Starting phenix.real_space_refine
on Sun Apr  5 12:25:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jzn_61929/04_2026/9jzn_61929.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jzn_61929/04_2026/9jzn_61929.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.15
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jzn_61929/04_2026/9jzn_61929.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jzn_61929/04_2026/9jzn_61929.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jzn_61929/04_2026/9jzn_61929.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jzn_61929/04_2026/9jzn_61929.map"
  }
  resolution = 3.15
  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=   0.007 sd=   0.114
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      52      5.16       5
     C    6656      2.51       5
     N    1776      2.21       5
     O    1944      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 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: 10428
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2607
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 316}
          Chain breaks: 2
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 1.62, per 1000 atoms: 0.16
  Number of scatterers: 10428
  At special positions: 0
  Unit cell: (102.808, 102.808, 97.016, 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      52     16.00
     O    1944      8.00
     N    1776      7.00
     C    6656      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: 0.65
  Conformation dependent library (CDL) restraints added in 492.5 milliseconds
  

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2504

  Finding SS restraints...
    Secondary structure from input PDB file:
      76 helices and 4 sheets defined
      62.2% alpha, 2.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 49 through 51
      No H-bonds generated for 'chain 'A' and resid 49 through 51'
    Processing helix  chain 'A' and resid 52 through 60
    Processing helix  chain 'A' and resid 62 through 67
    Processing helix  chain 'A' and resid 71 through 83
      removed outlier: 4.696A  pdb=" N   SER A  75 " --> pdb=" O   THR A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 94
      removed outlier: 3.726A  pdb=" N   ALA A  89 " --> pdb=" O   GLY A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 150
    Processing helix  chain 'A' and resid 152 through 158
    Processing helix  chain 'A' and resid 159 through 173
      removed outlier: 3.709A  pdb=" N   LYS A 163 " --> pdb=" O   ALA A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 182
    Processing helix  chain 'A' and resid 190 through 199
    Processing helix  chain 'A' and resid 202 through 211
    Processing helix  chain 'A' and resid 218 through 230
      removed outlier: 3.535A  pdb=" N   GLN A 225 " --> pdb=" O   GLU A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 248
    Processing helix  chain 'A' and resid 255 through 276
      removed outlier: 3.630A  pdb=" N   GLU A 261 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 283
    Processing helix  chain 'A' and resid 288 through 293
    Processing helix  chain 'A' and resid 299 through 314
    Processing helix  chain 'A' and resid 332 through 341
    Processing helix  chain 'A' and resid 354 through 365
    Processing helix  chain 'B' and resid 49 through 51
      No H-bonds generated for 'chain 'B' and resid 49 through 51'
    Processing helix  chain 'B' and resid 52 through 60
    Processing helix  chain 'B' and resid 62 through 67
    Processing helix  chain 'B' and resid 71 through 83
      removed outlier: 4.696A  pdb=" N   SER B  75 " --> pdb=" O   THR B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 94
      removed outlier: 3.726A  pdb=" N   ALA B  89 " --> pdb=" O   GLY B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 150
    Processing helix  chain 'B' and resid 152 through 158
    Processing helix  chain 'B' and resid 159 through 173
      removed outlier: 3.709A  pdb=" N   LYS B 163 " --> pdb=" O   ALA B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 182
    Processing helix  chain 'B' and resid 190 through 199
    Processing helix  chain 'B' and resid 202 through 211
    Processing helix  chain 'B' and resid 218 through 230
      removed outlier: 3.535A  pdb=" N   GLN B 225 " --> pdb=" O   GLU B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 248
    Processing helix  chain 'B' and resid 255 through 276
      removed outlier: 3.630A  pdb=" N   GLU B 261 " --> pdb=" O   VAL B 257 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 283
    Processing helix  chain 'B' and resid 288 through 293
    Processing helix  chain 'B' and resid 299 through 314
    Processing helix  chain 'B' and resid 332 through 341
    Processing helix  chain 'B' and resid 354 through 365
    Processing helix  chain 'C' and resid 49 through 51
      No H-bonds generated for 'chain 'C' and resid 49 through 51'
    Processing helix  chain 'C' and resid 52 through 60
    Processing helix  chain 'C' and resid 62 through 67
    Processing helix  chain 'C' and resid 71 through 83
      removed outlier: 4.696A  pdb=" N   SER C  75 " --> pdb=" O   THR C  71 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 94
      removed outlier: 3.726A  pdb=" N   ALA C  89 " --> pdb=" O   GLY C  85 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 129 through 150
    Processing helix  chain 'C' and resid 152 through 158
    Processing helix  chain 'C' and resid 159 through 173
      removed outlier: 3.709A  pdb=" N   LYS C 163 " --> pdb=" O   ALA C 159 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 177 through 182
    Processing helix  chain 'C' and resid 190 through 199
    Processing helix  chain 'C' and resid 202 through 211
    Processing helix  chain 'C' and resid 218 through 230
      removed outlier: 3.535A  pdb=" N   GLN C 225 " --> pdb=" O   GLU C 221 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 235 through 248
    Processing helix  chain 'C' and resid 255 through 276
      removed outlier: 3.630A  pdb=" N   GLU C 261 " --> pdb=" O   VAL C 257 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 279 through 283
    Processing helix  chain 'C' and resid 288 through 293
    Processing helix  chain 'C' and resid 299 through 314
    Processing helix  chain 'C' and resid 332 through 341
    Processing helix  chain 'C' and resid 354 through 365
    Processing helix  chain 'D' and resid 49 through 51
      No H-bonds generated for 'chain 'D' and resid 49 through 51'
    Processing helix  chain 'D' and resid 52 through 60
    Processing helix  chain 'D' and resid 62 through 67
    Processing helix  chain 'D' and resid 71 through 83
      removed outlier: 4.696A  pdb=" N   SER D  75 " --> pdb=" O   THR D  71 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 85 through 94
      removed outlier: 3.726A  pdb=" N   ALA D  89 " --> pdb=" O   GLY D  85 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 129 through 150
    Processing helix  chain 'D' and resid 152 through 158
    Processing helix  chain 'D' and resid 159 through 173
      removed outlier: 3.709A  pdb=" N   LYS D 163 " --> pdb=" O   ALA D 159 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 177 through 182
    Processing helix  chain 'D' and resid 190 through 199
    Processing helix  chain 'D' and resid 202 through 211
    Processing helix  chain 'D' and resid 218 through 230
      removed outlier: 3.535A  pdb=" N   GLN D 225 " --> pdb=" O   GLU D 221 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 235 through 248
    Processing helix  chain 'D' and resid 255 through 276
      removed outlier: 3.630A  pdb=" N   GLU D 261 " --> pdb=" O   VAL D 257 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 279 through 283
    Processing helix  chain 'D' and resid 288 through 293
    Processing helix  chain 'D' and resid 299 through 314
    Processing helix  chain 'D' and resid 332 through 341
    Processing helix  chain 'D' and resid 354 through 365
    Processing sheet with id=1, first strand: chain 'A' and resid 99 through 105
      removed outlier: 6.908A  pdb=" N   VAL A 113 " --> pdb=" O   LEU A 101 " (cutoff:3.500A)
    Processing sheet with id=2, first strand: chain 'B' and resid 99 through 105
      removed outlier: 6.908A  pdb=" N   VAL B 113 " --> pdb=" O   LEU B 101 " (cutoff:3.500A)
    Processing sheet with id=3, first strand: chain 'C' and resid 99 through 105
      removed outlier: 6.908A  pdb=" N   VAL C 113 " --> pdb=" O   LEU C 101 " (cutoff:3.500A)
    Processing sheet with id=4, first strand: chain 'D' and resid 99 through 105
      removed outlier: 6.908A  pdb=" N   VAL D 113 " --> pdb=" O   LEU D 101 " (cutoff:3.500A)

    536 hydrogen bonds defined for protein.
    1536 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: 1.73

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2088
        1.33 -     1.45: 2596
        1.45 -     1.57: 5880
        1.57 -     1.70: 4
        1.70 -     1.82: 88
  Bond restraints: 10656
  Sorted by residual:
  bond pdb=" CA  SER D  99 "
       pdb=" CB  SER D  99 "
    ideal  model  delta    sigma   weight residual
    1.532  1.445  0.087 1.58e-02 4.01e+03 3.02e+01
  bond pdb=" CA  SER A  99 "
       pdb=" CB  SER A  99 "
    ideal  model  delta    sigma   weight residual
    1.532  1.445  0.087 1.58e-02 4.01e+03 3.02e+01
  bond pdb=" CA  SER C  99 "
       pdb=" CB  SER C  99 "
    ideal  model  delta    sigma   weight residual
    1.532  1.445  0.087 1.58e-02 4.01e+03 3.02e+01
  bond pdb=" CA  SER B  99 "
       pdb=" CB  SER B  99 "
    ideal  model  delta    sigma   weight residual
    1.532  1.445  0.087 1.58e-02 4.01e+03 3.02e+01
  bond pdb=" CA  SER B 135 "
       pdb=" CB  SER B 135 "
    ideal  model  delta    sigma   weight residual
    1.528  1.456  0.072 1.56e-02 4.11e+03 2.16e+01
  ... (remaining 10651 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 10896
        1.80 -     3.60: 2992
        3.60 -     5.40: 440
        5.40 -     7.21: 92
        7.21 -     9.01: 12
  Bond angle restraints: 14432
  Sorted by residual:
  angle pdb=" N   PRO A 218 "
        pdb=" CA  PRO A 218 "
        pdb=" CB  PRO A 218 "
      ideal   model   delta    sigma   weight residual
     101.83  106.91   -5.08 8.40e-01 1.42e+00 3.65e+01
  angle pdb=" N   PRO C 218 "
        pdb=" CA  PRO C 218 "
        pdb=" CB  PRO C 218 "
      ideal   model   delta    sigma   weight residual
     101.83  106.91   -5.08 8.40e-01 1.42e+00 3.65e+01
  angle pdb=" N   PRO B 218 "
        pdb=" CA  PRO B 218 "
        pdb=" CB  PRO B 218 "
      ideal   model   delta    sigma   weight residual
     101.83  106.91   -5.08 8.40e-01 1.42e+00 3.65e+01
  angle pdb=" N   PRO D 218 "
        pdb=" CA  PRO D 218 "
        pdb=" CB  PRO D 218 "
      ideal   model   delta    sigma   weight residual
     101.83  106.91   -5.08 8.40e-01 1.42e+00 3.65e+01
  angle pdb=" CA  THR B  73 "
        pdb=" CB  THR B  73 "
        pdb=" OG1 THR B  73 "
      ideal   model   delta    sigma   weight residual
     109.60  100.59    9.01 1.50e+00 4.44e-01 3.61e+01
  ... (remaining 14427 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    25.91: 6236
       25.91 -    51.81: 116
       51.81 -    77.72: 80
       77.72 -   103.62: 0
      103.62 -   129.53: 4
  Dihedral angle restraints: 6436
    sinusoidal: 2564
      harmonic: 3872
  Sorted by residual:
  dihedral pdb=" CA  SER C 217 "
           pdb=" C   SER C 217 "
           pdb=" N   PRO C 218 "
           pdb=" CA  PRO C 218 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   50.47  129.53     0      5.00e+00 4.00e-02 6.71e+02
  dihedral pdb=" CA  SER B 217 "
           pdb=" C   SER B 217 "
           pdb=" N   PRO B 218 "
           pdb=" CA  PRO B 218 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   50.47  129.53     0      5.00e+00 4.00e-02 6.71e+02
  dihedral pdb=" CA  SER A 217 "
           pdb=" C   SER A 217 "
           pdb=" N   PRO A 218 "
           pdb=" CA  PRO A 218 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   50.47  129.53     0      5.00e+00 4.00e-02 6.71e+02
  ... (remaining 6433 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.071: 984
       0.071 -    0.141: 480
       0.141 -    0.212: 144
       0.212 -    0.282: 36
       0.282 -    0.353: 4
  Chirality restraints: 1648
  Sorted by residual:
  chirality pdb=" CA  ASP C 195 "
            pdb=" N   ASP C 195 "
            pdb=" C   ASP C 195 "
            pdb=" CB  ASP C 195 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.11e+00
  chirality pdb=" CA  ASP D 195 "
            pdb=" N   ASP D 195 "
            pdb=" C   ASP D 195 "
            pdb=" CB  ASP D 195 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.11e+00
  chirality pdb=" CA  ASP B 195 "
            pdb=" N   ASP B 195 "
            pdb=" C   ASP B 195 "
            pdb=" CB  ASP B 195 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.11e+00
  ... (remaining 1645 not shown)

  Planarity restraints: 1840
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 202 "    0.076 2.00e-02 2.50e+03   4.40e-02 4.84e+01
        pdb=" CG  TRP D 202 "   -0.058 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 202 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 202 "   -0.068 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 202 "    0.015 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 202 "   -0.023 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 202 "   -0.034 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 202 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 202 "    0.018 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 202 "    0.054 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 202 "   -0.076 2.00e-02 2.50e+03   4.40e-02 4.84e+01
        pdb=" CG  TRP A 202 "    0.058 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 202 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 202 "    0.068 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 202 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 202 "    0.023 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 202 "    0.034 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 202 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 202 "   -0.018 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 202 "   -0.054 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 202 "   -0.076 2.00e-02 2.50e+03   4.40e-02 4.84e+01
        pdb=" CG  TRP B 202 "    0.058 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 202 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 202 "    0.068 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 202 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 202 "    0.023 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 202 "    0.034 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 202 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 202 "   -0.018 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 202 "   -0.054 2.00e-02 2.50e+03
  ... (remaining 1837 not shown)

  Histogram of nonbonded interaction distances:
        2.47 -     2.96: 5028
        2.96 -     3.44: 11212
        3.44 -     3.93: 18452
        3.93 -     4.41: 21644
        4.41 -     4.90: 33652
  Nonbonded interactions: 89988
  Sorted by model distance:
  nonbonded pdb=" O   PHE C 206 "
            pdb=" OG  SER C 209 "
     model   vdw
     2.471 3.040
  nonbonded pdb=" O   PHE D 206 "
            pdb=" OG  SER D 209 "
     model   vdw
     2.471 3.040
  nonbonded pdb=" O   PHE B 206 "
            pdb=" OG  SER B 209 "
     model   vdw
     2.471 3.040
  nonbonded pdb=" O   PHE A 206 "
            pdb=" OG  SER A 209 "
     model   vdw
     2.471 3.040
  nonbonded pdb=" O   ALA C 277 "
            pdb=" N   LEU C 279 "
     model   vdw
     2.489 3.120
  ... (remaining 89983 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.34 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.440
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
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      :  0.012   0.087  10656  Z= 0.737
  Angle     :  1.680   9.007  14432  Z= 1.157
  Chirality :  0.091   0.353   1648
  Planarity :  0.014   0.091   1840
  Dihedral  : 13.584 129.527   3932
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  5.99 %
    Favored  : 93.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.26 %
    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 (0.20), residues: 1320
  helix: -1.80 (0.16), residues: 752
  sheet:  None (None), residues: 0
  loop : -1.53 (0.24), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.004   ARG B 362 
 TYR   0.050   0.011   TYR D 244 
 PHE   0.075   0.011   PHE A 118 
 TRP   0.076   0.022   TRP A 202 
 HIS   0.009   0.003   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.01193 (10656)
  covalent geometry    : angle       1.67987 (14432)
  hydrogen bonds       : bond        0.19126 (  536)
  hydrogen bonds       : angle       6.92736 ( 1536)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  332 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 328
  time to evaluate  : 0.326 
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   86 LEU cc_start: 0.8672 (tp) cc_final: 0.8462 (tp)
REVERT: A  170 MET cc_start: 0.8535 (mmp) cc_final: 0.7927 (mmp)
REVERT: A  264 ASP cc_start: 0.8942 (m-30) cc_final: 0.8688 (t0)
REVERT: B   86 LEU cc_start: 0.8677 (tp) cc_final: 0.8466 (tp)
REVERT: B  170 MET cc_start: 0.8537 (mmp) cc_final: 0.7929 (mmp)
REVERT: B  264 ASP cc_start: 0.8943 (m-30) cc_final: 0.8689 (t0)
REVERT: C   86 LEU cc_start: 0.8673 (tp) cc_final: 0.8463 (tp)
REVERT: C  170 MET cc_start: 0.8534 (mmp) cc_final: 0.7927 (mmp)
REVERT: C  264 ASP cc_start: 0.8942 (m-30) cc_final: 0.8687 (t0)
REVERT: D   86 LEU cc_start: 0.8673 (tp) cc_final: 0.8462 (tp)
REVERT: D  170 MET cc_start: 0.8539 (mmp) cc_final: 0.7928 (mmp)
REVERT: D  264 ASP cc_start: 0.8942 (m-30) cc_final: 0.8686 (t0)
REVERT: D  290 ASP cc_start: 0.8408 (m-30) cc_final: 0.8207 (m-30)
  outliers start: 4
  outliers final: 0
  residues processed: 332
  average time/residue: 0.1232
  time to fit residues: 53.3957
Evaluate side-chains
  212 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:   20.0000
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 326 GLN
A 335 GLN
B 326 GLN
B 335 GLN
C 326 GLN
C 335 GLN
D 326 GLN
D 335 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.140097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.104154 restraints weight = 13988.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 2.63
r_work: 0.3193 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3220
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3220 r_free = 0.3220    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3219 r_free = 0.3219    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3219
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.2952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  10656  Z= 0.128
  Angle     :  0.578   5.273  14432  Z= 0.297
  Chirality :  0.038   0.134   1648
  Planarity :  0.005   0.060   1840
  Dihedral  :  5.555  72.468   1436
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  1.21 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  : 10.21 %
    Favored  : 89.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.26 %
    Twisted General : 0.32 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.22), residues: 1320
  helix:  1.05 (0.18), residues: 788
  sheet:  None (None), residues: 0
  loop : -0.22 (0.26), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 338 
 TYR   0.026   0.002   TYR B 339 
 PHE   0.007   0.001   PHE A 206 
 TRP   0.003   0.001   TRP D 309 
 HIS   0.002   0.001   HIS C 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (10656)
  covalent geometry    : angle       0.57807 (14432)
  hydrogen bonds       : bond        0.04767 (  536)
  hydrogen bonds       : angle       4.20085 ( 1536)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 232
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 ASP cc_start: 0.8312 (m-30) cc_final: 0.8110 (m-30)
REVERT: A   68 MET cc_start: 0.8597 (mtp) cc_final: 0.8202 (mtp)
REVERT: A  135 SER cc_start: 0.8953 (m) cc_final: 0.8734 (p)
REVERT: A  160 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7481 (tm-30)
REVERT: A  223 MET cc_start: 0.7940 (mmm) cc_final: 0.7309 (mmm)
REVERT: A  339 TYR cc_start: 0.7839 (m-80) cc_final: 0.7635 (m-10)
REVERT: A  362 ARG cc_start: 0.8526 (ttm110) cc_final: 0.8054 (mpp80)
REVERT: B   52 ASP cc_start: 0.8313 (m-30) cc_final: 0.8111 (m-30)
REVERT: B   68 MET cc_start: 0.8594 (mtp) cc_final: 0.8200 (mtp)
REVERT: B  135 SER cc_start: 0.8959 (m) cc_final: 0.8738 (p)
REVERT: B  160 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7483 (tm-30)
REVERT: B  223 MET cc_start: 0.7942 (mmm) cc_final: 0.7312 (mmm)
REVERT: B  339 TYR cc_start: 0.7839 (m-80) cc_final: 0.7637 (m-10)
REVERT: B  362 ARG cc_start: 0.8533 (ttm110) cc_final: 0.8058 (mpp80)
REVERT: C   52 ASP cc_start: 0.8314 (m-30) cc_final: 0.8113 (m-30)
REVERT: C   68 MET cc_start: 0.8609 (mtp) cc_final: 0.8211 (mtp)
REVERT: C  135 SER cc_start: 0.8955 (m) cc_final: 0.8735 (p)
REVERT: C  160 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7483 (tm-30)
REVERT: C  223 MET cc_start: 0.7948 (mmm) cc_final: 0.7318 (mmm)
REVERT: C  339 TYR cc_start: 0.7840 (m-80) cc_final: 0.7638 (m-10)
REVERT: C  362 ARG cc_start: 0.8547 (ttm110) cc_final: 0.8069 (mpp80)
REVERT: D   52 ASP cc_start: 0.8311 (m-30) cc_final: 0.8111 (m-30)
REVERT: D   68 MET cc_start: 0.8598 (mtp) cc_final: 0.8202 (mtp)
REVERT: D  135 SER cc_start: 0.8957 (m) cc_final: 0.8736 (p)
REVERT: D  160 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7482 (tm-30)
REVERT: D  223 MET cc_start: 0.7941 (mmm) cc_final: 0.7314 (mmm)
REVERT: D  339 TYR cc_start: 0.7840 (m-80) cc_final: 0.7636 (m-10)
REVERT: D  362 ARG cc_start: 0.8531 (ttm110) cc_final: 0.8057 (mpp80)
  outliers start: 4
  outliers final: 0
  residues processed: 236
  average time/residue: 0.0938
  time to fit residues: 31.3533
Evaluate side-chains
  220 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 63 optimal weight:   20.0000
   chunk 22 optimal weight:    1.9990
   chunk 45 optimal weight:    9.9990
   chunk 106 optimal weight:    8.9990
   chunk 112 optimal weight:    9.9990
   chunk 61 optimal weight:   20.0000
   chunk 77 optimal weight:    8.9990
   chunk 27 optimal weight:    9.9990
   chunk 1 optimal weight:   10.0000
   chunk 126 optimal weight:   20.0000
   overall best weight:    6.7990

-------------------------------------------------------------------------------
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 = 0.3725 r_free = 0.3725 target = 0.135200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.098118 restraints weight = 14817.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 2.68
r_work: 0.3075 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3104
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3104
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.3710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036  10656  Z= 0.259
  Angle     :  0.642   5.332  14432  Z= 0.328
  Chirality :  0.042   0.134   1648
  Planarity :  0.005   0.056   1840
  Dihedral  :  5.437  71.809   1436
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  2.12 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  : 13.73 %
    Favored  : 85.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.26 %
    Twisted General : 0.32 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.23), residues: 1320
  helix:  1.15 (0.19), residues: 788
  sheet:  None (None), residues: 0
  loop : -0.11 (0.26), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 338 
 TYR   0.018   0.003   TYR D 339 
 PHE   0.013   0.002   PHE C  69 
 TRP   0.006   0.002   TRP B 309 
 HIS   0.007   0.001   HIS D  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00629 (10656)
  covalent geometry    : angle       0.64227 (14432)
  hydrogen bonds       : bond        0.05281 (  536)
  hydrogen bonds       : angle       4.09749 ( 1536)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 216
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 ASP cc_start: 0.8350 (m-30) cc_final: 0.7962 (m-30)
REVERT: A  119 TYR cc_start: 0.9230 (p90) cc_final: 0.8485 (p90)
REVERT: A  247 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8455 (mt-10)
REVERT: B   52 ASP cc_start: 0.8354 (m-30) cc_final: 0.7963 (m-30)
REVERT: B  119 TYR cc_start: 0.9229 (p90) cc_final: 0.8483 (p90)
REVERT: B  247 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8452 (mt-10)
REVERT: C   52 ASP cc_start: 0.8356 (m-30) cc_final: 0.7969 (m-30)
REVERT: C  119 TYR cc_start: 0.9233 (p90) cc_final: 0.8487 (p90)
REVERT: C  247 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8449 (mt-10)
REVERT: D   52 ASP cc_start: 0.8352 (m-30) cc_final: 0.7964 (m-30)
REVERT: D  119 TYR cc_start: 0.9230 (p90) cc_final: 0.8485 (p90)
REVERT: D  247 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8446 (mt-10)
  outliers start: 4
  outliers final: 0
  residues processed: 220
  average time/residue: 0.0919
  time to fit residues: 28.9984
Evaluate side-chains
  208 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 70 optimal weight:    6.9990
   chunk 87 optimal weight:    0.9980
   chunk 34 optimal weight:    9.9990
   chunk 100 optimal weight:   10.0000
   chunk 47 optimal weight:    9.9990
   chunk 10 optimal weight:    0.9990
   chunk 116 optimal weight:    0.0980
   chunk 71 optimal weight:    0.9980
   chunk 61 optimal weight:    5.9990
   chunk 97 optimal weight:    0.0050
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
A 186 GLN
A 335 GLN
B 186 GLN
B 335 GLN
C  35 GLN
C 335 GLN
D  35 GLN
D 335 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.140018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.103040 restraints weight = 14344.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 2.73
r_work: 0.3168 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3194
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3194 r_free = 0.3194    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3193 r_free = 0.3193    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3193
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.4026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10656  Z= 0.104
  Angle     :  0.511   5.076  14432  Z= 0.263
  Chirality :  0.037   0.160   1648
  Planarity :  0.004   0.047   1840
  Dihedral  :  4.858  60.940   1436
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 14.17 %
    Favored  : 85.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.26 %
    Twisted General : 0.32 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.23), residues: 1320
  helix:  1.61 (0.19), residues: 792
  sheet:  None (None), residues: 0
  loop : -0.04 (0.25), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 338 
 TYR   0.017   0.001   TYR A 339 
 PHE   0.009   0.001   PHE C  69 
 TRP   0.005   0.001   TRP A 202 
 HIS   0.001   0.000   HIS B 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 (10656)
  covalent geometry    : angle       0.51051 (14432)
  hydrogen bonds       : bond        0.03981 (  536)
  hydrogen bonds       : angle       3.73840 ( 1536)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 232
  time to evaluate  : 0.385 
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: A   52 ASP cc_start: 0.8198 (m-30) cc_final: 0.7800 (m-30)
REVERT: A   62 ASP cc_start: 0.7829 (p0) cc_final: 0.7377 (p0)
REVERT: A   63 GLN cc_start: 0.8641 (tp40) cc_final: 0.8432 (tp40)
REVERT: A  119 TYR cc_start: 0.9170 (p90) cc_final: 0.8550 (p90)
REVERT: A  160 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7549 (tm-30)
REVERT: A  161 GLN cc_start: 0.8380 (mp10) cc_final: 0.8176 (mp10)
REVERT: A  223 MET cc_start: 0.8357 (mmm) cc_final: 0.7838 (mmm)
REVERT: A  339 TYR cc_start: 0.7952 (m-10) cc_final: 0.7746 (m-10)
REVERT: B   52 ASP cc_start: 0.8191 (m-30) cc_final: 0.7788 (m-30)
REVERT: B   62 ASP cc_start: 0.7826 (p0) cc_final: 0.7383 (p0)
REVERT: B   63 GLN cc_start: 0.8643 (tp40) cc_final: 0.8436 (tp40)
REVERT: B  119 TYR cc_start: 0.9167 (p90) cc_final: 0.8538 (p90)
REVERT: B  160 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7541 (tm-30)
REVERT: B  161 GLN cc_start: 0.8380 (mp10) cc_final: 0.8175 (mp10)
REVERT: B  214 ASP cc_start: 0.8235 (p0) cc_final: 0.8030 (p0)
REVERT: B  223 MET cc_start: 0.8353 (mmm) cc_final: 0.7837 (mmm)
REVERT: B  339 TYR cc_start: 0.7945 (m-10) cc_final: 0.7739 (m-10)
REVERT: C   52 ASP cc_start: 0.8203 (m-30) cc_final: 0.7800 (m-30)
REVERT: C   62 ASP cc_start: 0.7829 (p0) cc_final: 0.7381 (p0)
REVERT: C   63 GLN cc_start: 0.8639 (tp40) cc_final: 0.8432 (tp40)
REVERT: C  119 TYR cc_start: 0.9173 (p90) cc_final: 0.8550 (p90)
REVERT: C  160 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7539 (tm-30)
REVERT: C  161 GLN cc_start: 0.8373 (mp10) cc_final: 0.8167 (mp10)
REVERT: C  214 ASP cc_start: 0.8246 (p0) cc_final: 0.8040 (p0)
REVERT: C  223 MET cc_start: 0.8358 (mmm) cc_final: 0.7842 (mmm)
REVERT: C  339 TYR cc_start: 0.7949 (m-10) cc_final: 0.7745 (m-10)
REVERT: D   52 ASP cc_start: 0.8196 (m-30) cc_final: 0.7795 (m-30)
REVERT: D   62 ASP cc_start: 0.7848 (p0) cc_final: 0.7394 (p0)
REVERT: D   63 GLN cc_start: 0.8650 (tp40) cc_final: 0.8439 (tp40)
REVERT: D  119 TYR cc_start: 0.9166 (p90) cc_final: 0.8541 (p90)
REVERT: D  160 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7546 (tm-30)
REVERT: D  161 GLN cc_start: 0.8384 (mp10) cc_final: 0.8181 (mp10)
REVERT: D  223 MET cc_start: 0.8355 (mmm) cc_final: 0.7838 (mmm)
REVERT: D  339 TYR cc_start: 0.7949 (m-10) cc_final: 0.7743 (m-10)
  outliers start: 8
  outliers final: 4
  residues processed: 236
  average time/residue: 0.0864
  time to fit residues: 29.4782
Evaluate side-chains
  200 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 196
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain C residue  105 VAL
Chi-restraints excluded: chain D residue  105 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 109 optimal weight:    5.9990
   chunk 56 optimal weight:    6.9990
   chunk 44 optimal weight:    4.9990
   chunk 121 optimal weight:    6.9990
   chunk 40 optimal weight:    9.9990
   chunk 3 optimal weight:    4.9990
   chunk 75 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   chunk 111 optimal weight:   10.0000
   chunk 39 optimal weight:   10.0000
   chunk 5 optimal weight:    4.9990
   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 335 GLN
B 335 GLN
C 335 GLN
D 335 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.136253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.099377 restraints weight = 14403.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 2.71
r_work: 0.3104 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3131
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3131 r_free = 0.3131    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3131 r_free = 0.3131    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3131
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.4145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024  10656  Z= 0.167
  Angle     :  0.543   5.260  14432  Z= 0.279
  Chirality :  0.039   0.144   1648
  Planarity :  0.004   0.048   1840
  Dihedral  :  4.852  61.609   1436
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 14.88 %
    Favored  : 84.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.26 %
    Twisted General : 0.32 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.29 (0.23), residues: 1320
  helix:  1.54 (0.19), residues: 792
  sheet:  None (None), residues: 0
  loop : -0.12 (0.25), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 341 
 TYR   0.022   0.002   TYR A 308 
 PHE   0.010   0.001   PHE A 222 
 TRP   0.004   0.001   TRP A 309 
 HIS   0.004   0.001   HIS D  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (10656)
  covalent geometry    : angle       0.54275 (14432)
  hydrogen bonds       : bond        0.04367 (  536)
  hydrogen bonds       : angle       3.69201 ( 1536)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 196
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 ASP cc_start: 0.8244 (m-30) cc_final: 0.7876 (m-30)
REVERT: A  119 TYR cc_start: 0.9243 (p90) cc_final: 0.8737 (p90)
REVERT: A  160 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7680 (tm-30)
REVERT: A  223 MET cc_start: 0.8509 (mmm) cc_final: 0.7821 (mmm)
REVERT: B   52 ASP cc_start: 0.8238 (m-30) cc_final: 0.7867 (m-30)
REVERT: B  119 TYR cc_start: 0.9241 (p90) cc_final: 0.8728 (p90)
REVERT: B  160 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7684 (tm-30)
REVERT: B  214 ASP cc_start: 0.8262 (p0) cc_final: 0.8054 (p0)
REVERT: B  223 MET cc_start: 0.8507 (mmm) cc_final: 0.7811 (mmm)
REVERT: C   52 ASP cc_start: 0.8247 (m-30) cc_final: 0.7879 (m-30)
REVERT: C  119 TYR cc_start: 0.9243 (p90) cc_final: 0.8738 (p90)
REVERT: C  160 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7671 (tm-30)
REVERT: C  214 ASP cc_start: 0.8266 (p0) cc_final: 0.8056 (p0)
REVERT: C  223 MET cc_start: 0.8507 (mmm) cc_final: 0.7812 (mmm)
REVERT: D   52 ASP cc_start: 0.8245 (m-30) cc_final: 0.7875 (m-30)
REVERT: D  119 TYR cc_start: 0.9241 (p90) cc_final: 0.8734 (p90)
REVERT: D  160 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7680 (tm-30)
REVERT: D  223 MET cc_start: 0.8503 (mmm) cc_final: 0.7811 (mmm)
REVERT: D  362 ARG cc_start: 0.8657 (ttm110) cc_final: 0.8218 (mtt90)
  outliers start: 12
  outliers final: 7
  residues processed: 204
  average time/residue: 0.0839
  time to fit residues: 24.8028
Evaluate side-chains
  187 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 180
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  356 GLU
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  356 GLU
Chi-restraints excluded: chain C residue  105 VAL
Chi-restraints excluded: chain C residue  356 GLU
Chi-restraints excluded: chain D residue  105 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 59 optimal weight:   30.0000
   chunk 10 optimal weight:   10.0000
   chunk 14 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   chunk 123 optimal weight:    7.9990
   chunk 100 optimal weight:    5.9990
   chunk 61 optimal weight:   20.0000
   chunk 34 optimal weight:    0.3980
   chunk 99 optimal weight:    9.9990
   chunk 109 optimal weight:    0.9990
   overall best weight:    3.6788

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

Flipped N/Q/H residues before XYZ refinement:
A 186 GLN
B 186 GLN
C 186 GLN
D 186 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.136817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.100176 restraints weight = 14558.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 2.72
r_work: 0.3113 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3142
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3142 r_free = 0.3142    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3142 r_free = 0.3142    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3142
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.4412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10656  Z= 0.160
  Angle     :  0.558   6.450  14432  Z= 0.287
  Chirality :  0.038   0.153   1648
  Planarity :  0.004   0.051   1840
  Dihedral  :  4.743  60.152   1436
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  1.82 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 16.64 %
    Favored  : 82.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.26 %
    Twisted General : 0.32 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.29 (0.23), residues: 1320
  helix:  1.54 (0.19), residues: 792
  sheet:  None (None), residues: 0
  loop : -0.12 (0.25), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 338 
 TYR   0.010   0.001   TYR B 244 
 PHE   0.008   0.001   PHE B 280 
 TRP   0.004   0.001   TRP D 309 
 HIS   0.004   0.001   HIS B  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (10656)
  covalent geometry    : angle       0.55775 (14432)
  hydrogen bonds       : bond        0.04230 (  536)
  hydrogen bonds       : angle       3.66739 ( 1536)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 204
  time to evaluate  : 0.307 
Fit side-chains
REVERT: A   52 ASP cc_start: 0.8297 (m-30) cc_final: 0.7948 (m-30)
REVERT: A   63 GLN cc_start: 0.8626 (tp40) cc_final: 0.8081 (tp40)
REVERT: A  119 TYR cc_start: 0.9190 (p90) cc_final: 0.8657 (p90)
REVERT: A  161 GLN cc_start: 0.8404 (mp10) cc_final: 0.8186 (mp10)
REVERT: A  223 MET cc_start: 0.8538 (mmm) cc_final: 0.7829 (mmm)
REVERT: A  274 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8518 (tm-30)
REVERT: A  362 ARG cc_start: 0.8669 (ttm110) cc_final: 0.8214 (mtt90)
REVERT: B   52 ASP cc_start: 0.8283 (m-30) cc_final: 0.7935 (m-30)
REVERT: B   63 GLN cc_start: 0.8629 (tp40) cc_final: 0.8082 (tp40)
REVERT: B  119 TYR cc_start: 0.9185 (p90) cc_final: 0.8647 (p90)
REVERT: B  161 GLN cc_start: 0.8396 (mp10) cc_final: 0.8177 (mp10)
REVERT: B  223 MET cc_start: 0.8522 (mmm) cc_final: 0.7808 (mmm)
REVERT: B  362 ARG cc_start: 0.8669 (ttm110) cc_final: 0.8212 (mtt90)
REVERT: C   52 ASP cc_start: 0.8294 (m-30) cc_final: 0.7943 (m-30)
REVERT: C   63 GLN cc_start: 0.8626 (tp40) cc_final: 0.8078 (tp40)
REVERT: C  119 TYR cc_start: 0.9184 (p90) cc_final: 0.8651 (p90)
REVERT: C  161 GLN cc_start: 0.8398 (mp10) cc_final: 0.8179 (mp10)
REVERT: C  223 MET cc_start: 0.8522 (mmm) cc_final: 0.7808 (mmm)
REVERT: C  362 ARG cc_start: 0.8665 (ttm110) cc_final: 0.8214 (mtt90)
REVERT: D   52 ASP cc_start: 0.8295 (m-30) cc_final: 0.7944 (m-30)
REVERT: D   63 GLN cc_start: 0.8629 (tp40) cc_final: 0.8078 (tp40)
REVERT: D  119 TYR cc_start: 0.9184 (p90) cc_final: 0.8650 (p90)
REVERT: D  161 GLN cc_start: 0.8400 (mp10) cc_final: 0.8182 (mp10)
REVERT: D  223 MET cc_start: 0.8519 (mmm) cc_final: 0.7803 (mmm)
REVERT: D  362 ARG cc_start: 0.8664 (ttm110) cc_final: 0.8207 (mtt90)
  outliers start: 14
  outliers final: 3
  residues processed: 211
  average time/residue: 0.0832
  time to fit residues: 25.8744
Evaluate side-chains
  196 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 193
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain C residue  169 MET
Chi-restraints excluded: chain D residue  169 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 17 optimal weight:    0.2980
   chunk 118 optimal weight:    0.2980
   chunk 42 optimal weight:    7.9990
   chunk 104 optimal weight:    0.8980
   chunk 99 optimal weight:   10.0000
   chunk 125 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 84 optimal weight:    9.9990
   chunk 12 optimal weight:    4.9990
   chunk 112 optimal weight:    2.9990
   chunk 9 optimal weight:    8.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.3795 r_free = 0.3795 target = 0.138507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.102378 restraints weight = 14298.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 2.70
r_work: 0.3162 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3189
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3189 r_free = 0.3189    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3189 r_free = 0.3189    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3189
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.4620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10656  Z= 0.103
  Angle     :  0.528  10.134  14432  Z= 0.268
  Chirality :  0.036   0.144   1648
  Planarity :  0.004   0.046   1840
  Dihedral  :  4.509  57.537   1436
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 16.46 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.26 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.51 (0.23), residues: 1320
  helix:  1.77 (0.19), residues: 792
  sheet:  None (None), residues: 0
  loop : -0.12 (0.25), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 338 
 TYR   0.023   0.002   TYR D 308 
 PHE   0.007   0.001   PHE D 206 
 TRP   0.006   0.001   TRP C 202 
 HIS   0.002   0.000   HIS D 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 (10656)
  covalent geometry    : angle       0.52818 (14432)
  hydrogen bonds       : bond        0.03666 (  536)
  hydrogen bonds       : angle       3.56290 ( 1536)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 198
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 ASP cc_start: 0.8088 (m-30) cc_final: 0.7657 (m-30)
REVERT: A  119 TYR cc_start: 0.9186 (p90) cc_final: 0.8670 (p90)
REVERT: A  223 MET cc_start: 0.8467 (mmm) cc_final: 0.7801 (mmm)
REVERT: A  274 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8475 (tm-30)
REVERT: A  360 ILE cc_start: 0.8251 (mm) cc_final: 0.7896 (mt)
REVERT: B   52 ASP cc_start: 0.8081 (m-30) cc_final: 0.7652 (m-30)
REVERT: B  119 TYR cc_start: 0.9179 (p90) cc_final: 0.8663 (p90)
REVERT: B  223 MET cc_start: 0.8462 (mmm) cc_final: 0.7797 (mmm)
REVERT: B  360 ILE cc_start: 0.8256 (mm) cc_final: 0.7901 (mt)
REVERT: C   52 ASP cc_start: 0.8091 (m-30) cc_final: 0.7662 (m-30)
REVERT: C  119 TYR cc_start: 0.9179 (p90) cc_final: 0.8667 (p90)
REVERT: C  223 MET cc_start: 0.8469 (mmm) cc_final: 0.7788 (mmm)
REVERT: C  360 ILE cc_start: 0.8259 (mm) cc_final: 0.7903 (mt)
REVERT: D   52 ASP cc_start: 0.8091 (m-30) cc_final: 0.7660 (m-30)
REVERT: D  119 TYR cc_start: 0.9178 (p90) cc_final: 0.8665 (p90)
REVERT: D  223 MET cc_start: 0.8460 (mmm) cc_final: 0.7792 (mmm)
REVERT: D  360 ILE cc_start: 0.8236 (mm) cc_final: 0.7868 (mt)
  outliers start: 11
  outliers final: 11
  residues processed: 206
  average time/residue: 0.0817
  time to fit residues: 24.8769
Evaluate side-chains
  197 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 186
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  356 GLU
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  356 GLU
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  169 MET
Chi-restraints excluded: chain C residue  356 GLU
Chi-restraints excluded: chain D residue   72 VAL
Chi-restraints excluded: chain D residue  169 MET
Chi-restraints excluded: chain D residue  356 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 120 optimal weight:    0.9990
   chunk 107 optimal weight:    0.0040
   chunk 96 optimal weight:   20.0000
   chunk 100 optimal weight:    8.9990
   chunk 80 optimal weight:    9.9990
   chunk 43 optimal weight:    9.9990
   chunk 70 optimal weight:   10.0000
   chunk 32 optimal weight:   20.0000
   chunk 106 optimal weight:    5.9990
   chunk 30 optimal weight:    7.9990
   overall best weight:    3.8000

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

Flipped N/Q/H residues before XYZ refinement:
B  35 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.136027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.099217 restraints weight = 14487.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 2.73
r_work: 0.3117 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3148
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3147 r_free = 0.3147    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3147
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.4590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10656  Z= 0.163
  Angle     :  0.577  11.532  14432  Z= 0.291
  Chirality :  0.038   0.140   1648
  Planarity :  0.004   0.050   1840
  Dihedral  :  4.540  57.562   1436
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  1.52 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 16.90 %
    Favored  : 82.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.26 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.23), residues: 1320
  helix:  1.69 (0.19), residues: 792
  sheet:  None (None), residues: 0
  loop : -0.12 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 338 
 TYR   0.010   0.001   TYR D 244 
 PHE   0.008   0.001   PHE A 280 
 TRP   0.004   0.001   TRP A 309 
 HIS   0.004   0.001   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (10656)
  covalent geometry    : angle       0.57714 (14432)
  hydrogen bonds       : bond        0.04111 (  536)
  hydrogen bonds       : angle       3.71220 ( 1536)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 184
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A   52 ASP cc_start: 0.8222 (m-30) cc_final: 0.7860 (m-30)
REVERT: A  119 TYR cc_start: 0.9130 (p90) cc_final: 0.8611 (p90)
REVERT: A  223 MET cc_start: 0.8511 (mmm) cc_final: 0.7719 (mmm)
REVERT: A  360 ILE cc_start: 0.8239 (mm) cc_final: 0.7898 (mt)
REVERT: A  362 ARG cc_start: 0.8684 (ttm110) cc_final: 0.8248 (mpp80)
REVERT: B   52 ASP cc_start: 0.8218 (m-30) cc_final: 0.7855 (m-30)
REVERT: B  119 TYR cc_start: 0.9126 (p90) cc_final: 0.8607 (p90)
REVERT: B  223 MET cc_start: 0.8506 (mmm) cc_final: 0.7720 (mmm)
REVERT: B  360 ILE cc_start: 0.8246 (mm) cc_final: 0.7904 (mt)
REVERT: B  362 ARG cc_start: 0.8682 (ttm110) cc_final: 0.8246 (mpp80)
REVERT: C   52 ASP cc_start: 0.8227 (m-30) cc_final: 0.7863 (m-30)
REVERT: C  119 TYR cc_start: 0.9124 (p90) cc_final: 0.8604 (p90)
REVERT: C  223 MET cc_start: 0.8513 (mmm) cc_final: 0.7725 (mmm)
REVERT: C  360 ILE cc_start: 0.8249 (mm) cc_final: 0.7907 (mt)
REVERT: C  362 ARG cc_start: 0.8684 (ttm110) cc_final: 0.8250 (mpp80)
REVERT: D   52 ASP cc_start: 0.8224 (m-30) cc_final: 0.7857 (m-30)
REVERT: D  119 TYR cc_start: 0.9125 (p90) cc_final: 0.8609 (p90)
REVERT: D  223 MET cc_start: 0.8508 (mmm) cc_final: 0.7716 (mmm)
REVERT: D  274 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8423 (tm-30)
REVERT: D  360 ILE cc_start: 0.8252 (mm) cc_final: 0.7912 (mt)
REVERT: D  362 ARG cc_start: 0.8680 (ttm110) cc_final: 0.8246 (mpp80)
  outliers start: 11
  outliers final: 10
  residues processed: 192
  average time/residue: 0.0763
  time to fit residues: 22.0527
Evaluate side-chains
  191 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 181
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  356 GLU
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  356 GLU
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  169 MET
Chi-restraints excluded: chain C residue  356 GLU
Chi-restraints excluded: chain D residue   72 VAL
Chi-restraints excluded: chain D residue  169 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 88 optimal weight:    0.5980
   chunk 110 optimal weight:    1.9990
   chunk 101 optimal weight:   10.0000
   chunk 105 optimal weight:    0.9990
   chunk 7 optimal weight:   10.0000
   chunk 80 optimal weight:    8.9990
   chunk 30 optimal weight:   20.0000
   chunk 81 optimal weight:    0.0670
   chunk 48 optimal weight:   10.0000
   chunk 112 optimal weight:    0.7980
   chunk 64 optimal weight:    6.9990
   overall best weight:    0.8922

-------------------------------------------------------------------------------
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 = 0.3805 r_free = 0.3805 target = 0.139639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.102752 restraints weight = 14288.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 2.74
r_work: 0.3165 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3101
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3101 r_free = 0.3101    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3101 r_free = 0.3101    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3101
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.4753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  10656  Z= 0.102
  Angle     :  0.545  12.119  14432  Z= 0.274
  Chirality :  0.036   0.138   1648
  Planarity :  0.004   0.047   1840
  Dihedral  :  4.412  56.873   1436
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 17.08 %
    Favored  : 81.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.26 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.68 (0.23), residues: 1320
  helix:  1.93 (0.19), residues: 792
  sheet:  None (None), residues: 0
  loop : -0.10 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 338 
 TYR   0.007   0.001   TYR D 244 
 PHE   0.007   0.001   PHE A 206 
 TRP   0.006   0.001   TRP A 202 
 HIS   0.001   0.000   HIS A 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 (10656)
  covalent geometry    : angle       0.54519 (14432)
  hydrogen bonds       : bond        0.03570 (  536)
  hydrogen bonds       : angle       3.62559 ( 1536)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 185
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 ASP cc_start: 0.8010 (m-30) cc_final: 0.7647 (m-30)
REVERT: A  119 TYR cc_start: 0.9038 (p90) cc_final: 0.8580 (p90)
REVERT: A  360 ILE cc_start: 0.8207 (mm) cc_final: 0.7903 (mt)
REVERT: B   52 ASP cc_start: 0.8006 (m-30) cc_final: 0.7641 (m-30)
REVERT: B  119 TYR cc_start: 0.9033 (p90) cc_final: 0.8577 (p90)
REVERT: B  360 ILE cc_start: 0.8206 (mm) cc_final: 0.7902 (mt)
REVERT: C   52 ASP cc_start: 0.8015 (m-30) cc_final: 0.7651 (m-30)
REVERT: C  119 TYR cc_start: 0.9033 (p90) cc_final: 0.8576 (p90)
REVERT: C  360 ILE cc_start: 0.8213 (mm) cc_final: 0.7910 (mt)
REVERT: D   52 ASP cc_start: 0.8008 (m-30) cc_final: 0.7645 (m-30)
REVERT: D  119 TYR cc_start: 0.9030 (p90) cc_final: 0.8574 (p90)
REVERT: D  360 ILE cc_start: 0.8209 (mm) cc_final: 0.7905 (mt)
  outliers start: 11
  outliers final: 11
  residues processed: 192
  average time/residue: 0.0883
  time to fit residues: 24.3543
Evaluate side-chains
  188 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 177
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  356 GLU
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  356 GLU
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  169 MET
Chi-restraints excluded: chain C residue  356 GLU
Chi-restraints excluded: chain D residue   72 VAL
Chi-restraints excluded: chain D residue  169 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 83 optimal weight:    0.0770
   chunk 74 optimal weight:    0.8980
   chunk 102 optimal weight:    9.9990
   chunk 15 optimal weight:    7.9990
   chunk 30 optimal weight:    8.9990
   chunk 4 optimal weight:    4.9990
   chunk 65 optimal weight:    7.9990
   chunk 131 optimal weight:    8.9990
   chunk 29 optimal weight:    5.9990
   chunk 55 optimal weight:    6.9990
   chunk 107 optimal weight:   10.0000
   overall best weight:    3.7944

-------------------------------------------------------------------------------
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 = 0.3779 r_free = 0.3779 target = 0.137142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.099988 restraints weight = 14400.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3215 rms_B_bonded: 2.74
r_work: 0.3082 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3081
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3081 r_free = 0.3081    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3081 r_free = 0.3081    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3081
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.4745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10656  Z= 0.166
  Angle     :  0.609  12.186  14432  Z= 0.308
  Chirality :  0.039   0.145   1648
  Planarity :  0.004   0.051   1840
  Dihedral  :  4.459  57.709   1436
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  1.59 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 17.61 %
    Favored  : 81.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.26 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.62 (0.23), residues: 1320
  helix:  1.79 (0.19), residues: 792
  sheet:  None (None), residues: 0
  loop :  0.04 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 341 
 TYR   0.011   0.001   TYR A 244 
 PHE   0.009   0.001   PHE C 222 
 TRP   0.004   0.001   TRP B 309 
 HIS   0.004   0.001   HIS B  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 (10656)
  covalent geometry    : angle       0.60934 (14432)
  hydrogen bonds       : bond        0.04010 (  536)
  hydrogen bonds       : angle       3.67755 ( 1536)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 174
  time to evaluate  : 0.372 
Fit side-chains
REVERT: A   52 ASP cc_start: 0.8067 (m-30) cc_final: 0.7722 (m-30)
REVERT: A  119 TYR cc_start: 0.9128 (p90) cc_final: 0.8614 (p90)
REVERT: A  360 ILE cc_start: 0.8236 (mm) cc_final: 0.7940 (mt)
REVERT: A  362 ARG cc_start: 0.8747 (ttm110) cc_final: 0.8293 (mpp80)
REVERT: B   52 ASP cc_start: 0.8058 (m-30) cc_final: 0.7714 (m-30)
REVERT: B  119 TYR cc_start: 0.9122 (p90) cc_final: 0.8605 (p90)
REVERT: B  360 ILE cc_start: 0.8234 (mm) cc_final: 0.7939 (mt)
REVERT: B  362 ARG cc_start: 0.8748 (ttm110) cc_final: 0.8295 (mpp80)
REVERT: C   52 ASP cc_start: 0.8075 (m-30) cc_final: 0.7728 (m-30)
REVERT: C  119 TYR cc_start: 0.9121 (p90) cc_final: 0.8600 (p90)
REVERT: C  360 ILE cc_start: 0.8244 (mm) cc_final: 0.7948 (mt)
REVERT: C  362 ARG cc_start: 0.8747 (ttm110) cc_final: 0.8295 (mpp80)
REVERT: D   52 ASP cc_start: 0.8071 (m-30) cc_final: 0.7725 (m-30)
REVERT: D  119 TYR cc_start: 0.9123 (p90) cc_final: 0.8605 (p90)
REVERT: D  360 ILE cc_start: 0.8237 (mm) cc_final: 0.7942 (mt)
REVERT: D  362 ARG cc_start: 0.8743 (ttm110) cc_final: 0.8290 (mpp80)
  outliers start: 12
  outliers final: 8
  residues processed: 182
  average time/residue: 0.0736
  time to fit residues: 20.4599
Evaluate side-chains
  181 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 173
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  169 MET
Chi-restraints excluded: chain D residue   72 VAL
Chi-restraints excluded: chain D residue  169 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 8 optimal weight:    9.9990
   chunk 12 optimal weight:    4.9990
   chunk 73 optimal weight:    8.9990
   chunk 67 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 48 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9990
   chunk 35 optimal weight:    9.9990
   chunk 110 optimal weight:    2.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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 = 0.3791 r_free = 0.3791 target = 0.138021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.100995 restraints weight = 14414.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 2.74
r_work: 0.3143 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3172
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3172 r_free = 0.3172    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3172 r_free = 0.3172    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3172
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.4811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10656  Z= 0.131
  Angle     :  0.573  11.975  14432  Z= 0.290
  Chirality :  0.038   0.140   1648
  Planarity :  0.004   0.051   1840
  Dihedral  :  4.416  57.230   1436
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  1.29 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 17.78 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.26 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.70 (0.23), residues: 1320
  helix:  1.88 (0.19), residues: 788
  sheet:  None (None), residues: 0
  loop :  0.04 (0.27), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 341 
 TYR   0.010   0.001   TYR A 244 
 PHE   0.009   0.001   PHE B 222 
 TRP   0.004   0.001   TRP D 202 
 HIS   0.003   0.001   HIS C  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (10656)
  covalent geometry    : angle       0.57265 (14432)
  hydrogen bonds       : bond        0.03797 (  536)
  hydrogen bonds       : angle       3.63875 ( 1536)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1961.67 seconds
wall clock time: 34 minutes 28.92 seconds (2068.92 seconds total)