Starting phenix.real_space_refine
on Tue Mar  3 18:01:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9e01_47345/03_2026/9e01_47345.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9e01_47345/03_2026/9e01_47345.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9e01_47345/03_2026/9e01_47345.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9e01_47345/03_2026/9e01_47345.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9e01_47345/03_2026/9e01_47345.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9e01_47345/03_2026/9e01_47345.map"
  }
  resolution = 2.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.012
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      51      5.16       5
     C    5112      2.51       5
     N    1197      2.21       5
     O    1278      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7638
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "B"
      Number of atoms: 504
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 504
          Classifications: {'peptide': 64}
          Link IDs: {'PTRANS': 2, 'TRANS': 61}
    Chain: "A"
      Number of atoms: 1845
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 232, 1832
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 16, 'TRANS': 215}
      Conformer: "B"
        Number of residues, atoms: 232, 1832
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 16, 'TRANS': 215}
          bond proxies already assigned to first conformer: 1870
    Chain: "G"
      Number of atoms: 196
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 196
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "C"
      Number of atoms: 1845
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 232, 1832
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 16, 'TRANS': 215}
      Conformer: "B"
        Number of residues, atoms: 232, 1832
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 16, 'TRANS': 215}
          bond proxies already assigned to first conformer: 1870
    Chain: "E"
      Number of atoms: 1845
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 232, 1832
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 16, 'TRANS': 215}
      Conformer: "B"
        Number of residues, atoms: 232, 1832
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 16, 'TRANS': 215}
          bond proxies already assigned to first conformer: 1870
    Chain: "D"
      Number of atoms: 504
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 504
          Classifications: {'peptide': 64}
          Link IDs: {'PTRANS': 2, 'TRANS': 61}
    Chain: "F"
      Number of atoms: 504
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 504
          Classifications: {'peptide': 64}
          Link IDs: {'PTRANS': 2, 'TRANS': 61}
    Chain: "H"
      Number of atoms: 196
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 196
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "I"
      Number of atoms: 196
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 196
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "E"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 3.19, per 1000 atoms: 0.42
  Number of scatterers: 7638
  At special positions: 0
  Unit cell: (97.02, 101.178, 85.239, 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      51     16.00
     O    1278      8.00
     N    1197      7.00
     C    5112      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: 0.64
  Conformation dependent library (CDL) restraints added in 482.5 milliseconds
  

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1854

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 3 sheets defined
      88.0% alpha, 1.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'B' and resid 5 through 20
    Processing helix  chain 'B' and resid 24 through 64
    Processing helix  chain 'A' and resid 8 through 35
      removed outlier: 3.555A  pdb=" N   HIS A  12 " --> pdb=" O   PRO A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 53
      Proline residue:  A  48  - end of helix
      removed outlier: 3.587A  pdb=" N   GLN A  52 " --> pdb=" O   PRO A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 83
      Proline residue:  A  71  - end of helix
    Processing helix  chain 'A' and resid 83 through 96
    Processing helix  chain 'A' and resid 100 through 128
      removed outlier: 3.928A  pdb=" N   LEU A 106 " --> pdb=" O   HIS A 102 " (cutoff:3.500A)
      Proline residue:  A 109  - end of helix
      removed outlier: 3.583A  pdb=" N   LEU A 116 " --> pdb=" O   VAL A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 138
      removed outlier: 3.500A  pdb=" N   PHE A 136 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 182
      removed outlier: 3.739A  pdb=" N   GLU A 170 " --> pdb=" O   GLY A 166 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   VAL A 171 " --> pdb=" O   VAL A 167 " (cutoff:3.500A)
      Proline residue:  A 172  - end of helix
    Processing helix  chain 'A' and resid 185 through 192
    Processing helix  chain 'A' and resid 192 through 208
      removed outlier: 3.580A  pdb=" N   PHE A 201 " --> pdb=" O   LEU A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 235
      Proline residue:  A 221  - end of helix
      removed outlier: 4.001A  pdb=" N   PHE A 235 " --> pdb=" O   PHE A 231 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 2 through 27
      removed outlier: 8.231A  pdb=" N   ILE G  22 " --> pdb=" O   GLY G  18 " (cutoff:3.500A)
      removed outlier: 9.578A  pdb=" N   ALA G  23 " --> pdb=" O   THR G  19 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   SER G  24 " --> pdb=" O   SER G  20 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   LEU G  25 " --> pdb=" O   GLY G  21 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 8 through 36
      removed outlier: 3.561A  pdb=" N   HIS C  12 " --> pdb=" O   PRO C   8 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   TYR C  36 " --> pdb=" O   LEU C  32 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 37 through 53
      Proline residue:  C  48  - end of helix
      removed outlier: 3.591A  pdb=" N   GLN C  52 " --> pdb=" O   PRO C  48 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 65 through 83
      Proline residue:  C  71  - end of helix
    Processing helix  chain 'C' and resid 83 through 96
    Processing helix  chain 'C' and resid 100 through 128
      removed outlier: 3.983A  pdb=" N   LEU C 106 " --> pdb=" O   HIS C 102 " (cutoff:3.500A)
      Proline residue:  C 109  - end of helix
      removed outlier: 3.569A  pdb=" N   LEU C 116 " --> pdb=" O   VAL C 112 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   MET C 122 " --> pdb=" O   PHE C 118 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 128 through 138
    Processing helix  chain 'C' and resid 150 through 181
      removed outlier: 3.814A  pdb=" N   GLU C 170 " --> pdb=" O   GLY C 166 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   VAL C 171 " --> pdb=" O   VAL C 167 " (cutoff:3.500A)
      Proline residue:  C 172  - end of helix
    Processing helix  chain 'C' and resid 185 through 192
    Processing helix  chain 'C' and resid 192 through 208
      removed outlier: 3.540A  pdb=" N   PHE C 201 " --> pdb=" O   LEU C 197 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 211 through 235
      Proline residue:  C 221  - end of helix
      removed outlier: 3.525A  pdb=" N   ARG C 234 " --> pdb=" O   VAL C 230 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   PHE C 235 " --> pdb=" O   PHE C 231 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 8 through 35
      removed outlier: 3.541A  pdb=" N   HIS E  12 " --> pdb=" O   PRO E   8 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 37 through 53
      Proline residue:  E  48  - end of helix
      removed outlier: 3.573A  pdb=" N   GLN E  52 " --> pdb=" O   PRO E  48 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 65 through 83
      Proline residue:  E  71  - end of helix
    Processing helix  chain 'E' and resid 83 through 96
    Processing helix  chain 'E' and resid 100 through 128
      removed outlier: 4.017A  pdb=" N   LEU E 106 " --> pdb=" O   HIS E 102 " (cutoff:3.500A)
      Proline residue:  E 109  - end of helix
      removed outlier: 3.596A  pdb=" N   LEU E 116 " --> pdb=" O   VAL E 112 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 128 through 138
    Processing helix  chain 'E' and resid 150 through 182
      removed outlier: 3.695A  pdb=" N   GLU E 170 " --> pdb=" O   GLY E 166 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL E 171 " --> pdb=" O   VAL E 167 " (cutoff:3.500A)
      Proline residue:  E 172  - end of helix
    Processing helix  chain 'E' and resid 185 through 192
    Processing helix  chain 'E' and resid 192 through 208
      removed outlier: 3.577A  pdb=" N   PHE E 201 " --> pdb=" O   LEU E 197 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 211 through 235
      Proline residue:  E 221  - end of helix
      removed outlier: 3.992A  pdb=" N   PHE E 235 " --> pdb=" O   PHE E 231 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 5 through 20
    Processing helix  chain 'D' and resid 24 through 64
    Processing helix  chain 'F' and resid 5 through 20
    Processing helix  chain 'F' and resid 24 through 64
    Processing helix  chain 'H' and resid 2 through 21
    Processing helix  chain 'H' and resid 21 through 27
      removed outlier: 3.993A  pdb=" N   LEU H  25 " --> pdb=" O   GLY H  21 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 2 through 27
      removed outlier: 8.249A  pdb=" N   ILE I  22 " --> pdb=" O   GLY I  18 " (cutoff:3.500A)
      removed outlier: 9.625A  pdb=" N   ALA I  23 " --> pdb=" O   THR I  19 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   SER I  24 " --> pdb=" O   SER I  20 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LEU I  25 " --> pdb=" O   GLY I  21 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61
    Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 147
    Processing sheet with id=AA3, first strand: chain 'C' and resid 59 through 61
      removed outlier: 6.689A  pdb=" N   MET C  59 " --> pdb=" O   GLN E 146 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3

    614 hydrogen bonds defined for protein.
    1839 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.23

  Time building geometry restraints manager: 0.84 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2280
        1.34 -     1.46: 1686
        1.46 -     1.58: 3777
        1.58 -     1.69: 0
        1.69 -     1.81: 87
  Bond restraints: 7830
  Sorted by residual:
  bond pdb=" CA  VAL A 147 "
       pdb=" CB  VAL A 147 "
    ideal  model  delta    sigma   weight residual
    1.540  1.529  0.011 1.36e-02 5.41e+03 7.08e-01
  bond pdb=" CB  ASP H   2 "
       pdb=" CG  ASP H   2 "
    ideal  model  delta    sigma   weight residual
    1.516  1.537 -0.021 2.50e-02 1.60e+03 6.83e-01
  bond pdb=" CA  ILE C 220 "
       pdb=" CB  ILE C 220 "
    ideal  model  delta    sigma   weight residual
    1.534  1.539 -0.005 6.80e-03 2.16e+04 4.82e-01
  bond pdb=" CA  ILE C 220 "
       pdb=" C   ILE C 220 "
    ideal  model  delta    sigma   weight residual
    1.520  1.525 -0.006 8.80e-03 1.29e+04 4.30e-01
  bond pdb=" CG  PRO C  97 "
       pdb=" CD  PRO C  97 "
    ideal  model  delta    sigma   weight residual
    1.503  1.481  0.022 3.40e-02 8.65e+02 4.04e-01
  ... (remaining 7825 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.08: 10411
        1.08 -     2.15: 162
        2.15 -     3.23: 49
        3.23 -     4.31: 10
        4.31 -     5.38: 30
  Bond angle restraints: 10662
  Sorted by residual:
  angle pdb=" C   ASP H   2 "
        pdb=" CA  ASP H   2 "
        pdb=" CB  ASP H   2 "
      ideal   model   delta    sigma   weight residual
     110.45  113.85   -3.40 1.73e+00 3.34e-01 3.87e+00
  angle pdb=" CA  ASP H   2 "
        pdb=" CB  ASP H   2 "
        pdb=" CG  ASP H   2 "
      ideal   model   delta    sigma   weight residual
     112.60  114.15   -1.55 1.00e+00 1.00e+00 2.40e+00
  angle pdb=" CB  MET A 163 "
        pdb=" CG  MET A 163 "
        pdb=" SD  MET A 163 "
      ideal   model   delta    sigma   weight residual
     112.70  117.29   -4.59 3.00e+00 1.11e-01 2.34e+00
  angle pdb=" CB  ASP H   2 "
        pdb=" CG  ASP H   2 "
        pdb=" OD1 ASP H   2 "
      ideal   model   delta    sigma   weight residual
     118.40  121.89   -3.49 2.30e+00 1.89e-01 2.30e+00
  angle pdb=" N   LEU E 218 "
        pdb=" CA  LEU E 218 "
        pdb=" C   LEU E 218 "
      ideal   model   delta    sigma   weight residual
     113.41  111.56    1.85 1.22e+00 6.72e-01 2.29e+00
  ... (remaining 10657 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.58: 4072
       12.58 -    25.15: 373
       25.15 -    37.73: 129
       37.73 -    50.30: 52
       50.30 -    62.88: 18
  Dihedral angle restraints: 4644
    sinusoidal: 1788
      harmonic: 2856
  Sorted by residual:
  dihedral pdb=" CA  MET F   1 "
           pdb=" C   MET F   1 "
           pdb=" N   PHE F   2 "
           pdb=" CA  PHE F   2 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.74   16.26     0      5.00e+00 4.00e-02 1.06e+01
  dihedral pdb=" CB  ARG H   4 "
           pdb=" CG  ARG H   4 "
           pdb=" CD  ARG H   4 "
           pdb=" NE  ARG H   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.28   58.28     3      1.50e+01 4.44e-03 9.46e+00
  dihedral pdb=" CB  MET E 159 "
           pdb=" CG  MET E 159 "
           pdb=" SD  MET E 159 "
           pdb=" CE  MET E 159 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  122.61   57.39     3      1.50e+01 4.44e-03 9.44e+00
  ... (remaining 4641 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 745
       0.025 -    0.050: 316
       0.050 -    0.075: 160
       0.075 -    0.100: 58
       0.100 -    0.125: 11
  Chirality restraints: 1290
  Sorted by residual:
  chirality pdb=" CA  PRO C 221 "
            pdb=" N   PRO C 221 "
            pdb=" C   PRO C 221 "
            pdb=" CB  PRO C 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 3.92e-01
  chirality pdb=" CA  ILE F   4 "
            pdb=" N   ILE F   4 "
            pdb=" C   ILE F   4 "
            pdb=" CB  ILE F   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.56e-01
  chirality pdb=" CA  ILE D   4 "
            pdb=" N   ILE D   4 "
            pdb=" C   ILE D   4 "
            pdb=" CB  ILE D   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.11 2.00e-01 2.50e+01 3.08e-01
  ... (remaining 1287 not shown)

  Planarity restraints: 1299
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 220 "    0.024 5.00e-02 4.00e+02   3.60e-02 2.07e+00
        pdb=" N   PRO C 221 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO C 221 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO C 221 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C   7 "   -0.019 5.00e-02 4.00e+02   2.94e-02 1.38e+00
        pdb=" N   PRO C   8 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO C   8 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C   8 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A   7 "   -0.019 5.00e-02 4.00e+02   2.91e-02 1.35e+00
        pdb=" N   PRO A   8 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A   8 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A   8 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 1296 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1346
        2.76 -     3.29: 7611
        3.29 -     3.83: 12752
        3.83 -     4.36: 14899
        4.36 -     4.90: 25926
  Nonbonded interactions: 62534
  Sorted by model distance:
  nonbonded pdb=" O   PHE G   6 "
            pdb=" OG  SER G  10 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" O   GLY A 204 "
            pdb=" OG1 THR A 208 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" O   GLY E 204 "
            pdb=" OG1 THR E 208 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   PHE H   6 "
            pdb=" OG  SER H  10 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" OG1 THR A  62 "
            pdb=" OD2 ASP A 150 "
     model   vdw
     2.248 3.040
  ... (remaining 62529 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 'A' and (resid 5 through 6 or resid 8 through 42 or resid 44 through 236) \ 
)
  selection = (chain 'C' and (resid 5 through 6 or resid 8 through 42 or resid 44 through 236) \ 
)
  selection = (chain 'E' and (resid 5 through 6 or resid 8 through 42 or resid 44 through 236) \ 
)
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
}

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=0.37 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             13.010
  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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.570
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
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      :  0.002   0.030   7830  Z= 0.098
  Angle     :  0.460   5.382  10662  Z= 0.218
  Chirality :  0.037   0.125   1290
  Planarity :  0.004   0.036   1299
  Dihedral  : 12.604  62.876   2790
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 12.10 %
    Favored  : 86.83 %
  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 are not related in a simple way.
  whole:  1.95 (0.27), residues: 957
  helix:  1.51 (0.19), residues: 777
  sheet:  None (None), residues: 0
  loop :  0.62 (0.46), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG I   5 
 TYR   0.018   0.001   TYR A  42 
 PHE   0.014   0.001   PHE E 118 
 TRP   0.006   0.001   TRP E 180 
 HIS   0.002   0.001   HIS A 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 7830)
  covalent geometry    : angle       0.45987 (10662)
  hydrogen bonds       : bond        0.20529 (  614)
  hydrogen bonds       : angle       6.58213 ( 1839)

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

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

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 118
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A  169 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7185 (t80)
REVERT: C  178 LEU cc_start: 0.8353 (mt) cc_final: 0.8128 (mp)
REVERT: C  222 MET cc_start: 0.6145 (mtm) cc_final: 0.5869 (mtm)
REVERT: I   13 MET cc_start: 0.8339 (mtt) cc_final: 0.8134 (mtm)
  outliers start: 9
  outliers final: 7
  residues processed: 124
  average time/residue: 0.4691
  time to fit residues: 62.0646
Evaluate side-chains
  125 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 117
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  169 PHE
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue   64 VAL
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue  158 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.3980
   chunk 65 optimal weight:    0.0970
   chunk 62 optimal weight:    0.0170
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    0.4980
   chunk 45 optimal weight:    0.0970
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.2214

-------------------------------------------------------------------------------
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 = 0.4030 r_free = 0.4030 target = 0.163132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.134699 restraints weight = 22762.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 2.83
r_work: 0.3479 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3477
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3477 r_free = 0.3477    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3477 r_free = 0.3477    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3477
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.1099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7830  Z= 0.145
  Angle     :  0.535   5.564  10662  Z= 0.268
  Chirality :  0.039   0.114   1290
  Planarity :  0.005   0.032   1299
  Dihedral  :  4.712  54.055   1052
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 10.79 %
    Favored  : 87.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.14 (0.28), residues: 957
  helix:  2.31 (0.18), residues: 813
  sheet:  None (None), residues: 0
  loop :  0.83 (0.54), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG I   5 
 TYR   0.022   0.001   TYR A  42 
 PHE   0.018   0.001   PHE E 232 
 TRP   0.005   0.001   TRP E  92 
 HIS   0.001   0.000   HIS A 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 7830)
  covalent geometry    : angle       0.53471 (10662)
  hydrogen bonds       : bond        0.05242 (  614)
  hydrogen bonds       : angle       4.16266 ( 1839)

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

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

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A   15 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6657 (tm-30)
REVERT: C  159 MET cc_start: 0.8381 (mmt) cc_final: 0.8147 (mmt)
REVERT: C  178 LEU cc_start: 0.8135 (mt) cc_final: 0.7880 (mp)
REVERT: C  222 MET cc_start: 0.5897 (mtm) cc_final: 0.5639 (mtm)
REVERT: E   15 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6658 (tm-30)
REVERT: E  146 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7996 (tt0)
REVERT: I   13 MET cc_start: 0.7687 (mtt) cc_final: 0.7476 (mtm)
  outliers start: 17
  outliers final: 5
  residues processed: 130
  average time/residue: 0.4351
  time to fit residues: 60.5207
Evaluate side-chains
  125 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 117
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue   51 LYS
Chi-restraints excluded: chain E residue   15 GLU
Chi-restraints excluded: chain E residue  146 GLN
Chi-restraints excluded: chain E residue  181 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 92 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 78 optimal weight:    0.8980
   chunk 47 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0770
   chunk 39 optimal weight:    0.0970
   chunk 84 optimal weight:    0.7980
   chunk 43 optimal weight:    0.1980
   overall best weight:    0.3536

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

Flipped N/Q/H residues before XYZ refinement:
E  52 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.162089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.134024 restraints weight = 26797.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 3.41
r_work: 0.3456 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3460
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3460 r_free = 0.3460    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3460 r_free = 0.3460    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3460
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.1407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7830  Z= 0.162
  Angle     :  0.533   6.207  10662  Z= 0.262
  Chirality :  0.040   0.119   1290
  Planarity :  0.004   0.031   1299
  Dihedral  :  4.249  56.947   1045
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 11.15 %
    Favored  : 86.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.08 (0.27), residues: 957
  helix:  2.26 (0.18), residues: 810
  sheet:  None (None), residues: 0
  loop :  0.90 (0.53), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG I   5 
 TYR   0.026   0.001   TYR A  42 
 PHE   0.015   0.001   PHE C 124 
 TRP   0.007   0.001   TRP E  92 
 HIS   0.002   0.001   HIS A 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 7830)
  covalent geometry    : angle       0.53283 (10662)
  hydrogen bonds       : bond        0.04733 (  614)
  hydrogen bonds       : angle       3.95486 ( 1839)

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

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

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 122
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A   15 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6640 (tm-30)
REVERT: C  122 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7676 (mtt)
REVERT: C  146 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8026 (tt0)
REVERT: C  178 LEU cc_start: 0.8161 (mt) cc_final: 0.7903 (mp)
REVERT: C  222 MET cc_start: 0.5997 (mtm) cc_final: 0.5795 (mtm)
REVERT: C  231 PHE cc_start: 0.8254 (t80) cc_final: 0.8046 (t80)
REVERT: E   15 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6686 (tm-30)
REVERT: E  122 MET cc_start: 0.8159 (mmm) cc_final: 0.7878 (mtp)
REVERT: E  146 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8017 (tt0)
REVERT: E  178 LEU cc_start: 0.7681 (mt) cc_final: 0.7404 (mp)
REVERT: I   13 MET cc_start: 0.7695 (mtt) cc_final: 0.7480 (mtm)
  outliers start: 18
  outliers final: 8
  residues processed: 127
  average time/residue: 0.4516
  time to fit residues: 61.2458
Evaluate side-chains
  135 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue   51 LYS
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  146 GLN
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain E residue   15 GLU
Chi-restraints excluded: chain E residue  146 GLN
Chi-restraints excluded: chain E residue  158 VAL
Chi-restraints excluded: chain E residue  181 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9980
   chunk 72 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 77 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 91 optimal weight:    0.2980
   chunk 50 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0980
   chunk 29 optimal weight:    0.1980
   overall best weight:    0.3580

-------------------------------------------------------------------------------
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 = 0.4016 r_free = 0.4016 target = 0.162118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.133579 restraints weight = 27055.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3651 rms_B_bonded: 3.40
r_work: 0.3454 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3457
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3457 r_free = 0.3457    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3457 r_free = 0.3457    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3457
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.1542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7830  Z= 0.159
  Angle     :  0.524   6.256  10662  Z= 0.257
  Chirality :  0.040   0.116   1290
  Planarity :  0.004   0.031   1299
  Dihedral  :  4.284  59.462   1045
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 11.15 %
    Favored  : 86.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.10 (0.27), residues: 957
  helix:  2.28 (0.18), residues: 810
  sheet:  None (None), residues: 0
  loop :  0.89 (0.52), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG I   5 
 TYR   0.028   0.002   TYR A  42 
 PHE   0.019   0.001   PHE A 232 
 TRP   0.007   0.001   TRP E  92 
 HIS   0.002   0.001   HIS A 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 7830)
  covalent geometry    : angle       0.52429 (10662)
  hydrogen bonds       : bond        0.04395 (  614)
  hydrogen bonds       : angle       3.84989 ( 1839)

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

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

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.296 
Fit side-chains
REVERT: A   15 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6626 (tm-30)
REVERT: C  122 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7728 (mtt)
REVERT: C  146 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8019 (tt0)
REVERT: C  178 LEU cc_start: 0.8164 (mt) cc_final: 0.7907 (mp)
REVERT: E   15 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6678 (tm-30)
REVERT: E  146 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8020 (tt0)
REVERT: E  178 LEU cc_start: 0.7749 (mt) cc_final: 0.7487 (mp)
REVERT: F    1 MET cc_start: 0.3803 (mpp) cc_final: 0.3326 (mpp)
  outliers start: 19
  outliers final: 8
  residues processed: 128
  average time/residue: 0.4461
  time to fit residues: 61.2913
Evaluate side-chains
  134 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue   51 LYS
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  146 GLN
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain E residue   15 GLU
Chi-restraints excluded: chain E residue  146 GLN
Chi-restraints excluded: chain E residue  158 VAL
Chi-restraints excluded: chain E residue  181 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 88 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9980
   chunk 92 optimal weight:    0.8980
   chunk 77 optimal weight:    0.5980
   chunk 52 optimal weight:    0.7980
   chunk 12 optimal weight:    0.3980
   chunk 0 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0770
   chunk 90 optimal weight:    0.5980
   chunk 83 optimal weight:    4.9990
   chunk 20 optimal weight:    0.0870
   overall best weight:    0.3516

-------------------------------------------------------------------------------
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 = 0.4015 r_free = 0.4015 target = 0.162047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.133647 restraints weight = 26574.976|
|-----------------------------------------------------------------------------|
r_work (start): 0.3653 rms_B_bonded: 3.38
r_work: 0.3460 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3462
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3462 r_free = 0.3462    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3462 r_free = 0.3462    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3462
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.1610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7830  Z= 0.158
  Angle     :  0.523   6.368  10662  Z= 0.257
  Chirality :  0.039   0.114   1290
  Planarity :  0.004   0.031   1299
  Dihedral  :  4.276  58.455   1045
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 10.91 %
    Favored  : 86.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.12 (0.27), residues: 957
  helix:  2.29 (0.18), residues: 810
  sheet:  None (None), residues: 0
  loop :  0.90 (0.53), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H   5 
 TYR   0.029   0.002   TYR A  42 
 PHE   0.016   0.001   PHE C 232 
 TRP   0.008   0.001   TRP E  92 
 HIS   0.002   0.001   HIS A 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 7830)
  covalent geometry    : angle       0.52349 (10662)
  hydrogen bonds       : bond        0.04310 (  614)
  hydrogen bonds       : angle       3.80062 ( 1839)

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

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

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 122
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A   15 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6593 (tm-30)
REVERT: A  146 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.8036 (tt0)
REVERT: C  122 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7752 (mtt)
REVERT: C  146 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8047 (tt0)
REVERT: C  178 LEU cc_start: 0.8168 (mt) cc_final: 0.7913 (mp)
REVERT: E   15 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6667 (tm-30)
REVERT: E  146 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8001 (tt0)
REVERT: E  178 LEU cc_start: 0.7805 (mt) cc_final: 0.7533 (mp)
REVERT: E  220 ILE cc_start: 0.6673 (OUTLIER) cc_final: 0.6400 (tp)
REVERT: F    1 MET cc_start: 0.3754 (mpp) cc_final: 0.3315 (mpp)
REVERT: I   13 MET cc_start: 0.7761 (mtt) cc_final: 0.7517 (mtm)
  outliers start: 22
  outliers final: 10
  residues processed: 130
  average time/residue: 0.4710
  time to fit residues: 65.2625
Evaluate side-chains
  137 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  146 GLN
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue   51 LYS
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  146 GLN
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain E residue   15 GLU
Chi-restraints excluded: chain E residue   51 LYS
Chi-restraints excluded: chain E residue  146 GLN
Chi-restraints excluded: chain E residue  158 VAL
Chi-restraints excluded: chain E residue  181 MET
Chi-restraints excluded: chain E residue  220 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 79 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 50 optimal weight:    0.5980
   chunk 56 optimal weight:    0.3980
   chunk 33 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 42 optimal weight:    0.2980
   chunk 27 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 62 optimal weight:    0.2980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.4008 r_free = 0.4008 target = 0.161320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.133060 restraints weight = 21098.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.3653 rms_B_bonded: 2.73
r_work: 0.3456 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3454
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3454 r_free = 0.3454    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3454 r_free = 0.3454    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3454
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.1637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   7830  Z= 0.193
  Angle     :  0.549   6.674  10662  Z= 0.271
  Chirality :  0.041   0.121   1290
  Planarity :  0.004   0.031   1299
  Dihedral  :  4.340  58.095   1045
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 11.03 %
    Favored  : 86.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.95 (0.27), residues: 957
  helix:  2.17 (0.18), residues: 810
  sheet:  None (None), residues: 0
  loop :  0.87 (0.52), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H   5 
 TYR   0.031   0.002   TYR A  42 
 PHE   0.017   0.001   PHE A 232 
 TRP   0.009   0.001   TRP E  92 
 HIS   0.003   0.001   HIS A 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 ( 7830)
  covalent geometry    : angle       0.54854 (10662)
  hydrogen bonds       : bond        0.04488 (  614)
  hydrogen bonds       : angle       3.83532 ( 1839)

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

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

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.277 
Fit side-chains
REVERT: A   15 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6578 (tm-30)
REVERT: A  146 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.8045 (tt0)
REVERT: C  122 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7789 (mtt)
REVERT: C  146 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8045 (tt0)
REVERT: C  178 LEU cc_start: 0.8224 (mt) cc_final: 0.7971 (mp)
REVERT: C  236 TYR cc_start: 0.6105 (OUTLIER) cc_final: 0.5685 (t80)
REVERT: E   15 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6629 (tm-30)
REVERT: E  146 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7978 (tt0)
REVERT: E  178 LEU cc_start: 0.7824 (mt) cc_final: 0.7564 (mp)
REVERT: E  220 ILE cc_start: 0.6745 (OUTLIER) cc_final: 0.6463 (tp)
REVERT: F    1 MET cc_start: 0.3657 (mpp) cc_final: 0.3257 (mpp)
  outliers start: 23
  outliers final: 12
  residues processed: 128
  average time/residue: 0.4496
  time to fit residues: 61.5378
Evaluate side-chains
  138 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 118
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  146 GLN
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue   51 LYS
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  146 GLN
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain E residue   15 GLU
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue  146 GLN
Chi-restraints excluded: chain E residue  158 VAL
Chi-restraints excluded: chain E residue  181 MET
Chi-restraints excluded: chain E residue  220 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 42 optimal weight:    0.3980
   chunk 83 optimal weight:    0.8980
   chunk 61 optimal weight:    0.6980
   chunk 68 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 70 optimal weight:    0.1980
   chunk 60 optimal weight:    0.1980
   chunk 6 optimal weight:    0.9980
   chunk 39 optimal weight:    0.2980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.3580

-------------------------------------------------------------------------------
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 = 0.4013 r_free = 0.4013 target = 0.161748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.133687 restraints weight = 25733.589|
|-----------------------------------------------------------------------------|
r_work (start): 0.3660 rms_B_bonded: 3.07
r_work: 0.3455 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3454
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3454 r_free = 0.3454    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3454 r_free = 0.3454    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3454
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7830  Z= 0.159
  Angle     :  0.527   6.358  10662  Z= 0.260
  Chirality :  0.040   0.140   1290
  Planarity :  0.004   0.032   1299
  Dihedral  :  4.269  56.349   1045
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 11.15 %
    Favored  : 85.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.06 (0.27), residues: 957
  helix:  2.24 (0.18), residues: 810
  sheet:  None (None), residues: 0
  loop :  0.92 (0.53), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H   5 
 TYR   0.031   0.002   TYR A  42 
 PHE   0.011   0.001   PHE E 232 
 TRP   0.008   0.001   TRP E  92 
 HIS   0.002   0.001   HIS C 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 7830)
  covalent geometry    : angle       0.52748 (10662)
  hydrogen bonds       : bond        0.04261 (  614)
  hydrogen bonds       : angle       3.77695 ( 1839)

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

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

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A   15 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6605 (tm-30)
REVERT: A  146 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.8042 (tt0)
REVERT: A  236 TYR cc_start: 0.5975 (OUTLIER) cc_final: 0.5646 (t80)
REVERT: C  122 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7798 (mtt)
REVERT: C  146 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8048 (tt0)
REVERT: C  178 LEU cc_start: 0.8219 (mt) cc_final: 0.7963 (mp)
REVERT: C  236 TYR cc_start: 0.6149 (OUTLIER) cc_final: 0.5708 (t80)
REVERT: E   15 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6675 (tm-30)
REVERT: E  146 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7986 (tt0)
REVERT: E  178 LEU cc_start: 0.7844 (mt) cc_final: 0.7577 (mp)
REVERT: E  220 ILE cc_start: 0.6749 (OUTLIER) cc_final: 0.6479 (tp)
REVERT: F    1 MET cc_start: 0.3452 (mpp) cc_final: 0.3134 (mpp)
  outliers start: 25
  outliers final: 12
  residues processed: 134
  average time/residue: 0.4323
  time to fit residues: 62.0302
Evaluate side-chains
  140 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  146 GLN
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue   51 LYS
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  146 GLN
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain E residue   15 GLU
Chi-restraints excluded: chain E residue   51 LYS
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue  146 GLN
Chi-restraints excluded: chain E residue  158 VAL
Chi-restraints excluded: chain E residue  181 MET
Chi-restraints excluded: chain E residue  220 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 70 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 91 optimal weight:    0.1980
   chunk 58 optimal weight:    0.0770
   chunk 22 optimal weight:    0.5980
   chunk 35 optimal weight:    0.7980
   chunk 73 optimal weight:    0.5980
   chunk 20 optimal weight:    0.1980
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.3338

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
E 139 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.161913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.134024 restraints weight = 24417.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 2.96
r_work: 0.3461 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3460
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3460 r_free = 0.3460    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3460 r_free = 0.3460    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3460
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.1736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7830  Z= 0.154
  Angle     :  0.527   6.412  10662  Z= 0.260
  Chirality :  0.039   0.137   1290
  Planarity :  0.004   0.034   1299
  Dihedral  :  4.219  54.164   1045
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 11.74 %
    Favored  : 85.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.10 (0.27), residues: 957
  helix:  2.27 (0.18), residues: 810
  sheet:  None (None), residues: 0
  loop :  0.93 (0.53), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H   5 
 TYR   0.030   0.002   TYR A  42 
 PHE   0.021   0.001   PHE C 232 
 TRP   0.008   0.001   TRP E  92 
 HIS   0.002   0.001   HIS A 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 7830)
  covalent geometry    : angle       0.52700 (10662)
  hydrogen bonds       : bond        0.04200 (  614)
  hydrogen bonds       : angle       3.75035 ( 1839)

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

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

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 117
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A   15 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6602 (tm-30)
REVERT: A  146 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.8033 (tt0)
REVERT: A  236 TYR cc_start: 0.5971 (OUTLIER) cc_final: 0.5619 (t80)
REVERT: C  122 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7808 (mtt)
REVERT: C  146 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8057 (tt0)
REVERT: C  178 LEU cc_start: 0.8219 (mt) cc_final: 0.7964 (mp)
REVERT: C  236 TYR cc_start: 0.6131 (OUTLIER) cc_final: 0.5692 (t80)
REVERT: E   15 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6615 (tm-30)
REVERT: E  146 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7989 (tt0)
REVERT: E  220 ILE cc_start: 0.6767 (OUTLIER) cc_final: 0.6502 (tp)
REVERT: E  236 TYR cc_start: 0.5796 (OUTLIER) cc_final: 0.5565 (t80)
  outliers start: 23
  outliers final: 11
  residues processed: 129
  average time/residue: 0.4557
  time to fit residues: 63.1829
Evaluate side-chains
  138 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  146 GLN
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue   51 LYS
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  146 GLN
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain E residue   15 GLU
Chi-restraints excluded: chain E residue   51 LYS
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue  146 GLN
Chi-restraints excluded: chain E residue  158 VAL
Chi-restraints excluded: chain E residue  181 MET
Chi-restraints excluded: chain E residue  220 ILE
Chi-restraints excluded: chain E residue  236 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0980
   chunk 74 optimal weight:    2.9990
   chunk 67 optimal weight:    0.0060
   chunk 8 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 39 optimal weight:    0.2980
   chunk 68 optimal weight:    0.6980
   chunk 84 optimal weight:    0.8980
   chunk 65 optimal weight:    0.2980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.2596

-------------------------------------------------------------------------------
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 = 0.4021 r_free = 0.4021 target = 0.162468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.133770 restraints weight = 27614.736|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 3.59
r_work: 0.3456 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3454
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3454 r_free = 0.3454    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3454 r_free = 0.3454    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3454
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.1794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7830  Z= 0.137
  Angle     :  0.520   6.500  10662  Z= 0.257
  Chirality :  0.039   0.147   1290
  Planarity :  0.004   0.035   1299
  Dihedral  :  4.149  51.842   1045
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 11.98 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.23 (0.27), residues: 957
  helix:  2.36 (0.18), residues: 810
  sheet:  None (None), residues: 0
  loop :  0.98 (0.53), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG I   5 
 TYR   0.029   0.001   TYR A  42 
 PHE   0.016   0.001   PHE A 231 
 TRP   0.008   0.001   TRP E  92 
 HIS   0.002   0.001   HIS C 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 7830)
  covalent geometry    : angle       0.52033 (10662)
  hydrogen bonds       : bond        0.04069 (  614)
  hydrogen bonds       : angle       3.71653 ( 1839)

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

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

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 121
  time to evaluate  : 0.174 
Fit side-chains
REVERT: A   15 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6646 (tm-30)
REVERT: A  146 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.8043 (tt0)
REVERT: A  236 TYR cc_start: 0.5952 (OUTLIER) cc_final: 0.5597 (t80)
REVERT: C  122 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7824 (mtt)
REVERT: C  146 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8049 (tt0)
REVERT: C  178 LEU cc_start: 0.8181 (mt) cc_final: 0.7906 (mp)
REVERT: C  236 TYR cc_start: 0.6115 (OUTLIER) cc_final: 0.5679 (t80)
REVERT: E   15 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6718 (tm-30)
REVERT: E  146 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7996 (tt0)
REVERT: E  220 ILE cc_start: 0.6633 (OUTLIER) cc_final: 0.6396 (tp)
REVERT: E  236 TYR cc_start: 0.5782 (OUTLIER) cc_final: 0.5536 (t80)
  outliers start: 23
  outliers final: 10
  residues processed: 133
  average time/residue: 0.4435
  time to fit residues: 63.1644
Evaluate side-chains
  141 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  146 GLN
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain C residue   51 LYS
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  146 GLN
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain E residue    6 THR
Chi-restraints excluded: chain E residue   15 GLU
Chi-restraints excluded: chain E residue   51 LYS
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue  146 GLN
Chi-restraints excluded: chain E residue  158 VAL
Chi-restraints excluded: chain E residue  181 MET
Chi-restraints excluded: chain E residue  220 ILE
Chi-restraints excluded: chain E residue  236 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 43 optimal weight:    0.0980
   chunk 47 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   chunk 83 optimal weight:    0.0980
   chunk 9 optimal weight:    0.1980
   chunk 67 optimal weight:    0.0050
   chunk 64 optimal weight:    0.6980
   chunk 48 optimal weight:    0.5980
   chunk 46 optimal weight:    0.4980
   chunk 80 optimal weight:    0.9990
   overall best weight:    0.1794

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

Flipped N/Q/H residues before XYZ refinement:
E 139 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.163063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.134884 restraints weight = 30318.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 4.05
r_work: 0.3459 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3456
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3456 r_free = 0.3456    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3456 r_free = 0.3456    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3456
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.1864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7830  Z= 0.120
  Angle     :  0.505   5.917  10662  Z= 0.249
  Chirality :  0.038   0.151   1290
  Planarity :  0.004   0.038   1299
  Dihedral  :  3.756  50.876   1043
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 12.34 %
    Favored  : 85.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.43 (0.27), residues: 957
  helix:  2.50 (0.18), residues: 810
  sheet:  None (None), residues: 0
  loop :  1.05 (0.53), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG I   5 
 TYR   0.026   0.001   TYR A  42 
 PHE   0.021   0.001   PHE C 232 
 TRP   0.008   0.001   TRP E  92 
 HIS   0.001   0.001   HIS C 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 7830)
  covalent geometry    : angle       0.50483 (10662)
  hydrogen bonds       : bond        0.03857 (  614)
  hydrogen bonds       : angle       3.66247 ( 1839)

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

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

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 121
  time to evaluate  : 0.212 
Fit side-chains
REVERT: A   15 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6690 (tm-30)
REVERT: A  146 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.8067 (tt0)
REVERT: A  236 TYR cc_start: 0.5942 (OUTLIER) cc_final: 0.5616 (t80)
REVERT: C  122 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7794 (mtt)
REVERT: C  146 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7970 (tt0)
REVERT: C  178 LEU cc_start: 0.8185 (mt) cc_final: 0.7922 (mp)
REVERT: C  236 TYR cc_start: 0.6099 (OUTLIER) cc_final: 0.5703 (t80)
REVERT: E   15 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6675 (tm-30)
REVERT: E  220 ILE cc_start: 0.6677 (OUTLIER) cc_final: 0.6463 (tp)
REVERT: E  236 TYR cc_start: 0.5758 (OUTLIER) cc_final: 0.5534 (t80)
  outliers start: 22
  outliers final: 10
  residues processed: 134
  average time/residue: 0.4425
  time to fit residues: 63.3466
Evaluate side-chains
  139 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  146 GLN
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain C residue   51 LYS
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue   64 VAL
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  146 GLN
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain E residue    6 THR
Chi-restraints excluded: chain E residue   15 GLU
Chi-restraints excluded: chain E residue   51 LYS
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue  158 VAL
Chi-restraints excluded: chain E residue  220 ILE
Chi-restraints excluded: chain E residue  236 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 75 optimal weight:    0.7980
   chunk 2 optimal weight:    0.2980
   chunk 23 optimal weight:    0.5980
   chunk 87 optimal weight:    0.6980
   chunk 28 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 39 optimal weight:    0.0970
   chunk 34 optimal weight:    0.1980
   chunk 18 optimal weight:    0.0980
   chunk 31 optimal weight:    0.0570
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.1496

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

Flipped N/Q/H residues before XYZ refinement:
C 139 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.163871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.135160 restraints weight = 28264.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 3.72
r_work: 0.3465 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3463
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3463 r_free = 0.3463    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3463 r_free = 0.3463    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3463
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.1910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7830  Z= 0.116
  Angle     :  0.503   5.868  10662  Z= 0.248
  Chirality :  0.038   0.147   1290
  Planarity :  0.004   0.038   1299
  Dihedral  :  3.728  50.357   1043
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 12.69 %
    Favored  : 85.17 %
  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 are not related in a simple way.
  whole:  3.58 (0.27), residues: 957
  helix:  2.59 (0.18), residues: 813
  sheet:  None (None), residues: 0
  loop :  1.06 (0.55), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H   5 
 TYR   0.025   0.001   TYR A  42 
 PHE   0.015   0.001   PHE A 231 
 TRP   0.008   0.001   TRP E  92 
 HIS   0.001   0.001   HIS E 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7830)
  covalent geometry    : angle       0.50263 (10662)
  hydrogen bonds       : bond        0.03792 (  614)
  hydrogen bonds       : angle       3.63262 ( 1839)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3291.94 seconds
wall clock time: 56 minutes 38.35 seconds (3398.35 seconds total)