Starting phenix.real_space_refine
on Tue Aug  4 11:44:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9pei_71563/08_2026/9pei_71563.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9pei_71563/08_2026/9pei_71563.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9pei_71563/08_2026/9pei_71563.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9pei_71563/08_2026/9pei_71563.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9pei_71563/08_2026/9pei_71563.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9pei_71563/08_2026/9pei_71563.cif"
  }
  resolution = 3.9
  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=   0.001 sd=   0.016
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: 3
    Type Number    sf(0)   Gaussians
     C    1026      2.51       5
     N     198      2.21       5
     O     198      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 1422
  Number of models: 1
  Model: ""
    Number of chains: 36
    Chain: "M"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'TRANS': 7}
    Chain: "M"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "N"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'TRANS': 7}
    Chain: "N"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'TRANS': 7}
    Chain: "D"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "L"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'TRANS': 7}
    Chain: "L"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "O"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'TRANS': 7}
    Chain: "O"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "P"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'TRANS': 7}
    Chain: "P"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "Q"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'TRANS': 7}
    Chain: "Q"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'TRANS': 7}
    Chain: "R"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "S"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'TRANS': 7}
    Chain: "S"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "T"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'TRANS': 7}
    Chain: "T"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "U"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'TRANS': 7}
    Chain: "U"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "V"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'TRANS': 7}
    Chain: "V"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "F"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'TRANS': 7}
    Chain: "F"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "X"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'TRANS': 7}
    Chain: "X"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "E"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'TRANS': 7}
    Chain: "E"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "W"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'TRANS': 7}
    Chain: "W"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "G"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'TRANS': 7}
    Chain: "G"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "Y"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'TRANS': 7}
    Chain: "Y"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.66, per 1000 atoms: 0.46
  Number of scatterers: 1422
  At special positions: 0
  Unit cell: (73.04, 98.77, 78.02, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     198      8.00
     N     198      7.00
     C    1026      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=18, symmetry=0
  Number of additional bonds: simple=18, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.31
  Conformation dependent library (CDL) restraints added in 57.1 milliseconds
  

  216 Ramachandran restraints generated.
    108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  252

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 38.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.04
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'M' and resid 2 through 6
    Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 6
    Processing sheet with id=AA3, first strand: chain 'O' and resid 2 through 6
      removed outlier: 3.537A  pdb=" N   GLU P   4 " --> pdb=" O   GLU O   4 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'Q' and resid 2 through 6
    Processing sheet with id=AA5, first strand: chain 'U' and resid 2 through 6
    Processing sheet with id=AA6, first strand: chain 'F' and resid 3 through 6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 3 through 6
    Processing sheet with id=AA8, first strand: chain 'G' and resid 3 through 6
      removed outlier: 6.826A  pdb=" N   PHE G   3 " --> pdb=" O   GLU Y   4 " (cutoff:3.500A)
      removed outlier: 8.234A  pdb=" N   LYS Y   6 " --> pdb=" O   PHE G   3 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   PHE G   5 " --> pdb=" O   LYS Y   6 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    32 hydrogen bonds defined for protein.
    72 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: 0.18

  Time building geometry restraints manager: 0.16 seconds

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

  Histogram of bond lengths:
        1.18 -     1.26: 184
        1.26 -     1.33: 121
        1.33 -     1.41: 433
        1.41 -     1.48: 181
        1.48 -     1.56: 539
  Bond restraints: 1458
  Sorted by residual:
  bond pdb=" C   PHE W   7 "
       pdb=" N   GLY W   8 "
    ideal  model  delta    sigma   weight residual
    1.329  1.431 -0.102 1.40e-02 5.10e+03 5.30e+01
  bond pdb=" C   PHE R   7 "
       pdb=" N   GLY R   8 "
    ideal  model  delta    sigma   weight residual
    1.329  1.430 -0.101 1.40e-02 5.10e+03 5.25e+01
  bond pdb=" C   PHE S   7 "
       pdb=" N   GLY S   8 "
    ideal  model  delta    sigma   weight residual
    1.329  1.430 -0.101 1.40e-02 5.10e+03 5.24e+01
  bond pdb=" C   PHE O   7 "
       pdb=" N   GLY O   8 "
    ideal  model  delta    sigma   weight residual
    1.329  1.430 -0.101 1.40e-02 5.10e+03 5.24e+01
  bond pdb=" C   PHE Q   7 "
       pdb=" N   GLY Q   8 "
    ideal  model  delta    sigma   weight residual
    1.329  1.430 -0.101 1.40e-02 5.10e+03 5.22e+01
  ... (remaining 1453 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     9.02: 1836
        9.02 -    18.05: 14
       18.05 -    27.07: 11
       27.07 -    36.09: 6
       36.09 -    45.12: 5
  Bond angle restraints: 1872
  Sorted by residual:
  angle pdb=" O   PHE U   7 "
        pdb=" C   PHE U   7 "
        pdb=" N   GLY U   8 "
      ideal   model   delta    sigma   weight residual
     122.43   77.51   44.92 1.34e+00 5.57e-01 1.12e+03
  angle pdb=" O   PHE O   7 "
        pdb=" C   PHE O   7 "
        pdb=" N   GLY O   8 "
      ideal   model   delta    sigma   weight residual
     122.43   79.09   43.34 1.34e+00 5.57e-01 1.05e+03
  angle pdb=" O   PHE M   7 "
        pdb=" C   PHE M   7 "
        pdb=" N   GLY M   8 "
      ideal   model   delta    sigma   weight residual
     122.61   86.24   36.37 1.32e+00 5.74e-01 7.59e+02
  angle pdb=" CA  PHE U   7 "
        pdb=" C   PHE U   7 "
        pdb=" N   GLY U   8 "
      ideal   model   delta    sigma   weight residual
     118.14  153.44  -35.30 1.31e+00 5.83e-01 7.26e+02
  angle pdb=" C   PHE U   7 "
        pdb=" N   GLY U   8 "
        pdb=" CA  GLY U   8 "
      ideal   model   delta    sigma   weight residual
     121.70  166.82  -45.12 1.80e+00 3.09e-01 6.28e+02
  ... (remaining 1867 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    36.00: 722
       36.00 -    72.00: 16
       72.00 -   108.00: 0
      108.00 -   144.00: 0
      144.00 -   180.00: 18
  Dihedral angle restraints: 756
    sinusoidal: 378
      harmonic: 378
  Sorted by residual:
  dihedral pdb=" CH3 ACE Y   0 "
           pdb=" C   ACE Y   0 "
           pdb=" N   PHE Y   1 "
           pdb=" CA  PHE Y   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00   -0.00 -180.00     1      5.00e+00 4.00e-02 7.68e+02
  dihedral pdb=" CH3 ACE R   0 "
           pdb=" C   ACE R   0 "
           pdb=" N   PHE R   1 "
           pdb=" CA  PHE R   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00   -0.01 -179.99     1      5.00e+00 4.00e-02 7.68e+02
  dihedral pdb=" CH3 ACE D   0 "
           pdb=" C   ACE D   0 "
           pdb=" N   PHE D   1 "
           pdb=" CA  PHE D   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00   -0.01 -179.99     1      5.00e+00 4.00e-02 7.68e+02
  ... (remaining 753 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.018: 55
       0.018 -    0.035: 51
       0.035 -    0.052: 15
       0.052 -    0.070: 4
       0.070 -    0.087: 1
  Chirality restraints: 126
  Sorted by residual:
  chirality pdb=" CA  GLU R   4 "
            pdb=" N   GLU R   4 "
            pdb=" C   GLU R   4 "
            pdb=" CB  GLU R   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.60   -0.09 2.00e-01 2.50e+01 1.89e-01
  chirality pdb=" CA  LYS E   2 "
            pdb=" N   LYS E   2 "
            pdb=" C   LYS E   2 "
            pdb=" CB  LYS E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.57   -0.06 2.00e-01 2.50e+01 1.01e-01
  chirality pdb=" CA  PHE T   5 "
            pdb=" N   PHE T   5 "
            pdb=" C   PHE T   5 "
            pdb=" CB  PHE T   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.45    0.06 2.00e-01 2.50e+01 8.25e-02
  ... (remaining 123 not shown)

  Planarity restraints: 234
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE Q   7 "    0.097 2.00e-02 2.50e+03   1.70e-01 2.88e+02
        pdb=" C   PHE Q   7 "   -0.293 2.00e-02 2.50e+03
        pdb=" O   PHE Q   7 "    0.113 2.00e-02 2.50e+03
        pdb=" N   GLY Q   8 "    0.083 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE M   7 "    0.068 2.00e-02 2.50e+03   9.96e-02 9.93e+01
        pdb=" C   PHE M   7 "   -0.172 2.00e-02 2.50e+03
        pdb=" O   PHE M   7 "    0.044 2.00e-02 2.50e+03
        pdb=" N   GLY M   8 "    0.060 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE O   7 "   -0.069 2.00e-02 2.50e+03   9.68e-02 9.37e+01
        pdb=" C   PHE O   7 "    0.166 2.00e-02 2.50e+03
        pdb=" O   PHE O   7 "   -0.035 2.00e-02 2.50e+03
        pdb=" N   GLY O   8 "   -0.062 2.00e-02 2.50e+03
  ... (remaining 231 not shown)

  Histogram of nonbonded interaction distances:
        2.38 -     2.89: 525
        2.89 -     3.39: 908
        3.39 -     3.89: 1910
        3.89 -     4.40: 2034
        4.40 -     4.90: 3402
  Nonbonded interactions: 8779
  Sorted by model distance:
  nonbonded pdb=" N   PHE G   7 "
            pdb=" N   GLY G   8 "
     model   vdw
     2.382 2.560
  nonbonded pdb=" N   PHE F   7 "
            pdb=" N   GLY F   8 "
     model   vdw
     2.384 2.560
  nonbonded pdb=" N   GLU O   4 "
            pdb=" OE1 GLU O   4 "
     model   vdw
     2.389 3.120
  nonbonded pdb=" N   GLU U   4 "
            pdb=" OE1 GLU U   4 "
     model   vdw
     2.399 3.120
  nonbonded pdb=" N   PHE E   7 "
            pdb=" N   GLY E   8 "
     model   vdw
     2.411 2.560
  ... (remaining 8774 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
  selection = chain 'O'
  selection = chain 'P'
  selection = chain 'Q'
  selection = chain 'R'
  selection = chain 'S'
  selection = chain 'T'
  selection = chain 'U'
  selection = chain 'V'
  selection = chain 'W'
  selection = chain 'X'
  selection = chain 'Y'
}

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:             5.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     3.940
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.000
  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:1.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
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      :  0.021   0.135   1476  Z= 1.190
  Angle     :  3.907  45.116   1872  Z= 2.553
  Chirality :  0.026   0.087    126
  Planarity :  0.019   0.170    234
  Dihedral  : 36.651 179.999    504
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 10.32 %
    Favored  : 88.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.79 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.88 (0.45), residues: 108
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.95 (0.34), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.017   0.001   PHE M   5 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.02062 /  1.17 ( 1458)
  covalent geometry    : angle       3.90685 /  2.55 ( 1872)
  hydrogen bonds       : bond        0.28183 / 14.51 (   32)
  hydrogen bonds       : angle      18.10561 / 11.38 (   72)
  Misc. bond           : bond        0.02192 /  1.18 (   18)

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

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

  216 Ramachandran restraints generated.
    108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  216 Ramachandran restraints generated.
    108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.036 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M    2 LYS cc_start: 0.8101 (mttt) cc_final: 0.7880 (tptt)
REVERT: D    2 LYS cc_start: 0.7470 (mttt) cc_final: 0.7146 (pttm)
REVERT: Q    2 LYS cc_start: 0.8174 (mttt) cc_final: 0.7382 (tppt)
REVERT: R    6 LYS cc_start: 0.8315 (mmmt) cc_final: 0.8020 (mmmm)
REVERT: S    2 LYS cc_start: 0.8697 (mttt) cc_final: 0.8354 (mmmt)
REVERT: T    2 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.7775 (mptt)
REVERT: W    2 LYS cc_start: 0.8615 (mttt) cc_final: 0.8358 (tppt)
REVERT: G    6 LYS cc_start: 0.8598 (mttt) cc_final: 0.8335 (pttm)
  outliers start: 2
  outliers final: 1
  residues processed: 57
  average time/residue: 0.1299
  time to fit residues: 7.7451
Evaluate side-chains
  44 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 42
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Q residue    1 PHE
Chi-restraints excluded: chain T residue    2 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.8980
   overall best weight:   50.0000

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.067288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.060990 restraints weight = 12597.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.062128 restraints weight = 6452.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.062907 restraints weight = 4094.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.063475 restraints weight = 2894.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.063825 restraints weight = 2209.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          1.1721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.061   0.213   1476  Z= 2.587
  Angle     :  3.218  20.731   1872  Z= 1.648
  Chirality :  0.148   0.442    126
  Planarity :  0.020   0.114    234
  Dihedral  : 37.277 175.993    168
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 98.80
  Ramachandran Plot:
    Outliers :  0.93 %
    Allowed  :  9.26 %
    Favored  : 89.81 %
  Rotamer:
    Outliers : 18.25 %
    Allowed  : 36.51 %
    Favored  : 45.24 %
  Cbeta Deviations :  0.79 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.38 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.16 (0.56), residues: 108
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.16 (0.43), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.077   0.013   PHE D   3 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.06137 /  2.60 ( 1458)
  covalent geometry    : angle       3.21761 /  1.65 ( 1872)
  hydrogen bonds       : bond        0.13557 /  8.17 (   32)
  hydrogen bonds       : angle      14.27106 /  8.97 (   72)
  Misc. bond           : bond        0.00490 /  0.26 (   18)

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

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

  216 Ramachandran restraints generated.
    108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  216 Ramachandran restraints generated.
    108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 25
  time to evaluate  : 0.061 
Fit side-chains
REVERT: M    2 LYS cc_start: 0.8853 (mttt) cc_final: 0.8240 (tptt)
REVERT: D    2 LYS cc_start: 0.9091 (mttt) cc_final: 0.8767 (pttm)
REVERT: D    6 LYS cc_start: 0.5178 (OUTLIER) cc_final: 0.3916 (pttm)
REVERT: Q    1 PHE cc_start: 0.9414 (OUTLIER) cc_final: 0.9150 (m-80)
REVERT: Q    6 LYS cc_start: 0.8994 (mmtp) cc_final: 0.8569 (mmtm)
REVERT: R    6 LYS cc_start: 0.8592 (mmmt) cc_final: 0.8212 (mmtm)
REVERT: S    2 LYS cc_start: 0.9244 (mttt) cc_final: 0.8293 (mmmt)
REVERT: T    2 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.8633 (mtmm)
REVERT: U    2 LYS cc_start: 0.4258 (tptt) cc_final: 0.4019 (tptp)
REVERT: X    6 LYS cc_start: 0.5683 (OUTLIER) cc_final: 0.5296 (mmmt)
REVERT: W    2 LYS cc_start: 0.8981 (mttt) cc_final: 0.8265 (tppt)
REVERT: Y    2 LYS cc_start: 0.5187 (OUTLIER) cc_final: 0.4947 (mmmt)
  outliers start: 23
  outliers final: 11
  residues processed: 46
  average time/residue: 0.1570
  time to fit residues: 7.5740
Evaluate side-chains
  37 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 21
  time to evaluate  : 0.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue    3 PHE
Chi-restraints excluded: chain N residue    5 PHE
Chi-restraints excluded: chain D residue    6 LYS
Chi-restraints excluded: chain L residue    3 PHE
Chi-restraints excluded: chain L residue    5 PHE
Chi-restraints excluded: chain P residue    5 PHE
Chi-restraints excluded: chain Q residue    1 PHE
Chi-restraints excluded: chain S residue    1 PHE
Chi-restraints excluded: chain T residue    2 LYS
Chi-restraints excluded: chain U residue    3 PHE
Chi-restraints excluded: chain X residue    5 PHE
Chi-restraints excluded: chain X residue    6 LYS
Chi-restraints excluded: chain E residue    6 LYS
Chi-restraints excluded: chain W residue    5 PHE
Chi-restraints excluded: chain Y residue    2 LYS
Chi-restraints excluded: chain Y residue    5 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.9990
   overall best weight:   50.0000

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.071444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.064398 restraints weight = 10575.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.065388 restraints weight = 5951.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.066080 restraints weight = 4044.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.066476 restraints weight = 3131.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.066827 restraints weight = 2559.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          1.4001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.061   0.199   1476  Z= 2.557
  Angle     :  3.121  15.074   1872  Z= 1.672
  Chirality :  0.130   0.350    126
  Planarity :  0.015   0.054    234
  Dihedral  : 31.263 175.060    168
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 109.66
  Ramachandran Plot:
    Outliers :  1.85 %
    Allowed  : 16.67 %
    Favored  : 81.48 %
  Rotamer:
    Outliers : 36.51 %
    Allowed  : 26.98 %
    Favored  : 36.51 %
  Cbeta Deviations :  3.17 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 7.14 %

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: -5.61 (0.59), residues: 108
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.27 (0.45), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.073   0.011   PHE S   1 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.06109 /  2.57 ( 1458)
  covalent geometry    : angle       3.12055 /  1.67 ( 1872)
  hydrogen bonds       : bond        0.18252 / 11.42 (   32)
  hydrogen bonds       : angle      14.04747 /  8.65 (   72)
  Misc. bond           : bond        0.00298 /  0.15 (   18)

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

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

  216 Ramachandran restraints generated.
    108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  216 Ramachandran restraints generated.
    108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 16
  time to evaluate  : 0.057 
Fit side-chains
REVERT: L    6 LYS cc_start: 0.4383 (OUTLIER) cc_final: 0.3283 (mmmt)
REVERT: Q    1 PHE cc_start: 0.9472 (OUTLIER) cc_final: 0.8984 (m-80)
REVERT: Q    7 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7719 (t80)
REVERT: R    6 LYS cc_start: 0.8674 (mmmt) cc_final: 0.8278 (mmtm)
REVERT: S    2 LYS cc_start: 0.9278 (mttt) cc_final: 0.8400 (mmmt)
REVERT: S    6 LYS cc_start: 0.9000 (mmtm) cc_final: 0.8796 (mmtm)
REVERT: T    6 LYS cc_start: 0.9027 (mmtt) cc_final: 0.8632 (mmmt)
REVERT: U    1 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.8765 (m-80)
REVERT: V    1 PHE cc_start: 0.9403 (OUTLIER) cc_final: 0.8514 (m-80)
REVERT: F    4 GLU cc_start: 0.4776 (OUTLIER) cc_final: 0.3583 (pm20)
REVERT: X    2 LYS cc_start: 0.3632 (OUTLIER) cc_final: 0.2588 (mmmt)
REVERT: E    4 GLU cc_start: 0.4426 (OUTLIER) cc_final: 0.3018 (pm20)
REVERT: W    2 LYS cc_start: 0.9039 (mttt) cc_final: 0.8336 (mmmt)
REVERT: G    4 GLU cc_start: 0.3813 (OUTLIER) cc_final: 0.2385 (pm20)
REVERT: G    6 LYS cc_start: 0.4518 (OUTLIER) cc_final: 0.4306 (pttm)
REVERT: Y    2 LYS cc_start: 0.4434 (OUTLIER) cc_final: 0.3290 (mmmt)
  outliers start: 46
  outliers final: 20
  residues processed: 59
  average time/residue: 0.1269
  time to fit residues: 7.9053
Evaluate side-chains
  45 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 14
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue    3 PHE
Chi-restraints excluded: chain N residue    5 PHE
Chi-restraints excluded: chain L residue    3 PHE
Chi-restraints excluded: chain L residue    5 PHE
Chi-restraints excluded: chain L residue    6 LYS
Chi-restraints excluded: chain O residue    1 PHE
Chi-restraints excluded: chain O residue    5 PHE
Chi-restraints excluded: chain P residue    2 LYS
Chi-restraints excluded: chain P residue    5 PHE
Chi-restraints excluded: chain Q residue    1 PHE
Chi-restraints excluded: chain Q residue    7 PHE
Chi-restraints excluded: chain R residue    3 PHE
Chi-restraints excluded: chain R residue    4 GLU
Chi-restraints excluded: chain S residue    1 PHE
Chi-restraints excluded: chain S residue    3 PHE
Chi-restraints excluded: chain U residue    1 PHE
Chi-restraints excluded: chain U residue    3 PHE
Chi-restraints excluded: chain V residue    1 PHE
Chi-restraints excluded: chain F residue    4 GLU
Chi-restraints excluded: chain X residue    2 LYS
Chi-restraints excluded: chain X residue    3 PHE
Chi-restraints excluded: chain X residue    5 PHE
Chi-restraints excluded: chain E residue    4 GLU
Chi-restraints excluded: chain W residue    4 GLU
Chi-restraints excluded: chain W residue    5 PHE
Chi-restraints excluded: chain W residue    6 LYS
Chi-restraints excluded: chain W residue    7 PHE
Chi-restraints excluded: chain G residue    4 GLU
Chi-restraints excluded: chain G residue    6 LYS
Chi-restraints excluded: chain Y residue    2 LYS
Chi-restraints excluded: chain Y residue    5 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    1.9990
   overall best weight:   50.0000

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.074396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.067451 restraints weight = 9840.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.068375 restraints weight = 5685.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.068925 restraints weight = 3912.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.069394 restraints weight = 3098.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.069666 restraints weight = 2517.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          1.4730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.060   0.218   1476  Z= 2.530
  Angle     :  3.068  14.075   1872  Z= 1.645
  Chirality :  0.125   0.329    126
  Planarity :  0.014   0.045    234
  Dihedral  : 32.377 174.722    164
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 117.28
  Ramachandran Plot:
    Outliers :  1.85 %
    Allowed  : 27.78 %
    Favored  : 70.37 %
  Rotamer:
    Outliers : 34.92 %
    Allowed  : 28.57 %
    Favored  : 36.51 %
  Cbeta Deviations :  1.59 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 8.73 %

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: -6.45 (0.57), residues: 108
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.91 (0.44), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.075   0.010   PHE X   5 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.06061 /  2.55 ( 1458)
  covalent geometry    : angle       3.06754 /  1.64 ( 1872)
  hydrogen bonds       : bond        0.19119 / 11.72 (   32)
  hydrogen bonds       : angle      14.03117 /  8.79 (   72)
  Misc. bond           : bond        0.00246 /  0.14 (   18)

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

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

  216 Ramachandran restraints generated.
    108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  216 Ramachandran restraints generated.
    108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 12
  time to evaluate  : 0.061 
Fit side-chains
REVERT: D    6 LYS cc_start: 0.4556 (OUTLIER) cc_final: 0.3043 (pttm)
REVERT: L    6 LYS cc_start: 0.4244 (OUTLIER) cc_final: 0.3277 (mmmt)
REVERT: O    2 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8481 (mmtm)
REVERT: Q    1 PHE cc_start: 0.9483 (OUTLIER) cc_final: 0.9015 (m-80)
REVERT: R    6 LYS cc_start: 0.8669 (mmmt) cc_final: 0.8330 (mmtp)
REVERT: S    2 LYS cc_start: 0.9283 (mttt) cc_final: 0.8522 (mmmt)
REVERT: S    6 LYS cc_start: 0.9031 (mmtm) cc_final: 0.8620 (mmmt)
REVERT: T    6 LYS cc_start: 0.9145 (mmtt) cc_final: 0.8705 (mmmt)
REVERT: U    1 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.8488 (m-80)
REVERT: V    1 PHE cc_start: 0.9381 (OUTLIER) cc_final: 0.8585 (m-80)
REVERT: F    4 GLU cc_start: 0.4594 (OUTLIER) cc_final: 0.3476 (pm20)
REVERT: X    2 LYS cc_start: 0.3569 (OUTLIER) cc_final: 0.2541 (mmmt)
REVERT: E    4 GLU cc_start: 0.4329 (OUTLIER) cc_final: 0.2746 (pm20)
REVERT: W    2 LYS cc_start: 0.9002 (mttt) cc_final: 0.8320 (mmmt)
REVERT: G    4 GLU cc_start: 0.4222 (OUTLIER) cc_final: 0.2588 (pm20)
  outliers start: 44
  outliers final: 24
  residues processed: 55
  average time/residue: 0.1054
  time to fit residues: 6.1892
Evaluate side-chains
  45 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 11
  time to evaluate  : 0.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue    1 PHE
Chi-restraints excluded: chain N residue    3 PHE
Chi-restraints excluded: chain N residue    5 PHE
Chi-restraints excluded: chain D residue    2 LYS
Chi-restraints excluded: chain D residue    6 LYS
Chi-restraints excluded: chain L residue    1 PHE
Chi-restraints excluded: chain L residue    3 PHE
Chi-restraints excluded: chain L residue    5 PHE
Chi-restraints excluded: chain L residue    6 LYS
Chi-restraints excluded: chain O residue    1 PHE
Chi-restraints excluded: chain O residue    2 LYS
Chi-restraints excluded: chain O residue    3 PHE
Chi-restraints excluded: chain P residue    2 LYS
Chi-restraints excluded: chain P residue    7 PHE
Chi-restraints excluded: chain Q residue    1 PHE
Chi-restraints excluded: chain Q residue    7 PHE
Chi-restraints excluded: chain S residue    1 PHE
Chi-restraints excluded: chain S residue    3 PHE
Chi-restraints excluded: chain U residue    1 PHE
Chi-restraints excluded: chain U residue    3 PHE
Chi-restraints excluded: chain U residue    5 PHE
Chi-restraints excluded: chain V residue    1 PHE
Chi-restraints excluded: chain F residue    4 GLU
Chi-restraints excluded: chain X residue    2 LYS
Chi-restraints excluded: chain X residue    3 PHE
Chi-restraints excluded: chain X residue    5 PHE
Chi-restraints excluded: chain E residue    4 GLU
Chi-restraints excluded: chain W residue    1 PHE
Chi-restraints excluded: chain W residue    4 GLU
Chi-restraints excluded: chain W residue    5 PHE
Chi-restraints excluded: chain W residue    6 LYS
Chi-restraints excluded: chain G residue    4 GLU
Chi-restraints excluded: chain Y residue    3 PHE
Chi-restraints excluded: chain Y residue    5 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.9990
   overall best weight:   50.0000

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.073709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.067096 restraints weight = 10039.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.067989 restraints weight = 5823.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.068566 restraints weight = 4049.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.069036 restraints weight = 3161.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.069215 restraints weight = 2552.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          1.5028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.060   0.216   1476  Z= 2.525
  Angle     :  3.054  14.405   1872  Z= 1.628
  Chirality :  0.127   0.314    126
  Planarity :  0.014   0.046    234
  Dihedral  : 32.775 174.705    164
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 118.01
  Ramachandran Plot:
    Outliers :  0.93 %
    Allowed  : 32.41 %
    Favored  : 66.67 %
  Rotamer:
    Outliers : 38.89 %
    Allowed  : 24.60 %
    Favored  : 36.51 %
  Cbeta Deviations :  0.79 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 8.73 %

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: -6.55 (0.58), residues: 108
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.99 (0.44), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.075   0.010   PHE X   5 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.06054 /  2.54 ( 1458)
  covalent geometry    : angle       3.05391 /  1.63 ( 1872)
  hydrogen bonds       : bond        0.19097 / 11.68 (   32)
  hydrogen bonds       : angle      14.49513 /  9.10 (   72)
  Misc. bond           : bond        0.00269 /  0.15 (   18)

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

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

  216 Ramachandran restraints generated.
    108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  216 Ramachandran restraints generated.
    108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 10
  time to evaluate  : 0.063 
Fit side-chains
REVERT: D    4 GLU cc_start: 0.4088 (OUTLIER) cc_final: 0.3877 (pm20)
REVERT: D    6 LYS cc_start: 0.4576 (OUTLIER) cc_final: 0.3081 (pttm)
REVERT: L    2 LYS cc_start: 0.3813 (OUTLIER) cc_final: 0.2387 (mmmt)
REVERT: O    2 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8486 (mmtm)
REVERT: Q    1 PHE cc_start: 0.9494 (OUTLIER) cc_final: 0.9019 (m-80)
REVERT: R    6 LYS cc_start: 0.8670 (mmmt) cc_final: 0.8298 (mmtp)
REVERT: S    2 LYS cc_start: 0.9385 (mttt) cc_final: 0.8761 (mmmt)
REVERT: S    6 LYS cc_start: 0.9017 (mmtm) cc_final: 0.8630 (mmmt)
REVERT: T    6 LYS cc_start: 0.9098 (mmtt) cc_final: 0.8765 (mmmt)
REVERT: V    1 PHE cc_start: 0.9284 (OUTLIER) cc_final: 0.8538 (m-80)
REVERT: F    4 GLU cc_start: 0.4608 (OUTLIER) cc_final: 0.3434 (pm20)
REVERT: X    2 LYS cc_start: 0.3518 (OUTLIER) cc_final: 0.2546 (mmmt)
REVERT: X    6 LYS cc_start: 0.4161 (OUTLIER) cc_final: 0.3549 (mmmt)
REVERT: W    2 LYS cc_start: 0.8992 (mttt) cc_final: 0.8306 (mmmt)
REVERT: G    4 GLU cc_start: 0.3942 (OUTLIER) cc_final: 0.3236 (pp20)
REVERT: Y    1 PHE cc_start: 0.9406 (OUTLIER) cc_final: 0.9169 (m-80)
REVERT: Y    2 LYS cc_start: 0.4581 (OUTLIER) cc_final: 0.3409 (mmmt)
  outliers start: 49
  outliers final: 25
  residues processed: 58
  average time/residue: 0.1160
  time to fit residues: 7.1517
Evaluate side-chains
  47 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 10
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue    1 PHE
Chi-restraints excluded: chain N residue    3 PHE
Chi-restraints excluded: chain N residue    5 PHE
Chi-restraints excluded: chain D residue    2 LYS
Chi-restraints excluded: chain D residue    4 GLU
Chi-restraints excluded: chain D residue    6 LYS
Chi-restraints excluded: chain L residue    2 LYS
Chi-restraints excluded: chain L residue    6 LYS
Chi-restraints excluded: chain O residue    2 LYS
Chi-restraints excluded: chain O residue    3 PHE
Chi-restraints excluded: chain O residue    5 PHE
Chi-restraints excluded: chain P residue    2 LYS
Chi-restraints excluded: chain P residue    7 PHE
Chi-restraints excluded: chain Q residue    1 PHE
Chi-restraints excluded: chain Q residue    7 PHE
Chi-restraints excluded: chain R residue    1 PHE
Chi-restraints excluded: chain S residue    1 PHE
Chi-restraints excluded: chain S residue    3 PHE
Chi-restraints excluded: chain S residue    5 PHE
Chi-restraints excluded: chain U residue    3 PHE
Chi-restraints excluded: chain U residue    5 PHE
Chi-restraints excluded: chain V residue    1 PHE
Chi-restraints excluded: chain F residue    4 GLU
Chi-restraints excluded: chain X residue    2 LYS
Chi-restraints excluded: chain X residue    3 PHE
Chi-restraints excluded: chain X residue    5 PHE
Chi-restraints excluded: chain X residue    6 LYS
Chi-restraints excluded: chain E residue    7 PHE
Chi-restraints excluded: chain W residue    1 PHE
Chi-restraints excluded: chain W residue    4 GLU
Chi-restraints excluded: chain W residue    5 PHE
Chi-restraints excluded: chain W residue    6 LYS
Chi-restraints excluded: chain G residue    4 GLU
Chi-restraints excluded: chain Y residue    1 PHE
Chi-restraints excluded: chain Y residue    2 LYS
Chi-restraints excluded: chain Y residue    3 PHE
Chi-restraints excluded: chain Y residue    5 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.9990
   overall best weight:   50.0000

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.072010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.065166 restraints weight = 9523.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.066082 restraints weight = 5640.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.066692 restraints weight = 3959.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.067138 restraints weight = 3088.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.067466 restraints weight = 2530.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          1.5230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.060   0.212   1476  Z= 2.517
  Angle     :  3.049  14.316   1872  Z= 1.632
  Chirality :  0.130   0.307    126
  Planarity :  0.014   0.046    234
  Dihedral  : 32.852 174.991    164
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 119.10
  Ramachandran Plot:
    Outliers :  0.93 %
    Allowed  : 34.26 %
    Favored  : 64.81 %
  Rotamer:
    Outliers : 39.68 %
    Allowed  : 23.81 %
    Favored  : 36.51 %
  Cbeta Deviations :  0.79 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 10.32 %

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: -6.69 (0.58), residues: 108
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.09 (0.44), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.075   0.010   PHE X   5 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.06041 /  2.53 ( 1458)
  covalent geometry    : angle       3.04856 /  1.63 ( 1872)
  hydrogen bonds       : bond        0.19480 / 11.86 (   32)
  hydrogen bonds       : angle      14.91155 /  9.34 (   72)
  Misc. bond           : bond        0.00266 /  0.14 (   18)

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

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

  216 Ramachandran restraints generated.
    108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  216 Ramachandran restraints generated.
    108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 11
  time to evaluate  : 0.078 
Fit side-chains
REVERT: D    6 LYS cc_start: 0.4573 (OUTLIER) cc_final: 0.3178 (pttm)
REVERT: L    2 LYS cc_start: 0.3865 (OUTLIER) cc_final: 0.2427 (mmmt)
REVERT: O    2 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8331 (mmtm)
REVERT: Q    1 PHE cc_start: 0.9489 (OUTLIER) cc_final: 0.9022 (m-80)
REVERT: R    6 LYS cc_start: 0.8678 (mmmt) cc_final: 0.8337 (mmtm)
REVERT: S    2 LYS cc_start: 0.9378 (mttt) cc_final: 0.8746 (mmmt)
REVERT: S    6 LYS cc_start: 0.9036 (mmtm) cc_final: 0.8676 (mmmt)
REVERT: T    6 LYS cc_start: 0.9117 (mmtt) cc_final: 0.8781 (mmmt)
REVERT: U    1 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8428 (m-80)
REVERT: V    1 PHE cc_start: 0.9261 (OUTLIER) cc_final: 0.8528 (m-80)
REVERT: F    2 LYS cc_start: 0.6306 (OUTLIER) cc_final: 0.5847 (pttm)
REVERT: F    4 GLU cc_start: 0.4566 (OUTLIER) cc_final: 0.3451 (pm20)
REVERT: X    2 LYS cc_start: 0.3586 (OUTLIER) cc_final: 0.2599 (mmmt)
REVERT: X    6 LYS cc_start: 0.4217 (OUTLIER) cc_final: 0.3565 (mmmt)
REVERT: W    2 LYS cc_start: 0.8993 (mttt) cc_final: 0.8363 (mmmt)
REVERT: Y    2 LYS cc_start: 0.4623 (OUTLIER) cc_final: 0.3424 (mmmt)
  outliers start: 50
  outliers final: 30
  residues processed: 60
  average time/residue: 0.1257
  time to fit residues: 7.9955
Evaluate side-chains
  52 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 11
  time to evaluate  : 0.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue    3 PHE
Chi-restraints excluded: chain N residue    5 PHE
Chi-restraints excluded: chain N residue    6 LYS
Chi-restraints excluded: chain D residue    2 LYS
Chi-restraints excluded: chain D residue    6 LYS
Chi-restraints excluded: chain L residue    2 LYS
Chi-restraints excluded: chain L residue    3 PHE
Chi-restraints excluded: chain L residue    5 PHE
Chi-restraints excluded: chain L residue    6 LYS
Chi-restraints excluded: chain O residue    2 LYS
Chi-restraints excluded: chain O residue    3 PHE
Chi-restraints excluded: chain O residue    5 PHE
Chi-restraints excluded: chain P residue    2 LYS
Chi-restraints excluded: chain P residue    5 PHE
Chi-restraints excluded: chain P residue    7 PHE
Chi-restraints excluded: chain Q residue    1 PHE
Chi-restraints excluded: chain Q residue    7 PHE
Chi-restraints excluded: chain R residue    1 PHE
Chi-restraints excluded: chain R residue    4 GLU
Chi-restraints excluded: chain S residue    1 PHE
Chi-restraints excluded: chain S residue    3 PHE
Chi-restraints excluded: chain S residue    5 PHE
Chi-restraints excluded: chain U residue    1 PHE
Chi-restraints excluded: chain U residue    3 PHE
Chi-restraints excluded: chain U residue    5 PHE
Chi-restraints excluded: chain V residue    1 PHE
Chi-restraints excluded: chain F residue    2 LYS
Chi-restraints excluded: chain F residue    4 GLU
Chi-restraints excluded: chain X residue    2 LYS
Chi-restraints excluded: chain X residue    3 PHE
Chi-restraints excluded: chain X residue    5 PHE
Chi-restraints excluded: chain X residue    6 LYS
Chi-restraints excluded: chain E residue    7 PHE
Chi-restraints excluded: chain W residue    1 PHE
Chi-restraints excluded: chain W residue    4 GLU
Chi-restraints excluded: chain W residue    5 PHE
Chi-restraints excluded: chain W residue    6 LYS
Chi-restraints excluded: chain G residue    2 LYS
Chi-restraints excluded: chain Y residue    2 LYS
Chi-restraints excluded: chain Y residue    3 PHE
Chi-restraints excluded: chain Y residue    5 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.9990
   overall best weight:   50.0000

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.073348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.066390 restraints weight = 11688.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.067397 restraints weight = 6398.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.068097 restraints weight = 4312.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.068535 restraints weight = 3220.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.068897 restraints weight = 2626.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          1.5268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.060   0.209   1476  Z= 2.514
  Angle     :  3.049  14.174   1872  Z= 1.629
  Chirality :  0.128   0.289    126
  Planarity :  0.014   0.047    234
  Dihedral  : 32.785 175.912    164
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 118.01
  Ramachandran Plot:
    Outliers :  0.93 %
    Allowed  : 35.19 %
    Favored  : 63.89 %
  Rotamer:
    Outliers : 39.68 %
    Allowed  : 24.60 %
    Favored  : 35.71 %
  Cbeta Deviations :  0.79 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 8.73 %

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: -6.77 (0.56), residues: 108
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.16 (0.43), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.075   0.010   PHE X   5 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.06037 /  2.53 ( 1458)
  covalent geometry    : angle       3.04881 /  1.63 ( 1872)
  hydrogen bonds       : bond        0.19290 / 11.74 (   32)
  hydrogen bonds       : angle      14.86537 /  9.33 (   72)
  Misc. bond           : bond        0.00274 /  0.15 (   18)

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

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

  216 Ramachandran restraints generated.
    108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  216 Ramachandran restraints generated.
    108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 12
  time to evaluate  : 0.061 
Fit side-chains
REVERT: D    6 LYS cc_start: 0.4581 (OUTLIER) cc_final: 0.3110 (pttm)
REVERT: L    2 LYS cc_start: 0.3764 (OUTLIER) cc_final: 0.2342 (mmmt)
REVERT: O    2 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8337 (mmtm)
REVERT: Q    1 PHE cc_start: 0.9501 (OUTLIER) cc_final: 0.9030 (m-80)
REVERT: R    6 LYS cc_start: 0.8665 (mmmt) cc_final: 0.8297 (mmtm)
REVERT: S    2 LYS cc_start: 0.9399 (mttt) cc_final: 0.8740 (mmmt)
REVERT: S    6 LYS cc_start: 0.9043 (mmtm) cc_final: 0.8676 (mmmt)
REVERT: T    6 LYS cc_start: 0.9090 (mmtt) cc_final: 0.8743 (mmmt)
REVERT: U    1 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8464 (m-80)
REVERT: V    1 PHE cc_start: 0.9277 (OUTLIER) cc_final: 0.8584 (m-80)
REVERT: F    4 GLU cc_start: 0.4524 (OUTLIER) cc_final: 0.3377 (pm20)
REVERT: X    2 LYS cc_start: 0.3504 (OUTLIER) cc_final: 0.2536 (mmmt)
REVERT: X    6 LYS cc_start: 0.4144 (OUTLIER) cc_final: 0.3539 (mmmt)
REVERT: W    2 LYS cc_start: 0.8995 (mttt) cc_final: 0.8352 (mmmt)
REVERT: Y    1 PHE cc_start: 0.9391 (OUTLIER) cc_final: 0.9135 (m-80)
REVERT: Y    2 LYS cc_start: 0.4637 (OUTLIER) cc_final: 0.3442 (mmmt)
  outliers start: 50
  outliers final: 33
  residues processed: 61
  average time/residue: 0.1257
  time to fit residues: 8.1244
Evaluate side-chains
  55 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 11
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue    2 LYS
Chi-restraints excluded: chain M residue    5 PHE
Chi-restraints excluded: chain N residue    1 PHE
Chi-restraints excluded: chain N residue    3 PHE
Chi-restraints excluded: chain N residue    5 PHE
Chi-restraints excluded: chain N residue    6 LYS
Chi-restraints excluded: chain D residue    2 LYS
Chi-restraints excluded: chain D residue    6 LYS
Chi-restraints excluded: chain L residue    2 LYS
Chi-restraints excluded: chain L residue    3 PHE
Chi-restraints excluded: chain L residue    5 PHE
Chi-restraints excluded: chain L residue    6 LYS
Chi-restraints excluded: chain O residue    2 LYS
Chi-restraints excluded: chain O residue    3 PHE
Chi-restraints excluded: chain O residue    5 PHE
Chi-restraints excluded: chain P residue    2 LYS
Chi-restraints excluded: chain P residue    7 PHE
Chi-restraints excluded: chain Q residue    1 PHE
Chi-restraints excluded: chain Q residue    7 PHE
Chi-restraints excluded: chain R residue    1 PHE
Chi-restraints excluded: chain R residue    4 GLU
Chi-restraints excluded: chain S residue    1 PHE
Chi-restraints excluded: chain S residue    3 PHE
Chi-restraints excluded: chain S residue    5 PHE
Chi-restraints excluded: chain U residue    1 PHE
Chi-restraints excluded: chain U residue    3 PHE
Chi-restraints excluded: chain U residue    5 PHE
Chi-restraints excluded: chain V residue    1 PHE
Chi-restraints excluded: chain F residue    2 LYS
Chi-restraints excluded: chain F residue    4 GLU
Chi-restraints excluded: chain X residue    2 LYS
Chi-restraints excluded: chain X residue    3 PHE
Chi-restraints excluded: chain X residue    5 PHE
Chi-restraints excluded: chain X residue    6 LYS
Chi-restraints excluded: chain E residue    7 PHE
Chi-restraints excluded: chain W residue    1 PHE
Chi-restraints excluded: chain W residue    4 GLU
Chi-restraints excluded: chain W residue    5 PHE
Chi-restraints excluded: chain W residue    6 LYS
Chi-restraints excluded: chain G residue    2 LYS
Chi-restraints excluded: chain Y residue    1 PHE
Chi-restraints excluded: chain Y residue    2 LYS
Chi-restraints excluded: chain Y residue    3 PHE
Chi-restraints excluded: chain Y residue    5 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    1.9990
   overall best weight:   50.0000

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.073443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.066685 restraints weight = 9997.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.067601 restraints weight = 5833.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.068257 restraints weight = 4065.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.068652 restraints weight = 3087.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.068984 restraints weight = 2587.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          1.5295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.060   0.209   1476  Z= 2.510
  Angle     :  3.077  14.049   1872  Z= 1.637
  Chirality :  0.129   0.293    126
  Planarity :  0.014   0.047    234
  Dihedral  : 32.671 170.889    164
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 116.92
  Ramachandran Plot:
    Outliers :  0.93 %
    Allowed  : 33.33 %
    Favored  : 65.74 %
  Rotamer:
    Outliers : 39.68 %
    Allowed  : 24.60 %
    Favored  : 35.71 %
  Cbeta Deviations :  0.79 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 8.73 %

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: -6.84 (0.54), residues: 108
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.21 (0.41), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.075   0.010   PHE X   5 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.06032 /  2.53 ( 1458)
  covalent geometry    : angle       3.07690 /  1.64 ( 1872)
  hydrogen bonds       : bond        0.19415 / 11.78 (   32)
  hydrogen bonds       : angle      14.87988 /  9.34 (   72)
  Misc. bond           : bond        0.00272 /  0.14 (   18)

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

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

  216 Ramachandran restraints generated.
    108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  216 Ramachandran restraints generated.
    108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 12
  time to evaluate  : 0.060 
Fit side-chains
REVERT: D    6 LYS cc_start: 0.4646 (OUTLIER) cc_final: 0.3186 (pttm)
REVERT: L    2 LYS cc_start: 0.3872 (OUTLIER) cc_final: 0.2385 (mmmt)
REVERT: O    2 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8347 (mmtm)
REVERT: Q    1 PHE cc_start: 0.9487 (OUTLIER) cc_final: 0.9021 (m-80)
REVERT: R    6 LYS cc_start: 0.8677 (mmmt) cc_final: 0.8337 (mmtm)
REVERT: S    2 LYS cc_start: 0.9377 (mttt) cc_final: 0.8728 (mmmt)
REVERT: S    6 LYS cc_start: 0.9061 (mmtm) cc_final: 0.8710 (mmmt)
REVERT: T    6 LYS cc_start: 0.9091 (mmtt) cc_final: 0.8755 (mmmt)
REVERT: U    1 PHE cc_start: 0.8973 (OUTLIER) cc_final: 0.8432 (m-80)
REVERT: V    1 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.8580 (m-80)
REVERT: F    4 GLU cc_start: 0.4611 (OUTLIER) cc_final: 0.3461 (pm20)
REVERT: X    2 LYS cc_start: 0.3625 (OUTLIER) cc_final: 0.2640 (mmmt)
REVERT: X    6 LYS cc_start: 0.4308 (OUTLIER) cc_final: 0.3690 (mmmt)
REVERT: E    6 LYS cc_start: 0.4689 (OUTLIER) cc_final: 0.4208 (pttp)
REVERT: W    2 LYS cc_start: 0.9005 (mttt) cc_final: 0.8388 (mmmt)
REVERT: Y    1 PHE cc_start: 0.9386 (OUTLIER) cc_final: 0.9125 (m-80)
REVERT: Y    2 LYS cc_start: 0.4727 (OUTLIER) cc_final: 0.3522 (mmmt)
  outliers start: 50
  outliers final: 34
  residues processed: 61
  average time/residue: 0.1290
  time to fit residues: 8.3476
Evaluate side-chains
  58 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 12
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue    2 LYS
Chi-restraints excluded: chain M residue    5 PHE
Chi-restraints excluded: chain N residue    1 PHE
Chi-restraints excluded: chain N residue    3 PHE
Chi-restraints excluded: chain N residue    5 PHE
Chi-restraints excluded: chain N residue    6 LYS
Chi-restraints excluded: chain D residue    2 LYS
Chi-restraints excluded: chain D residue    6 LYS
Chi-restraints excluded: chain L residue    2 LYS
Chi-restraints excluded: chain L residue    3 PHE
Chi-restraints excluded: chain L residue    5 PHE
Chi-restraints excluded: chain L residue    6 LYS
Chi-restraints excluded: chain O residue    2 LYS
Chi-restraints excluded: chain O residue    3 PHE
Chi-restraints excluded: chain O residue    5 PHE
Chi-restraints excluded: chain P residue    2 LYS
Chi-restraints excluded: chain P residue    7 PHE
Chi-restraints excluded: chain Q residue    1 PHE
Chi-restraints excluded: chain Q residue    7 PHE
Chi-restraints excluded: chain R residue    1 PHE
Chi-restraints excluded: chain R residue    4 GLU
Chi-restraints excluded: chain S residue    1 PHE
Chi-restraints excluded: chain S residue    3 PHE
Chi-restraints excluded: chain S residue    5 PHE
Chi-restraints excluded: chain U residue    1 PHE
Chi-restraints excluded: chain U residue    3 PHE
Chi-restraints excluded: chain U residue    5 PHE
Chi-restraints excluded: chain V residue    1 PHE
Chi-restraints excluded: chain F residue    2 LYS
Chi-restraints excluded: chain F residue    4 GLU
Chi-restraints excluded: chain X residue    2 LYS
Chi-restraints excluded: chain X residue    3 PHE
Chi-restraints excluded: chain X residue    5 PHE
Chi-restraints excluded: chain X residue    6 LYS
Chi-restraints excluded: chain E residue    6 LYS
Chi-restraints excluded: chain E residue    7 PHE
Chi-restraints excluded: chain W residue    1 PHE
Chi-restraints excluded: chain W residue    4 GLU
Chi-restraints excluded: chain W residue    5 PHE
Chi-restraints excluded: chain W residue    6 LYS
Chi-restraints excluded: chain W residue    7 PHE
Chi-restraints excluded: chain G residue    2 LYS
Chi-restraints excluded: chain Y residue    1 PHE
Chi-restraints excluded: chain Y residue    2 LYS
Chi-restraints excluded: chain Y residue    3 PHE
Chi-restraints excluded: chain Y residue    5 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.9990
   overall best weight:   50.0000

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.073495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.066374 restraints weight = 12131.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.067377 restraints weight = 6620.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.068102 restraints weight = 4488.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.068623 restraints weight = 3341.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.068929 restraints weight = 2680.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          1.5318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.060   0.209   1476  Z= 2.506
  Angle     :  3.072  14.162   1872  Z= 1.635
  Chirality :  0.129   0.290    126
  Planarity :  0.014   0.047    234
  Dihedral  : 32.715 172.067    164
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 119.83
  Ramachandran Plot:
    Outliers :  1.85 %
    Allowed  : 33.33 %
    Favored  : 64.81 %
  Rotamer:
    Outliers : 40.48 %
    Allowed  : 23.81 %
    Favored  : 35.71 %
  Cbeta Deviations :  1.59 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 8.73 %

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: -6.96 (0.53), residues: 108
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.30 (0.41), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.075   0.010   PHE X   5 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.06025 /  2.52 ( 1458)
  covalent geometry    : angle       3.07228 /  1.63 ( 1872)
  hydrogen bonds       : bond        0.19395 / 11.76 (   32)
  hydrogen bonds       : angle      14.91020 /  9.36 (   72)
  Misc. bond           : bond        0.00276 /  0.15 (   18)

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

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

  216 Ramachandran restraints generated.
    108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  216 Ramachandran restraints generated.
    108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 12
  time to evaluate  : 0.061 
Fit side-chains
REVERT: D    6 LYS cc_start: 0.4631 (OUTLIER) cc_final: 0.3429 (pttm)
REVERT: L    2 LYS cc_start: 0.3880 (OUTLIER) cc_final: 0.2383 (mmmt)
REVERT: O    2 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8345 (mmtm)
REVERT: Q    1 PHE cc_start: 0.9485 (OUTLIER) cc_final: 0.9020 (m-80)
REVERT: R    6 LYS cc_start: 0.8672 (mmmt) cc_final: 0.8342 (mmtm)
REVERT: S    2 LYS cc_start: 0.9376 (mttt) cc_final: 0.8725 (mmmt)
REVERT: S    6 LYS cc_start: 0.9067 (mmtm) cc_final: 0.8756 (mmmt)
REVERT: T    6 LYS cc_start: 0.9092 (mmtt) cc_final: 0.8757 (mmmt)
REVERT: U    1 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8429 (m-80)
REVERT: V    1 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.8563 (m-80)
REVERT: F    4 GLU cc_start: 0.4625 (OUTLIER) cc_final: 0.3479 (pm20)
REVERT: X    2 LYS cc_start: 0.3626 (OUTLIER) cc_final: 0.2641 (mmmt)
REVERT: X    6 LYS cc_start: 0.4313 (OUTLIER) cc_final: 0.3688 (mmmt)
REVERT: E    6 LYS cc_start: 0.4746 (OUTLIER) cc_final: 0.4262 (pttp)
REVERT: W    2 LYS cc_start: 0.9011 (mttt) cc_final: 0.8394 (mmmt)
REVERT: Y    1 PHE cc_start: 0.9381 (OUTLIER) cc_final: 0.9119 (m-80)
REVERT: Y    2 LYS cc_start: 0.4727 (OUTLIER) cc_final: 0.3523 (mmmt)
  outliers start: 51
  outliers final: 35
  residues processed: 62
  average time/residue: 0.1232
  time to fit residues: 8.0735
Evaluate side-chains
  58 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 11
  time to evaluate  : 0.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue    2 LYS
Chi-restraints excluded: chain M residue    5 PHE
Chi-restraints excluded: chain N residue    1 PHE
Chi-restraints excluded: chain N residue    3 PHE
Chi-restraints excluded: chain N residue    5 PHE
Chi-restraints excluded: chain N residue    6 LYS
Chi-restraints excluded: chain D residue    2 LYS
Chi-restraints excluded: chain D residue    6 LYS
Chi-restraints excluded: chain L residue    2 LYS
Chi-restraints excluded: chain L residue    3 PHE
Chi-restraints excluded: chain L residue    5 PHE
Chi-restraints excluded: chain L residue    6 LYS
Chi-restraints excluded: chain O residue    2 LYS
Chi-restraints excluded: chain O residue    3 PHE
Chi-restraints excluded: chain O residue    5 PHE
Chi-restraints excluded: chain P residue    2 LYS
Chi-restraints excluded: chain P residue    5 PHE
Chi-restraints excluded: chain P residue    7 PHE
Chi-restraints excluded: chain Q residue    1 PHE
Chi-restraints excluded: chain Q residue    7 PHE
Chi-restraints excluded: chain R residue    1 PHE
Chi-restraints excluded: chain R residue    4 GLU
Chi-restraints excluded: chain S residue    1 PHE
Chi-restraints excluded: chain S residue    3 PHE
Chi-restraints excluded: chain S residue    5 PHE
Chi-restraints excluded: chain U residue    1 PHE
Chi-restraints excluded: chain U residue    3 PHE
Chi-restraints excluded: chain U residue    5 PHE
Chi-restraints excluded: chain V residue    1 PHE
Chi-restraints excluded: chain F residue    2 LYS
Chi-restraints excluded: chain F residue    4 GLU
Chi-restraints excluded: chain X residue    2 LYS
Chi-restraints excluded: chain X residue    3 PHE
Chi-restraints excluded: chain X residue    5 PHE
Chi-restraints excluded: chain X residue    6 LYS
Chi-restraints excluded: chain E residue    6 LYS
Chi-restraints excluded: chain E residue    7 PHE
Chi-restraints excluded: chain W residue    1 PHE
Chi-restraints excluded: chain W residue    4 GLU
Chi-restraints excluded: chain W residue    5 PHE
Chi-restraints excluded: chain W residue    6 LYS
Chi-restraints excluded: chain W residue    7 PHE
Chi-restraints excluded: chain G residue    2 LYS
Chi-restraints excluded: chain Y residue    1 PHE
Chi-restraints excluded: chain Y residue    2 LYS
Chi-restraints excluded: chain Y residue    3 PHE
Chi-restraints excluded: chain Y residue    5 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.9990
   overall best weight:   50.0000

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.073564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.066752 restraints weight = 10094.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.067693 restraints weight = 5885.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.068280 restraints weight = 4073.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.068758 restraints weight = 3198.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.069043 restraints weight = 2591.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          1.5329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.060   0.209   1476  Z= 2.505
  Angle     :  3.077  14.150   1872  Z= 1.635
  Chirality :  0.129   0.297    126
  Planarity :  0.014   0.047    234
  Dihedral  : 32.722 172.334    164
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 118.74
  Ramachandran Plot:
    Outliers :  1.85 %
    Allowed  : 34.26 %
    Favored  : 63.89 %
  Rotamer:
    Outliers : 40.48 %
    Allowed  : 24.60 %
    Favored  : 34.92 %
  Cbeta Deviations :  1.59 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 8.73 %

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: -7.01 (0.53), residues: 108
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.34 (0.41), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.075   0.010   PHE X   5 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.06022 /  2.52 ( 1458)
  covalent geometry    : angle       3.07714 /  1.64 ( 1872)
  hydrogen bonds       : bond        0.19432 / 11.78 (   32)
  hydrogen bonds       : angle      14.92250 /  9.35 (   72)
  Misc. bond           : bond        0.00273 /  0.15 (   18)

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

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

  216 Ramachandran restraints generated.
    108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  216 Ramachandran restraints generated.
    108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 12
  time to evaluate  : 0.058 
Fit side-chains
REVERT: D    6 LYS cc_start: 0.4629 (OUTLIER) cc_final: 0.3429 (pttm)
REVERT: L    2 LYS cc_start: 0.3879 (OUTLIER) cc_final: 0.2382 (mmmt)
REVERT: O    2 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8343 (mmtm)
REVERT: Q    1 PHE cc_start: 0.9485 (OUTLIER) cc_final: 0.9021 (m-80)
REVERT: R    6 LYS cc_start: 0.8673 (mmmt) cc_final: 0.8328 (mmtm)
REVERT: S    2 LYS cc_start: 0.9372 (mttt) cc_final: 0.8726 (mmmt)
REVERT: S    6 LYS cc_start: 0.9072 (mmtm) cc_final: 0.8789 (mmmt)
REVERT: T    6 LYS cc_start: 0.9095 (mmtt) cc_final: 0.8759 (mmmt)
REVERT: U    1 PHE cc_start: 0.8970 (OUTLIER) cc_final: 0.8430 (m-80)
REVERT: V    1 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8584 (m-80)
REVERT: F    4 GLU cc_start: 0.4625 (OUTLIER) cc_final: 0.3482 (pm20)
REVERT: X    2 LYS cc_start: 0.3621 (OUTLIER) cc_final: 0.2638 (mmmt)
REVERT: X    6 LYS cc_start: 0.4306 (OUTLIER) cc_final: 0.3679 (mmmt)
REVERT: E    6 LYS cc_start: 0.4733 (OUTLIER) cc_final: 0.4246 (pttp)
REVERT: W    2 LYS cc_start: 0.9008 (mttt) cc_final: 0.8393 (mmmt)
REVERT: Y    1 PHE cc_start: 0.9379 (OUTLIER) cc_final: 0.9116 (m-80)
REVERT: Y    2 LYS cc_start: 0.4650 (OUTLIER) cc_final: 0.3451 (mmmt)
  outliers start: 51
  outliers final: 35
  residues processed: 62
  average time/residue: 0.1280
  time to fit residues: 8.3733
Evaluate side-chains
  59 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 12
  time to evaluate  : 0.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue    2 LYS
Chi-restraints excluded: chain M residue    5 PHE
Chi-restraints excluded: chain N residue    1 PHE
Chi-restraints excluded: chain N residue    3 PHE
Chi-restraints excluded: chain N residue    5 PHE
Chi-restraints excluded: chain N residue    6 LYS
Chi-restraints excluded: chain D residue    2 LYS
Chi-restraints excluded: chain D residue    6 LYS
Chi-restraints excluded: chain L residue    2 LYS
Chi-restraints excluded: chain L residue    3 PHE
Chi-restraints excluded: chain L residue    5 PHE
Chi-restraints excluded: chain L residue    6 LYS
Chi-restraints excluded: chain O residue    2 LYS
Chi-restraints excluded: chain O residue    3 PHE
Chi-restraints excluded: chain O residue    5 PHE
Chi-restraints excluded: chain P residue    2 LYS
Chi-restraints excluded: chain P residue    5 PHE
Chi-restraints excluded: chain P residue    7 PHE
Chi-restraints excluded: chain Q residue    1 PHE
Chi-restraints excluded: chain Q residue    7 PHE
Chi-restraints excluded: chain R residue    1 PHE
Chi-restraints excluded: chain R residue    4 GLU
Chi-restraints excluded: chain S residue    1 PHE
Chi-restraints excluded: chain S residue    3 PHE
Chi-restraints excluded: chain S residue    5 PHE
Chi-restraints excluded: chain U residue    1 PHE
Chi-restraints excluded: chain U residue    3 PHE
Chi-restraints excluded: chain U residue    5 PHE
Chi-restraints excluded: chain V residue    1 PHE
Chi-restraints excluded: chain F residue    2 LYS
Chi-restraints excluded: chain F residue    4 GLU
Chi-restraints excluded: chain X residue    2 LYS
Chi-restraints excluded: chain X residue    3 PHE
Chi-restraints excluded: chain X residue    5 PHE
Chi-restraints excluded: chain X residue    6 LYS
Chi-restraints excluded: chain E residue    6 LYS
Chi-restraints excluded: chain E residue    7 PHE
Chi-restraints excluded: chain W residue    1 PHE
Chi-restraints excluded: chain W residue    4 GLU
Chi-restraints excluded: chain W residue    5 PHE
Chi-restraints excluded: chain W residue    6 LYS
Chi-restraints excluded: chain W residue    7 PHE
Chi-restraints excluded: chain G residue    2 LYS
Chi-restraints excluded: chain Y residue    1 PHE
Chi-restraints excluded: chain Y residue    2 LYS
Chi-restraints excluded: chain Y residue    3 PHE
Chi-restraints excluded: chain Y residue    5 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    1.9990
   overall best weight:   50.0000

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.073680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.066610 restraints weight = 11837.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.067595 restraints weight = 6548.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.068293 restraints weight = 4488.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.068777 restraints weight = 3373.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.069100 restraints weight = 2726.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          1.5355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.060   0.208   1476  Z= 2.503
  Angle     :  3.074  14.185   1872  Z= 1.636
  Chirality :  0.130   0.297    126
  Planarity :  0.014   0.047    234
  Dihedral  : 32.763 172.567    164
  Min Nonbonded Distance : 1.891

Molprobity Statistics.
  All-atom Clashscore : 118.37
  Ramachandran Plot:
    Outliers :  0.93 %
    Allowed  : 35.19 %
    Favored  : 63.89 %
  Rotamer:
    Outliers : 40.48 %
    Allowed  : 23.81 %
    Favored  : 35.71 %
  Cbeta Deviations :  1.59 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 8.73 %

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: -7.06 (0.54), residues: 108
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.37 (0.41), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.075   0.010   PHE X   5 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.06018 /  2.52 ( 1458)
  covalent geometry    : angle       3.07377 /  1.64 ( 1872)
  hydrogen bonds       : bond        0.19507 / 11.80 (   32)
  hydrogen bonds       : angle      15.07469 /  9.44 (   72)
  Misc. bond           : bond        0.00272 /  0.15 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 425.73 seconds
wall clock time: 8 minutes 15.03 seconds (495.03 seconds total)