Starting phenix.real_space_refine
on Tue Mar 11 15:26:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7czb_30508/03_2025/7czb_30508.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7czb_30508/03_2025/7czb_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_2025/7czb_30508.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7czb_30508/03_2025/7czb_30508.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7czb_30508/03_2025/7czb_30508.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7czb_30508/03_2025/7czb_30508.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.008 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP: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: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP: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: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP: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: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 17
  Time building chain proxies: 3.94, per 1000 atoms: 0.63
  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: 1.26
  Conformation dependent library (CDL) restraints added in 762.2 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: 0.49
  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: 1.33

  Time building geometry restraints manager: 1.53 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: 0.02
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:             0.780
  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:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.310
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.640
-------------------------------------------------------------------------------
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= 0.314
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.95 (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
 TRP   0.012   0.001   TRP B 145 
 HIS   0.001   0.000   HIS A 181 
 PHE   0.030   0.002   PHE B 188 
 TYR   0.016   0.002   TYR A 183 
 ARG   0.005   0.001   ARG B 138 

*********************** 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  : 0.707 
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: 0.8369 (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: 0.8815 (m)
REVERT: B  104 PHE cc_start: 0.8742 (t80) cc_final: 0.8368 (t80)
REVERT: B  123 ILE cc_start: 0.8975 (mp) cc_final: 0.8457 (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: 0.8494 (t80)
REVERT: C  187 MET cc_start: 0.7799 (tmm) cc_final: 0.7245 (tmm)
REVERT: D   85 ARG cc_start: 0.8550 (mmt90) cc_final: 0.8145 (mmm-85)
REVERT: D  104 PHE cc_start: 0.8810 (t80) cc_final: 0.8351 (t80)
REVERT: D  106 TRP cc_start: 0.8995 (t60) cc_final: 0.8347 (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: 0.8460 (mm)
  outliers start: 3
  outliers final: 0
  residues processed: 234
  average time/residue: 0.1885
  time to fit residues: 56.8258
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  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 57 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   chunk 19 optimal weight:   10.0000
   chunk 38 optimal weight:   10.0000
   chunk 30 optimal weight:    0.8980
   chunk 59 optimal weight:    4.9990
   chunk 23 optimal weight:    9.9990
   chunk 36 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 137 ASN
D 172 ASN
D 177 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.142638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.116192 restraints weight = 14227.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.119220 restraints weight = 8501.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.121223 restraints weight = 6222.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6536  Z= 0.211
  Angle     :  0.776   8.970   8928  Z= 0.384
  Chirality :  0.045   0.224    964
  Planarity :  0.006   0.065   1084
  Dihedral  :  5.305  20.773    864
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.98 %
    Favored  : 88.02 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 20.60 %
    Favored  : 75.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.30 (0.29), residues: 768
  helix: -1.05 (0.23), residues: 454
  sheet:  None (None), residues: 0
  loop : -4.01 (0.33), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  53 
 HIS   0.000   0.000   HIS D 181 
 PHE   0.013   0.001   PHE B  91 
 TYR   0.014   0.002   TYR B  77 
 ARG   0.006   0.001   ARG A  49 

*********************** 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
  223 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 197
  time to evaluate  : 0.656 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 MET cc_start: 0.7431 (tmm) cc_final: 0.7021 (tmm)
REVERT: B  104 PHE cc_start: 0.8748 (t80) cc_final: 0.8315 (t80)
REVERT: B  106 TRP cc_start: 0.9025 (t60) cc_final: 0.8427 (t60)
REVERT: B  136 LEU cc_start: 0.8719 (mm) cc_final: 0.8320 (mm)
REVERT: C  187 MET cc_start: 0.7793 (tmm) cc_final: 0.7128 (tmm)
REVERT: D   16 ARG cc_start: 0.7264 (ptt180) cc_final: 0.6981 (ptp-170)
REVERT: D   85 ARG cc_start: 0.8618 (mmt90) cc_final: 0.8082 (mmm-85)
REVERT: D  104 PHE cc_start: 0.8789 (t80) cc_final: 0.8407 (t80)
  outliers start: 26
  outliers final: 16
  residues processed: 203
  average time/residue: 0.1658
  time to fit residues: 44.5329
Evaluate side-chains
  192 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 176
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
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   53 TRP
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 17 optimal weight:    0.8980
   chunk 60 optimal weight:    6.9990
   chunk 42 optimal weight:    6.9990
   chunk 41 optimal weight:    6.9990
   chunk 62 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 46 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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 = 0.3849 r_free = 0.3849 target = 0.138720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.111248 restraints weight = 14647.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.114246 restraints weight = 8885.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.116093 restraints weight = 6580.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
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      :  0.004   0.032   6536  Z= 0.263
  Angle     :  0.771   7.603   8928  Z= 0.379
  Chirality :  0.046   0.211    964
  Planarity :  0.005   0.066   1084
  Dihedral  :  5.069  20.612    864
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.98 %
    Favored  : 88.02 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 22.64 %
    Favored  : 71.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.61 (0.30), residues: 768
  helix: -0.45 (0.24), residues: 456
  sheet:  None (None), residues: 0
  loop : -3.81 (0.35), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D  53 
 HIS   0.001   0.000   HIS D 181 
 PHE   0.018   0.001   PHE B  91 
 TYR   0.017   0.002   TYR B  98 
 ARG   0.005   0.001   ARG C  49 

*********************** 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
  215 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 180
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 TYR cc_start: 0.6227 (OUTLIER) cc_final: 0.5900 (m-10)
REVERT: A  183 TYR cc_start: 0.8838 (t80) cc_final: 0.8600 (t80)
REVERT: A  187 MET cc_start: 0.7547 (tmm) cc_final: 0.6851 (tmm)
REVERT: B  104 PHE cc_start: 0.8770 (t80) cc_final: 0.8325 (t80)
REVERT: B  106 TRP cc_start: 0.9080 (t60) cc_final: 0.8497 (t60)
REVERT: C  140 MET cc_start: 0.7737 (mpp) cc_final: 0.7413 (mpp)
REVERT: C  187 MET cc_start: 0.7867 (tmm) cc_final: 0.7066 (tmm)
REVERT: D   85 ARG cc_start: 0.8658 (mmt90) cc_final: 0.8033 (tpp80)
REVERT: D  104 PHE cc_start: 0.8815 (t80) cc_final: 0.8439 (t80)
REVERT: D  118 MET cc_start: 0.6881 (tpp) cc_final: 0.6649 (tpt)
  outliers start: 35
  outliers final: 21
  residues processed: 193
  average time/residue: 0.1676
  time to fit residues: 42.7221
Evaluate side-chains
  192 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 170
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 TRP
Chi-restraints excluded: chain A residue   48 TYR
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   59 THR
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  120 LEU
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  121 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   99 LEU
Chi-restraints excluded: chain D residue  188 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 37 optimal weight:   10.0000
   chunk 39 optimal weight:    0.0980
   chunk 12 optimal weight:    1.9990
   chunk 70 optimal weight:    9.9990
   chunk 17 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3884 r_free = 0.3884 target = 0.141389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.114720 restraints weight = 14579.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.117740 restraints weight = 8600.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.119657 restraints weight = 6270.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.2681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6536  Z= 0.173
  Angle     :  0.722   8.203   8928  Z= 0.349
  Chirality :  0.044   0.205    964
  Planarity :  0.005   0.067   1084
  Dihedral  :  4.816  20.049    864
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.59 %
    Favored  : 88.41 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 25.63 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.08 (0.31), residues: 768
  helix:  0.05 (0.25), residues: 450
  sheet:  None (None), residues: 0
  loop : -3.65 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 133 
 HIS   0.001   0.000   HIS D 181 
 PHE   0.018   0.001   PHE B  91 
 TYR   0.015   0.001   TYR C  98 
 ARG   0.006   0.001   ARG B 138 

*********************** 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
  232 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 198
  time to evaluate  : 0.657 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 TYR cc_start: 0.6216 (OUTLIER) cc_final: 0.5816 (m-10)
REVERT: A   81 GLN cc_start: 0.9186 (tp40) cc_final: 0.8618 (tp40)
REVERT: A  183 TYR cc_start: 0.8820 (t80) cc_final: 0.8601 (t80)
REVERT: A  187 MET cc_start: 0.7631 (tmm) cc_final: 0.6858 (tmm)
REVERT: B  103 LEU cc_start: 0.9398 (mm) cc_final: 0.9131 (mm)
REVERT: B  104 PHE cc_start: 0.8775 (t80) cc_final: 0.8346 (t80)
REVERT: B  106 TRP cc_start: 0.9047 (t60) cc_final: 0.8453 (t60)
REVERT: C   48 TYR cc_start: 0.6258 (OUTLIER) cc_final: 0.6041 (m-10)
REVERT: C  140 MET cc_start: 0.7792 (mpp) cc_final: 0.7527 (mpp)
REVERT: C  178 LEU cc_start: 0.8609 (tt) cc_final: 0.8344 (pp)
REVERT: C  187 MET cc_start: 0.7874 (tmm) cc_final: 0.7091 (tmm)
REVERT: D   51 GLN cc_start: 0.7196 (tp-100) cc_final: 0.6903 (tp-100)
REVERT: D   85 ARG cc_start: 0.8592 (mmt90) cc_final: 0.8048 (tpp80)
REVERT: D  104 PHE cc_start: 0.8803 (t80) cc_final: 0.8454 (t80)
REVERT: D  112 THR cc_start: 0.9076 (m) cc_final: 0.8876 (p)
  outliers start: 34
  outliers final: 21
  residues processed: 215
  average time/residue: 0.1624
  time to fit residues: 46.4308
Evaluate side-chains
  203 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 180
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
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   48 TYR
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  175 ILE
Chi-restraints excluded: chain C residue   40 PHE
Chi-restraints excluded: chain C residue   42 TRP
Chi-restraints excluded: chain C residue   48 TYR
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   99 LEU
Chi-restraints excluded: chain D residue  101 MET
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0370
   chunk 31 optimal weight:    0.8980
   chunk 27 optimal weight:    0.4980
   chunk 72 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 22 optimal weight:    7.9990
   chunk 11 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.8862

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.141365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.114378 restraints weight = 14546.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.116752 restraints weight = 8842.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.119107 restraints weight = 6695.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.2884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6536  Z= 0.183
  Angle     :  0.725   7.698   8928  Z= 0.347
  Chirality :  0.044   0.204    964
  Planarity :  0.004   0.060   1084
  Dihedral  :  4.688  19.381    864
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.37 %
    Favored  : 87.63 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 27.20 %
    Favored  : 67.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.81 (0.32), residues: 768
  helix:  0.26 (0.25), residues: 452
  sheet:  None (None), residues: 0
  loop : -3.55 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 133 
 HIS   0.001   0.000   HIS D 181 
 PHE   0.016   0.001   PHE B  91 
 TYR   0.014   0.001   TYR C  82 
 ARG   0.006   0.001   ARG B 138 

*********************** 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
  225 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 190
  time to evaluate  : 0.703 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 TYR cc_start: 0.6263 (OUTLIER) cc_final: 0.6044 (m-10)
REVERT: A   81 GLN cc_start: 0.9178 (tp40) cc_final: 0.8957 (tp40)
REVERT: A  178 LEU cc_start: 0.8624 (tt) cc_final: 0.8308 (pp)
REVERT: A  183 TYR cc_start: 0.8841 (t80) cc_final: 0.8632 (t80)
REVERT: A  187 MET cc_start: 0.7750 (tmm) cc_final: 0.6924 (tmm)
REVERT: B   71 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7759 (tt)
REVERT: B  103 LEU cc_start: 0.9403 (mm) cc_final: 0.9141 (mm)
REVERT: B  104 PHE cc_start: 0.8766 (t80) cc_final: 0.8326 (t80)
REVERT: B  106 TRP cc_start: 0.9048 (t60) cc_final: 0.8475 (t60)
REVERT: B  187 MET cc_start: 0.7476 (tmm) cc_final: 0.6790 (tmm)
REVERT: C  140 MET cc_start: 0.7794 (mpp) cc_final: 0.7457 (mpp)
REVERT: C  178 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8342 (pp)
REVERT: C  187 MET cc_start: 0.7904 (tmm) cc_final: 0.7087 (tmm)
REVERT: D    9 ARG cc_start: 0.6510 (mtt180) cc_final: 0.6083 (mtm180)
REVERT: D   85 ARG cc_start: 0.8602 (mmt90) cc_final: 0.8136 (tpp80)
REVERT: D  104 PHE cc_start: 0.8795 (t80) cc_final: 0.8439 (t80)
  outliers start: 35
  outliers final: 25
  residues processed: 207
  average time/residue: 0.1772
  time to fit residues: 49.1385
Evaluate side-chains
  208 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 180
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 TRP
Chi-restraints excluded: chain A residue   48 TYR
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 A residue  188 PHE
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue   59 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  175 ILE
Chi-restraints excluded: chain C residue   42 TRP
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  144 PHE
Chi-restraints excluded: chain C residue  178 LEU
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  101 MET
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  175 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 59 optimal weight:    0.4980
   chunk 42 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0070
   chunk 9 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.5998

-------------------------------------------------------------------------------
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 = 0.3882 r_free = 0.3882 target = 0.141364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.115637 restraints weight = 14228.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.118623 restraints weight = 8415.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.120608 restraints weight = 6082.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.3040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6536  Z= 0.174
  Angle     :  0.723   8.839   8928  Z= 0.344
  Chirality :  0.044   0.201    964
  Planarity :  0.005   0.070   1084
  Dihedral  :  4.572  18.815    864
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.46 %
    Favored  : 88.54 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 28.30 %
    Favored  : 66.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.32), residues: 768
  helix:  0.44 (0.26), residues: 452
  sheet:  None (None), residues: 0
  loop : -3.50 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 133 
 HIS   0.001   0.000   HIS D 181 
 PHE   0.015   0.001   PHE B  91 
 TYR   0.014   0.001   TYR C  82 
 ARG   0.006   0.001   ARG D  49 

*********************** 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
  230 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 194
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 GLN cc_start: 0.9135 (tp40) cc_final: 0.8905 (tp40)
REVERT: A  178 LEU cc_start: 0.8589 (tt) cc_final: 0.8242 (pp)
REVERT: A  187 MET cc_start: 0.7730 (tmm) cc_final: 0.6887 (tmm)
REVERT: B   71 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7705 (tt)
REVERT: B  103 LEU cc_start: 0.9417 (mm) cc_final: 0.9158 (mm)
REVERT: B  104 PHE cc_start: 0.8777 (t80) cc_final: 0.8362 (t80)
REVERT: B  106 TRP cc_start: 0.9014 (t60) cc_final: 0.8463 (t60)
REVERT: B  187 MET cc_start: 0.7472 (tmm) cc_final: 0.6769 (tmm)
REVERT: C  178 LEU cc_start: 0.8566 (tt) cc_final: 0.8281 (pp)
REVERT: C  187 MET cc_start: 0.7930 (tmm) cc_final: 0.7046 (tmm)
REVERT: D    9 ARG cc_start: 0.6435 (mtt180) cc_final: 0.6041 (mtm180)
REVERT: D   85 ARG cc_start: 0.8537 (mmt90) cc_final: 0.8100 (tpp80)
REVERT: D  104 PHE cc_start: 0.8827 (t80) cc_final: 0.8484 (t80)
  outliers start: 36
  outliers final: 23
  residues processed: 214
  average time/residue: 0.1562
  time to fit residues: 44.9212
Evaluate side-chains
  204 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 180
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
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  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  118 MET
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  164 TYR
Chi-restraints excluded: chain B residue  175 ILE
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  144 PHE
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  101 MET
Chi-restraints excluded: chain D residue  164 TYR
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 10 optimal weight:    0.9980
   chunk 61 optimal weight:    9.9990
   chunk 54 optimal weight:    4.9990
   chunk 22 optimal weight:    8.9990
   chunk 68 optimal weight:    0.1980
   chunk 40 optimal weight:    4.9990
   chunk 75 optimal weight:    0.0670
   chunk 44 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 56 optimal weight:    9.9990
   chunk 67 optimal weight:    5.9990
   overall best weight:    0.8320

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

Flipped N/Q/H residues before XYZ refinement:
C 137 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.141517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.115715 restraints weight = 14521.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.118750 restraints weight = 8508.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.120736 restraints weight = 6132.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.3200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6536  Z= 0.187
  Angle     :  0.746  10.043   8928  Z= 0.352
  Chirality :  0.044   0.202    964
  Planarity :  0.005   0.066   1084
  Dihedral  :  4.544  18.912    864
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.85 %
    Favored  : 88.15 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 30.35 %
    Favored  : 64.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.32), residues: 768
  helix:  0.47 (0.26), residues: 456
  sheet:  None (None), residues: 0
  loop : -3.45 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 133 
 HIS   0.001   0.000   HIS A 181 
 PHE   0.014   0.001   PHE B  91 
 TYR   0.014   0.001   TYR C  82 
 ARG   0.007   0.001   ARG B 138 

*********************** 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
  216 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 186
  time to evaluate  : 0.739 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 GLN cc_start: 0.9141 (tp40) cc_final: 0.8903 (tp40)
REVERT: A  178 LEU cc_start: 0.8607 (tt) cc_final: 0.8270 (pp)
REVERT: A  187 MET cc_start: 0.7918 (tmm) cc_final: 0.6986 (tmm)
REVERT: B   51 GLN cc_start: 0.7241 (tp-100) cc_final: 0.7040 (tp-100)
REVERT: B   71 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7720 (tt)
REVERT: B  103 LEU cc_start: 0.9442 (mm) cc_final: 0.9175 (mm)
REVERT: B  104 PHE cc_start: 0.8820 (t80) cc_final: 0.8403 (t80)
REVERT: B  106 TRP cc_start: 0.9025 (t60) cc_final: 0.8455 (t60)
REVERT: B  187 MET cc_start: 0.7464 (tmm) cc_final: 0.6761 (tmm)
REVERT: C   81 GLN cc_start: 0.8940 (tp40) cc_final: 0.8300 (tp40)
REVERT: C  178 LEU cc_start: 0.8573 (tt) cc_final: 0.8288 (pp)
REVERT: C  187 MET cc_start: 0.7951 (tmm) cc_final: 0.7147 (tmm)
REVERT: D    9 ARG cc_start: 0.6448 (mtt180) cc_final: 0.6041 (mtm180)
REVERT: D   85 ARG cc_start: 0.8542 (mmt90) cc_final: 0.8102 (tpp80)
REVERT: D  104 PHE cc_start: 0.8836 (t80) cc_final: 0.8489 (t80)
  outliers start: 30
  outliers final: 24
  residues processed: 199
  average time/residue: 0.1533
  time to fit residues: 40.9108
Evaluate side-chains
  206 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 181
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
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  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  118 MET
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  164 TYR
Chi-restraints excluded: chain B residue  175 ILE
Chi-restraints excluded: chain C residue   42 TRP
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  144 PHE
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  101 MET
Chi-restraints excluded: chain D residue  175 ILE
Chi-restraints excluded: chain D residue  188 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 52 optimal weight:    0.0670
   chunk 49 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 70 optimal weight:    8.9990
   overall best weight:    0.7718

-------------------------------------------------------------------------------
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 = 0.3894 r_free = 0.3894 target = 0.142037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.115961 restraints weight = 14426.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.118859 restraints weight = 8489.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.120802 restraints weight = 6197.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.3317

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= 0.187
  Angle     :  0.749   9.052   8928  Z= 0.354
  Chirality :  0.044   0.199    964
  Planarity :  0.005   0.075   1084
  Dihedral  :  4.486  18.640    864
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.59 %
    Favored  : 88.41 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 30.35 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.44 (0.32), residues: 768
  helix:  0.55 (0.26), residues: 456
  sheet:  None (None), residues: 0
  loop : -3.41 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 133 
 HIS   0.001   0.000   HIS D 181 
 PHE   0.014   0.001   PHE B  91 
 TYR   0.015   0.001   TYR C 183 
 ARG   0.008   0.001   ARG B 138 

*********************** 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
  218 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 185
  time to evaluate  : 0.668 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 GLN cc_start: 0.9132 (tp40) cc_final: 0.8895 (tp40)
REVERT: A  178 LEU cc_start: 0.8623 (tt) cc_final: 0.8287 (pp)
REVERT: A  187 MET cc_start: 0.7922 (tmm) cc_final: 0.7072 (tmm)
REVERT: B   71 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7755 (tt)
REVERT: B  103 LEU cc_start: 0.9447 (mm) cc_final: 0.9173 (mm)
REVERT: B  104 PHE cc_start: 0.8880 (t80) cc_final: 0.8491 (t80)
REVERT: B  106 TRP cc_start: 0.9038 (t60) cc_final: 0.8476 (t60)
REVERT: B  187 MET cc_start: 0.7451 (tmm) cc_final: 0.6748 (tmm)
REVERT: C  178 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8309 (pp)
REVERT: C  187 MET cc_start: 0.7972 (tmm) cc_final: 0.7174 (tmm)
REVERT: D    9 ARG cc_start: 0.6455 (mtt180) cc_final: 0.6086 (mtm180)
REVERT: D   85 ARG cc_start: 0.8518 (mmt90) cc_final: 0.8091 (tpp80)
REVERT: D  104 PHE cc_start: 0.8845 (t80) cc_final: 0.8528 (t80)
  outliers start: 33
  outliers final: 20
  residues processed: 199
  average time/residue: 0.1588
  time to fit residues: 42.6091
Evaluate side-chains
  203 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 181
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   71 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  164 TYR
Chi-restraints excluded: chain B residue  175 ILE
Chi-restraints excluded: chain C residue   42 TRP
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  144 PHE
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  175 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 69 optimal weight:    0.7980
   chunk 12 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 15 optimal weight:    0.1980
   chunk 9 optimal weight:    0.9980
   chunk 74 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.3887 r_free = 0.3887 target = 0.141646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.115208 restraints weight = 14754.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.118168 restraints weight = 8751.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.120164 restraints weight = 6380.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.3406

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= 0.202
  Angle     :  0.783  10.011   8928  Z= 0.367
  Chirality :  0.044   0.199    964
  Planarity :  0.005   0.074   1084
  Dihedral  :  4.484  18.830    864
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.98 %
    Favored  : 88.02 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 31.13 %
    Favored  : 63.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.32), residues: 768
  helix:  0.55 (0.26), residues: 456
  sheet:  None (None), residues: 0
  loop : -3.39 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C 133 
 HIS   0.001   0.001   HIS D 181 
 PHE   0.014   0.001   PHE B  91 
 TYR   0.015   0.001   TYR A 183 
 ARG   0.009   0.001   ARG B 138 

*********************** 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
  209 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 178
  time to evaluate  : 0.688 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 GLN cc_start: 0.9141 (tp40) cc_final: 0.8888 (tp40)
REVERT: A  118 MET cc_start: 0.7582 (tpp) cc_final: 0.7315 (tpp)
REVERT: A  178 LEU cc_start: 0.8628 (tt) cc_final: 0.8283 (pp)
REVERT: A  187 MET cc_start: 0.7876 (tmm) cc_final: 0.7069 (tmm)
REVERT: B   71 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7751 (tt)
REVERT: B  103 LEU cc_start: 0.9466 (mm) cc_final: 0.9192 (mm)
REVERT: B  104 PHE cc_start: 0.8902 (t80) cc_final: 0.8518 (t80)
REVERT: B  106 TRP cc_start: 0.9044 (t60) cc_final: 0.8493 (t60)
REVERT: B  187 MET cc_start: 0.7496 (tmm) cc_final: 0.6791 (tmm)
REVERT: C  118 MET cc_start: 0.7667 (tpp) cc_final: 0.7421 (tpp)
REVERT: C  178 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8345 (pp)
REVERT: C  187 MET cc_start: 0.8038 (tmm) cc_final: 0.7211 (tmm)
REVERT: D    9 ARG cc_start: 0.6575 (mtt180) cc_final: 0.6223 (mtm180)
REVERT: D   85 ARG cc_start: 0.8520 (mmt90) cc_final: 0.8097 (tpp80)
REVERT: D  104 PHE cc_start: 0.8862 (t80) cc_final: 0.8509 (t80)
  outliers start: 31
  outliers final: 24
  residues processed: 192
  average time/residue: 0.1551
  time to fit residues: 39.9674
Evaluate side-chains
  203 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 177
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   59 THR
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  164 TYR
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 C residue  144 PHE
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  175 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 30 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 52 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0670
   chunk 21 optimal weight:    4.9990
   chunk 40 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.5718

-------------------------------------------------------------------------------
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 = 0.3904 r_free = 0.3904 target = 0.142991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.116807 restraints weight = 14644.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.119902 restraints weight = 8655.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.121878 restraints weight = 6245.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.3512

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= 0.186
  Angle     :  0.790   9.608   8928  Z= 0.370
  Chirality :  0.044   0.199    964
  Planarity :  0.005   0.070   1084
  Dihedral  :  4.446  18.150    864
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.85 %
    Favored  : 88.15 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 32.23 %
    Favored  : 63.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.37 (0.33), residues: 768
  helix:  0.59 (0.26), residues: 456
  sheet:  None (None), residues: 0
  loop : -3.37 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C 133 
 HIS   0.001   0.000   HIS D 181 
 PHE   0.013   0.001   PHE B  91 
 TYR   0.016   0.001   TYR A 183 
 ARG   0.009   0.001   ARG D 138 

********************** 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
  219 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 194
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 GLN cc_start: 0.9100 (tp40) cc_final: 0.8870 (tp40)
REVERT: A  118 MET cc_start: 0.7489 (tpp) cc_final: 0.7211 (tpp)
REVERT: A  140 MET cc_start: 0.7532 (mpp) cc_final: 0.7304 (mpp)
REVERT: A  178 LEU cc_start: 0.8613 (tt) cc_final: 0.8272 (pp)
REVERT: A  187 MET cc_start: 0.7880 (tmm) cc_final: 0.7068 (tmm)
REVERT: B   71 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7763 (tt)
REVERT: B  103 LEU cc_start: 0.9472 (mm) cc_final: 0.9201 (mm)
REVERT: B  104 PHE cc_start: 0.8878 (t80) cc_final: 0.8501 (t80)
REVERT: B  106 TRP cc_start: 0.9035 (t60) cc_final: 0.8487 (t60)
REVERT: B  187 MET cc_start: 0.7423 (tmm) cc_final: 0.6766 (tmm)
REVERT: C  118 MET cc_start: 0.7631 (tpp) cc_final: 0.7407 (tpp)
REVERT: C  178 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8315 (pp)
REVERT: C  187 MET cc_start: 0.7978 (tmm) cc_final: 0.7156 (tmm)
REVERT: D    9 ARG cc_start: 0.6562 (mtt180) cc_final: 0.6198 (mtm180)
REVERT: D   85 ARG cc_start: 0.8487 (mmt90) cc_final: 0.8069 (tpp80)
REVERT: D  104 PHE cc_start: 0.8857 (t80) cc_final: 0.8526 (t80)
  outliers start: 25
  outliers final: 20
  residues processed: 206
  average time/residue: 0.1548
  time to fit residues: 43.0486
Evaluate side-chains
  207 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 185
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   71 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  164 TYR
Chi-restraints excluded: chain B residue  175 ILE
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  175 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 12 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 29 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 70 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.3941 r_free = 0.3941 target = 0.144905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.118446 restraints weight = 14768.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.121509 restraints weight = 8960.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.123075 restraints weight = 6551.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.3611

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= 0.199
  Angle     :  0.787   9.228   8928  Z= 0.371
  Chirality :  0.045   0.202    964
  Planarity :  0.005   0.080   1084
  Dihedral  :  4.490  18.571    864
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.94 %
    Favored  : 89.06 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 32.23 %
    Favored  : 63.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.35 (0.33), residues: 768
  helix:  0.59 (0.26), residues: 456
  sheet:  None (None), residues: 0
  loop : -3.34 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C 133 
 HIS   0.002   0.001   HIS D 181 
 PHE   0.013   0.001   PHE B  91 
 TYR   0.021   0.001   TYR A 183 
 ARG   0.011   0.001   ARG D 138 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2182.47 seconds
wall clock time: 38 minutes 19.43 seconds (2299.43 seconds total)