Starting phenix.real_space_refine
on Fri Oct 10 10:17:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8olo_16960/10_2025/8olo_16960.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8olo_16960/10_2025/8olo_16960.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8olo_16960/10_2025/8olo_16960.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8olo_16960/10_2025/8olo_16960.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8olo_16960/10_2025/8olo_16960.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8olo_16960/10_2025/8olo_16960.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      10      5.16       5
     C    1520      2.51       5
     N     390      2.21       5
     O     410      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2330
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 233
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 233
          Classifications: {'peptide': 31}
          Link IDs: {'TRANS': 30}
  Restraints were copied for chains:
    D, B, C, E, F, G, H, I, J
  Time building chain proxies: 0.56, per 1000 atoms: 0.24
  Number of scatterers: 2330
  At special positions: 0
  Unit cell: (92.92, 50.904, 40.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      10     16.00
     O     410      8.00
     N     390      7.00
     C    1520      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.19
  Conformation dependent library (CDL) restraints added in 92.9 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  520

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 5 sheets defined
      0.0% alpha, 54.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 20
      removed outlier: 9.105A  pdb=" N   GLU A  11 " --> pdb=" O   VAL C  12 " (cutoff:3.500A)
      removed outlier: 10.329A  pdb=" N   HIS C  14 " --> pdb=" O   GLU A  11 " (cutoff:3.500A)
      removed outlier: 5.615A  pdb=" N   HIS A  13 " --> pdb=" O   HIS C  14 " (cutoff:3.500A)
      removed outlier: 8.309A  pdb=" N   LYS C  16 " --> pdb=" O   HIS A  13 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   GLN A  15 " --> pdb=" O   LYS C  16 " (cutoff:3.500A)
      removed outlier: 7.202A  pdb=" N   VAL C  18 " --> pdb=" O   GLN A  15 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   LEU A  17 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   PHE C  20 " --> pdb=" O   LEU A  17 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   PHE A  19 " --> pdb=" O   PHE C  20 " (cutoff:3.500A)
      removed outlier: 7.810A  pdb=" N   GLU C  22 " --> pdb=" O   PHE A  19 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 20
      removed outlier: 9.105A  pdb=" N   GLU A  11 " --> pdb=" O   VAL C  12 " (cutoff:3.500A)
      removed outlier: 10.329A  pdb=" N   HIS C  14 " --> pdb=" O   GLU A  11 " (cutoff:3.500A)
      removed outlier: 5.615A  pdb=" N   HIS A  13 " --> pdb=" O   HIS C  14 " (cutoff:3.500A)
      removed outlier: 8.309A  pdb=" N   LYS C  16 " --> pdb=" O   HIS A  13 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   GLN A  15 " --> pdb=" O   LYS C  16 " (cutoff:3.500A)
      removed outlier: 7.202A  pdb=" N   VAL C  18 " --> pdb=" O   GLN A  15 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   LEU A  17 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   PHE C  20 " --> pdb=" O   LEU A  17 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   PHE A  19 " --> pdb=" O   PHE C  20 " (cutoff:3.500A)
      removed outlier: 7.810A  pdb=" N   GLU C  22 " --> pdb=" O   PHE A  19 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   GLN E  15 " --> pdb=" O   HIS C  14 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   LYS C  16 " --> pdb=" O   GLN E  15 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   LEU E  17 " --> pdb=" O   LYS C  16 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   VAL C  18 " --> pdb=" O   LEU E  17 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   PHE E  19 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   PHE C  20 " --> pdb=" O   PHE E  19 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   ALA E  21 " --> pdb=" O   PHE C  20 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   GLU C  22 " --> pdb=" O   ALA E  21 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   GLN G  15 " --> pdb=" O   HIS E  14 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   LYS E  16 " --> pdb=" O   GLN G  15 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   LEU G  17 " --> pdb=" O   LYS E  16 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   VAL E  18 " --> pdb=" O   LEU G  17 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   PHE G  19 " --> pdb=" O   VAL E  18 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   PHE E  20 " --> pdb=" O   PHE G  19 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   ALA G  21 " --> pdb=" O   PHE E  20 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   GLU E  22 " --> pdb=" O   ALA G  21 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   GLN I  15 " --> pdb=" O   HIS G  14 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   LYS G  16 " --> pdb=" O   GLN I  15 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   LEU I  17 " --> pdb=" O   LYS G  16 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   VAL G  18 " --> pdb=" O   LEU I  17 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   PHE I  19 " --> pdb=" O   VAL G  18 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   PHE G  20 " --> pdb=" O   PHE I  19 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   ALA I  21 " --> pdb=" O   PHE G  20 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   GLU G  22 " --> pdb=" O   ALA I  21 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 30 through 32
      removed outlier: 6.124A  pdb=" N   ILE C  31 " --> pdb=" O   ILE E  32 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   ILE E  31 " --> pdb=" O   ILE G  32 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   ILE G  31 " --> pdb=" O   ILE I  32 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 24
      removed outlier: 6.368A  pdb=" N   GLU D  11 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
      removed outlier: 8.229A  pdb=" N   HIS B  14 " --> pdb=" O   GLU D  11 " (cutoff:3.500A)
      removed outlier: 8.975A  pdb=" N   HIS D  13 " --> pdb=" O   HIS B  14 " (cutoff:3.500A)
      removed outlier: 8.148A  pdb=" N   LYS B  16 " --> pdb=" O   HIS D  13 " (cutoff:3.500A)
      removed outlier: 9.082A  pdb=" N   GLN D  15 " --> pdb=" O   LYS B  16 " (cutoff:3.500A)
      removed outlier: 9.717A  pdb=" N   VAL B  18 " --> pdb=" O   GLN D  15 " (cutoff:3.500A)
      removed outlier: 9.003A  pdb=" N   LEU D  17 " --> pdb=" O   VAL B  18 " (cutoff:3.500A)
      removed outlier: 10.287A  pdb=" N   PHE B  20 " --> pdb=" O   LEU D  17 " (cutoff:3.500A)
      removed outlier: 8.945A  pdb=" N   PHE D  19 " --> pdb=" O   PHE B  20 " (cutoff:3.500A)
      removed outlier: 9.478A  pdb=" N   GLU B  22 " --> pdb=" O   PHE D  19 " (cutoff:3.500A)
      removed outlier: 5.713A  pdb=" N   ALA D  21 " --> pdb=" O   GLU B  22 " (cutoff:3.500A)
      removed outlier: 7.411A  pdb=" N   VAL B  24 " --> pdb=" O   ALA D  21 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ASP D  23 " --> pdb=" O   VAL B  24 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   GLN F  15 " --> pdb=" O   HIS D  14 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   LYS D  16 " --> pdb=" O   GLN F  15 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   LEU F  17 " --> pdb=" O   LYS D  16 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   VAL D  18 " --> pdb=" O   LEU F  17 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   PHE F  19 " --> pdb=" O   VAL D  18 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   PHE D  20 " --> pdb=" O   PHE F  19 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   ALA F  21 " --> pdb=" O   PHE D  20 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   GLU D  22 " --> pdb=" O   ALA F  21 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   GLN H  15 " --> pdb=" O   HIS F  14 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   LYS F  16 " --> pdb=" O   GLN H  15 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   LEU H  17 " --> pdb=" O   LYS F  16 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   VAL F  18 " --> pdb=" O   LEU H  17 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   PHE H  19 " --> pdb=" O   VAL F  18 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   PHE F  20 " --> pdb=" O   PHE H  19 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   ALA H  21 " --> pdb=" O   PHE F  20 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   GLU F  22 " --> pdb=" O   ALA H  21 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   VAL J  12 " --> pdb=" O   GLU H  11 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   HIS H  13 " --> pdb=" O   VAL J  12 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   HIS J  14 " --> pdb=" O   HIS H  13 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   ASP H  23 " --> pdb=" O   GLU J  22 " (cutoff:3.500A)
      removed outlier: 7.135A  pdb=" N   VAL J  24 " --> pdb=" O   ASP H  23 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 32
      removed outlier: 6.110A  pdb=" N   ILE D  31 " --> pdb=" O   ILE F  32 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   ILE F  31 " --> pdb=" O   ILE H  32 " (cutoff:3.500A)

    40 hydrogen bonds defined for protein.
    120 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: 0.33

  Time building geometry restraints manager: 0.26 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 515
        1.33 -     1.45: 518
        1.45 -     1.56: 1317
        1.56 -     1.68: 0
        1.68 -     1.80: 20
  Bond restraints: 2370
  Sorted by residual:
  bond pdb=" C   VAL H  12 "
       pdb=" O   VAL H  12 "
    ideal  model  delta    sigma   weight residual
    1.237  1.209  0.028 1.13e-02 7.83e+03 6.15e+00
  bond pdb=" C   VAL I  12 "
       pdb=" O   VAL I  12 "
    ideal  model  delta    sigma   weight residual
    1.237  1.209  0.028 1.13e-02 7.83e+03 6.13e+00
  bond pdb=" C   VAL C  12 "
       pdb=" O   VAL C  12 "
    ideal  model  delta    sigma   weight residual
    1.237  1.210  0.028 1.13e-02 7.83e+03 6.06e+00
  bond pdb=" C   VAL F  12 "
       pdb=" O   VAL F  12 "
    ideal  model  delta    sigma   weight residual
    1.237  1.210  0.028 1.13e-02 7.83e+03 5.96e+00
  bond pdb=" C   VAL D  12 "
       pdb=" O   VAL D  12 "
    ideal  model  delta    sigma   weight residual
    1.237  1.210  0.028 1.13e-02 7.83e+03 5.96e+00
  ... (remaining 2365 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 2961
        1.42 -     2.84: 184
        2.84 -     4.26: 15
        4.26 -     5.68: 0
        5.68 -     7.09: 20
  Bond angle restraints: 3180
  Sorted by residual:
  angle pdb=" C   HIS I  14 "
        pdb=" N   GLN I  15 "
        pdb=" CA  GLN I  15 "
      ideal   model   delta    sigma   weight residual
     122.95  130.04   -7.09 1.44e+00 4.82e-01 2.43e+01
  angle pdb=" C   HIS D  14 "
        pdb=" N   GLN D  15 "
        pdb=" CA  GLN D  15 "
      ideal   model   delta    sigma   weight residual
     122.95  130.04   -7.09 1.44e+00 4.82e-01 2.42e+01
  angle pdb=" C   HIS E  14 "
        pdb=" N   GLN E  15 "
        pdb=" CA  GLN E  15 "
      ideal   model   delta    sigma   weight residual
     122.95  130.02   -7.07 1.44e+00 4.82e-01 2.41e+01
  angle pdb=" C   HIS F  14 "
        pdb=" N   GLN F  15 "
        pdb=" CA  GLN F  15 "
      ideal   model   delta    sigma   weight residual
     122.95  130.02   -7.07 1.44e+00 4.82e-01 2.41e+01
  angle pdb=" C   HIS C  14 "
        pdb=" N   GLN C  15 "
        pdb=" CA  GLN C  15 "
      ideal   model   delta    sigma   weight residual
     122.95  130.02   -7.07 1.44e+00 4.82e-01 2.41e+01
  ... (remaining 3175 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.15: 1100
       10.15 -    20.30: 148
       20.30 -    30.46: 52
       30.46 -    40.61: 10
       40.61 -    50.76: 10
  Dihedral angle restraints: 1320
    sinusoidal: 490
      harmonic: 830
  Sorted by residual:
  dihedral pdb=" CA  ALA J  21 "
           pdb=" C   ALA J  21 "
           pdb=" N   GLU J  22 "
           pdb=" CA  GLU J  22 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.52  -15.48     0      5.00e+00 4.00e-02 9.58e+00
  dihedral pdb=" CA  ALA G  21 "
           pdb=" C   ALA G  21 "
           pdb=" N   GLU G  22 "
           pdb=" CA  GLU G  22 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.55  -15.45     0      5.00e+00 4.00e-02 9.55e+00
  dihedral pdb=" CA  ALA C  21 "
           pdb=" C   ALA C  21 "
           pdb=" N   GLU C  22 "
           pdb=" CA  GLU C  22 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.57  -15.43     0      5.00e+00 4.00e-02 9.52e+00
  ... (remaining 1317 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 223
       0.040 -    0.080: 57
       0.080 -    0.120: 40
       0.120 -    0.160: 20
       0.160 -    0.200: 20
  Chirality restraints: 360
  Sorted by residual:
  chirality pdb=" CA  VAL J  12 "
            pdb=" N   VAL J  12 "
            pdb=" C   VAL J  12 "
            pdb=" CB  VAL J  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 1.00e+00
  chirality pdb=" CA  VAL F  12 "
            pdb=" N   VAL F  12 "
            pdb=" C   VAL F  12 "
            pdb=" CB  VAL F  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 9.96e-01
  chirality pdb=" CA  VAL D  12 "
            pdb=" N   VAL D  12 "
            pdb=" C   VAL D  12 "
            pdb=" CB  VAL D  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 9.91e-01
  ... (remaining 357 not shown)

  Planarity restraints: 400
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU H  11 "    0.013 2.00e-02 2.50e+03   2.73e-02 7.46e+00
        pdb=" C   GLU H  11 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   GLU H  11 "    0.018 2.00e-02 2.50e+03
        pdb=" N   VAL H  12 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU J  11 "    0.013 2.00e-02 2.50e+03   2.73e-02 7.46e+00
        pdb=" C   GLU J  11 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   GLU J  11 "    0.018 2.00e-02 2.50e+03
        pdb=" N   VAL J  12 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B  11 "    0.013 2.00e-02 2.50e+03   2.73e-02 7.46e+00
        pdb=" C   GLU B  11 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   GLU B  11 "    0.018 2.00e-02 2.50e+03
        pdb=" N   VAL B  12 "    0.016 2.00e-02 2.50e+03
  ... (remaining 397 not shown)

  Histogram of nonbonded interaction distances:
        2.38 -     2.88: 772
        2.88 -     3.39: 1905
        3.39 -     3.89: 3892
        3.89 -     4.40: 4079
        4.40 -     4.90: 7896
  Nonbonded interactions: 18544
  Sorted by model distance:
  nonbonded pdb=" N   HIS H  14 "
            pdb=" O   HIS J  14 "
     model   vdw
     2.375 3.120
  nonbonded pdb=" OG  SER C  26 "
            pdb=" O   SER E  26 "
     model   vdw
     2.426 3.040
  nonbonded pdb=" O   TYR H  10 "
            pdb=" O   GLU J  11 "
     model   vdw
     2.443 3.040
  nonbonded pdb=" OG  SER D  26 "
            pdb=" O   SER F  26 "
     model   vdw
     2.473 3.040
  nonbonded pdb=" O   ASN A  27 "
            pdb=" N   LYS C  28 "
     model   vdw
     2.480 3.120
  ... (remaining 18539 not shown)

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

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:             2.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.610
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   2370  Z= 0.329
  Angle     :  0.869   7.094   3180  Z= 0.559
  Chirality :  0.072   0.200    360
  Planarity :  0.005   0.027    400
  Dihedral  : 11.692  50.761    800
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.19 (0.46), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.43 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR H  10 
 PHE   0.007   0.001   PHE C  20 
 HIS   0.004   0.002   HIS A  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00521 ( 2370)
  covalent geometry    : angle       0.86940 ( 3180)
  hydrogen bonds       : bond        0.19503 (   40)
  hydrogen bonds       : angle       8.76959 (  120)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.095 
Fit side-chains
REVERT: B   32 ILE cc_start: 0.8195 (mt) cc_final: 0.7841 (mm)
REVERT: G   10 TYR cc_start: 0.7448 (m-80) cc_final: 0.7195 (m-80)
REVERT: H   11 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7254 (mt-10)
REVERT: I   27 ASN cc_start: 0.5978 (t0) cc_final: 0.5684 (t0)
REVERT: J   32 ILE cc_start: 0.7882 (mt) cc_final: 0.7434 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.0395
  time to fit residues: 2.8023
Evaluate side-chains
  54 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    0.4980
   chunk 12 optimal weight:    3.9990
   chunk 24 optimal weight:    6.9990
   chunk 28 optimal weight:    8.9990
   chunk 13 optimal weight:   10.0000
   chunk 1 optimal weight:    7.9990
   chunk 8 optimal weight:    8.9990
   chunk 16 optimal weight:    9.9990
   chunk 15 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 25 optimal weight:   10.0000
   overall best weight:    4.4988

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

Flipped N/Q/H residues before XYZ refinement:
A  14 HIS
D  14 HIS
B  14 HIS
C  14 HIS
E  14 HIS
F  14 HIS
G  14 HIS
H  14 HIS
I  14 HIS
J  14 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.172012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.153825 restraints weight = 3393.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.158916 restraints weight = 1517.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.162964 restraints weight = 905.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.165158 restraints weight = 589.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.166620 restraints weight = 419.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.4187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.3751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.038   2370  Z= 0.286
  Angle     :  0.771   5.907   3180  Z= 0.420
  Chirality :  0.058   0.139    360
  Planarity :  0.003   0.013    400
  Dihedral  :  5.596  15.203    310
  Min Nonbonded Distance : 2.653

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 14.17 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.85 (0.37), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.93 (0.29), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR H  10 
 PHE   0.009   0.001   PHE J  20 
 HIS   0.005   0.002   HIS H  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00675 ( 2370)
  covalent geometry    : angle       0.77077 ( 3180)
  hydrogen bonds       : bond        0.05290 (   40)
  hydrogen bonds       : angle       7.17915 (  120)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 75
  time to evaluate  : 0.090 
Fit side-chains
REVERT: H   11 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7317 (mt-10)
  outliers start: 4
  outliers final: 2
  residues processed: 75
  average time/residue: 0.0371
  time to fit residues: 3.6208
Evaluate side-chains
  77 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 75
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 MET
Chi-restraints excluded: chain I residue   35 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   chunk 13 optimal weight:    8.9990
   chunk 6 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 1 optimal weight:    7.9990
   chunk 19 optimal weight:    1.9990
   chunk 8 optimal weight:    7.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** C  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.179207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.161665 restraints weight = 3372.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.166786 restraints weight = 1611.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.170347 restraints weight = 971.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.172465 restraints weight = 631.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.173988 restraints weight = 446.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.4261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.4122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   2370  Z= 0.160
  Angle     :  0.621   5.605   3180  Z= 0.340
  Chirality :  0.057   0.136    360
  Planarity :  0.002   0.010    400
  Dihedral  :  5.259  14.697    310
  Min Nonbonded Distance : 2.671

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 19.58 %
    Favored  : 77.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.40 (0.38), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.59 (0.29), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR A  10 
 PHE   0.005   0.001   PHE J  20 
 HIS   0.003   0.001   HIS F  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 2370)
  covalent geometry    : angle       0.62075 ( 3180)
  hydrogen bonds       : bond        0.04627 (   40)
  hydrogen bonds       : angle       7.37720 (  120)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.114 
Fit side-chains
REVERT: D   11 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7273 (mt-10)
REVERT: J   11 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7368 (mt-10)
REVERT: J   35 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.7153 (ptp)
  outliers start: 6
  outliers final: 2
  residues processed: 74
  average time/residue: 0.0380
  time to fit residues: 3.6630
Evaluate side-chains
  76 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 73
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain I residue   35 MET
Chi-restraints excluded: chain J residue   35 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 28 optimal weight:    7.9990
   chunk 9 optimal weight:    6.9990
   chunk 27 optimal weight:    5.9990
   chunk 26 optimal weight:    8.9990
   chunk 12 optimal weight:    0.7980
   chunk 5 optimal weight:    9.9990
   chunk 16 optimal weight:    6.9990
   chunk 14 optimal weight:    9.9990
   chunk 22 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   overall best weight:    3.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.178796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.161450 restraints weight = 3320.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.166439 restraints weight = 1472.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.169689 restraints weight = 844.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.172240 restraints weight = 559.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.173695 restraints weight = 388.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.4229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.4580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   2370  Z= 0.250
  Angle     :  0.713   5.201   3180  Z= 0.391
  Chirality :  0.058   0.160    360
  Planarity :  0.003   0.012    400
  Dihedral  :  5.624  14.707    310
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 14.17 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.53 (0.36), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.68 (0.27), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR C  10 
 PHE   0.006   0.001   PHE J  20 
 HIS   0.004   0.001   HIS H  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00591 ( 2370)
  covalent geometry    : angle       0.71335 ( 3180)
  hydrogen bonds       : bond        0.05130 (   40)
  hydrogen bonds       : angle       7.15285 (  120)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.100 
Fit side-chains
REVERT: D   15 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7589 (mt0)
REVERT: B   15 GLN cc_start: 0.8436 (mt0) cc_final: 0.8179 (mt0)
REVERT: G   10 TYR cc_start: 0.7674 (m-80) cc_final: 0.7411 (m-80)
REVERT: J   11 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7322 (mt-10)
REVERT: J   15 GLN cc_start: 0.8624 (mp10) cc_final: 0.8345 (mp10)
REVERT: J   35 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.6009 (tpt)
  outliers start: 16
  outliers final: 8
  residues processed: 80
  average time/residue: 0.0360
  time to fit residues: 3.7836
Evaluate side-chains
  84 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   15 GLN
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain G residue   12 VAL
Chi-restraints excluded: chain G residue   15 GLN
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain I residue   35 MET
Chi-restraints excluded: chain J residue   35 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 6 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 13 optimal weight:    9.9990
   chunk 11 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 21 optimal weight:    7.9990
   chunk 5 optimal weight:    1.9990
   chunk 20 optimal weight:   10.0000
   chunk 19 optimal weight:    0.4980
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** D  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  27 ASN
** H  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.188076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.171103 restraints weight = 3142.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.176254 restraints weight = 1442.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.179183 restraints weight = 832.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.181918 restraints weight = 567.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.183559 restraints weight = 383.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.4331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.4717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   2370  Z= 0.086
  Angle     :  0.549   5.694   3180  Z= 0.301
  Chirality :  0.056   0.138    360
  Planarity :  0.002   0.009    400
  Dihedral  :  5.060  13.567    310
  Min Nonbonded Distance : 2.679

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 18.75 %
    Favored  : 77.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.87 (0.40), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.18 (0.30), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR F  10 
 PHE   0.003   0.000   PHE J  19 
 HIS   0.003   0.001   HIS E  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00189 ( 2370)
  covalent geometry    : angle       0.54938 ( 3180)
  hydrogen bonds       : bond        0.03967 (   40)
  hydrogen bonds       : angle       7.31707 (  120)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.095 
Fit side-chains
REVERT: A   15 GLN cc_start: 0.7753 (mt0) cc_final: 0.5593 (tp40)
REVERT: B   15 GLN cc_start: 0.8162 (mt0) cc_final: 0.6102 (mm110)
REVERT: H   10 TYR cc_start: 0.7612 (m-80) cc_final: 0.7328 (m-80)
REVERT: J   11 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7057 (tt0)
REVERT: J   35 MET cc_start: 0.6819 (OUTLIER) cc_final: 0.4988 (tpt)
  outliers start: 10
  outliers final: 7
  residues processed: 73
  average time/residue: 0.0351
  time to fit residues: 3.4020
Evaluate side-chains
  78 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain C residue   27 ASN
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain I residue   15 GLN
Chi-restraints excluded: chain I residue   35 MET
Chi-restraints excluded: chain J residue   35 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 23 optimal weight:    9.9990
   chunk 26 optimal weight:    8.9990
   chunk 8 optimal weight:    9.9990
   chunk 9 optimal weight:    5.9990
   chunk 22 optimal weight:    8.9990
   chunk 28 optimal weight:    2.9990
   chunk 12 optimal weight:    6.9990
   chunk 11 optimal weight:    8.9990
   chunk 7 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 27 optimal weight:    0.2980
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
** D  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  27 ASN
** E  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 ASN
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  27 ASN
** I  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.182295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.165368 restraints weight = 3225.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.170122 restraints weight = 1454.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.173421 restraints weight = 835.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.175634 restraints weight = 546.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.177511 restraints weight = 390.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.4270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.4904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2370  Z= 0.155
  Angle     :  0.585   5.272   3180  Z= 0.322
  Chirality :  0.056   0.136    360
  Planarity :  0.002   0.011    400
  Dihedral  :  5.120  13.885    310
  Min Nonbonded Distance : 2.648

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 15.83 %
    Favored  : 78.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.89 (0.39), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.19 (0.30), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR F  10 
 PHE   0.003   0.001   PHE J  20 
 HIS   0.004   0.001   HIS G  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 2370)
  covalent geometry    : angle       0.58504 ( 3180)
  hydrogen bonds       : bond        0.04383 (   40)
  hydrogen bonds       : angle       7.03074 (  120)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.098 
Fit side-chains
REVERT: A   15 GLN cc_start: 0.8057 (mt0) cc_final: 0.5969 (tp-100)
REVERT: D   15 GLN cc_start: 0.8064 (mt0) cc_final: 0.7846 (mt0)
REVERT: G   13 HIS cc_start: 0.8697 (OUTLIER) cc_final: 0.7566 (p90)
  outliers start: 14
  outliers final: 8
  residues processed: 77
  average time/residue: 0.0374
  time to fit residues: 3.7671
Evaluate side-chains
  83 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain G residue   13 HIS
Chi-restraints excluded: chain G residue   15 GLN
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   35 MET
Chi-restraints excluded: chain I residue   15 GLN
Chi-restraints excluded: chain I residue   35 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 21 optimal weight:    6.9990
   chunk 10 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 29 optimal weight:    9.9990
   chunk 17 optimal weight:    4.9990
   chunk 7 optimal weight:    8.9990
   chunk 19 optimal weight:   10.0000
   chunk 14 optimal weight:    5.9990
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
** H  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.173154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.154956 restraints weight = 3252.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.159666 restraints weight = 1550.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.162807 restraints weight = 934.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.165039 restraints weight = 643.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.166829 restraints weight = 475.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.4205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.5253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   2370  Z= 0.265
  Angle     :  0.715   6.399   3180  Z= 0.390
  Chirality :  0.057   0.137    360
  Planarity :  0.003   0.013    400
  Dihedral  :  5.746  16.016    310
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  5.42 %
    Allowed  : 17.92 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.29 (0.38), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.50 (0.29), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR C  10 
 PHE   0.005   0.001   PHE J  20 
 HIS   0.005   0.001   HIS G  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00623 ( 2370)
  covalent geometry    : angle       0.71498 ( 3180)
  hydrogen bonds       : bond        0.05176 (   40)
  hydrogen bonds       : angle       7.07681 (  120)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.098 
Fit side-chains
REVERT: J   35 MET cc_start: 0.7929 (ppp) cc_final: 0.7107 (tpt)
  outliers start: 13
  outliers final: 9
  residues processed: 77
  average time/residue: 0.0347
  time to fit residues: 3.5363
Evaluate side-chains
  80 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain G residue   15 GLN
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   35 MET
Chi-restraints excluded: chain I residue   15 GLN
Chi-restraints excluded: chain I residue   35 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 26 optimal weight:    0.3980
   chunk 27 optimal weight:    3.9990
   chunk 17 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 3 optimal weight:    8.9990
   chunk 13 optimal weight:    8.9990
   chunk 21 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    1.8788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.173338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.156187 restraints weight = 3277.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.160887 restraints weight = 1575.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.164472 restraints weight = 945.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.166461 restraints weight = 615.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.167886 restraints weight = 434.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.4264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.5442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2370  Z= 0.145
  Angle     :  0.662   7.418   3180  Z= 0.344
  Chirality :  0.057   0.146    360
  Planarity :  0.002   0.009    400
  Dihedral  :  5.551  15.939    310
  Min Nonbonded Distance : 2.650

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 19.58 %
    Favored  : 76.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.08 (0.39), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.34 (0.30), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR F  10 
 PHE   0.003   0.001   PHE F  19 
 HIS   0.004   0.001   HIS F  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 2370)
  covalent geometry    : angle       0.66159 ( 3180)
  hydrogen bonds       : bond        0.04458 (   40)
  hydrogen bonds       : angle       7.21462 (  120)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.091 
Fit side-chains
REVERT: A   15 GLN cc_start: 0.8417 (mp10) cc_final: 0.5281 (tp40)
REVERT: G   13 HIS cc_start: 0.8706 (OUTLIER) cc_final: 0.7656 (p90)
REVERT: J   10 TYR cc_start: 0.7600 (m-80) cc_final: 0.5365 (p90)
  outliers start: 10
  outliers final: 9
  residues processed: 74
  average time/residue: 0.0360
  time to fit residues: 3.5101
Evaluate side-chains
  81 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain F residue   35 MET
Chi-restraints excluded: chain G residue   13 HIS
Chi-restraints excluded: chain G residue   15 GLN
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   35 MET
Chi-restraints excluded: chain I residue   15 GLN
Chi-restraints excluded: chain I residue   35 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 20 optimal weight:    5.9990
   chunk 15 optimal weight:    6.9990
   chunk 0 optimal weight:    6.9990
   chunk 14 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 23 optimal weight:    8.9990
   chunk 8 optimal weight:    7.9990
   chunk 24 optimal weight:    4.9990
   chunk 12 optimal weight:    9.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.174572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.157397 restraints weight = 3213.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.161974 restraints weight = 1439.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.164897 restraints weight = 821.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.167257 restraints weight = 546.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.168813 restraints weight = 383.400|
|-----------------------------------------------------------------------------|
r_work (final): 0.4200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.5617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.055   2370  Z= 0.338
  Angle     :  0.803   6.885   3180  Z= 0.429
  Chirality :  0.059   0.140    360
  Planarity :  0.003   0.016    400
  Dihedral  :  6.105  15.272    310
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 14.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 18.33 %
    Favored  : 77.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.44 (0.37), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.61 (0.29), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.011   0.002   TYR C  10 
 PHE   0.005   0.001   PHE J  20 
 HIS   0.006   0.002   HIS F  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00799 ( 2370)
  covalent geometry    : angle       0.80311 ( 3180)
  hydrogen bonds       : bond        0.05454 (   40)
  hydrogen bonds       : angle       7.05421 (  120)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.092 
Fit side-chains
REVERT: A   34 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7235 (tt)
REVERT: I   10 TYR cc_start: 0.7530 (m-80) cc_final: 0.5433 (p90)
REVERT: J   10 TYR cc_start: 0.7645 (m-80) cc_final: 0.5392 (p90)
REVERT: J   35 MET cc_start: 0.7970 (ttp) cc_final: 0.6225 (tpt)
  outliers start: 11
  outliers final: 10
  residues processed: 75
  average time/residue: 0.0328
  time to fit residues: 3.2623
Evaluate side-chains
  83 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain F residue   35 MET
Chi-restraints excluded: chain G residue   15 GLN
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   35 MET
Chi-restraints excluded: chain I residue   15 GLN
Chi-restraints excluded: chain I residue   35 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 16 optimal weight:    8.9990
   chunk 5 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 25 optimal weight:    7.9990
   chunk 14 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
C  15 GLN
** F  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.173322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.155257 restraints weight = 3388.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.159654 restraints weight = 1619.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.163206 restraints weight = 1009.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.165967 restraints weight = 675.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.167541 restraints weight = 470.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.4256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.5644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2370  Z= 0.135
  Angle     :  0.668   7.437   3180  Z= 0.349
  Chirality :  0.057   0.140    360
  Planarity :  0.002   0.009    400
  Dihedral  :  5.751  18.848    310
  Min Nonbonded Distance : 2.650

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 20.00 %
    Favored  : 75.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.21 (0.39), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.44 (0.30), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.001   TYR G  10 
 PHE   0.004   0.001   PHE J  19 
 HIS   0.004   0.001   HIS F  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 2370)
  covalent geometry    : angle       0.66780 ( 3180)
  hydrogen bonds       : bond        0.04553 (   40)
  hydrogen bonds       : angle       7.29827 (  120)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.089 
Fit side-chains
REVERT: A   34 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7360 (tt)
REVERT: F   13 HIS cc_start: 0.8300 (OUTLIER) cc_final: 0.7569 (p90)
REVERT: I   10 TYR cc_start: 0.7542 (m-80) cc_final: 0.5452 (p90)
REVERT: J   10 TYR cc_start: 0.7536 (m-80) cc_final: 0.5480 (p90)
REVERT: J   35 MET cc_start: 0.7710 (ttp) cc_final: 0.6028 (tpt)
  outliers start: 11
  outliers final: 9
  residues processed: 75
  average time/residue: 0.0344
  time to fit residues: 3.3611
Evaluate side-chains
  83 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain F residue   13 HIS
Chi-restraints excluded: chain F residue   35 MET
Chi-restraints excluded: chain G residue   15 GLN
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   35 MET
Chi-restraints excluded: chain I residue   15 GLN
Chi-restraints excluded: chain I residue   35 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 11 optimal weight:   10.0000
   chunk 19 optimal weight:    8.9990
   chunk 0 optimal weight:    7.9990
   chunk 12 optimal weight:    7.9990
   chunk 23 optimal weight:    0.0870
   chunk 24 optimal weight:   10.0000
   chunk 25 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 6 optimal weight:   10.0000
   chunk 8 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    2.4166

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

Flipped N/Q/H residues before XYZ refinement:
H  27 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.164643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.145492 restraints weight = 3451.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.150050 restraints weight = 1685.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.153380 restraints weight = 1020.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.155803 restraints weight = 693.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.157331 restraints weight = 499.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.4221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.5767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2370  Z= 0.169
  Angle     :  0.693   7.172   3180  Z= 0.364
  Chirality :  0.057   0.141    360
  Planarity :  0.002   0.009    400
  Dihedral  :  5.886  18.447    310
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.55 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 18.75 %
    Favored  : 76.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.16 (0.39), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.40 (0.30), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.008   0.002   TYR G  10 
 PHE   0.003   0.001   PHE J  20 
 HIS   0.004   0.001   HIS F  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 2370)
  covalent geometry    : angle       0.69264 ( 3180)
  hydrogen bonds       : bond        0.04786 (   40)
  hydrogen bonds       : angle       7.13373 (  120)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 630.66 seconds
wall clock time: 11 minutes 56.89 seconds (716.89 seconds total)