Starting phenix.real_space_refine
on Tue Feb  3 14:20:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9d2g_46495/02_2026/9d2g_46495.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9d2g_46495/02_2026/9d2g_46495.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9d2g_46495/02_2026/9d2g_46495.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9d2g_46495/02_2026/9d2g_46495.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9d2g_46495/02_2026/9d2g_46495.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9d2g_46495/02_2026/9d2g_46495.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
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       5      5.16       5
     C    2330      2.51       5
     N     595      2.21       5
     O     670      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3600
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 720
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 720
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 4, 'TRANS': 87}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 0.52, per 1000 atoms: 0.14
  Number of scatterers: 3600
  At special positions: 0
  Unit cell: (76.626, 81.356, 40.678, 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       5     16.00
     O     670      8.00
     N     595      7.00
     C    2330      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.26
  Conformation dependent library (CDL) restraints added in 134.4 milliseconds
  

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  880

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 48.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 12 through 16
      removed outlier: 6.661A  pdb=" N   MET B  13 " --> pdb=" O   VAL D  14 " (cutoff:3.500A)
      removed outlier: 8.168A  pdb=" N   VAL D  16 " --> pdb=" O   MET B  13 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   LYS B  15 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   MET A  13 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      removed outlier: 8.146A  pdb=" N   VAL B  16 " --> pdb=" O   MET A  13 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   LYS A  15 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 19 through 21
      removed outlier: 6.376A  pdb=" N   ALA B  19 " --> pdb=" O   VAL D  20 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   ALA A  19 " --> pdb=" O   VAL B  20 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 26 through 34
      removed outlier: 6.343A  pdb=" N   ASN B  27 " --> pdb=" O   VAL D  28 " (cutoff:3.500A)
      removed outlier: 7.856A  pdb=" N   VAL D  30 " --> pdb=" O   ASN B  27 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   ALA B  29 " --> pdb=" O   VAL D  30 " (cutoff:3.500A)
      removed outlier: 7.954A  pdb=" N   VAL D  32 " --> pdb=" O   ALA B  29 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   HIS B  31 " --> pdb=" O   VAL D  32 " (cutoff:3.500A)
      removed outlier: 8.140A  pdb=" N   ARG D  34 " --> pdb=" O   HIS B  31 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   PHE B  33 " --> pdb=" O   ARG D  34 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   ASN A  27 " --> pdb=" O   VAL B  28 " (cutoff:3.500A)
      removed outlier: 7.846A  pdb=" N   VAL B  30 " --> pdb=" O   ASN A  27 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   ALA A  29 " --> pdb=" O   VAL B  30 " (cutoff:3.500A)
      removed outlier: 7.945A  pdb=" N   VAL B  32 " --> pdb=" O   ALA A  29 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   HIS A  31 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 8.130A  pdb=" N   ARG B  34 " --> pdb=" O   HIS A  31 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   PHE A  33 " --> pdb=" O   ARG B  34 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 59 through 66
      removed outlier: 7.128A  pdb=" N   ALA D  60 " --> pdb=" O   THR B  59 " (cutoff:3.500A)
      removed outlier: 7.062A  pdb=" N   GLU B  61 " --> pdb=" O   ALA D  60 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   GLU D  62 " --> pdb=" O   GLU B  61 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   PHE D  64 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 7.088A  pdb=" N   ALA B  60 " --> pdb=" O   THR A  59 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   GLU A  61 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   GLU B  62 " --> pdb=" O   GLU A  61 " (cutoff:3.500A)
      removed outlier: 9.097A  pdb=" N   ALA A  60 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
      removed outlier: 9.747A  pdb=" N   GLU C  63 " --> pdb=" O   ALA A  60 " (cutoff:3.500A)
      removed outlier: 5.585A  pdb=" N   GLU A  62 " --> pdb=" O   GLU C  63 " (cutoff:3.500A)
      removed outlier: 7.607A  pdb=" N   VAL C  65 " --> pdb=" O   GLU A  62 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   PHE A  64 " --> pdb=" O   VAL C  65 " (cutoff:3.500A)
      removed outlier: 9.113A  pdb=" N   ALA C  60 " --> pdb=" O   GLU E  61 " (cutoff:3.500A)
      removed outlier: 9.758A  pdb=" N   GLU E  63 " --> pdb=" O   ALA C  60 " (cutoff:3.500A)
      removed outlier: 5.597A  pdb=" N   GLU C  62 " --> pdb=" O   GLU E  63 " (cutoff:3.500A)
      removed outlier: 7.624A  pdb=" N   VAL E  65 " --> pdb=" O   GLU C  62 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   PHE C  64 " --> pdb=" O   VAL E  65 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 69 through 75
      removed outlier: 6.729A  pdb=" N   TYR B  69 " --> pdb=" O   LYS D  70 " (cutoff:3.500A)
      removed outlier: 8.232A  pdb=" N   GLU D  72 " --> pdb=" O   TYR B  69 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   VAL B  71 " --> pdb=" O   GLU D  72 " (cutoff:3.500A)
      removed outlier: 7.912A  pdb=" N   ASP D  74 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 8.416A  pdb=" N   ILE B  73 " --> pdb=" O   ASP D  74 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   TYR A  69 " --> pdb=" O   LYS B  70 " (cutoff:3.500A)
      removed outlier: 8.206A  pdb=" N   GLU B  72 " --> pdb=" O   TYR A  69 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   VAL A  71 " --> pdb=" O   GLU B  72 " (cutoff:3.500A)
      removed outlier: 7.883A  pdb=" N   ASP B  74 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
      removed outlier: 8.370A  pdb=" N   ILE A  73 " --> pdb=" O   ASP B  74 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   THR C  75 " --> pdb=" O   ASP A  74 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   THR E  75 " --> pdb=" O   ASP C  74 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 79 through 80
      removed outlier: 6.457A  pdb=" N   TRP B  79 " --> pdb=" O   LYS D  80 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   TRP A  79 " --> pdb=" O   LYS B  80 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 92 through 99
      removed outlier: 6.762A  pdb=" N   VAL B  93 " --> pdb=" O   VAL D  94 " (cutoff:3.500A)
      removed outlier: 8.055A  pdb=" N   THR D  96 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   PHE B  95 " --> pdb=" O   THR D  96 " (cutoff:3.500A)
      removed outlier: 7.621A  pdb=" N   ASN D  98 " --> pdb=" O   PHE B  95 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   ALA B  97 " --> pdb=" O   ASN D  98 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   VAL A  93 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
      removed outlier: 8.052A  pdb=" N   THR B  96 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   PHE A  95 " --> pdb=" O   THR B  96 " (cutoff:3.500A)
      removed outlier: 7.623A  pdb=" N   ASN B  98 " --> pdb=" O   PHE A  95 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   ALA A  97 " --> pdb=" O   ASN B  98 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 104 through 108
      removed outlier: 6.460A  pdb=" N   ARG A 104 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 8.154A  pdb=" N   ILE C 107 " --> pdb=" O   ARG A 104 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   THR A 106 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   ARG C 104 " --> pdb=" O   TYR E 105 " (cutoff:3.500A)
      removed outlier: 8.153A  pdb=" N   ILE E 107 " --> pdb=" O   ARG C 104 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   THR C 106 " --> pdb=" O   ILE E 107 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 114 through 115
      removed outlier: 7.054A  pdb=" N   TYR A 114 " --> pdb=" O   SER C 115 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   TYR C 114 " --> pdb=" O   SER E 115 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 118 through 123
      removed outlier: 5.906A  pdb=" N   THR B 118 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   VAL D 121 " --> pdb=" O   THR B 118 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   ALA B 120 " --> pdb=" O   VAL D 121 " (cutoff:3.500A)
      removed outlier: 8.257A  pdb=" N   THR D 123 " --> pdb=" O   ALA B 120 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   VAL B 122 " --> pdb=" O   THR D 123 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   THR A 118 " --> pdb=" O   THR B 119 " (cutoff:3.500A)
      removed outlier: 7.751A  pdb=" N   VAL B 121 " --> pdb=" O   THR A 118 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   ALA A 120 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)
      removed outlier: 8.222A  pdb=" N   THR B 123 " --> pdb=" O   ALA A 120 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   VAL A 122 " --> pdb=" O   THR B 123 " (cutoff:3.500A)

    81 hydrogen bonds defined for protein.
    243 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.48

  Time building geometry restraints manager: 0.36 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1130
        1.34 -     1.46: 655
        1.46 -     1.57: 1890
        1.57 -     1.69: 0
        1.69 -     1.80: 10
  Bond restraints: 3685
  Sorted by residual:
  bond pdb=" CA  SER B 100 "
       pdb=" C   SER B 100 "
    ideal  model  delta    sigma   weight residual
    1.530  1.518  0.012 1.08e-02 8.57e+03 1.22e+00
  bond pdb=" CA  SER E 100 "
       pdb=" C   SER E 100 "
    ideal  model  delta    sigma   weight residual
    1.530  1.519  0.011 1.08e-02 8.57e+03 1.12e+00
  bond pdb=" CA  SER A 100 "
       pdb=" C   SER A 100 "
    ideal  model  delta    sigma   weight residual
    1.530  1.519  0.011 1.08e-02 8.57e+03 1.06e+00
  bond pdb=" CA  SER D 100 "
       pdb=" C   SER D 100 "
    ideal  model  delta    sigma   weight residual
    1.530  1.520  0.011 1.08e-02 8.57e+03 1.01e+00
  bond pdb=" CA  SER C 100 "
       pdb=" C   SER C 100 "
    ideal  model  delta    sigma   weight residual
    1.530  1.520  0.011 1.08e-02 8.57e+03 9.91e-01
  ... (remaining 3680 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 4858
        1.76 -     3.53: 130
        3.53 -     5.29: 12
        5.29 -     7.06: 10
        7.06 -     8.82: 5
  Bond angle restraints: 5015
  Sorted by residual:
  angle pdb=" C   ARG E  21 "
        pdb=" CA  ARG E  21 "
        pdb=" CB  ARG E  21 "
      ideal   model   delta    sigma   weight residual
     109.38  118.20   -8.82 2.03e+00 2.43e-01 1.89e+01
  angle pdb=" C   ARG B  21 "
        pdb=" CA  ARG B  21 "
        pdb=" CB  ARG B  21 "
      ideal   model   delta    sigma   weight residual
     109.38  118.19   -8.81 2.03e+00 2.43e-01 1.88e+01
  angle pdb=" C   ARG D  21 "
        pdb=" CA  ARG D  21 "
        pdb=" CB  ARG D  21 "
      ideal   model   delta    sigma   weight residual
     109.38  118.19   -8.81 2.03e+00 2.43e-01 1.88e+01
  angle pdb=" C   ARG A  21 "
        pdb=" CA  ARG A  21 "
        pdb=" CB  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     109.38  118.18   -8.80 2.03e+00 2.43e-01 1.88e+01
  angle pdb=" C   ARG C  21 "
        pdb=" CA  ARG C  21 "
        pdb=" CB  ARG C  21 "
      ideal   model   delta    sigma   weight residual
     109.38  118.16   -8.78 2.03e+00 2.43e-01 1.87e+01
  ... (remaining 5010 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.56: 1806
        9.56 -    19.13: 214
       19.13 -    28.69: 105
       28.69 -    38.26: 45
       38.26 -    47.82: 10
  Dihedral angle restraints: 2180
    sinusoidal: 825
      harmonic: 1355
  Sorted by residual:
  dihedral pdb=" CA  ILE E  26 "
           pdb=" C   ILE E  26 "
           pdb=" N   ASN E  27 "
           pdb=" CA  ASN E  27 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.02   17.98     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  ILE C  26 "
           pdb=" C   ILE C  26 "
           pdb=" N   ASN C  27 "
           pdb=" CA  ASN C  27 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.03   17.97     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  ILE A  26 "
           pdb=" C   ILE A  26 "
           pdb=" N   ASN A  27 "
           pdb=" CA  ASN A  27 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.04   17.96     0      5.00e+00 4.00e-02 1.29e+01
  ... (remaining 2177 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 287
       0.027 -    0.054: 156
       0.054 -    0.082: 54
       0.082 -    0.109: 57
       0.109 -    0.136: 36
  Chirality restraints: 590
  Sorted by residual:
  chirality pdb=" CA  VAL B  65 "
            pdb=" N   VAL B  65 "
            pdb=" C   VAL B  65 "
            pdb=" CB  VAL B  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.63e-01
  chirality pdb=" CA  VAL A  65 "
            pdb=" N   VAL A  65 "
            pdb=" C   VAL A  65 "
            pdb=" CB  VAL A  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.59e-01
  chirality pdb=" CA  VAL D  65 "
            pdb=" N   VAL D  65 "
            pdb=" C   VAL D  65 "
            pdb=" CB  VAL D  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.13 2.00e-01 2.50e+01 4.51e-01
  ... (remaining 587 not shown)

  Planarity restraints: 620
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER E 100 "   -0.007 2.00e-02 2.50e+03   1.40e-02 1.97e+00
        pdb=" C   SER E 100 "    0.024 2.00e-02 2.50e+03
        pdb=" O   SER E 100 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   GLY E 101 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 100 "   -0.007 2.00e-02 2.50e+03   1.39e-02 1.94e+00
        pdb=" C   SER B 100 "    0.024 2.00e-02 2.50e+03
        pdb=" O   SER B 100 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   GLY B 101 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER C 100 "   -0.007 2.00e-02 2.50e+03   1.39e-02 1.92e+00
        pdb=" C   SER C 100 "    0.024 2.00e-02 2.50e+03
        pdb=" O   SER C 100 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   GLY C 101 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 617 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 288
        2.75 -     3.29: 3309
        3.29 -     3.83: 5708
        3.83 -     4.36: 6674
        4.36 -     4.90: 11134
  Nonbonded interactions: 27113
  Sorted by model distance:
  nonbonded pdb=" O   SER E  85 "
            pdb=" OG  SER E  85 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" O   SER C  85 "
            pdb=" OG  SER C  85 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" O   SER A  85 "
            pdb=" OG  SER A  85 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" O   SER D  85 "
            pdb=" OG  SER D  85 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" O   SER B  85 "
            pdb=" OG  SER B  85 "
     model   vdw
     2.218 3.040
  ... (remaining 27108 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.620
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3685  Z= 0.146
  Angle     :  0.768   8.823   5015  Z= 0.424
  Chirality :  0.052   0.136    590
  Planarity :  0.005   0.028    620
  Dihedral  : 11.608  47.820   1300
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.44 (0.38), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.85 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  34 
 TYR   0.010   0.002   TYR D 114 
 PHE   0.023   0.003   PHE D  33 
 TRP   0.004   0.001   TRP D  79 
 HIS   0.001   0.000   HIS D  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3685)
  covalent geometry    : angle       0.76756 ( 5015)
  hydrogen bonds       : bond        0.21274 (   81)
  hydrogen bonds       : angle       8.60477 (  243)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.129 
Fit side-chains
REVERT: B   13 MET cc_start: 0.7202 (ttt) cc_final: 0.6581 (tmm)
REVERT: B   34 ARG cc_start: 0.7658 (ttt-90) cc_final: 0.7213 (ttt180)
REVERT: D   34 ARG cc_start: 0.7927 (ttt-90) cc_final: 0.7724 (ttt180)
REVERT: E   13 MET cc_start: 0.7568 (ttt) cc_final: 0.7180 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.0839
  time to fit residues: 5.4183
Evaluate side-chains
  44 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    7.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
A  90 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.130068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.107753 restraints weight = 3972.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3886 rms_B_bonded: 2.55
r_work: 0.3733 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3604 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.1230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   3685  Z= 0.195
  Angle     :  0.696   6.241   5015  Z= 0.381
  Chirality :  0.054   0.178    590
  Planarity :  0.005   0.037    620
  Dihedral  :  6.100  19.793    495
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  8.97 %
    Favored  : 90.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.44 (0.38), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.85 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 104 
 TYR   0.018   0.002   TYR B 114 
 PHE   0.021   0.003   PHE C  33 
 TRP   0.004   0.001   TRP A  79 
 HIS   0.003   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 ( 3685)
  covalent geometry    : angle       0.69565 ( 5015)
  hydrogen bonds       : bond        0.04158 (   81)
  hydrogen bonds       : angle       6.45450 (  243)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.180 
Fit side-chains
REVERT: B   13 MET cc_start: 0.7409 (ttt) cc_final: 0.6799 (tmm)
REVERT: B   34 ARG cc_start: 0.7975 (ttt-90) cc_final: 0.7289 (ttt180)
REVERT: E   13 MET cc_start: 0.7436 (ttt) cc_final: 0.7188 (tpp)
  outliers start: 1
  outliers final: 1
  residues processed: 48
  average time/residue: 0.0838
  time to fit residues: 4.8100
Evaluate side-chains
  41 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 40
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   23 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 41 optimal weight:    0.5980
   chunk 18 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 21 optimal weight:    0.1980
   chunk 42 optimal weight:    4.9990
   chunk 19 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 23 optimal weight:    6.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  90 HIS
A 124 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.138016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.116786 restraints weight = 3823.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.4014 rms_B_bonded: 2.46
r_work: 0.3890 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3765 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.1499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3685  Z= 0.108
  Angle     :  0.579   5.365   5015  Z= 0.312
  Chirality :  0.050   0.153    590
  Planarity :  0.004   0.042    620
  Dihedral  :  5.705  18.210    495
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  8.21 %
    Favored  : 91.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.55 (0.38), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.94 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  34 
 TYR   0.014   0.001   TYR B 114 
 PHE   0.014   0.002   PHE C  33 
 TRP   0.002   0.000   TRP C  79 
 HIS   0.002   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 3685)
  covalent geometry    : angle       0.57883 ( 5015)
  hydrogen bonds       : bond        0.03300 (   81)
  hydrogen bonds       : angle       5.96819 (  243)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 50
  time to evaluate  : 0.104 
Fit side-chains
REVERT: B   34 ARG cc_start: 0.7815 (ttt-90) cc_final: 0.7033 (ttt180)
REVERT: D   34 ARG cc_start: 0.8101 (ttt-90) cc_final: 0.7654 (ttt180)
REVERT: E   13 MET cc_start: 0.7229 (ttt) cc_final: 0.7020 (tpp)
  outliers start: 1
  outliers final: 1
  residues processed: 50
  average time/residue: 0.0716
  time to fit residues: 4.2752
Evaluate side-chains
  48 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 41 optimal weight:    0.0040
   chunk 40 optimal weight:    0.3980
   chunk 6 optimal weight:   10.0000
   chunk 10 optimal weight:    4.9990
   chunk 36 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 2 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 17 optimal weight:    7.9990
   overall best weight:    1.0798

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

Flipped N/Q/H residues before XYZ refinement:
A  90 HIS
A 124 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.137105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.115731 restraints weight = 3772.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3996 rms_B_bonded: 2.45
r_work: 0.3874 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3747 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.1762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3685  Z= 0.136
  Angle     :  0.607   5.290   5015  Z= 0.329
  Chirality :  0.051   0.158    590
  Planarity :  0.004   0.031    620
  Dihedral  :  5.738  18.340    495
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  8.97 %
    Favored  : 90.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.54 (0.37), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.93 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  34 
 TYR   0.013   0.001   TYR B 114 
 PHE   0.013   0.002   PHE A  33 
 TRP   0.003   0.001   TRP C  79 
 HIS   0.003   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 3685)
  covalent geometry    : angle       0.60689 ( 5015)
  hydrogen bonds       : bond        0.03437 (   81)
  hydrogen bonds       : angle       5.78264 (  243)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 49
  time to evaluate  : 0.087 
Fit side-chains
REVERT: C   13 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.6936 (tpp)
REVERT: E   13 MET cc_start: 0.7186 (ttt) cc_final: 0.6944 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 49
  average time/residue: 0.0992
  time to fit residues: 5.7116
Evaluate side-chains
  47 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 46
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   13 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 24 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 4 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0030
   overall best weight:    1.1596

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

Flipped N/Q/H residues before XYZ refinement:
A  90 HIS
A 124 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.135688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.115130 restraints weight = 3808.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.3992 rms_B_bonded: 2.43
r_work: 0.3867 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3741 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3685  Z= 0.141
  Angle     :  0.605   5.506   5015  Z= 0.329
  Chirality :  0.051   0.158    590
  Planarity :  0.004   0.031    620
  Dihedral  :  5.786  18.726    495
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  9.49 %
    Favored  : 90.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.57 (0.37), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.95 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  34 
 TYR   0.014   0.001   TYR B 114 
 PHE   0.013   0.002   PHE A  33 
 TRP   0.003   0.001   TRP E  79 
 HIS   0.003   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 3685)
  covalent geometry    : angle       0.60546 ( 5015)
  hydrogen bonds       : bond        0.03357 (   81)
  hydrogen bonds       : angle       5.60036 (  243)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 50
  time to evaluate  : 0.151 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.7229 (ptp-170) cc_final: 0.6409 (ptm-80)
REVERT: B   34 ARG cc_start: 0.7766 (ttt-90) cc_final: 0.6969 (ttt90)
REVERT: C   13 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6859 (tpp)
REVERT: E   13 MET cc_start: 0.7170 (ttt) cc_final: 0.6925 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 50
  average time/residue: 0.1089
  time to fit residues: 6.4120
Evaluate side-chains
  47 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 46
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   13 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 42 optimal weight:    7.9990
   chunk 30 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 28 optimal weight:    0.5980
   chunk 9 optimal weight:    5.9990
   chunk 6 optimal weight:    9.9990
   chunk 25 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    2.3188

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

Flipped N/Q/H residues before XYZ refinement:
A  90 HIS
B 124 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.131863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.110978 restraints weight = 3928.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3901 rms_B_bonded: 2.47
r_work: 0.3780 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3652 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.033   3685  Z= 0.251
  Angle     :  0.719   6.365   5015  Z= 0.397
  Chirality :  0.055   0.178    590
  Planarity :  0.005   0.036    620
  Dihedral  :  6.317  19.679    495
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 10.00 %
    Favored  : 89.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.51 (0.37), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.91 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  34 
 TYR   0.015   0.002   TYR A 114 
 PHE   0.019   0.003   PHE A  33 
 TRP   0.008   0.001   TRP E  79 
 HIS   0.004   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00604 ( 3685)
  covalent geometry    : angle       0.71902 ( 5015)
  hydrogen bonds       : bond        0.04437 (   81)
  hydrogen bonds       : angle       5.80995 (  243)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 54
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.7446 (ptp-170) cc_final: 0.6483 (ptm-80)
REVERT: B   21 ARG cc_start: 0.7643 (ptp-170) cc_final: 0.6689 (ptm-80)
REVERT: B   66 GLU cc_start: 0.7419 (tt0) cc_final: 0.6607 (tm-30)
REVERT: B   90 HIS cc_start: 0.7935 (m90) cc_final: 0.7732 (m90)
REVERT: C   21 ARG cc_start: 0.7222 (ptp-170) cc_final: 0.6526 (ptm-80)
REVERT: E   13 MET cc_start: 0.7211 (ttt) cc_final: 0.7000 (tpp)
REVERT: E   21 ARG cc_start: 0.7454 (ptp-170) cc_final: 0.7128 (ptm160)
  outliers start: 1
  outliers final: 1
  residues processed: 54
  average time/residue: 0.1156
  time to fit residues: 7.1825
Evaluate side-chains
  48 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   chunk 42 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 2 optimal weight:    5.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A  90 HIS
A 124 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.132948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.112100 restraints weight = 3939.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3934 rms_B_bonded: 2.48
r_work: 0.3811 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3684 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.2325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3685  Z= 0.175
  Angle     :  0.646   6.024   5015  Z= 0.354
  Chirality :  0.052   0.165    590
  Planarity :  0.004   0.031    620
  Dihedral  :  6.153  19.169    495
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 10.00 %
    Favored  : 89.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.53 (0.36), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.92 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  34 
 TYR   0.015   0.002   TYR B 114 
 PHE   0.013   0.002   PHE A  33 
 TRP   0.004   0.001   TRP B  79 
 HIS   0.003   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 3685)
  covalent geometry    : angle       0.64638 ( 5015)
  hydrogen bonds       : bond        0.03671 (   81)
  hydrogen bonds       : angle       5.63130 (  243)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 48
  time to evaluate  : 0.083 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.7403 (ptp-170) cc_final: 0.6435 (ptm-80)
REVERT: B   21 ARG cc_start: 0.7602 (ptp-170) cc_final: 0.6632 (ptm-80)
REVERT: B   34 ARG cc_start: 0.7740 (ttt-90) cc_final: 0.7455 (ttt90)
REVERT: B   90 HIS cc_start: 0.7917 (m90) cc_final: 0.7715 (m90)
REVERT: C   21 ARG cc_start: 0.7228 (ptp-170) cc_final: 0.6537 (ptm-80)
  outliers start: 1
  outliers final: 1
  residues processed: 48
  average time/residue: 0.0707
  time to fit residues: 3.9802
Evaluate side-chains
  47 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 46
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 1 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0030
   overall best weight:    0.6390

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

Flipped N/Q/H residues before XYZ refinement:
A  90 HIS
A 124 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.138591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.117455 restraints weight = 3788.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.4018 rms_B_bonded: 2.46
r_work: 0.3894 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3765 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.2373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3685  Z= 0.101
  Angle     :  0.571   5.490   5015  Z= 0.308
  Chirality :  0.050   0.149    590
  Planarity :  0.004   0.036    620
  Dihedral  :  5.720  17.931    495
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 10.26 %
    Favored  : 89.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.56 (0.36), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.94 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  34 
 TYR   0.014   0.001   TYR B 114 
 PHE   0.009   0.001   PHE A  33 
 TRP   0.001   0.000   TRP A  79 
 HIS   0.003   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 3685)
  covalent geometry    : angle       0.57051 ( 5015)
  hydrogen bonds       : bond        0.02677 (   81)
  hydrogen bonds       : angle       5.36038 (  243)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 51
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.7233 (ptp-170) cc_final: 0.6328 (ptm-80)
REVERT: B   21 ARG cc_start: 0.7500 (ptp-170) cc_final: 0.6566 (ptm-80)
REVERT: B   34 ARG cc_start: 0.7699 (ttt-90) cc_final: 0.6914 (ttt180)
REVERT: B   99 ASP cc_start: 0.7846 (t70) cc_final: 0.7490 (t70)
REVERT: C   21 ARG cc_start: 0.7097 (ptp-170) cc_final: 0.6530 (ttm170)
REVERT: E   13 MET cc_start: 0.7352 (tpp) cc_final: 0.7152 (tpp)
  outliers start: 1
  outliers final: 1
  residues processed: 51
  average time/residue: 0.0861
  time to fit residues: 5.1451
Evaluate side-chains
  47 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 46
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 20 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9980
   chunk 6 optimal weight:    8.9990
   chunk 38 optimal weight:    0.6980
   chunk 28 optimal weight:    0.7980
   chunk 9 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   chunk 40 optimal weight:    0.3980
   chunk 16 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A  90 HIS
A 124 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.136058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.115431 restraints weight = 3818.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.4005 rms_B_bonded: 2.41
r_work: 0.3881 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3754 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.2389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3685  Z= 0.124
  Angle     :  0.592   5.467   5015  Z= 0.322
  Chirality :  0.050   0.154    590
  Planarity :  0.004   0.042    620
  Dihedral  :  5.728  17.755    495
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.77 %
    Favored  : 89.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.56 (0.36), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.94 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D  34 
 TYR   0.014   0.001   TYR B 114 
 PHE   0.010   0.002   PHE A  33 
 TRP   0.002   0.001   TRP B  79 
 HIS   0.003   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 3685)
  covalent geometry    : angle       0.59238 ( 5015)
  hydrogen bonds       : bond        0.03051 (   81)
  hydrogen bonds       : angle       5.36469 (  243)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.7275 (ptp-170) cc_final: 0.6292 (ptm-80)
REVERT: B   21 ARG cc_start: 0.7503 (ptp-170) cc_final: 0.6587 (ptm-80)
REVERT: B   34 ARG cc_start: 0.7781 (ttt-90) cc_final: 0.7562 (ttt90)
REVERT: C   21 ARG cc_start: 0.7152 (ptp-170) cc_final: 0.6470 (ptm-80)
REVERT: E   13 MET cc_start: 0.7434 (tpp) cc_final: 0.7223 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.0862
  time to fit residues: 4.9005
Evaluate side-chains
  45 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 28 optimal weight:    0.4980
   chunk 2 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0970
   chunk 41 optimal weight:    4.9990
   chunk 6 optimal weight:    8.9990
   chunk 19 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A  90 HIS
A 124 ASN
B 124 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.134543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.113825 restraints weight = 3899.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.3980 rms_B_bonded: 2.43
r_work: 0.3856 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3728 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.2438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   3685  Z= 0.154
  Angle     :  0.618   5.644   5015  Z= 0.337
  Chirality :  0.051   0.160    590
  Planarity :  0.004   0.033    620
  Dihedral  :  5.863  18.274    495
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 10.77 %
    Favored  : 88.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.55 (0.36), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.94 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  34 
 TYR   0.014   0.002   TYR B 114 
 PHE   0.012   0.002   PHE A  33 
 TRP   0.003   0.001   TRP E  79 
 HIS   0.003   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 3685)
  covalent geometry    : angle       0.61812 ( 5015)
  hydrogen bonds       : bond        0.03404 (   81)
  hydrogen bonds       : angle       5.43155 (  243)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 48
  time to evaluate  : 0.086 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.7269 (ptp-170) cc_final: 0.6311 (ptm-80)
REVERT: B   21 ARG cc_start: 0.7553 (ptp-170) cc_final: 0.6606 (ptm-80)
REVERT: B   34 ARG cc_start: 0.7846 (ttt-90) cc_final: 0.7558 (ttt90)
REVERT: C   21 ARG cc_start: 0.7247 (ptp-170) cc_final: 0.6577 (ptm-80)
  outliers start: 1
  outliers final: 1
  residues processed: 49
  average time/residue: 0.1045
  time to fit residues: 5.9887
Evaluate side-chains
  47 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 46
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   58 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 20 optimal weight:    8.9990
   chunk 17 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 9 optimal weight:    5.9990
   chunk 8 optimal weight:    0.2980
   chunk 35 optimal weight:    1.9990
   overall best weight:    2.2586

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

Flipped N/Q/H residues before XYZ refinement:
A  90 HIS
A 124 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.131714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.110952 restraints weight = 3840.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.3923 rms_B_bonded: 2.44
r_work: 0.3799 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3672 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.2522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.031   3685  Z= 0.241
  Angle     :  0.702   6.061   5015  Z= 0.387
  Chirality :  0.055   0.172    590
  Planarity :  0.004   0.035    620
  Dihedral  :  6.256  19.400    495
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 10.77 %
    Favored  : 88.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.55 (0.36), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.94 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  34 
 TYR   0.015   0.002   TYR A 114 
 PHE   0.015   0.003   PHE A  33 
 TRP   0.007   0.001   TRP E  79 
 HIS   0.004   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00582 ( 3685)
  covalent geometry    : angle       0.70195 ( 5015)
  hydrogen bonds       : bond        0.04269 (   81)
  hydrogen bonds       : angle       5.62980 (  243)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 989.58 seconds
wall clock time: 17 minutes 34.49 seconds (1054.49 seconds total)