Starting phenix.real_space_refine
on Tue Mar  3 17:37:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qsz_53345/03_2026/9qsz_53345.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qsz_53345/03_2026/9qsz_53345.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qsz_53345/03_2026/9qsz_53345.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qsz_53345/03_2026/9qsz_53345.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qsz_53345/03_2026/9qsz_53345.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qsz_53345/03_2026/9qsz_53345.cif"
  }
  resolution = 3.0
  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=   0.002 sd=   0.065
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    4984      2.51       5
     N    1228      2.21       5
     O    1316      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 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: 7568
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1881
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 250, 1881
          Classifications: {'peptide': 250}
          Link IDs: {'PTRANS': 12, 'TRANS': 237}
    Chain: "A"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 8
          Unusual residues: {'PEO': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "D"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 1.29, per 1000 atoms: 0.17
  Number of scatterers: 7568
  At special positions: 0
  Unit cell: (80.51, 80.51, 67.23, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      40     16.00
     O    1316      8.00
     N    1228      7.00
     C    4984      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: 0.81
  Conformation dependent library (CDL) restraints added in 304.9 milliseconds
  

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1744

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 0 sheets defined
      76.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 49
      removed outlier: 3.725A  pdb=" N   SER A  42 " --> pdb=" O   PHE A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 79
      removed outlier: 3.514A  pdb=" N   ILE A  59 " --> pdb=" O   GLY A  55 " (cutoff:3.500A)
      removed outlier: 5.672A  pdb=" N   GLN A  76 " --> pdb=" O   LEU A  72 " (cutoff:3.500A)
      removed outlier: 5.566A  pdb=" N   VAL A  77 " --> pdb=" O   ILE A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 93
    Processing helix  chain 'A' and resid 99 through 123
      removed outlier: 3.761A  pdb=" N   ILE A 103 " --> pdb=" O   ILE A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 129
    Processing helix  chain 'A' and resid 156 through 179
    Processing helix  chain 'A' and resid 190 through 206
    Processing helix  chain 'A' and resid 215 through 230
      Proline residue:  A 222  - end of helix
      removed outlier: 3.583A  pdb=" N   GLY A 230 " --> pdb=" O   THR A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 236
      removed outlier: 4.152A  pdb=" N   ALA A 234 " --> pdb=" O   TRP A 231 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   VAL A 235 " --> pdb=" O   GLY A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 242
      removed outlier: 3.571A  pdb=" N   HIS A 241 " --> pdb=" O   THR A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 265
      Proline residue:  A 250  - end of helix
    Processing helix  chain 'A' and resid 266 through 269
    Processing helix  chain 'B' and resid 21 through 49
      removed outlier: 3.724A  pdb=" N   SER B  42 " --> pdb=" O   PHE B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 79
      removed outlier: 3.515A  pdb=" N   ILE B  59 " --> pdb=" O   GLY B  55 " (cutoff:3.500A)
      removed outlier: 5.672A  pdb=" N   GLN B  76 " --> pdb=" O   LEU B  72 " (cutoff:3.500A)
      removed outlier: 5.565A  pdb=" N   VAL B  77 " --> pdb=" O   ILE B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 93
    Processing helix  chain 'B' and resid 99 through 123
      removed outlier: 3.760A  pdb=" N   ILE B 103 " --> pdb=" O   ILE B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 129
    Processing helix  chain 'B' and resid 156 through 179
    Processing helix  chain 'B' and resid 190 through 206
    Processing helix  chain 'B' and resid 215 through 230
      Proline residue:  B 222  - end of helix
      removed outlier: 3.584A  pdb=" N   GLY B 230 " --> pdb=" O   THR B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 236
      removed outlier: 4.151A  pdb=" N   ALA B 234 " --> pdb=" O   TRP B 231 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   VAL B 235 " --> pdb=" O   GLY B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 242
      removed outlier: 3.571A  pdb=" N   HIS B 241 " --> pdb=" O   THR B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 265
      Proline residue:  B 250  - end of helix
    Processing helix  chain 'B' and resid 266 through 269
    Processing helix  chain 'C' and resid 21 through 49
      removed outlier: 3.725A  pdb=" N   SER C  42 " --> pdb=" O   PHE C  38 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 55 through 79
      removed outlier: 3.515A  pdb=" N   ILE C  59 " --> pdb=" O   GLY C  55 " (cutoff:3.500A)
      removed outlier: 5.672A  pdb=" N   GLN C  76 " --> pdb=" O   LEU C  72 " (cutoff:3.500A)
      removed outlier: 5.565A  pdb=" N   VAL C  77 " --> pdb=" O   ILE C  73 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 83 through 93
    Processing helix  chain 'C' and resid 99 through 123
      removed outlier: 3.761A  pdb=" N   ILE C 103 " --> pdb=" O   ILE C  99 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 123 through 129
    Processing helix  chain 'C' and resid 156 through 179
    Processing helix  chain 'C' and resid 190 through 206
    Processing helix  chain 'C' and resid 215 through 230
      Proline residue:  C 222  - end of helix
      removed outlier: 3.584A  pdb=" N   GLY C 230 " --> pdb=" O   THR C 226 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 231 through 236
      removed outlier: 4.152A  pdb=" N   ALA C 234 " --> pdb=" O   TRP C 231 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   VAL C 235 " --> pdb=" O   GLY C 232 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 237 through 242
      removed outlier: 3.571A  pdb=" N   HIS C 241 " --> pdb=" O   THR C 237 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 244 through 265
      Proline residue:  C 250  - end of helix
    Processing helix  chain 'C' and resid 266 through 269
    Processing helix  chain 'D' and resid 21 through 49
      removed outlier: 3.725A  pdb=" N   SER D  42 " --> pdb=" O   PHE D  38 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 79
      removed outlier: 3.515A  pdb=" N   ILE D  59 " --> pdb=" O   GLY D  55 " (cutoff:3.500A)
      removed outlier: 5.672A  pdb=" N   GLN D  76 " --> pdb=" O   LEU D  72 " (cutoff:3.500A)
      removed outlier: 5.566A  pdb=" N   VAL D  77 " --> pdb=" O   ILE D  73 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 83 through 93
    Processing helix  chain 'D' and resid 99 through 123
      removed outlier: 3.761A  pdb=" N   ILE D 103 " --> pdb=" O   ILE D  99 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 123 through 129
    Processing helix  chain 'D' and resid 156 through 179
    Processing helix  chain 'D' and resid 190 through 206
    Processing helix  chain 'D' and resid 215 through 230
      Proline residue:  D 222  - end of helix
      removed outlier: 3.585A  pdb=" N   GLY D 230 " --> pdb=" O   THR D 226 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 231 through 236
      removed outlier: 4.152A  pdb=" N   ALA D 234 " --> pdb=" O   TRP D 231 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   VAL D 235 " --> pdb=" O   GLY D 232 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 237 through 242
      removed outlier: 3.571A  pdb=" N   HIS D 241 " --> pdb=" O   THR D 237 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 244 through 265
      Proline residue:  D 250  - end of helix
    Processing helix  chain 'D' and resid 266 through 269

    525 hydrogen bonds defined for protein.
    1551 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: 1.21

  Time building geometry restraints manager: 1.02 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: 2332
        1.34 -     1.46: 1902
        1.46 -     1.58: 3470
        1.58 -     1.69: 0
        1.69 -     1.81: 60
  Bond restraints: 7764
  Sorted by residual:
  bond pdb=" CA  ILE A 178 "
       pdb=" C   ILE A 178 "
    ideal  model  delta    sigma   weight residual
    1.524  1.533 -0.009 1.33e-02 5.65e+03 4.65e-01
  bond pdb=" CA  ILE B 178 "
       pdb=" C   ILE B 178 "
    ideal  model  delta    sigma   weight residual
    1.524  1.533 -0.009 1.33e-02 5.65e+03 4.65e-01
  bond pdb=" CB  ILE C 166 "
       pdb=" CG2 ILE C 166 "
    ideal  model  delta    sigma   weight residual
    1.521  1.499  0.022 3.30e-02 9.18e+02 4.59e-01
  bond pdb=" CB  ILE A 166 "
       pdb=" CG2 ILE A 166 "
    ideal  model  delta    sigma   weight residual
    1.521  1.499  0.022 3.30e-02 9.18e+02 4.40e-01
  bond pdb=" CB  ILE B 166 "
       pdb=" CG2 ILE B 166 "
    ideal  model  delta    sigma   weight residual
    1.521  1.499  0.022 3.30e-02 9.18e+02 4.38e-01
  ... (remaining 7759 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.92: 10145
        0.92 -     1.84: 355
        1.84 -     2.77: 44
        2.77 -     3.69: 40
        3.69 -     4.61: 12
  Bond angle restraints: 10596
  Sorted by residual:
  angle pdb=" N   ALA C  74 "
        pdb=" CA  ALA C  74 "
        pdb=" C   ALA C  74 "
      ideal   model   delta    sigma   weight residual
     112.88  115.16   -2.28 1.29e+00 6.01e-01 3.11e+00
  angle pdb=" N   ALA B  74 "
        pdb=" CA  ALA B  74 "
        pdb=" C   ALA B  74 "
      ideal   model   delta    sigma   weight residual
     112.88  115.16   -2.28 1.29e+00 6.01e-01 3.11e+00
  angle pdb=" N   ALA D  74 "
        pdb=" CA  ALA D  74 "
        pdb=" C   ALA D  74 "
      ideal   model   delta    sigma   weight residual
     112.88  115.14   -2.26 1.29e+00 6.01e-01 3.08e+00
  angle pdb=" N   ASN B 183 "
        pdb=" CA  ASN B 183 "
        pdb=" C   ASN B 183 "
      ideal   model   delta    sigma   weight residual
     110.80  107.57    3.23 2.13e+00 2.20e-01 2.30e+00
  angle pdb=" N   ASN D 183 "
        pdb=" CA  ASN D 183 "
        pdb=" C   ASN D 183 "
      ideal   model   delta    sigma   weight residual
     110.80  107.59    3.21 2.13e+00 2.20e-01 2.27e+00
  ... (remaining 10591 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.97: 3633
       11.97 -    23.95: 395
       23.95 -    35.92: 164
       35.92 -    47.89: 56
       47.89 -    59.87: 44
  Dihedral angle restraints: 4292
    sinusoidal: 1524
      harmonic: 2768
  Sorted by residual:
  dihedral pdb=" CA  GLN B 164 "
           pdb=" CB  GLN B 164 "
           pdb=" CG  GLN B 164 "
           pdb=" CD  GLN B 164 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.13  -59.87     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CA  GLN A 164 "
           pdb=" CB  GLN A 164 "
           pdb=" CG  GLN A 164 "
           pdb=" CD  GLN A 164 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.17  -59.83     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CA  GLN D 164 "
           pdb=" CB  GLN D 164 "
           pdb=" CG  GLN D 164 "
           pdb=" CD  GLN D 164 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.18  -59.82     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 4289 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 686
       0.027 -    0.054: 343
       0.054 -    0.081: 142
       0.081 -    0.108: 37
       0.108 -    0.135: 8
  Chirality restraints: 1216
  Sorted by residual:
  chirality pdb=" CA  VAL A 186 "
            pdb=" N   VAL A 186 "
            pdb=" C   VAL A 186 "
            pdb=" CB  VAL A 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.13 2.00e-01 2.50e+01 4.55e-01
  chirality pdb=" CA  VAL C 186 "
            pdb=" N   VAL C 186 "
            pdb=" C   VAL C 186 "
            pdb=" CB  VAL C 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.37e-01
  chirality pdb=" CA  VAL B 186 "
            pdb=" N   VAL B 186 "
            pdb=" C   VAL B 186 "
            pdb=" CB  VAL B 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.36e-01
  ... (remaining 1213 not shown)

  Planarity restraints: 1332
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE C 113 "   -0.008 2.00e-02 2.50e+03   1.63e-02 2.65e+00
        pdb=" C   PHE C 113 "    0.028 2.00e-02 2.50e+03
        pdb=" O   PHE C 113 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   LEU C 114 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE D 113 "    0.008 2.00e-02 2.50e+03   1.62e-02 2.63e+00
        pdb=" C   PHE D 113 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   PHE D 113 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LEU D 114 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 113 "   -0.008 2.00e-02 2.50e+03   1.61e-02 2.60e+00
        pdb=" C   PHE A 113 "    0.028 2.00e-02 2.50e+03
        pdb=" O   PHE A 113 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   LEU A 114 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1329 not shown)

  Histogram of nonbonded interaction distances:
        2.64 -     3.09: 5646
        3.09 -     3.54: 8456
        3.54 -     4.00: 12219
        4.00 -     4.45: 16224
        4.45 -     4.90: 23701
  Nonbonded interactions: 66246
  Sorted by model distance:
  nonbonded pdb=" N   ASN A 183 "
            pdb=" O   ASN A 183 "
     model   vdw
     2.639 2.496
  nonbonded pdb=" N   ASN B 183 "
            pdb=" O   ASN B 183 "
     model   vdw
     2.639 2.496
  nonbonded pdb=" N   ASN C 183 "
            pdb=" O   ASN C 183 "
     model   vdw
     2.639 2.496
  nonbonded pdb=" N   ASN D 183 "
            pdb=" O   ASN D 183 "
     model   vdw
     2.640 2.496
  nonbonded pdb=" C   SER A 233 "
            pdb=" OG  SER A 233 "
     model   vdw
     2.650 2.616
  ... (remaining 66241 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.250
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
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   0.022   7764  Z= 0.111
  Angle     :  0.452   4.610  10596  Z= 0.251
  Chirality :  0.038   0.135   1216
  Planarity :  0.005   0.040   1332
  Dihedral  : 14.482  59.866   2548
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  : 16.67 %
    Favored  : 82.81 %
  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:  1.07 (0.28), residues: 992
  helix:  1.38 (0.20), residues: 680
  sheet:  None (None), residues: 0
  loop : -0.72 (0.42), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 218 
 TYR   0.006   0.001   TYR A 261 
 PHE   0.012   0.001   PHE D 165 
 TRP   0.003   0.001   TRP D 243 
 HIS   0.001   0.000   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 7764)
  covalent geometry    : angle       0.45197 (10596)
  hydrogen bonds       : bond        0.09841 (  525)
  hydrogen bonds       : angle       6.17398 ( 1551)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A   35 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7793 (tt)
REVERT: B   35 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7791 (tt)
REVERT: D  157 MET cc_start: 0.7847 (tpp) cc_final: 0.7551 (tpp)
REVERT: D  158 ILE cc_start: 0.7589 (mp) cc_final: 0.7306 (mm)
  outliers start: 4
  outliers final: 0
  residues processed: 87
  average time/residue: 0.2727
  time to fit residues: 26.3997
Evaluate side-chains
  72 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain B residue   35 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 159 ASN
B 159 ASN
C 159 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.133772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.106590 restraints weight = 7660.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 1.41
r_work: 0.2878 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2717 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.2929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7764  Z= 0.158
  Angle     :  0.552   6.106  10596  Z= 0.289
  Chirality :  0.042   0.138   1216
  Planarity :  0.005   0.037   1332
  Dihedral  :  4.107  35.327   1056
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 13.41 %
    Favored  : 82.29 %
  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:  1.55 (0.28), residues: 992
  helix:  1.86 (0.19), residues: 684
  sheet:  None (None), residues: 0
  loop : -0.90 (0.41), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  50 
 TYR   0.014   0.002   TYR B 104 
 PHE   0.014   0.001   PHE B 225 
 TRP   0.007   0.001   TRP B 242 
 HIS   0.004   0.001   HIS B 268 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 7764)
  covalent geometry    : angle       0.55226 (10596)
  hydrogen bonds       : bond        0.04050 (  525)
  hydrogen bonds       : angle       3.98858 ( 1551)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 72
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A  204 THR cc_start: 0.9097 (m) cc_final: 0.8881 (m)
REVERT: B  163 ASP cc_start: 0.8305 (t70) cc_final: 0.7878 (m-30)
REVERT: C   37 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8170 (ttt)
REVERT: D  210 SER cc_start: 0.8399 (t) cc_final: 0.8086 (p)
  outliers start: 33
  outliers final: 10
  residues processed: 95
  average time/residue: 0.2306
  time to fit residues: 24.8050
Evaluate side-chains
  76 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue  138 SER
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain C residue   37 MET
Chi-restraints excluded: chain C residue  138 SER
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain D residue   35 LEU
Chi-restraints excluded: chain D residue  138 SER
Chi-restraints excluded: chain D residue  233 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 22 optimal weight:    0.0270
   chunk 80 optimal weight:    0.7980
   chunk 82 optimal weight:    4.9990
   chunk 85 optimal weight:    0.0170
   chunk 74 optimal weight:    0.6980
   chunk 75 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   chunk 69 optimal weight:    0.2980
   chunk 60 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0020
   overall best weight:    0.2084

-------------------------------------------------------------------------------
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 = 0.3428 r_free = 0.3428 target = 0.135688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.109361 restraints weight = 7613.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 1.38
r_work: 0.2907 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2749 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.2991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7764  Z= 0.091
  Angle     :  0.429   4.379  10596  Z= 0.227
  Chirality :  0.038   0.135   1216
  Planarity :  0.004   0.037   1332
  Dihedral  :  3.475  14.673   1052
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 14.32 %
    Favored  : 82.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.16 (0.28), residues: 992
  helix:  2.37 (0.19), residues: 680
  sheet:  None (None), residues: 0
  loop : -0.72 (0.41), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  23 
 TYR   0.004   0.001   TYR D 212 
 PHE   0.010   0.001   PHE B 225 
 TRP   0.004   0.000   TRP C 243 
 HIS   0.002   0.000   HIS C  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00187 ( 7764)
  covalent geometry    : angle       0.42926 (10596)
  hydrogen bonds       : bond        0.03091 (  525)
  hydrogen bonds       : angle       3.85553 ( 1551)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 69
  time to evaluate  : 0.259 
Fit side-chains
REVERT: B   35 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8280 (tt)
REVERT: B  163 ASP cc_start: 0.8274 (t70) cc_final: 0.7878 (m-30)
REVERT: C  219 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7522 (m-30)
REVERT: C  233 SER cc_start: 0.8634 (OUTLIER) cc_final: 0.8210 (p)
REVERT: C  263 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7869 (mp)
REVERT: D  210 SER cc_start: 0.8269 (t) cc_final: 0.8000 (p)
  outliers start: 28
  outliers final: 12
  residues processed: 86
  average time/residue: 0.2514
  time to fit residues: 24.3518
Evaluate side-chains
  74 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  157 MET
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  219 ASP
Chi-restraints excluded: chain C residue  233 SER
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain D residue   35 LEU
Chi-restraints excluded: chain D residue  138 SER
Chi-restraints excluded: chain D residue  197 LEU
Chi-restraints excluded: chain D residue  233 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 93 optimal weight:    3.9990
   chunk 89 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 83 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 92 optimal weight:    0.8980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3373 r_free = 0.3373 target = 0.131421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.104612 restraints weight = 7804.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3020 rms_B_bonded: 1.42
r_work: 0.2834 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2673 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.3725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7764  Z= 0.123
  Angle     :  0.479   4.491  10596  Z= 0.256
  Chirality :  0.040   0.143   1216
  Planarity :  0.004   0.040   1332
  Dihedral  :  3.682  16.599   1052
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 14.71 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.07 (0.28), residues: 992
  helix:  2.28 (0.19), residues: 680
  sheet:  None (None), residues: 0
  loop : -0.71 (0.40), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 188 
 TYR   0.013   0.001   TYR C 261 
 PHE   0.014   0.001   PHE B 225 
 TRP   0.006   0.001   TRP A 244 
 HIS   0.002   0.000   HIS D 268 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 7764)
  covalent geometry    : angle       0.47857 (10596)
  hydrogen bonds       : bond        0.03700 (  525)
  hydrogen bonds       : angle       3.87600 ( 1551)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 79
  time to evaluate  : 0.205 
Fit side-chains
REVERT: A  163 ASP cc_start: 0.8422 (t0) cc_final: 0.7770 (m-30)
REVERT: A  219 ASP cc_start: 0.8280 (m-30) cc_final: 0.7791 (m-30)
REVERT: B  163 ASP cc_start: 0.8369 (t70) cc_final: 0.7736 (m-30)
REVERT: C   37 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8441 (ttt)
REVERT: C  210 SER cc_start: 0.8305 (t) cc_final: 0.7802 (p)
REVERT: C  219 ASP cc_start: 0.8123 (m-30) cc_final: 0.7659 (m-30)
REVERT: C  263 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8062 (mp)
REVERT: D  210 SER cc_start: 0.8374 (t) cc_final: 0.8092 (p)
  outliers start: 31
  outliers final: 16
  residues processed: 98
  average time/residue: 0.2558
  time to fit residues: 28.1505
Evaluate side-chains
  91 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain B residue  138 SER
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  197 LEU
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain C residue   35 LEU
Chi-restraints excluded: chain C residue   37 MET
Chi-restraints excluded: chain C residue  138 SER
Chi-restraints excluded: chain C residue  157 MET
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain D residue   35 LEU
Chi-restraints excluded: chain D residue  138 SER
Chi-restraints excluded: chain D residue  233 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 76 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 89 optimal weight:    3.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
B 133 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.133645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.106566 restraints weight = 7724.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 1.43
r_work: 0.2886 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2730 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
moved from start:          0.3997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7764  Z= 0.126
  Angle     :  0.470   5.005  10596  Z= 0.249
  Chirality :  0.040   0.141   1216
  Planarity :  0.004   0.040   1332
  Dihedral  :  3.690  16.085   1052
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 14.71 %
    Favored  : 80.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.04 (0.28), residues: 992
  helix:  2.23 (0.19), residues: 680
  sheet:  None (None), residues: 0
  loop : -0.65 (0.41), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  23 
 TYR   0.008   0.001   TYR A 261 
 PHE   0.012   0.001   PHE C 165 
 TRP   0.004   0.001   TRP D 242 
 HIS   0.002   0.000   HIS D  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 7764)
  covalent geometry    : angle       0.47032 (10596)
  hydrogen bonds       : bond        0.03518 (  525)
  hydrogen bonds       : angle       3.86928 ( 1551)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 73
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A  163 ASP cc_start: 0.8392 (t0) cc_final: 0.7800 (m-30)
REVERT: A  178 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7501 (mp)
REVERT: A  210 SER cc_start: 0.8390 (t) cc_final: 0.7827 (p)
REVERT: A  219 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7686 (m-30)
REVERT: B  163 ASP cc_start: 0.8324 (t70) cc_final: 0.7730 (m-30)
REVERT: B  210 SER cc_start: 0.8465 (t) cc_final: 0.8098 (p)
REVERT: C  210 SER cc_start: 0.8330 (t) cc_final: 0.7858 (p)
REVERT: C  219 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7587 (m-30)
REVERT: C  263 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8092 (mp)
REVERT: D  210 SER cc_start: 0.8345 (t) cc_final: 0.8031 (p)
  outliers start: 34
  outliers final: 19
  residues processed: 93
  average time/residue: 0.2511
  time to fit residues: 26.2928
Evaluate side-chains
  93 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 70
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  178 ILE
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  219 ASP
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  138 SER
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain C residue   35 LEU
Chi-restraints excluded: chain C residue  138 SER
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  219 ASP
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain D residue   35 LEU
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue  138 SER
Chi-restraints excluded: chain D residue  197 LEU
Chi-restraints excluded: chain D residue  233 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0770
   chunk 59 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 85 optimal weight:    3.9990
   chunk 74 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.7742

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

Flipped N/Q/H residues before XYZ refinement:
B 133 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.132548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.104996 restraints weight = 7760.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 1.45
r_work: 0.2876 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2717 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.4154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7764  Z= 0.111
  Angle     :  0.454   4.987  10596  Z= 0.241
  Chirality :  0.039   0.139   1216
  Planarity :  0.004   0.040   1332
  Dihedral  :  3.610  16.087   1052
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 15.49 %
    Favored  : 80.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.18 (0.28), residues: 992
  helix:  2.32 (0.19), residues: 680
  sheet:  None (None), residues: 0
  loop : -0.54 (0.42), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  23 
 TYR   0.008   0.001   TYR C 261 
 PHE   0.011   0.001   PHE D 225 
 TRP   0.003   0.001   TRP D 243 
 HIS   0.002   0.000   HIS D  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 7764)
  covalent geometry    : angle       0.45424 (10596)
  hydrogen bonds       : bond        0.03351 (  525)
  hydrogen bonds       : angle       3.80972 ( 1551)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 77
  time to evaluate  : 0.262 
Fit side-chains
REVERT: A  163 ASP cc_start: 0.8321 (t0) cc_final: 0.7729 (m-30)
REVERT: A  178 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7488 (mp)
REVERT: A  210 SER cc_start: 0.8424 (t) cc_final: 0.7844 (p)
REVERT: A  219 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7671 (m-30)
REVERT: B  163 ASP cc_start: 0.8301 (t70) cc_final: 0.7731 (m-30)
REVERT: B  210 SER cc_start: 0.8383 (t) cc_final: 0.7963 (p)
REVERT: C  210 SER cc_start: 0.8252 (t) cc_final: 0.7812 (p)
REVERT: C  219 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7636 (m-30)
REVERT: C  263 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8092 (mp)
REVERT: D  210 SER cc_start: 0.8297 (t) cc_final: 0.7958 (p)
  outliers start: 31
  outliers final: 18
  residues processed: 95
  average time/residue: 0.2470
  time to fit residues: 26.5044
Evaluate side-chains
  94 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 72
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  178 ILE
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  219 ASP
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  138 SER
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  157 MET
Chi-restraints excluded: chain B residue  197 LEU
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain C residue   35 LEU
Chi-restraints excluded: chain C residue  138 SER
Chi-restraints excluded: chain C residue  219 ASP
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain D residue   35 LEU
Chi-restraints excluded: chain D residue  138 SER
Chi-restraints excluded: chain D residue  197 LEU
Chi-restraints excluded: chain D residue  233 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 15 optimal weight:    0.5980
   chunk 67 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0980
   chunk 25 optimal weight:    6.9990
   chunk 77 optimal weight:    0.9990
   chunk 90 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 99 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3394 r_free = 0.3394 target = 0.133048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.106312 restraints weight = 7711.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3058 rms_B_bonded: 1.41
r_work: 0.2881 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2723 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.4239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7764  Z= 0.103
  Angle     :  0.447   4.468  10596  Z= 0.237
  Chirality :  0.039   0.138   1216
  Planarity :  0.004   0.040   1332
  Dihedral  :  3.573  15.833   1052
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 15.49 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.28 (0.28), residues: 992
  helix:  2.39 (0.19), residues: 680
  sheet:  None (None), residues: 0
  loop : -0.49 (0.42), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  23 
 TYR   0.007   0.001   TYR C 261 
 PHE   0.010   0.001   PHE D 225 
 TRP   0.003   0.000   TRP A 128 
 HIS   0.002   0.000   HIS C  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 7764)
  covalent geometry    : angle       0.44691 (10596)
  hydrogen bonds       : bond        0.03220 (  525)
  hydrogen bonds       : angle       3.78907 ( 1551)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 71
  time to evaluate  : 0.174 
Fit side-chains
REVERT: A  163 ASP cc_start: 0.8340 (t0) cc_final: 0.7768 (m-30)
REVERT: A  178 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7528 (mp)
REVERT: A  210 SER cc_start: 0.8357 (t) cc_final: 0.7836 (p)
REVERT: A  263 LEU cc_start: 0.8566 (mp) cc_final: 0.8128 (mp)
REVERT: B  163 ASP cc_start: 0.8330 (t70) cc_final: 0.7762 (m-30)
REVERT: B  210 SER cc_start: 0.8388 (t) cc_final: 0.7957 (p)
REVERT: C  210 SER cc_start: 0.8266 (t) cc_final: 0.7834 (p)
REVERT: C  219 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7642 (m-30)
REVERT: C  263 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8147 (mp)
REVERT: D  163 ASP cc_start: 0.8360 (t0) cc_final: 0.7604 (m-30)
REVERT: D  210 SER cc_start: 0.8307 (t) cc_final: 0.7964 (p)
  outliers start: 27
  outliers final: 17
  residues processed: 88
  average time/residue: 0.2597
  time to fit residues: 25.5099
Evaluate side-chains
  87 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 67
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  178 ILE
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  138 SER
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain C residue   35 LEU
Chi-restraints excluded: chain C residue  138 SER
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  219 ASP
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain D residue   35 LEU
Chi-restraints excluded: chain D residue  138 SER
Chi-restraints excluded: chain D residue  233 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 25 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 37 optimal weight:    6.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.3352 r_free = 0.3352 target = 0.130095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.103097 restraints weight = 7794.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 1.43
r_work: 0.2810 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2652 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.4367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7764  Z= 0.148
  Angle     :  0.497   5.050  10596  Z= 0.264
  Chirality :  0.042   0.151   1216
  Planarity :  0.004   0.041   1332
  Dihedral  :  3.781  17.143   1052
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 15.62 %
    Favored  : 81.12 %
  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:  2.04 (0.28), residues: 992
  helix:  2.17 (0.19), residues: 684
  sheet:  None (None), residues: 0
  loop : -0.53 (0.42), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  23 
 TYR   0.011   0.001   TYR C 261 
 PHE   0.013   0.001   PHE B 225 
 TRP   0.005   0.001   TRP D 242 
 HIS   0.002   0.001   HIS C  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 7764)
  covalent geometry    : angle       0.49715 (10596)
  hydrogen bonds       : bond        0.03770 (  525)
  hydrogen bonds       : angle       3.89631 ( 1551)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 75
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A  163 ASP cc_start: 0.8445 (t0) cc_final: 0.7839 (m-30)
REVERT: A  178 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7594 (mp)
REVERT: A  210 SER cc_start: 0.8462 (t) cc_final: 0.7924 (p)
REVERT: A  219 ASP cc_start: 0.8151 (m-30) cc_final: 0.7685 (m-30)
REVERT: A  263 LEU cc_start: 0.8633 (mp) cc_final: 0.8196 (mp)
REVERT: B  163 ASP cc_start: 0.8401 (t70) cc_final: 0.7801 (m-30)
REVERT: B  210 SER cc_start: 0.8438 (t) cc_final: 0.8016 (p)
REVERT: C  210 SER cc_start: 0.8373 (t) cc_final: 0.7887 (p)
REVERT: C  219 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7672 (m-30)
REVERT: C  263 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8199 (mp)
REVERT: D  210 SER cc_start: 0.8426 (t) cc_final: 0.8017 (p)
  outliers start: 25
  outliers final: 19
  residues processed: 92
  average time/residue: 0.2505
  time to fit residues: 25.8382
Evaluate side-chains
  96 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 74
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  178 ILE
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  138 SER
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain C residue   35 LEU
Chi-restraints excluded: chain C residue  138 SER
Chi-restraints excluded: chain C residue  157 MET
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  219 ASP
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain D residue   35 LEU
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue  138 SER
Chi-restraints excluded: chain D residue  233 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 53 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 73 optimal weight:    4.9990
   chunk 63 optimal weight:    0.6980
   chunk 79 optimal weight:    0.8980
   chunk 82 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3370 r_free = 0.3370 target = 0.131243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.104402 restraints weight = 7746.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 1.42
r_work: 0.2903 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2745 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.4405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7764  Z= 0.116
  Angle     :  0.465   4.671  10596  Z= 0.247
  Chirality :  0.040   0.140   1216
  Planarity :  0.004   0.041   1332
  Dihedral  :  3.693  16.505   1052
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 15.10 %
    Favored  : 81.12 %
  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:  2.14 (0.28), residues: 992
  helix:  2.27 (0.19), residues: 680
  sheet:  None (None), residues: 0
  loop : -0.51 (0.42), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  23 
 TYR   0.008   0.001   TYR C 261 
 PHE   0.011   0.001   PHE D 225 
 TRP   0.003   0.001   TRP D 243 
 HIS   0.002   0.000   HIS B  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 7764)
  covalent geometry    : angle       0.46535 (10596)
  hydrogen bonds       : bond        0.03425 (  525)
  hydrogen bonds       : angle       3.84993 ( 1551)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 77
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A  163 ASP cc_start: 0.8354 (t0) cc_final: 0.7782 (m-30)
REVERT: A  178 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7528 (mp)
REVERT: A  210 SER cc_start: 0.8434 (t) cc_final: 0.7881 (p)
REVERT: A  219 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7658 (m-30)
REVERT: B  163 ASP cc_start: 0.8330 (t70) cc_final: 0.7770 (m-30)
REVERT: B  210 SER cc_start: 0.8416 (t) cc_final: 0.7993 (p)
REVERT: C  210 SER cc_start: 0.8340 (t) cc_final: 0.7849 (p)
REVERT: C  219 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7631 (m-30)
REVERT: C  263 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8206 (mp)
REVERT: D  163 ASP cc_start: 0.8320 (t0) cc_final: 0.7651 (m-30)
REVERT: D  210 SER cc_start: 0.8423 (t) cc_final: 0.7982 (p)
REVERT: D  219 ASP cc_start: 0.8091 (m-30) cc_final: 0.7615 (m-30)
  outliers start: 29
  outliers final: 21
  residues processed: 93
  average time/residue: 0.2569
  time to fit residues: 26.8317
Evaluate side-chains
  99 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 74
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  178 ILE
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  219 ASP
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  138 SER
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain C residue   35 LEU
Chi-restraints excluded: chain C residue  138 SER
Chi-restraints excluded: chain C residue  157 MET
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  219 ASP
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain D residue   35 LEU
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue  138 SER
Chi-restraints excluded: chain D residue  233 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 53 optimal weight:   10.0000
   chunk 50 optimal weight:    0.9990
   chunk 86 optimal weight:    0.0970
   chunk 13 optimal weight:    0.2980
   chunk 66 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0470
   chunk 70 optimal weight:    0.8980
   chunk 71 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.4678

-------------------------------------------------------------------------------
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 = 0.3396 r_free = 0.3396 target = 0.133369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.106858 restraints weight = 7665.604|
|-----------------------------------------------------------------------------|
r_work (start): 0.3092 rms_B_bonded: 1.41
r_work: 0.2916 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2759 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.4419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7764  Z= 0.097
  Angle     :  0.441   4.431  10596  Z= 0.234
  Chirality :  0.039   0.178   1216
  Planarity :  0.004   0.040   1332
  Dihedral  :  3.536  15.896   1052
  Min Nonbonded Distance : 2.647

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 16.02 %
    Favored  : 80.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.36 (0.28), residues: 992
  helix:  2.42 (0.19), residues: 680
  sheet:  None (None), residues: 0
  loop : -0.40 (0.43), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  23 
 TYR   0.005   0.001   TYR C 261 
 PHE   0.011   0.001   PHE C 113 
 TRP   0.004   0.000   TRP A 243 
 HIS   0.002   0.000   HIS C  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 7764)
  covalent geometry    : angle       0.44121 (10596)
  hydrogen bonds       : bond        0.03098 (  525)
  hydrogen bonds       : angle       3.80583 ( 1551)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 72
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A  163 ASP cc_start: 0.8306 (t0) cc_final: 0.7738 (m-30)
REVERT: A  178 ILE cc_start: 0.7756 (OUTLIER) cc_final: 0.7489 (mp)
REVERT: A  210 SER cc_start: 0.8303 (t) cc_final: 0.7806 (p)
REVERT: A  219 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7641 (m-30)
REVERT: B  163 ASP cc_start: 0.8311 (t70) cc_final: 0.7805 (m-30)
REVERT: B  210 SER cc_start: 0.8365 (t) cc_final: 0.7929 (p)
REVERT: B  263 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8233 (mp)
REVERT: C  163 ASP cc_start: 0.8331 (t0) cc_final: 0.7596 (m-30)
REVERT: C  210 SER cc_start: 0.8199 (t) cc_final: 0.7742 (p)
REVERT: C  219 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7626 (m-30)
REVERT: D  163 ASP cc_start: 0.8272 (t0) cc_final: 0.7593 (m-30)
REVERT: D  210 SER cc_start: 0.8303 (t) cc_final: 0.7929 (p)
  outliers start: 24
  outliers final: 15
  residues processed: 86
  average time/residue: 0.2574
  time to fit residues: 24.7369
Evaluate side-chains
  89 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  178 ILE
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  219 ASP
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  138 SER
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain C residue   35 LEU
Chi-restraints excluded: chain C residue  138 SER
Chi-restraints excluded: chain C residue  157 MET
Chi-restraints excluded: chain C residue  219 ASP
Chi-restraints excluded: chain D residue   35 LEU
Chi-restraints excluded: chain D residue  138 SER
Chi-restraints excluded: chain D residue  233 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 77 optimal weight:    0.7980
   chunk 25 optimal weight:    6.9990
   chunk 48 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 64 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 41 optimal weight:    6.9990
   chunk 98 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3376 r_free = 0.3376 target = 0.131842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.105305 restraints weight = 7677.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.3085 rms_B_bonded: 1.41
r_work: 0.2905 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2747 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.4465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7764  Z= 0.118
  Angle     :  0.465   4.498  10596  Z= 0.248
  Chirality :  0.040   0.199   1216
  Planarity :  0.004   0.041   1332
  Dihedral  :  3.623  16.227   1052
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 16.02 %
    Favored  : 80.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.26 (0.28), residues: 992
  helix:  2.34 (0.19), residues: 680
  sheet:  None (None), residues: 0
  loop : -0.43 (0.42), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  23 
 TYR   0.009   0.001   TYR C 261 
 PHE   0.012   0.001   PHE D 225 
 TRP   0.003   0.001   TRP A 242 
 HIS   0.002   0.000   HIS B  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7764)
  covalent geometry    : angle       0.46473 (10596)
  hydrogen bonds       : bond        0.03389 (  525)
  hydrogen bonds       : angle       3.82442 ( 1551)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1703.64 seconds
wall clock time: 29 minutes 52.52 seconds (1792.52 seconds total)