  4.445  18.388    864
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.20 %
    Favored  : 88.80 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 28.93 %
    Favored  : 65.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.50 (0.33), residues: 768
  helix:  0.47 (0.26), residues: 456
  sheet:  None (None), residues: 0
  loop : -3.38 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 189 
 TYR   0.013   0.001   TYR C  82 
 PHE   0.014   0.001   PHE D 184 
 TRP   0.016   0.001   TRP C 133 
 HIS   0.002   0.000   HIS D 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 6536)
  covalent geometry    : angle       0.74732 ( 8928)
  hydrogen bonds       : bond        0.03482 (  300)
  hydrogen bonds       : angle       4.07612 (  870)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 193
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8628 (tp40)
REVERT: A   97 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8329 (p0)
REVERT: A  178 LEU cc_start: 0.8566 (tt) cc_final: 0.8241 (pp)
REVERT: A  187 MET cc_start: 0.7826 (tmm) cc_final: 0.7010 (tmm)
REVERT: B    9 ARG cc_start: 0.6552 (mtt180) cc_final: 0.6176 (mtm180)
REVERT: B   71 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7741 (tt)
REVERT: B  103 LEU cc_start: 0.9443 (mm) cc_final: 0.9204 (mm)
REVERT: B  104 PHE cc_start: 0.8840 (t80) cc_final: 0.8424 (t80)
REVERT: C   81 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8182 (tp40)
REVERT: C  178 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8260 (pp)
REVERT: C  187 MET cc_start: 0.7934 (tmm) cc_final: 0.7094 (tmm)
REVERT: D  104 PHE cc_start: 0.8850 (t80) cc_final: 0.8486 (t80)
  outliers start: 33
  outliers final: 22
  residues processed: 206
  average time/residue: 0.0640
  time to fit residues: 18.1082
Evaluate side-chains
  211 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 186
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  164 TYR
Chi-restraints excluded: chain B residue  175 ILE
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  178 LEU
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   57 THR
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  136 LEU
Chi-restraints excluded: chain D residue  188 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9980
   chunk 32 optimal weight:   10.0000
   chunk 26 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 43 optimal weight:    0.6980
   chunk 59 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0370
   chunk 19 optimal weight:    8.9990
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
D 181 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.143866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.117713 restraints weight = 14675.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.120852 restraints weight = 8659.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.122746 restraints weight = 6223.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.124091 restraints weight = 5108.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.124894 restraints weight = 4467.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.3606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6536  Z= 0.130
  Angle     :  0.771   9.486   8928  Z= 0.365
  Chirality :  0.044   0.200    964
  Planarity :  0.005   0.073   1084
  Dihedral  :  4.434  18.303    864
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.33 %
    Favored  : 88.67 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 30.97 %
    Favored  : 64.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.49 (0.33), residues: 768
  helix:  0.49 (0.26), residues: 456
  sheet:  None (None), residues: 0
  loop : -3.40 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D 138 
 TYR   0.013   0.001   TYR C  82 
 PHE   0.012   0.001   PHE B 144 
 TRP   0.018   0.001   TRP C 133 
 HIS   0.001   0.000   HIS D 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6536)
  covalent geometry    : angle       0.77060 ( 8928)
  hydrogen bonds       : bond        0.03565 (  300)
  hydrogen bonds       : angle       4.11265 (  870)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 193
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 GLN cc_start: 0.8836 (mm-40) cc_final: 0.8201 (tp40)
REVERT: A   97 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8358 (p0)
REVERT: A  140 MET cc_start: 0.7520 (mpp) cc_final: 0.7273 (mpp)
REVERT: A  178 LEU cc_start: 0.8582 (tt) cc_final: 0.8263 (pp)
REVERT: A  187 MET cc_start: 0.7836 (tmm) cc_final: 0.7041 (tmm)
REVERT: B    9 ARG cc_start: 0.6544 (mtt180) cc_final: 0.6180 (mtm180)
REVERT: B   71 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7720 (tt)
REVERT: B  103 LEU cc_start: 0.9435 (mm) cc_final: 0.9190 (mm)
REVERT: B  104 PHE cc_start: 0.8893 (t80) cc_final: 0.8512 (t80)
REVERT: B  135 GLN cc_start: 0.9108 (mm-40) cc_final: 0.8893 (mm-40)
REVERT: C   81 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8186 (tp40)
REVERT: C  178 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8283 (pp)
REVERT: C  187 MET cc_start: 0.7984 (tmm) cc_final: 0.7182 (tmm)
REVERT: D  104 PHE cc_start: 0.8853 (t80) cc_final: 0.8453 (t80)
  outliers start: 27
  outliers final: 21
  residues processed: 206
  average time/residue: 0.0661
  time to fit residues: 18.7604
Evaluate side-chains
  210 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 186
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  175 ILE
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  178 LEU
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   57 THR
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  175 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 58 optimal weight:    0.4980
   chunk 53 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 36 optimal weight:    0.6980
   chunk 44 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
D 181 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.145557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.120362 restraints weight = 14185.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.123361 restraints weight = 8402.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.125388 restraints weight = 6047.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.126535 restraints weight = 4897.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.126843 restraints weight = 4300.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.3700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6536  Z= 0.132
  Angle     :  0.772   9.517   8928  Z= 0.367
  Chirality :  0.044   0.200    964
  Planarity :  0.005   0.081   1084
  Dihedral  :  4.403  18.231    864
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.07 %
    Favored  : 88.93 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 30.50 %
    Favored  : 64.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.44 (0.33), residues: 768
  helix:  0.49 (0.26), residues: 458
  sheet:  None (None), residues: 0
  loop : -3.34 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 138 
 TYR   0.013   0.001   TYR A  82 
 PHE   0.016   0.001   PHE B 144 
 TRP   0.023   0.001   TRP D 133 
 HIS   0.001   0.000   HIS D 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 6536)
  covalent geometry    : angle       0.77240 ( 8928)
  hydrogen bonds       : bond        0.03639 (  300)
  hydrogen bonds       : angle       4.13130 (  870)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 193
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8223 (tp40)
REVERT: A   97 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.8299 (p0)
REVERT: A  178 LEU cc_start: 0.8584 (tt) cc_final: 0.8259 (pp)
REVERT: A  187 MET cc_start: 0.7788 (tmm) cc_final: 0.7068 (tmm)
REVERT: B    9 ARG cc_start: 0.6522 (mtt180) cc_final: 0.6156 (mtm180)
REVERT: B   71 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7745 (tt)
REVERT: B  103 LEU cc_start: 0.9427 (mm) cc_final: 0.9190 (mm)
REVERT: B  104 PHE cc_start: 0.8907 (t80) cc_final: 0.8525 (t80)
REVERT: C   81 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8184 (tp40)
REVERT: C  178 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8251 (pp)
REVERT: C  187 MET cc_start: 0.7975 (tmm) cc_final: 0.7196 (tmm)
REVERT: D  104 PHE cc_start: 0.8838 (t80) cc_final: 0.8458 (t80)
REVERT: D  187 MET cc_start: 0.7261 (tmm) cc_final: 0.7003 (tmm)
  outliers start: 30
  outliers final: 22
  residues processed: 207
  average time/residue: 0.0678
  time to fit residues: 19.1213
Evaluate side-chains
  211 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 186
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  175 ILE
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  178 LEU
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   57 THR
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  175 ILE
Chi-restraints excluded: chain D residue  188 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 58 optimal weight:    0.1980
   chunk 20 optimal weight:    0.1980
   chunk 16 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 51 optimal weight:   10.0000
   chunk 56 optimal weight:    9.9990
   chunk 44 optimal weight:    0.8980
   chunk 40 optimal weight:    4.9990
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
A 137 ASN
C  75 ASN
D 181 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.146627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.120594 restraints weight = 14486.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.123618 restraints weight = 8743.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.125435 restraints weight = 6379.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.126767 restraints weight = 5273.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.127414 restraints weight = 4629.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.3814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6536  Z= 0.134
  Angle     :  0.804   9.324   8928  Z= 0.383
  Chirality :  0.045   0.222    964
  Planarity :  0.005   0.080   1084
  Dihedral  :  4.485  21.191    864
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.94 %
    Favored  : 89.06 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 31.29 %
    Favored  : 64.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.42 (0.32), residues: 768
  helix:  0.54 (0.26), residues: 454
  sheet:  None (None), residues: 0
  loop : -3.34 (0.36), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 138 
 TYR   0.014   0.001   TYR C 183 
 PHE   0.015   0.001   PHE B 144 
 TRP   0.021   0.001   TRP D 133 
 HIS   0.002   0.000   HIS D 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 6536)
  covalent geometry    : angle       0.80413 ( 8928)
  hydrogen bonds       : bond        0.03607 (  300)
  hydrogen bonds       : angle       4.23788 (  870)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1128.86 seconds
wall clock time: 20 minutes 0.58 seconds (1200.58 seconds total)