Starting phenix.real_space_refine
on Sun Apr  5 17:44:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9uxi_64584/04_2026/9uxi_64584.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9uxi_64584/04_2026/9uxi_64584.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9uxi_64584/04_2026/9uxi_64584.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9uxi_64584/04_2026/9uxi_64584.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9uxi_64584/04_2026/9uxi_64584.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9uxi_64584/04_2026/9uxi_64584.cif"
  }
  resolution = 3.64
  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=   0.004
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      38      5.16       5
     C    7520      2.51       5
     N    2058      2.21       5
     O    2346      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11962
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2843
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 350, 2843
          Classifications: {'peptide': 350}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 341}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 3138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 388, 3138
          Classifications: {'peptide': 388}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 379}
    Chain: "B"
      Number of atoms: 2843
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 350, 2843
          Classifications: {'peptide': 350}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 341}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 3138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 388, 3138
          Classifications: {'peptide': 388}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 379}
  Time building chain proxies: 2.09, per 1000 atoms: 0.17
  Number of scatterers: 11962
  At special positions: 0
  Unit cell: (143.5, 90.2, 125.46, 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      38     16.00
     O    2346      8.00
     N    2058      7.00
     C    7520      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: 0.61
  Conformation dependent library (CDL) restraints added in 532.5 milliseconds
  

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2808

  Finding SS restraints...
    Secondary structure from input PDB file:
      73 helices and 4 sheets defined
      69.9% alpha, 2.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 29
    Processing helix  chain 'A' and resid 70 through 87
    Processing helix  chain 'A' and resid 90 through 94
    Processing helix  chain 'A' and resid 106 through 115
    Processing helix  chain 'A' and resid 117 through 132
    Processing helix  chain 'A' and resid 136 through 147
      removed outlier: 4.278A  pdb=" N   ASN A 141 " --> pdb=" O   PRO A 137 " (cutoff:3.500A)
      removed outlier: 4.784A  pdb=" N   TYR A 142 " --> pdb=" O   SER A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 159
    Processing helix  chain 'A' and resid 168 through 180
    Processing helix  chain 'A' and resid 185 through 187
      No H-bonds generated for 'chain 'A' and resid 185 through 187'
    Processing helix  chain 'A' and resid 188 through 210
    Processing helix  chain 'A' and resid 217 through 234
      removed outlier: 3.630A  pdb=" N   TYR A 232 " --> pdb=" O   ILE A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 258
    Processing helix  chain 'A' and resid 259 through 269
    Processing helix  chain 'A' and resid 271 through 295
    Processing helix  chain 'A' and resid 299 through 325
    Processing helix  chain 'A' and resid 329 through 345
    Processing helix  chain 'A' and resid 346 through 348
      No H-bonds generated for 'chain 'A' and resid 346 through 348'
    Processing helix  chain 'A' and resid 356 through 370
    Processing helix  chain 'A' and resid 378 through 383
    Processing helix  chain 'C' and resid 2 through 29
    Processing helix  chain 'C' and resid 70 through 86
    Processing helix  chain 'C' and resid 106 through 115
    Processing helix  chain 'C' and resid 117 through 132
    Processing helix  chain 'C' and resid 139 through 147
    Processing helix  chain 'C' and resid 149 through 159
    Processing helix  chain 'C' and resid 168 through 181
    Processing helix  chain 'C' and resid 185 through 187
      No H-bonds generated for 'chain 'C' and resid 185 through 187'
    Processing helix  chain 'C' and resid 188 through 210
      removed outlier: 3.653A  pdb=" N   LYS C 210 " --> pdb=" O   LEU C 206 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 218 through 232
    Processing helix  chain 'C' and resid 248 through 258
    Processing helix  chain 'C' and resid 259 through 267
    Processing helix  chain 'C' and resid 271 through 295
    Processing helix  chain 'C' and resid 299 through 325
    Processing helix  chain 'C' and resid 329 through 345
    Processing helix  chain 'C' and resid 346 through 348
      No H-bonds generated for 'chain 'C' and resid 346 through 348'
    Processing helix  chain 'C' and resid 356 through 370
    Processing helix  chain 'C' and resid 378 through 384
    Processing helix  chain 'B' and resid 17 through 29
    Processing helix  chain 'B' and resid 70 through 87
    Processing helix  chain 'B' and resid 106 through 115
    Processing helix  chain 'B' and resid 117 through 132
    Processing helix  chain 'B' and resid 136 through 147
      removed outlier: 4.234A  pdb=" N   ASN B 141 " --> pdb=" O   PRO B 137 " (cutoff:3.500A)
      removed outlier: 4.765A  pdb=" N   TYR B 142 " --> pdb=" O   SER B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 149 through 159
    Processing helix  chain 'B' and resid 168 through 180
    Processing helix  chain 'B' and resid 185 through 187
      No H-bonds generated for 'chain 'B' and resid 185 through 187'
    Processing helix  chain 'B' and resid 188 through 210
    Processing helix  chain 'B' and resid 217 through 234
      removed outlier: 3.631A  pdb=" N   TYR B 232 " --> pdb=" O   ILE B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 258
    Processing helix  chain 'B' and resid 259 through 269
    Processing helix  chain 'B' and resid 271 through 295
    Processing helix  chain 'B' and resid 299 through 325
    Processing helix  chain 'B' and resid 329 through 345
    Processing helix  chain 'B' and resid 346 through 348
      No H-bonds generated for 'chain 'B' and resid 346 through 348'
    Processing helix  chain 'B' and resid 356 through 370
    Processing helix  chain 'B' and resid 378 through 383
    Processing helix  chain 'D' and resid 2 through 29
    Processing helix  chain 'D' and resid 70 through 86
    Processing helix  chain 'D' and resid 106 through 115
    Processing helix  chain 'D' and resid 117 through 132
    Processing helix  chain 'D' and resid 139 through 147
    Processing helix  chain 'D' and resid 149 through 159
    Processing helix  chain 'D' and resid 168 through 181
    Processing helix  chain 'D' and resid 185 through 187
      No H-bonds generated for 'chain 'D' and resid 185 through 187'
    Processing helix  chain 'D' and resid 188 through 210
      removed outlier: 3.704A  pdb=" N   LYS D 210 " --> pdb=" O   LEU D 206 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 218 through 233
    Processing helix  chain 'D' and resid 248 through 258
    Processing helix  chain 'D' and resid 259 through 267
    Processing helix  chain 'D' and resid 271 through 295
    Processing helix  chain 'D' and resid 299 through 325
    Processing helix  chain 'D' and resid 329 through 345
    Processing helix  chain 'D' and resid 346 through 348
      No H-bonds generated for 'chain 'D' and resid 346 through 348'
    Processing helix  chain 'D' and resid 356 through 370
    Processing helix  chain 'D' and resid 378 through 384
    Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36
    Processing sheet with id=AA2, first strand: chain 'C' and resid 160 through 164
      removed outlier: 6.067A  pdb=" N   PHE C  96 " --> pdb=" O   THR C 161 " (cutoff:3.500A)
      removed outlier: 7.607A  pdb=" N   ILE C 163 " --> pdb=" O   PHE C  96 " (cutoff:3.500A)
      removed outlier: 6.048A  pdb=" N   LEU C  98 " --> pdb=" O   ILE C 163 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   PHE C  53 " --> pdb=" O   LEU C  97 " (cutoff:3.500A)
      removed outlier: 7.750A  pdb=" N   PHE C  99 " --> pdb=" O   PHE C  53 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   GLN C  55 " --> pdb=" O   PHE C  99 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   GLU C  44 " --> pdb=" O   GLY C  36 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 35 through 36
    Processing sheet with id=AA4, first strand: chain 'D' and resid 160 through 164
      removed outlier: 6.049A  pdb=" N   PHE D  96 " --> pdb=" O   THR D 161 " (cutoff:3.500A)
      removed outlier: 7.592A  pdb=" N   ILE D 163 " --> pdb=" O   PHE D  96 " (cutoff:3.500A)
      removed outlier: 6.042A  pdb=" N   LEU D  98 " --> pdb=" O   ILE D 163 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   PHE D  53 " --> pdb=" O   LEU D  97 " (cutoff:3.500A)
      removed outlier: 7.737A  pdb=" N   PHE D  99 " --> pdb=" O   PHE D  53 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   GLN D  55 " --> pdb=" O   PHE D  99 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   GLU D  44 " --> pdb=" O   GLY D  36 " (cutoff:3.500A)

    754 hydrogen bonds defined for protein.
    2238 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: 1.74

  Time building geometry restraints manager: 0.93 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3998
        1.35 -     1.46: 2816
        1.46 -     1.58: 5332
        1.58 -     1.69: 0
        1.69 -     1.81: 52
  Bond restraints: 12198
  Sorted by residual:
  bond pdb=" C   ALA A 169 "
       pdb=" O   ALA A 169 "
    ideal  model  delta    sigma   weight residual
    1.244  1.236  0.008 1.00e-02 1.00e+04 5.73e-01
  bond pdb=" CA  ALA A 169 "
       pdb=" C   ALA A 169 "
    ideal  model  delta    sigma   weight residual
    1.520  1.529 -0.008 1.23e-02 6.61e+03 4.52e-01
  bond pdb=" C   ALA B 169 "
       pdb=" O   ALA B 169 "
    ideal  model  delta    sigma   weight residual
    1.244  1.237  0.007 1.00e-02 1.00e+04 4.29e-01
  bond pdb=" C   ALA A 169 "
       pdb=" N   PRO A 170 "
    ideal  model  delta    sigma   weight residual
    1.335  1.344 -0.009 1.36e-02 5.41e+03 4.04e-01
  bond pdb=" CA  THR D 214 "
       pdb=" C   THR D 214 "
    ideal  model  delta    sigma   weight residual
    1.531  1.524  0.007 1.12e-02 7.97e+03 3.65e-01
  ... (remaining 12193 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 16429
        2.10 -     4.19: 56
        4.19 -     6.29: 5
        6.29 -     8.39: 0
        8.39 -    10.49: 2
  Bond angle restraints: 16492
  Sorted by residual:
  angle pdb=" CA  LEU B 197 "
        pdb=" CB  LEU B 197 "
        pdb=" CG  LEU B 197 "
      ideal   model   delta    sigma   weight residual
     116.30  126.79  -10.49 3.50e+00 8.16e-02 8.98e+00
  angle pdb=" CA  LEU A 197 "
        pdb=" CB  LEU A 197 "
        pdb=" CG  LEU A 197 "
      ideal   model   delta    sigma   weight residual
     116.30  126.74  -10.44 3.50e+00 8.16e-02 8.90e+00
  angle pdb=" C   SER B 168 "
        pdb=" N   ALA B 169 "
        pdb=" CA  ALA B 169 "
      ideal   model   delta    sigma   weight residual
     120.26  122.61   -2.35 1.34e+00 5.57e-01 3.09e+00
  angle pdb=" C   SER A 168 "
        pdb=" N   ALA A 169 "
        pdb=" CA  ALA A 169 "
      ideal   model   delta    sigma   weight residual
     120.26  122.60   -2.34 1.34e+00 5.57e-01 3.05e+00
  angle pdb=" N   ARG A 211 "
        pdb=" CA  ARG A 211 "
        pdb=" C   ARG A 211 "
      ideal   model   delta    sigma   weight residual
     113.38  111.66    1.72 1.17e+00 7.31e-01 2.16e+00
  ... (remaining 16487 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.93: 7007
       14.93 -    29.87: 269
       29.87 -    44.80: 57
       44.80 -    59.73: 9
       59.73 -    74.67: 4
  Dihedral angle restraints: 7346
    sinusoidal: 3002
      harmonic: 4344
  Sorted by residual:
  dihedral pdb=" CA  ARG D 328 "
           pdb=" CB  ARG D 328 "
           pdb=" CG  ARG D 328 "
           pdb=" CD  ARG D 328 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -109.90   49.90     3      1.50e+01 4.44e-03 8.83e+00
  dihedral pdb=" CA  ARG C 328 "
           pdb=" CB  ARG C 328 "
           pdb=" CG  ARG C 328 "
           pdb=" CD  ARG C 328 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -131.70  -48.30     3      1.50e+01 4.44e-03 8.62e+00
  dihedral pdb=" CA  ILE D  58 "
           pdb=" CB  ILE D  58 "
           pdb=" CG1 ILE D  58 "
           pdb=" CD1 ILE D  58 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  107.66  -47.66     3      1.50e+01 4.44e-03 8.53e+00
  ... (remaining 7343 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 1199
       0.025 -    0.049: 391
       0.049 -    0.074: 132
       0.074 -    0.099: 65
       0.099 -    0.123: 19
  Chirality restraints: 1806
  Sorted by residual:
  chirality pdb=" CA  ILE A  95 "
            pdb=" N   ILE A  95 "
            pdb=" C   ILE A  95 "
            pdb=" CB  ILE A  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.81e-01
  chirality pdb=" CA  ILE B  95 "
            pdb=" N   ILE B  95 "
            pdb=" C   ILE B  95 "
            pdb=" CB  ILE B  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.70e-01
  chirality pdb=" CA  ILE B 237 "
            pdb=" N   ILE B 237 "
            pdb=" C   ILE B 237 "
            pdb=" CB  ILE B 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.28e-01
  ... (remaining 1803 not shown)

  Planarity restraints: 2134
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C 328 "   -0.019 5.00e-02 4.00e+02   2.82e-02 1.27e+00
        pdb=" N   PRO C 329 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO C 329 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO C 329 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 328 "   -0.019 5.00e-02 4.00e+02   2.82e-02 1.27e+00
        pdb=" N   PRO B 329 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO B 329 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B 329 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 328 "   -0.019 5.00e-02 4.00e+02   2.81e-02 1.26e+00
        pdb=" N   PRO A 329 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO A 329 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 329 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 2131 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 39
        2.68 -     3.23: 12235
        3.23 -     3.79: 20076
        3.79 -     4.34: 26256
        4.34 -     4.90: 41972
  Nonbonded interactions: 100578
  Sorted by model distance:
  nonbonded pdb=" CE1 TYR C 194 "
            pdb=" OD2 ASP D 202 "
     model   vdw
     2.119 3.340
  nonbonded pdb=" OD1 ASP C 202 "
            pdb=" OH  TYR D  20 "
     model   vdw
     2.125 3.040
  nonbonded pdb=" OH  TYR C  20 "
            pdb=" OD1 ASP D 202 "
     model   vdw
     2.127 3.040
  nonbonded pdb=" OD2 ASP C 202 "
            pdb=" CE1 TYR D 194 "
     model   vdw
     2.131 3.340
  nonbonded pdb=" CD1 TYR C 194 "
            pdb=" OD2 ASP D 202 "
     model   vdw
     2.325 3.340
  ... (remaining 100573 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'
}
ncs_group {
  reference = 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.440
  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:          0.250
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.390
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6169
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   0.014  12198  Z= 0.088
  Angle     :  0.375  10.487  16492  Z= 0.200
  Chirality :  0.032   0.123   1806
  Planarity :  0.002   0.028   2134
  Dihedral  :  8.668  74.669   4538
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.13 %
    Favored  : 98.64 %
  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:  3.74 (0.23), residues: 1464
  helix:  3.40 (0.16), residues: 1000
  sheet:  0.22 (0.66), residues: 72
  loop :  0.39 (0.33), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 181 
 TYR   0.007   0.001   TYR A 338 
 PHE   0.007   0.001   PHE A 125 
 TRP   0.007   0.001   TRP C 375 
 HIS   0.002   0.000   HIS B 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00167 (12198)
  covalent geometry    : angle       0.37463 (16492)
  hydrogen bonds       : bond        0.10968 (  754)
  hydrogen bonds       : angle       4.40524 ( 2238)

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

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

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 263
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 LEU cc_start: 0.8147 (mt) cc_final: 0.7744 (mt)
REVERT: A  337 LEU cc_start: 0.9018 (tp) cc_final: 0.8703 (tp)
REVERT: C   37 PHE cc_start: 0.7013 (t80) cc_final: 0.6362 (t80)
REVERT: C   47 THR cc_start: 0.4250 (m) cc_final: 0.3974 (p)
REVERT: C  163 ILE cc_start: 0.6640 (pt) cc_final: 0.6430 (pt)
REVERT: C  188 HIS cc_start: 0.6589 (m-70) cc_final: 0.6352 (m-70)
REVERT: C  340 GLU cc_start: 0.7477 (tp30) cc_final: 0.7260 (tp30)
REVERT: B  337 LEU cc_start: 0.9049 (tp) cc_final: 0.8796 (tp)
REVERT: D   37 PHE cc_start: 0.6914 (t80) cc_final: 0.6182 (t80)
REVERT: D  340 GLU cc_start: 0.7467 (tp30) cc_final: 0.7263 (tp30)
  outliers start: 3
  outliers final: 0
  residues processed: 266
  average time/residue: 0.1191
  time to fit residues: 44.1323
Evaluate side-chains
  108 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    8.9990
   chunk 124 optimal weight:   20.0000
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    9.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 266 ASN
C 105 HIS
C 134 HIS
C 188 HIS
B  79 ASN
B 234 GLN
B 252 GLN
B 266 ASN
D 105 HIS
D 134 HIS
** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.071847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.051025 restraints weight = 65405.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.052373 restraints weight = 39489.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.053296 restraints weight = 27829.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.054022 restraints weight = 22331.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.054469 restraints weight = 19352.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.2766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  12198  Z= 0.214
  Angle     :  0.640  12.712  16492  Z= 0.321
  Chirality :  0.041   0.202   1806
  Planarity :  0.003   0.034   2134
  Dihedral  :  3.597  13.732   1616
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 15.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  8.17 %
    Favored  : 90.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.03 (0.22), residues: 1464
  helix:  2.83 (0.16), residues: 1010
  sheet: -0.23 (0.73), residues: 58
  loop :  0.15 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 217 
 TYR   0.018   0.002   TYR C 162 
 PHE   0.025   0.002   PHE D 358 
 TRP   0.016   0.002   TRP C  80 
 HIS   0.007   0.001   HIS C 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 (12198)
  covalent geometry    : angle       0.64047 (16492)
  hydrogen bonds       : bond        0.03622 (  754)
  hydrogen bonds       : angle       4.21426 ( 2238)

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

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

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 144
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 SER cc_start: 0.8373 (m) cc_final: 0.7887 (p)
REVERT: A  189 LEU cc_start: 0.9639 (pt) cc_final: 0.9210 (mt)
REVERT: A  193 MET cc_start: 0.9517 (mmm) cc_final: 0.9204 (mmp)
REVERT: A  367 MET cc_start: 0.9267 (mmm) cc_final: 0.8941 (mmm)
REVERT: C  126 ASP cc_start: 0.9009 (t0) cc_final: 0.8459 (m-30)
REVERT: C  191 GLU cc_start: 0.9164 (mp0) cc_final: 0.8961 (mp0)
REVERT: C  193 MET cc_start: 0.9315 (mmm) cc_final: 0.8989 (mmm)
REVERT: C  195 GLU cc_start: 0.9256 (tt0) cc_final: 0.8626 (tt0)
REVERT: C  310 LEU cc_start: 0.9611 (mp) cc_final: 0.9358 (mt)
REVERT: C  340 GLU cc_start: 0.9402 (tp30) cc_final: 0.8566 (tp30)
REVERT: B   79 ASN cc_start: 0.9431 (m-40) cc_final: 0.9192 (m110)
REVERT: B  115 SER cc_start: 0.8346 (m) cc_final: 0.7847 (p)
REVERT: B  189 LEU cc_start: 0.9786 (mt) cc_final: 0.9460 (mt)
REVERT: B  193 MET cc_start: 0.9484 (mmm) cc_final: 0.9220 (mmp)
REVERT: B  367 MET cc_start: 0.9248 (mmm) cc_final: 0.8913 (mmm)
REVERT: D  155 ARG cc_start: 0.8390 (mtp180) cc_final: 0.8187 (ttm-80)
REVERT: D  191 GLU cc_start: 0.9118 (mp0) cc_final: 0.8524 (mm-30)
REVERT: D  193 MET cc_start: 0.9232 (mmm) cc_final: 0.8911 (mmm)
REVERT: D  195 GLU cc_start: 0.9175 (tt0) cc_final: 0.8951 (tt0)
REVERT: D  310 LEU cc_start: 0.9596 (mp) cc_final: 0.9340 (mt)
REVERT: D  340 GLU cc_start: 0.9394 (tp30) cc_final: 0.8443 (tp30)
REVERT: D  351 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8632 (tm-30)
  outliers start: 17
  outliers final: 10
  residues processed: 155
  average time/residue: 0.0977
  time to fit residues: 22.4665
Evaluate side-chains
  120 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 CYS
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  242 CYS
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  242 CYS
Chi-restraints excluded: chain B residue  339 ILE
Chi-restraints excluded: chain D residue  364 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 131 optimal weight:   10.0000
   chunk 77 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 133 optimal weight:    5.9990
   chunk 78 optimal weight:    0.0030
   chunk 38 optimal weight:    9.9990
   chunk 121 optimal weight:    0.0980
   chunk 49 optimal weight:    6.9990
   chunk 111 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9990
   chunk 53 optimal weight:   10.0000
   overall best weight:    1.4196

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 365 HIS
** C  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 352 ASN
B 365 HIS
** D   4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  31 ASN
D 188 HIS
D 352 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.073621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.053113 restraints weight = 64106.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.054643 restraints weight = 37896.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.055638 restraints weight = 26618.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.056395 restraints weight = 20978.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.056836 restraints weight = 17657.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.2995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  12198  Z= 0.123
  Angle     :  0.536   9.432  16492  Z= 0.263
  Chirality :  0.037   0.132   1806
  Planarity :  0.003   0.034   2134
  Dihedral  :  3.557  13.263   1616
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  8.40 %
    Favored  : 90.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.96 (0.22), residues: 1464
  helix:  2.84 (0.16), residues: 1010
  sheet: -0.51 (0.69), residues: 58
  loop :  0.01 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 181 
 TYR   0.024   0.001   TYR D 162 
 PHE   0.023   0.002   PHE D  99 
 TRP   0.010   0.001   TRP D  12 
 HIS   0.003   0.001   HIS C 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (12198)
  covalent geometry    : angle       0.53570 (16492)
  hydrogen bonds       : bond        0.03188 (  754)
  hydrogen bonds       : angle       3.93277 ( 2238)

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

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

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 137
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 SER cc_start: 0.8322 (m) cc_final: 0.7813 (p)
REVERT: A  189 LEU cc_start: 0.9622 (pt) cc_final: 0.9230 (mt)
REVERT: A  193 MET cc_start: 0.9510 (mmm) cc_final: 0.9220 (mmm)
REVERT: A  367 MET cc_start: 0.9255 (mmm) cc_final: 0.8934 (mmm)
REVERT: C  160 PHE cc_start: 0.7221 (t80) cc_final: 0.6797 (t80)
REVERT: C  193 MET cc_start: 0.9247 (mmm) cc_final: 0.8883 (mmm)
REVERT: C  310 LEU cc_start: 0.9608 (mp) cc_final: 0.9350 (mt)
REVERT: C  340 GLU cc_start: 0.9365 (tp30) cc_final: 0.8388 (tp30)
REVERT: C  367 MET cc_start: 0.9327 (mpp) cc_final: 0.9053 (mpp)
REVERT: B   34 CYS cc_start: 0.9041 (m) cc_final: 0.8652 (t)
REVERT: B   79 ASN cc_start: 0.9405 (m-40) cc_final: 0.9173 (m110)
REVERT: B  178 LYS cc_start: 0.9848 (mtpt) cc_final: 0.9600 (ptpp)
REVERT: B  189 LEU cc_start: 0.9782 (mt) cc_final: 0.9441 (mt)
REVERT: B  193 MET cc_start: 0.9515 (mmm) cc_final: 0.9244 (mmm)
REVERT: B  367 MET cc_start: 0.9243 (mmm) cc_final: 0.8889 (mmm)
REVERT: D   19 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8144 (mt-10)
REVERT: D  195 GLU cc_start: 0.9262 (tt0) cc_final: 0.8999 (tt0)
REVERT: D  310 LEU cc_start: 0.9587 (mp) cc_final: 0.9324 (mt)
REVERT: D  340 GLU cc_start: 0.9359 (tp30) cc_final: 0.8408 (tp30)
REVERT: D  351 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8544 (tm-30)
REVERT: D  367 MET cc_start: 0.9316 (mpp) cc_final: 0.9048 (mpp)
  outliers start: 14
  outliers final: 9
  residues processed: 145
  average time/residue: 0.1030
  time to fit residues: 21.9750
Evaluate side-chains
  122 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 113
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 CYS
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  242 CYS
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  242 CYS
Chi-restraints excluded: chain D residue  364 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 45 optimal weight:    8.9990
   chunk 128 optimal weight:    0.9980
   chunk 137 optimal weight:    8.9990
   chunk 91 optimal weight:    2.9990
   chunk 73 optimal weight:   10.0000
   chunk 144 optimal weight:    3.9990
   chunk 84 optimal weight:    8.9990
   chunk 102 optimal weight:    4.9990
   chunk 119 optimal weight:    4.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C   4 ASN
** C  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 234 GLN
D  18 GLN
D 188 HIS
** D 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.070028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.048561 restraints weight = 62596.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.049826 restraints weight = 38762.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.050594 restraints weight = 27327.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.051362 restraints weight = 22775.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.051596 restraints weight = 19754.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.3437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12198  Z= 0.184
  Angle     :  0.553  12.592  16492  Z= 0.283
  Chirality :  0.038   0.186   1806
  Planarity :  0.003   0.034   2134
  Dihedral  :  3.635  14.176   1616
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 14.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 10.14 %
    Favored  : 88.88 %
  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:  2.67 (0.22), residues: 1464
  helix:  2.64 (0.16), residues: 1010
  sheet: -0.52 (0.79), residues: 40
  loop : -0.21 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 181 
 TYR   0.021   0.001   TYR D 162 
 PHE   0.025   0.002   PHE D  99 
 TRP   0.011   0.002   TRP D  12 
 HIS   0.005   0.001   HIS B 365 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (12198)
  covalent geometry    : angle       0.55314 (16492)
  hydrogen bonds       : bond        0.03233 (  754)
  hydrogen bonds       : angle       4.08593 ( 2238)

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

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

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 SER cc_start: 0.8366 (m) cc_final: 0.7860 (p)
REVERT: A  173 LEU cc_start: 0.9484 (mt) cc_final: 0.9240 (mt)
REVERT: A  189 LEU cc_start: 0.9630 (pt) cc_final: 0.9220 (mt)
REVERT: A  193 MET cc_start: 0.9532 (mmm) cc_final: 0.9224 (mmm)
REVERT: A  367 MET cc_start: 0.9222 (mmm) cc_final: 0.8995 (mmm)
REVERT: C    1 MET cc_start: 0.3919 (ttt) cc_final: 0.3411 (ttt)
REVERT: C  126 ASP cc_start: 0.8906 (t0) cc_final: 0.8332 (m-30)
REVERT: C  193 MET cc_start: 0.9367 (mmm) cc_final: 0.8973 (mmm)
REVERT: C  219 LYS cc_start: 0.9749 (tttt) cc_final: 0.9464 (tppt)
REVERT: C  340 GLU cc_start: 0.9423 (tp30) cc_final: 0.8489 (tp30)
REVERT: C  367 MET cc_start: 0.9371 (mpp) cc_final: 0.9095 (mpp)
REVERT: B   34 CYS cc_start: 0.9194 (m) cc_final: 0.8339 (p)
REVERT: B   79 ASN cc_start: 0.9434 (m-40) cc_final: 0.9194 (m-40)
REVERT: B  189 LEU cc_start: 0.9764 (mt) cc_final: 0.9469 (mt)
REVERT: B  193 MET cc_start: 0.9536 (mmm) cc_final: 0.9265 (mmm)
REVERT: B  367 MET cc_start: 0.9212 (mmm) cc_final: 0.8969 (mmm)
REVERT: D  193 MET cc_start: 0.9237 (mmm) cc_final: 0.8937 (mmm)
REVERT: D  195 GLU cc_start: 0.9297 (tt0) cc_final: 0.9002 (tt0)
REVERT: D  340 GLU cc_start: 0.9418 (tp30) cc_final: 0.8451 (tp30)
REVERT: D  351 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8703 (tm-30)
REVERT: D  367 MET cc_start: 0.9389 (mpp) cc_final: 0.9111 (mpp)
  outliers start: 13
  outliers final: 8
  residues processed: 130
  average time/residue: 0.1022
  time to fit residues: 19.8282
Evaluate side-chains
  116 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 CYS
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  242 CYS
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain D residue  364 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 87 optimal weight:    8.9990
   chunk 24 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 90 optimal weight:    0.3980
   chunk 51 optimal weight:    8.9990
   chunk 142 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9980
   chunk 145 optimal weight:    3.9990
   chunk 140 optimal weight:    1.9990
   chunk 93 optimal weight:    6.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** C  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 365 HIS
D 188 HIS
** D 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 365 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.072507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.052086 restraints weight = 65783.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.053573 restraints weight = 38401.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.054499 restraints weight = 26559.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.055221 restraints weight = 21106.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.055665 restraints weight = 18165.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.3512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  12198  Z= 0.108
  Angle     :  0.509  10.813  16492  Z= 0.255
  Chirality :  0.037   0.155   1806
  Planarity :  0.003   0.033   2134
  Dihedral  :  3.606  18.050   1616
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 11.35 %
    Favored  : 87.82 %
  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:  2.77 (0.22), residues: 1464
  helix:  2.75 (0.16), residues: 1010
  sheet: -0.47 (0.82), residues: 40
  loop : -0.30 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 155 
 TYR   0.018   0.001   TYR C 306 
 PHE   0.019   0.001   PHE D  99 
 TRP   0.013   0.001   TRP D  12 
 HIS   0.003   0.001   HIS A 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 (12198)
  covalent geometry    : angle       0.50874 (16492)
  hydrogen bonds       : bond        0.03054 (  754)
  hydrogen bonds       : angle       3.83161 ( 2238)

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

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

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 LEU cc_start: 0.9501 (mt) cc_final: 0.9253 (mt)
REVERT: A  189 LEU cc_start: 0.9633 (pt) cc_final: 0.9220 (mt)
REVERT: A  193 MET cc_start: 0.9475 (mmm) cc_final: 0.9162 (mmm)
REVERT: A  367 MET cc_start: 0.9251 (mmm) cc_final: 0.9045 (mmm)
REVERT: C    1 MET cc_start: 0.3787 (ttt) cc_final: 0.3207 (ttt)
REVERT: C   37 PHE cc_start: 0.8215 (t80) cc_final: 0.7826 (t80)
REVERT: C  126 ASP cc_start: 0.8890 (t0) cc_final: 0.8284 (m-30)
REVERT: C  193 MET cc_start: 0.9310 (mmm) cc_final: 0.8968 (mmm)
REVERT: C  310 LEU cc_start: 0.9654 (mp) cc_final: 0.9374 (mt)
REVERT: C  340 GLU cc_start: 0.9388 (tp30) cc_final: 0.8420 (tp30)
REVERT: C  367 MET cc_start: 0.9354 (mpp) cc_final: 0.9010 (mpp)
REVERT: B   34 CYS cc_start: 0.9181 (m) cc_final: 0.8322 (p)
REVERT: B   79 ASN cc_start: 0.9411 (m-40) cc_final: 0.9168 (m110)
REVERT: B  178 LYS cc_start: 0.9850 (mtpt) cc_final: 0.9580 (ptpp)
REVERT: B  189 LEU cc_start: 0.9760 (mt) cc_final: 0.9426 (mt)
REVERT: B  193 MET cc_start: 0.9516 (mmm) cc_final: 0.9201 (mmm)
REVERT: B  367 MET cc_start: 0.9239 (mmm) cc_final: 0.9020 (mmm)
REVERT: D  195 GLU cc_start: 0.9232 (tt0) cc_final: 0.8935 (tt0)
REVERT: D  310 LEU cc_start: 0.9639 (mp) cc_final: 0.9357 (mt)
REVERT: D  340 GLU cc_start: 0.9396 (tp30) cc_final: 0.8386 (tp30)
REVERT: D  351 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8544 (tm-30)
REVERT: D  367 MET cc_start: 0.9371 (mpp) cc_final: 0.9034 (mpp)
  outliers start: 11
  outliers final: 7
  residues processed: 121
  average time/residue: 0.1013
  time to fit residues: 18.3546
Evaluate side-chains
  97 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  242 CYS
Chi-restraints excluded: chain D residue  364 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   chunk 85 optimal weight:    9.9990
   chunk 54 optimal weight:    9.9990
   chunk 109 optimal weight:    2.9990
   chunk 100 optimal weight:    6.9990
   chunk 99 optimal weight:    3.9990
   chunk 127 optimal weight:    4.9990
   chunk 3 optimal weight:   10.0000
   chunk 112 optimal weight:   20.0000
   chunk 130 optimal weight:    2.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 266 ASN
** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 317 GLN
** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 188 HIS
D 266 ASN
** D 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.068902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.047915 restraints weight = 62848.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.049059 restraints weight = 38456.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.049857 restraints weight = 27270.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.050590 restraints weight = 22564.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.050885 restraints weight = 19529.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.3940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  12198  Z= 0.262
  Angle     :  0.597   8.554  16492  Z= 0.318
  Chirality :  0.040   0.274   1806
  Planarity :  0.003   0.033   2134
  Dihedral  :  3.818  16.922   1616
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 16.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 12.33 %
    Favored  : 86.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.27 (0.22), residues: 1464
  helix:  2.41 (0.16), residues: 1008
  sheet: -1.12 (0.64), residues: 60
  loop : -0.48 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 181 
 TYR   0.020   0.002   TYR D 162 
 PHE   0.025   0.002   PHE D 358 
 TRP   0.018   0.002   TRP C  80 
 HIS   0.006   0.001   HIS B 365 

Details of bonding type rmsd
  covalent geometry    : bond        0.00521 (12198)
  covalent geometry    : angle       0.59725 (16492)
  hydrogen bonds       : bond        0.03487 (  754)
  hydrogen bonds       : angle       4.26284 ( 2238)

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

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

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 LEU cc_start: 0.9499 (mt) cc_final: 0.9248 (mt)
REVERT: A  189 LEU cc_start: 0.9640 (pt) cc_final: 0.9047 (tt)
REVERT: A  193 MET cc_start: 0.9547 (mmm) cc_final: 0.9153 (mmm)
REVERT: A  340 GLU cc_start: 0.9787 (mm-30) cc_final: 0.9320 (mm-30)
REVERT: C    1 MET cc_start: 0.3880 (ttt) cc_final: 0.3265 (ttt)
REVERT: C  126 ASP cc_start: 0.8981 (t0) cc_final: 0.8447 (m-30)
REVERT: C  191 GLU cc_start: 0.9172 (mp0) cc_final: 0.8778 (pm20)
REVERT: C  193 MET cc_start: 0.9398 (mmm) cc_final: 0.8997 (mmm)
REVERT: C  340 GLU cc_start: 0.9474 (tp30) cc_final: 0.8505 (tp30)
REVERT: C  367 MET cc_start: 0.9384 (mpp) cc_final: 0.9074 (mpp)
REVERT: B   79 ASN cc_start: 0.9468 (m-40) cc_final: 0.9217 (m-40)
REVERT: B  189 LEU cc_start: 0.9734 (mt) cc_final: 0.9453 (mt)
REVERT: B  193 MET cc_start: 0.9536 (mmm) cc_final: 0.9255 (mmm)
REVERT: D  173 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.8841 (mm)
REVERT: D  195 GLU cc_start: 0.9325 (tt0) cc_final: 0.9091 (tt0)
REVERT: D  340 GLU cc_start: 0.9469 (tp30) cc_final: 0.8521 (tp30)
REVERT: D  351 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8627 (tm-30)
REVERT: D  367 MET cc_start: 0.9382 (mpp) cc_final: 0.9105 (mpp)
  outliers start: 15
  outliers final: 11
  residues processed: 99
  average time/residue: 0.1103
  time to fit residues: 16.0381
Evaluate side-chains
  101 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 CYS
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  373 ILE
Chi-restraints excluded: chain C residue  146 PHE
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  236 THR
Chi-restraints excluded: chain B residue  373 ILE
Chi-restraints excluded: chain D residue  173 LEU
Chi-restraints excluded: chain D residue  364 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 93 optimal weight:    0.8980
   chunk 101 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 136 optimal weight:    4.9990
   chunk 88 optimal weight:    7.9990
   chunk 64 optimal weight:    0.7980
   chunk 53 optimal weight:   10.0000
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** C  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 266 ASN
** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 266 ASN
** D 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.072021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.051458 restraints weight = 65102.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.052933 restraints weight = 38313.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.053849 restraints weight = 26685.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.054618 restraints weight = 21293.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.055010 restraints weight = 18160.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.3898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  12198  Z= 0.111
  Angle     :  0.516  10.728  16492  Z= 0.258
  Chirality :  0.037   0.216   1806
  Planarity :  0.003   0.034   2134
  Dihedral  :  3.638  19.659   1616
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 12.71 %
    Favored  : 86.61 %
  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:  2.66 (0.22), residues: 1464
  helix:  2.69 (0.16), residues: 1008
  sheet: -0.49 (0.80), residues: 42
  loop : -0.38 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 174 
 TYR   0.015   0.001   TYR D 162 
 PHE   0.016   0.001   PHE D  37 
 TRP   0.015   0.001   TRP D  12 
 HIS   0.004   0.001   HIS D 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (12198)
  covalent geometry    : angle       0.51638 (16492)
  hydrogen bonds       : bond        0.03104 (  754)
  hydrogen bonds       : angle       3.84914 ( 2238)

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

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

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 LEU cc_start: 0.9520 (mt) cc_final: 0.9259 (mt)
REVERT: A  189 LEU cc_start: 0.9627 (pt) cc_final: 0.9221 (mt)
REVERT: A  193 MET cc_start: 0.9477 (mmm) cc_final: 0.9127 (mmm)
REVERT: A  310 LEU cc_start: 0.9724 (mp) cc_final: 0.9303 (pp)
REVERT: A  340 GLU cc_start: 0.9741 (mm-30) cc_final: 0.9274 (mm-30)
REVERT: A  367 MET cc_start: 0.9279 (mmm) cc_final: 0.9009 (mmm)
REVERT: C    1 MET cc_start: 0.3564 (ttt) cc_final: 0.2898 (ttt)
REVERT: C  126 ASP cc_start: 0.8930 (t0) cc_final: 0.8369 (m-30)
REVERT: C  193 MET cc_start: 0.9286 (mmm) cc_final: 0.8965 (mmm)
REVERT: C  340 GLU cc_start: 0.9403 (tp30) cc_final: 0.8382 (tp30)
REVERT: C  367 MET cc_start: 0.9372 (mpp) cc_final: 0.9123 (mpp)
REVERT: B   34 CYS cc_start: 0.8988 (m) cc_final: 0.8047 (p)
REVERT: B   79 ASN cc_start: 0.9437 (m-40) cc_final: 0.9178 (m-40)
REVERT: B  189 LEU cc_start: 0.9731 (mt) cc_final: 0.9460 (mt)
REVERT: B  193 MET cc_start: 0.9520 (mmm) cc_final: 0.9184 (mmm)
REVERT: B  342 LEU cc_start: 0.9713 (OUTLIER) cc_final: 0.9452 (mm)
REVERT: B  367 MET cc_start: 0.9269 (mmm) cc_final: 0.9068 (mmm)
REVERT: D  193 MET cc_start: 0.8967 (mtm) cc_final: 0.8683 (ptt)
REVERT: D  340 GLU cc_start: 0.9409 (tp30) cc_final: 0.8377 (tp30)
REVERT: D  351 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8507 (tm-30)
REVERT: D  367 MET cc_start: 0.9370 (mpp) cc_final: 0.9115 (mpp)
  outliers start: 9
  outliers final: 6
  residues processed: 103
  average time/residue: 0.1027
  time to fit residues: 15.7928
Evaluate side-chains
  96 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain D residue  364 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 20 optimal weight:    9.9990
   chunk 75 optimal weight:    6.9990
   chunk 71 optimal weight:    0.9980
   chunk 118 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 39 optimal weight:    9.9990
   chunk 73 optimal weight:   10.0000
   chunk 134 optimal weight:    3.9990
   chunk 95 optimal weight:    0.5980
   chunk 107 optimal weight:    6.9990
   chunk 50 optimal weight:    8.9990
   overall best weight:    2.7186

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

Flipped N/Q/H residues before XYZ refinement:
A 317 GLN
** A 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 266 ASN
** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 352 ASN
** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D   4 ASN
** D 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.069484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.048207 restraints weight = 60670.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.049301 restraints weight = 37445.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.050018 restraints weight = 27038.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.050816 restraints weight = 22624.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.051111 restraints weight = 19619.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.4126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12198  Z= 0.189
  Angle     :  0.547   8.812  16492  Z= 0.285
  Chirality :  0.038   0.196   1806
  Planarity :  0.003   0.035   2134
  Dihedral  :  3.746  18.544   1616
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 14.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 13.54 %
    Favored  : 85.63 %
  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:  2.43 (0.22), residues: 1464
  helix:  2.53 (0.16), residues: 1008
  sheet: -1.07 (0.65), residues: 60
  loop : -0.43 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 181 
 TYR   0.016   0.001   TYR D 162 
 PHE   0.020   0.002   PHE D 358 
 TRP   0.020   0.002   TRP C  80 
 HIS   0.005   0.001   HIS C 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 (12198)
  covalent geometry    : angle       0.54711 (16492)
  hydrogen bonds       : bond        0.03266 (  754)
  hydrogen bonds       : angle       4.05193 ( 2238)

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

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

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 LEU cc_start: 0.9493 (mt) cc_final: 0.9231 (mt)
REVERT: A  189 LEU cc_start: 0.9630 (pt) cc_final: 0.9231 (mt)
REVERT: A  193 MET cc_start: 0.9505 (mmm) cc_final: 0.9176 (mmm)
REVERT: A  340 GLU cc_start: 0.9773 (mm-30) cc_final: 0.9296 (mm-30)
REVERT: A  367 MET cc_start: 0.9223 (mmm) cc_final: 0.8995 (mmm)
REVERT: C  126 ASP cc_start: 0.8976 (t0) cc_final: 0.8441 (m-30)
REVERT: C  191 GLU cc_start: 0.9121 (mp0) cc_final: 0.8760 (pm20)
REVERT: C  193 MET cc_start: 0.9352 (mmm) cc_final: 0.8962 (mmm)
REVERT: C  310 LEU cc_start: 0.9611 (mp) cc_final: 0.9320 (mt)
REVERT: C  340 GLU cc_start: 0.9434 (tp30) cc_final: 0.8452 (tp30)
REVERT: C  367 MET cc_start: 0.9374 (mpp) cc_final: 0.9066 (mpp)
REVERT: B   34 CYS cc_start: 0.8980 (m) cc_final: 0.8065 (p)
REVERT: B   79 ASN cc_start: 0.9459 (m-40) cc_final: 0.9204 (m-40)
REVERT: B  189 LEU cc_start: 0.9735 (mt) cc_final: 0.9460 (mt)
REVERT: B  193 MET cc_start: 0.9510 (mmm) cc_final: 0.9239 (mmm)
REVERT: B  342 LEU cc_start: 0.9747 (OUTLIER) cc_final: 0.9456 (mm)
REVERT: B  367 MET cc_start: 0.9213 (mmm) cc_final: 0.8984 (mmm)
REVERT: D  191 GLU cc_start: 0.9170 (mp0) cc_final: 0.8747 (pm20)
REVERT: D  195 GLU cc_start: 0.9294 (tt0) cc_final: 0.8955 (tt0)
REVERT: D  310 LEU cc_start: 0.9596 (mp) cc_final: 0.9309 (mt)
REVERT: D  340 GLU cc_start: 0.9443 (tp30) cc_final: 0.8482 (tp30)
REVERT: D  351 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8552 (tm-30)
REVERT: D  367 MET cc_start: 0.9373 (mpp) cc_final: 0.9045 (mpp)
  outliers start: 11
  outliers final: 8
  residues processed: 96
  average time/residue: 0.1135
  time to fit residues: 16.0019
Evaluate side-chains
  97 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  197 LEU
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  373 ILE
Chi-restraints excluded: chain D residue  364 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 57 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 46 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 121 optimal weight:    0.5980
   chunk 143 optimal weight:    3.9990
   chunk 83 optimal weight:    6.9990
   chunk 87 optimal weight:    0.5980
   chunk 113 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
C  31 ASN
** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 266 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.072182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.050936 restraints weight = 61066.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.052248 restraints weight = 36802.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.053070 restraints weight = 25823.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.053830 restraints weight = 21198.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.054311 restraints weight = 18224.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.4113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  12198  Z= 0.104
  Angle     :  0.525   9.423  16492  Z= 0.261
  Chirality :  0.037   0.179   1806
  Planarity :  0.003   0.035   2134
  Dihedral  :  3.602  19.802   1616
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 13.84 %
    Favored  : 85.40 %
  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:  2.73 (0.22), residues: 1464
  helix:  2.76 (0.16), residues: 1008
  sheet: -0.35 (0.84), residues: 42
  loop : -0.44 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  25 
 TYR   0.017   0.001   TYR C 306 
 PHE   0.016   0.001   PHE D  37 
 TRP   0.017   0.001   TRP D  12 
 HIS   0.005   0.001   HIS C 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 (12198)
  covalent geometry    : angle       0.52521 (16492)
  hydrogen bonds       : bond        0.03051 (  754)
  hydrogen bonds       : angle       3.76538 ( 2238)

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

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

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 LEU cc_start: 0.9620 (pt) cc_final: 0.9160 (mt)
REVERT: A  193 MET cc_start: 0.9441 (mmm) cc_final: 0.9103 (mmm)
REVERT: A  310 LEU cc_start: 0.9730 (mp) cc_final: 0.9298 (pp)
REVERT: A  340 GLU cc_start: 0.9726 (mm-30) cc_final: 0.9270 (mm-30)
REVERT: A  367 MET cc_start: 0.9274 (mmm) cc_final: 0.8992 (mmm)
REVERT: C  126 ASP cc_start: 0.8937 (t0) cc_final: 0.8431 (m-30)
REVERT: C  191 GLU cc_start: 0.9015 (mp0) cc_final: 0.8353 (pm20)
REVERT: C  193 MET cc_start: 0.9274 (mmm) cc_final: 0.9044 (mmm)
REVERT: C  310 LEU cc_start: 0.9621 (mp) cc_final: 0.9333 (mt)
REVERT: C  340 GLU cc_start: 0.9424 (tp30) cc_final: 0.8417 (tp30)
REVERT: C  367 MET cc_start: 0.9348 (mpp) cc_final: 0.9031 (mpp)
REVERT: B   34 CYS cc_start: 0.8941 (m) cc_final: 0.7985 (p)
REVERT: B   79 ASN cc_start: 0.9438 (m-40) cc_final: 0.9174 (m-40)
REVERT: B  189 LEU cc_start: 0.9740 (mt) cc_final: 0.9474 (mt)
REVERT: B  193 MET cc_start: 0.9437 (mmm) cc_final: 0.9147 (mmm)
REVERT: B  342 LEU cc_start: 0.9726 (OUTLIER) cc_final: 0.9457 (mm)
REVERT: D  191 GLU cc_start: 0.9053 (mp0) cc_final: 0.8642 (pm20)
REVERT: D  310 LEU cc_start: 0.9613 (mp) cc_final: 0.9333 (mt)
REVERT: D  340 GLU cc_start: 0.9416 (tp30) cc_final: 0.8391 (tp30)
REVERT: D  351 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8444 (tm-30)
REVERT: D  367 MET cc_start: 0.9355 (mpp) cc_final: 0.9036 (mpp)
  outliers start: 10
  outliers final: 8
  residues processed: 108
  average time/residue: 0.0984
  time to fit residues: 15.6557
Evaluate side-chains
  96 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  197 LEU
Chi-restraints excluded: chain B residue  236 THR
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain D residue  118 THR
Chi-restraints excluded: chain D residue  364 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 1 optimal weight:    7.9990
   chunk 111 optimal weight:    9.9990
   chunk 35 optimal weight:    6.9990
   chunk 37 optimal weight:    0.0970
   chunk 45 optimal weight:    0.0980
   chunk 57 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 63 optimal weight:   10.0000
   chunk 102 optimal weight:    0.1980
   chunk 39 optimal weight:    6.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3695 r_free = 0.3695 target = 0.072551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.051258 restraints weight = 61340.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.052618 restraints weight = 37188.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 16)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.053236 restraints weight = 26401.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.054177 restraints weight = 21557.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.054493 restraints weight = 18369.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.4226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  12198  Z= 0.102
  Angle     :  0.540  12.087  16492  Z= 0.266
  Chirality :  0.037   0.174   1806
  Planarity :  0.003   0.035   2134
  Dihedral  :  3.731  32.659   1616
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 14.37 %
    Favored  : 84.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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:  2.80 (0.22), residues: 1464
  helix:  2.78 (0.16), residues: 1010
  sheet: -0.25 (1.28), residues: 24
  loop : -0.35 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 155 
 TYR   0.017   0.001   TYR C 306 
 PHE   0.016   0.001   PHE D  37 
 TRP   0.018   0.001   TRP C  12 
 HIS   0.006   0.001   HIS C 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 (12198)
  covalent geometry    : angle       0.54032 (16492)
  hydrogen bonds       : bond        0.02982 (  754)
  hydrogen bonds       : angle       3.71676 ( 2238)

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

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

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 LEU cc_start: 0.9648 (pt) cc_final: 0.9056 (mt)
REVERT: A  310 LEU cc_start: 0.9726 (mp) cc_final: 0.9286 (pp)
REVERT: A  340 GLU cc_start: 0.9719 (mm-30) cc_final: 0.9264 (mm-30)
REVERT: A  367 MET cc_start: 0.9292 (mmm) cc_final: 0.8999 (mmm)
REVERT: C  126 ASP cc_start: 0.8939 (t0) cc_final: 0.8415 (m-30)
REVERT: C  193 MET cc_start: 0.9268 (mmm) cc_final: 0.9051 (mmm)
REVERT: C  310 LEU cc_start: 0.9625 (mp) cc_final: 0.9354 (mt)
REVERT: C  340 GLU cc_start: 0.9428 (tp30) cc_final: 0.8433 (tp30)
REVERT: C  367 MET cc_start: 0.9290 (mpp) cc_final: 0.9009 (mpp)
REVERT: B   34 CYS cc_start: 0.8960 (m) cc_final: 0.8006 (p)
REVERT: B   79 ASN cc_start: 0.9430 (m-40) cc_final: 0.9164 (m-40)
REVERT: B  340 GLU cc_start: 0.9759 (mm-30) cc_final: 0.9186 (mm-30)
REVERT: B  342 LEU cc_start: 0.9719 (OUTLIER) cc_final: 0.9441 (mm)
REVERT: D  193 MET cc_start: 0.9108 (mtm) cc_final: 0.8899 (mtm)
REVERT: D  310 LEU cc_start: 0.9604 (mp) cc_final: 0.9330 (mt)
REVERT: D  340 GLU cc_start: 0.9418 (tp30) cc_final: 0.8415 (tp30)
REVERT: D  351 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8420 (tm-30)
REVERT: D  367 MET cc_start: 0.9280 (mpp) cc_final: 0.8999 (mpp)
  outliers start: 10
  outliers final: 7
  residues processed: 100
  average time/residue: 0.1106
  time to fit residues: 16.3743
Evaluate side-chains
  98 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  197 LEU
Chi-restraints excluded: chain B residue  236 THR
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain D residue  118 THR
Chi-restraints excluded: chain D residue  364 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 58 optimal weight:    7.9990
   chunk 72 optimal weight:    0.3980
   chunk 21 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 103 optimal weight:    0.8980
   chunk 121 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 43 optimal weight:    9.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 145 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.072162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.050836 restraints weight = 61191.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.052151 restraints weight = 37575.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.053079 restraints weight = 26659.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.053798 restraints weight = 21640.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.053994 restraints weight = 18674.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.4373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12198  Z= 0.121
  Angle     :  0.553  12.861  16492  Z= 0.276
  Chirality :  0.038   0.218   1806
  Planarity :  0.003   0.035   2134
  Dihedral  :  3.822  38.283   1616
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 14.37 %
    Favored  : 84.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.73 (0.22), residues: 1464
  helix:  2.76 (0.16), residues: 1008
  sheet: -0.33 (1.22), residues: 24
  loop : -0.42 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 155 
 TYR   0.016   0.001   TYR C 306 
 PHE   0.031   0.002   PHE C  96 
 TRP   0.021   0.001   TRP C  80 
 HIS   0.005   0.001   HIS D 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (12198)
  covalent geometry    : angle       0.55296 (16492)
  hydrogen bonds       : bond        0.03001 (  754)
  hydrogen bonds       : angle       3.76302 ( 2238)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2012.71 seconds
wall clock time: 35 minutes 46.77 seconds (2146.77 seconds total)