Starting phenix.real_space_refine
on Fri Aug 22 17:09:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gyx_34379/08_2025/8gyx_34379.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gyx_34379/08_2025/8gyx_34379.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gyx_34379/08_2025/8gyx_34379.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gyx_34379/08_2025/8gyx_34379.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gyx_34379/08_2025/8gyx_34379.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gyx_34379/08_2025/8gyx_34379.cif"
  }
  resolution = 3.7
  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=   0.004 sd=   0.108
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: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     Mg      4      5.21       5
     S      48      5.16       5
     C    4050      2.51       5
     N     978      2.21       5
     O    1036      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6118
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 3005
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 380, 3005
          Classifications: {'peptide': 380}
          Link IDs: {'PTRANS': 17, 'TRANS': 362}
    Chain: "B"
      Number of atoms: 54
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 54
          Unusual residues: {' MG': 2, 'POV': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Restraints were copied for chains:
    A
  Time building chain proxies: 1.58, per 1000 atoms: 0.26
  Number of scatterers: 6118
  At special positions: 0
  Unit cell: (108.07, 90.95, 72.76, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      48     16.00
     P       2     15.00
     Mg      4     11.99
     O    1036      8.00
     N     978      7.00
     C    4050      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: 0.47
  Conformation dependent library (CDL) restraints added in 279.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1424

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 0 sheets defined
      80.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'B' and resid 28 through 36
    Processing helix  chain 'B' and resid 44 through 53
      removed outlier: 3.808A  pdb=" N   GLU B  53 " --> pdb=" O   LYS B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 64 through 79
      removed outlier: 3.966A  pdb=" N   GLY B  70 " --> pdb=" O   PRO B  66 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   TYR B  71 " --> pdb=" O   LEU B  67 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ARG B  77 " --> pdb=" O   GLU B  73 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ARG B  78 " --> pdb=" O   TRP B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 107
    Processing helix  chain 'B' and resid 115 through 143
      removed outlier: 3.922A  pdb=" N   TYR B 119 " --> pdb=" O   PRO B 115 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ILE B 135 " --> pdb=" O   SER B 131 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ASP B 136 " --> pdb=" O   LEU B 132 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   GLY B 137 " --> pdb=" O   ASP B 133 " (cutoff:3.500A)
      removed outlier: 4.845A  pdb=" N   LYS B 138 " --> pdb=" O   ALA B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 174
      removed outlier: 3.595A  pdb=" N   LEU B 160 " --> pdb=" O   GLY B 156 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   VAL B 163 " --> pdb=" O   SER B 159 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   PHE B 164 " --> pdb=" O   LEU B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 177
      No H-bonds generated for 'chain 'B' and resid 175 through 177'
    Processing helix  chain 'B' and resid 178 through 204
    Processing helix  chain 'B' and resid 212 through 237
      removed outlier: 3.540A  pdb=" N   LEU B 225 " --> pdb=" O   ILE B 221 " (cutoff:3.500A)
      Proline residue:  B 232  - end of helix
    Processing helix  chain 'B' and resid 245 through 247
      No H-bonds generated for 'chain 'B' and resid 245 through 247'
    Processing helix  chain 'B' and resid 248 through 272
      removed outlier: 3.702A  pdb=" N   VAL B 268 " --> pdb=" O   ASN B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 279
    Processing helix  chain 'B' and resid 287 through 307
      removed outlier: 3.884A  pdb=" N   LEU B 291 " --> pdb=" O   LEU B 287 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   HIS B 292 " --> pdb=" O   SER B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 315
    Processing helix  chain 'B' and resid 315 through 341
    Processing helix  chain 'B' and resid 348 through 350
      No H-bonds generated for 'chain 'B' and resid 348 through 350'
    Processing helix  chain 'B' and resid 351 through 363
    Processing helix  chain 'B' and resid 368 through 400
    Processing helix  chain 'A' and resid 29 through 36
    Processing helix  chain 'A' and resid 44 through 53
      removed outlier: 3.808A  pdb=" N   GLU A  53 " --> pdb=" O   LYS A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 79
      removed outlier: 3.967A  pdb=" N   GLY A  70 " --> pdb=" O   PRO A  66 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   TYR A  71 " --> pdb=" O   LEU A  67 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ARG A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ARG A  78 " --> pdb=" O   TRP A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 107
    Processing helix  chain 'A' and resid 115 through 143
      removed outlier: 3.922A  pdb=" N   TYR A 119 " --> pdb=" O   PRO A 115 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ILE A 135 " --> pdb=" O   SER A 131 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ASP A 136 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   GLY A 137 " --> pdb=" O   ASP A 133 " (cutoff:3.500A)
      removed outlier: 4.846A  pdb=" N   LYS A 138 " --> pdb=" O   ALA A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 174
      removed outlier: 3.596A  pdb=" N   LEU A 160 " --> pdb=" O   GLY A 156 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   VAL A 163 " --> pdb=" O   SER A 159 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   PHE A 164 " --> pdb=" O   LEU A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 177
      No H-bonds generated for 'chain 'A' and resid 175 through 177'
    Processing helix  chain 'A' and resid 178 through 204
    Processing helix  chain 'A' and resid 212 through 237
      removed outlier: 3.540A  pdb=" N   LEU A 225 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      Proline residue:  A 232  - end of helix
    Processing helix  chain 'A' and resid 245 through 247
      No H-bonds generated for 'chain 'A' and resid 245 through 247'
    Processing helix  chain 'A' and resid 248 through 272
      removed outlier: 3.703A  pdb=" N   VAL A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 287 through 307
      removed outlier: 3.885A  pdb=" N   LEU A 291 " --> pdb=" O   LEU A 287 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   HIS A 292 " --> pdb=" O   SER A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 315
    Processing helix  chain 'A' and resid 315 through 341
    Processing helix  chain 'A' and resid 348 through 350
      No H-bonds generated for 'chain 'A' and resid 348 through 350'
    Processing helix  chain 'A' and resid 351 through 363
    Processing helix  chain 'A' and resid 368 through 400

    439 hydrogen bonds defined for protein.
    1305 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.77

  Time building geometry restraints manager: 0.60 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 898
        1.32 -     1.44: 1812
        1.44 -     1.57: 3498
        1.57 -     1.69: 12
        1.69 -     1.81: 66
  Bond restraints: 6286
  Sorted by residual:
  bond pdb=" O12 POV A 501 "
       pdb=" P   POV A 501 "
    ideal  model  delta    sigma   weight residual
    1.657  1.601  0.056 2.00e-02 2.50e+03 7.96e+00
  bond pdb=" O12 POV B 501 "
       pdb=" P   POV B 501 "
    ideal  model  delta    sigma   weight residual
    1.657  1.601  0.056 2.00e-02 2.50e+03 7.81e+00
  bond pdb=" CB  ASN B 144 "
       pdb=" CG  ASN B 144 "
    ideal  model  delta    sigma   weight residual
    1.516  1.576 -0.060 2.50e-02 1.60e+03 5.80e+00
  bond pdb=" CB  ASN A 144 "
       pdb=" CG  ASN A 144 "
    ideal  model  delta    sigma   weight residual
    1.516  1.576 -0.060 2.50e-02 1.60e+03 5.77e+00
  bond pdb=" CA  ASN A 144 "
       pdb=" CB  ASN A 144 "
    ideal  model  delta    sigma   weight residual
    1.529  1.567 -0.038 1.62e-02 3.81e+03 5.49e+00
  ... (remaining 6281 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.64: 8317
        3.64 -     7.27: 197
        7.27 -    10.91: 22
       10.91 -    14.54: 4
       14.54 -    18.18: 4
  Bond angle restraints: 8544
  Sorted by residual:
  angle pdb=" CB  MET A 339 "
        pdb=" CG  MET A 339 "
        pdb=" SD  MET A 339 "
      ideal   model   delta    sigma   weight residual
     112.70  130.88  -18.18 3.00e+00 1.11e-01 3.67e+01
  angle pdb=" CB  MET B 339 "
        pdb=" CG  MET B 339 "
        pdb=" SD  MET B 339 "
      ideal   model   delta    sigma   weight residual
     112.70  130.87  -18.17 3.00e+00 1.11e-01 3.67e+01
  angle pdb=" CA  PRO B 148 "
        pdb=" N   PRO B 148 "
        pdb=" CD  PRO B 148 "
      ideal   model   delta    sigma   weight residual
     112.00  104.61    7.39 1.40e+00 5.10e-01 2.79e+01
  angle pdb=" CA  PRO A 148 "
        pdb=" N   PRO A 148 "
        pdb=" CD  PRO A 148 "
      ideal   model   delta    sigma   weight residual
     112.00  104.64    7.36 1.40e+00 5.10e-01 2.76e+01
  angle pdb=" CA  ASN B 144 "
        pdb=" CB  ASN B 144 "
        pdb=" CG  ASN B 144 "
      ideal   model   delta    sigma   weight residual
     112.60  117.61   -5.01 1.00e+00 1.00e+00 2.51e+01
  ... (remaining 8539 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.09: 3233
       18.09 -    36.17: 305
       36.17 -    54.26: 90
       54.26 -    72.34: 20
       72.34 -    90.43: 6
  Dihedral angle restraints: 3654
    sinusoidal: 1446
      harmonic: 2208
  Sorted by residual:
  dihedral pdb=" C   ASN B 144 "
           pdb=" N   ASN B 144 "
           pdb=" CA  ASN B 144 "
           pdb=" CB  ASN B 144 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.96    9.36     0      2.50e+00 1.60e-01 1.40e+01
  dihedral pdb=" C   ASN A 144 "
           pdb=" N   ASN A 144 "
           pdb=" CA  ASN A 144 "
           pdb=" CB  ASN A 144 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.92    9.32     0      2.50e+00 1.60e-01 1.39e+01
  dihedral pdb=" CA  ASP B 348 "
           pdb=" CB  ASP B 348 "
           pdb=" CG  ASP B 348 "
           pdb=" OD1 ASP B 348 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.29   59.29     1      2.00e+01 2.50e-03 1.17e+01
  ... (remaining 3651 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 796
       0.082 -    0.164: 142
       0.164 -    0.245: 34
       0.245 -    0.327: 2
       0.327 -    0.409: 4
  Chirality restraints: 978
  Sorted by residual:
  chirality pdb=" CB  ILE A 222 "
            pdb=" CA  ILE A 222 "
            pdb=" CG1 ILE A 222 "
            pdb=" CG2 ILE A 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.24    0.41 2.00e-01 2.50e+01 4.18e+00
  chirality pdb=" CB  ILE B 222 "
            pdb=" CA  ILE B 222 "
            pdb=" CG1 ILE B 222 "
            pdb=" CG2 ILE B 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.24    0.41 2.00e-01 2.50e+01 4.17e+00
  chirality pdb=" CA  PRO A 148 "
            pdb=" N   PRO A 148 "
            pdb=" C   PRO A 148 "
            pdb=" CB  PRO A 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.38    0.34 2.00e-01 2.50e+01 2.89e+00
  ... (remaining 975 not shown)

  Planarity restraints: 1040
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C28 POV B 501 "   -0.096 2.00e-02 2.50e+03   2.38e-01 5.67e+02
        pdb=" C29 POV B 501 "    0.317 2.00e-02 2.50e+03
        pdb="C210 POV B 501 "   -0.325 2.00e-02 2.50e+03
        pdb="C211 POV B 501 "    0.104 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C28 POV A 501 "    0.096 2.00e-02 2.50e+03   2.38e-01 5.66e+02
        pdb=" C29 POV A 501 "   -0.317 2.00e-02 2.50e+03
        pdb="C210 POV A 501 "    0.325 2.00e-02 2.50e+03
        pdb="C211 POV A 501 "   -0.104 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 147 "   -0.071 5.00e-02 4.00e+02   1.03e-01 1.69e+01
        pdb=" N   PRO A 148 "    0.178 5.00e-02 4.00e+02
        pdb=" CA  PRO A 148 "   -0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO A 148 "   -0.057 5.00e-02 4.00e+02
  ... (remaining 1037 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 316
        2.75 -     3.28: 6486
        3.28 -     3.82: 10094
        3.82 -     4.36: 11692
        4.36 -     4.90: 20113
  Nonbonded interactions: 48701
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 133 "
            pdb="MG    MG A 502 "
     model   vdw
     2.208 2.170
  nonbonded pdb=" OD1 ASP B 133 "
            pdb="MG    MG B 502 "
     model   vdw
     2.208 2.170
  nonbonded pdb=" OD2 ASP B 158 "
            pdb="MG    MG B 503 "
     model   vdw
     2.234 2.170
  nonbonded pdb=" OD2 ASP A 158 "
            pdb="MG    MG A 503 "
     model   vdw
     2.235 2.170
  nonbonded pdb=" OG1 THR A 143 "
            pdb=" OG  SER A 145 "
     model   vdw
     2.261 3.040
  ... (remaining 48696 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.700
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.420
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.000
  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:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
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      :  0.007   0.060   6286  Z= 0.356
  Angle     :  1.358  18.179   8544  Z= 0.780
  Chirality :  0.072   0.409    978
  Planarity :  0.014   0.238   1040
  Dihedral  : 16.071  90.426   2230
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 19.64 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.28), residues: 756
  helix:  0.85 (0.20), residues: 548
  sheet:  None (None), residues: 0
  loop :  0.67 (0.45), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.003   ARG A  50 
 TYR   0.046   0.005   TYR B 387 
 PHE   0.056   0.003   PHE B 260 
 TRP   0.022   0.003   TRP B  74 
 HIS   0.031   0.004   HIS A  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00683 ( 6286)
  covalent geometry    : angle       1.35818 ( 8544)
  hydrogen bonds       : bond        0.20796 (  439)
  hydrogen bonds       : angle       6.77726 ( 1305)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 163
  time to evaluate  : 0.165 
Fit side-chains
REVERT: B  131 SER cc_start: 0.8853 (m) cc_final: 0.8614 (m)
REVERT: B  267 ARG cc_start: 0.7786 (ptm160) cc_final: 0.7433 (ptm160)
REVERT: A  131 SER cc_start: 0.8866 (m) cc_final: 0.8658 (m)
  outliers start: 2
  outliers final: 2
  residues processed: 164
  average time/residue: 0.0776
  time to fit residues: 16.3053
Evaluate side-chains
  160 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 158
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain A residue  149 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    9.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B 130 GLN
B 197 HIS
** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 217 GLN
A  57 GLN
A 130 GLN
A 197 HIS
** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 217 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.172856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.135069 restraints weight = 7369.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.140783 restraints weight = 3660.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.144689 restraints weight = 2390.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.146990 restraints weight = 1834.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.148525 restraints weight = 1565.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6286  Z= 0.159
  Angle     :  0.642  10.156   8544  Z= 0.335
  Chirality :  0.043   0.151    978
  Planarity :  0.005   0.061   1040
  Dihedral  : 10.967  87.849    898
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 18.43 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.66 (0.29), residues: 756
  helix:  2.10 (0.20), residues: 570
  sheet:  None (None), residues: 0
  loop :  0.84 (0.49), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  50 
 TYR   0.015   0.002   TYR A 362 
 PHE   0.019   0.002   PHE A 358 
 TRP   0.010   0.001   TRP B  74 
 HIS   0.006   0.001   HIS B  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 6286)
  covalent geometry    : angle       0.64193 ( 8544)
  hydrogen bonds       : bond        0.06222 (  439)
  hydrogen bonds       : angle       4.64065 ( 1305)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 193
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
REVERT: B   69 GLN cc_start: 0.8668 (tp40) cc_final: 0.8453 (tp40)
REVERT: B  131 SER cc_start: 0.8920 (m) cc_final: 0.8717 (m)
REVERT: B  219 PHE cc_start: 0.7412 (t80) cc_final: 0.6957 (m-10)
REVERT: B  267 ARG cc_start: 0.7973 (ptm160) cc_final: 0.7601 (ptm160)
REVERT: B  347 HIS cc_start: 0.8132 (p90) cc_final: 0.7562 (p90)
REVERT: B  360 ASP cc_start: 0.9044 (t70) cc_final: 0.8651 (t0)
REVERT: B  362 TYR cc_start: 0.9059 (t80) cc_final: 0.8609 (t80)
REVERT: A   50 ARG cc_start: 0.7801 (ttm110) cc_final: 0.7576 (ttp-110)
REVERT: A   69 GLN cc_start: 0.8648 (tp40) cc_final: 0.8431 (tp40)
REVERT: A  119 TYR cc_start: 0.8735 (m-10) cc_final: 0.8400 (m-10)
REVERT: A  219 PHE cc_start: 0.7439 (t80) cc_final: 0.6961 (m-10)
REVERT: A  347 HIS cc_start: 0.8151 (p90) cc_final: 0.7384 (p-80)
REVERT: A  360 ASP cc_start: 0.9057 (t70) cc_final: 0.8687 (t0)
REVERT: A  362 TYR cc_start: 0.9059 (t80) cc_final: 0.8630 (t80)
  outliers start: 23
  outliers final: 17
  residues processed: 207
  average time/residue: 0.0765
  time to fit residues: 20.5516
Evaluate side-chains
  202 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 185
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  365 SER
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  157 CYS
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  365 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 41 optimal weight:   10.0000
   chunk 71 optimal weight:    0.5980
   chunk 51 optimal weight:    0.6980
   chunk 18 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9980
   chunk 10 optimal weight:    7.9990
   chunk 4 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B  47 GLN
B  57 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.169471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.128264 restraints weight = 7560.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.134009 restraints weight = 3934.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.138005 restraints weight = 2658.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.140496 restraints weight = 2078.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.142175 restraints weight = 1783.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6286  Z= 0.145
  Angle     :  0.587   9.387   8544  Z= 0.308
  Chirality :  0.042   0.144    978
  Planarity :  0.005   0.043   1040
  Dihedral  : 10.218  81.989    898
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 22.05 %
    Favored  : 74.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.87 (0.30), residues: 756
  helix:  2.27 (0.21), residues: 568
  sheet:  None (None), residues: 0
  loop :  0.91 (0.48), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  50 
 TYR   0.015   0.002   TYR B 304 
 PHE   0.027   0.002   PHE A 234 
 TRP   0.015   0.001   TRP B  74 
 HIS   0.005   0.001   HIS A 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6286)
  covalent geometry    : angle       0.58744 ( 8544)
  hydrogen bonds       : bond        0.05483 (  439)
  hydrogen bonds       : angle       4.38921 ( 1305)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 191
  time to evaluate  : 0.164 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8500 (tp40) cc_final: 0.8251 (tp40)
REVERT: B   78 ARG cc_start: 0.8454 (mmm160) cc_final: 0.7991 (mmm-85)
REVERT: B  119 TYR cc_start: 0.8819 (m-10) cc_final: 0.8577 (m-10)
REVERT: B  201 TYR cc_start: 0.8834 (t80) cc_final: 0.8623 (t80)
REVERT: B  219 PHE cc_start: 0.7537 (t80) cc_final: 0.7100 (m-10)
REVERT: B  252 LEU cc_start: 0.8781 (mt) cc_final: 0.8482 (mt)
REVERT: B  313 GLU cc_start: 0.7871 (mp0) cc_final: 0.7581 (mp0)
REVERT: B  347 HIS cc_start: 0.8278 (p90) cc_final: 0.8004 (p90)
REVERT: B  360 ASP cc_start: 0.8848 (t70) cc_final: 0.8380 (t0)
REVERT: B  362 TYR cc_start: 0.8998 (t80) cc_final: 0.8701 (t80)
REVERT: A   69 GLN cc_start: 0.8504 (tp40) cc_final: 0.8289 (tp40)
REVERT: A  119 TYR cc_start: 0.8799 (m-10) cc_final: 0.8579 (m-10)
REVERT: A  201 TYR cc_start: 0.8829 (t80) cc_final: 0.8607 (t80)
REVERT: A  219 PHE cc_start: 0.7532 (t80) cc_final: 0.7135 (m-10)
REVERT: A  252 LEU cc_start: 0.8773 (mt) cc_final: 0.8474 (mt)
REVERT: A  305 LYS cc_start: 0.8732 (mmtt) cc_final: 0.8531 (mmmt)
REVERT: A  347 HIS cc_start: 0.8298 (p90) cc_final: 0.8032 (p90)
REVERT: A  360 ASP cc_start: 0.8879 (t70) cc_final: 0.8448 (t0)
REVERT: A  362 TYR cc_start: 0.9011 (t80) cc_final: 0.8772 (t80)
  outliers start: 24
  outliers final: 18
  residues processed: 204
  average time/residue: 0.0804
  time to fit residues: 20.9909
Evaluate side-chains
  205 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 187
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   47 GLN
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  365 SER
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  157 CYS
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  365 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 3 optimal weight:   10.0000
   chunk 14 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 5 optimal weight:    7.9990
   chunk 41 optimal weight:    7.9990
   chunk 24 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 217 GLN
B 224 HIS
** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 217 GLN
A 224 HIS
** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.161892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.124757 restraints weight = 7809.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.129973 restraints weight = 3986.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.133334 restraints weight = 2660.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.135431 restraints weight = 2083.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.136577 restraints weight = 1793.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.3312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   6286  Z= 0.228
  Angle     :  0.654  10.552   8544  Z= 0.343
  Chirality :  0.046   0.191    978
  Planarity :  0.005   0.044   1040
  Dihedral  : 10.015  83.352    898
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  6.19 %
    Allowed  : 21.75 %
    Favored  : 72.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.53 (0.30), residues: 756
  helix:  2.06 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop :  0.60 (0.47), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  55 
 TYR   0.018   0.002   TYR B 304 
 PHE   0.019   0.002   PHE A 323 
 TRP   0.008   0.001   TRP B 181 
 HIS   0.005   0.001   HIS B 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 ( 6286)
  covalent geometry    : angle       0.65380 ( 8544)
  hydrogen bonds       : bond        0.06105 (  439)
  hydrogen bonds       : angle       4.59413 ( 1305)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 225
  time to evaluate  : 0.160 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8592 (tp40) cc_final: 0.8339 (tp40)
REVERT: B   78 ARG cc_start: 0.8597 (mmm160) cc_final: 0.8163 (mmm-85)
REVERT: B   98 CYS cc_start: 0.8500 (m) cc_final: 0.7821 (m)
REVERT: B  149 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8725 (tt)
REVERT: B  199 GLN cc_start: 0.8843 (tm-30) cc_final: 0.8433 (tm-30)
REVERT: B  252 LEU cc_start: 0.8918 (mt) cc_final: 0.8658 (mt)
REVERT: B  360 ASP cc_start: 0.8907 (t70) cc_final: 0.8497 (t0)
REVERT: B  362 TYR cc_start: 0.9110 (t80) cc_final: 0.8658 (t80)
REVERT: A   69 GLN cc_start: 0.8628 (tp40) cc_final: 0.8368 (tp40)
REVERT: A  119 TYR cc_start: 0.8863 (m-10) cc_final: 0.8640 (m-10)
REVERT: A  149 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8717 (tt)
REVERT: A  199 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8379 (tm-30)
REVERT: A  252 LEU cc_start: 0.8904 (mt) cc_final: 0.8636 (mt)
REVERT: A  360 ASP cc_start: 0.8923 (t70) cc_final: 0.8530 (t0)
REVERT: A  362 TYR cc_start: 0.9097 (t80) cc_final: 0.8679 (t80)
  outliers start: 41
  outliers final: 34
  residues processed: 249
  average time/residue: 0.0769
  time to fit residues: 24.6258
Evaluate side-chains
  235 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 199
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  248 ILE
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  309 VAL
Chi-restraints excluded: chain B residue  365 SER
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  157 CYS
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  365 SER
Chi-restraints excluded: chain A residue  390 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 71 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 46 optimal weight:    0.1980
   chunk 54 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 44 optimal weight:    0.0980
   chunk 41 optimal weight:    6.9990
   chunk 42 optimal weight:    6.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
B  47 GLN
** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  46 HIS
** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 224 HIS
A 398 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.170720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.133061 restraints weight = 7777.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.138792 restraints weight = 3785.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.142484 restraints weight = 2457.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.144778 restraints weight = 1900.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.145850 restraints weight = 1624.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.3582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6286  Z= 0.135
  Angle     :  0.607  12.243   8544  Z= 0.309
  Chirality :  0.041   0.159    978
  Planarity :  0.005   0.039   1040
  Dihedral  :  9.567  79.931    898
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 28.25 %
    Favored  : 67.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.70 (0.30), residues: 756
  helix:  2.17 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop :  0.68 (0.48), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  50 
 TYR   0.017   0.001   TYR B 201 
 PHE   0.036   0.001   PHE A 234 
 TRP   0.007   0.001   TRP A 117 
 HIS   0.004   0.001   HIS A 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 6286)
  covalent geometry    : angle       0.60660 ( 8544)
  hydrogen bonds       : bond        0.05200 (  439)
  hydrogen bonds       : angle       4.25775 ( 1305)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 191
  time to evaluate  : 0.215 
Fit side-chains
REVERT: B   50 ARG cc_start: 0.8312 (ttm110) cc_final: 0.7601 (ttt180)
REVERT: B   69 GLN cc_start: 0.8199 (tp40) cc_final: 0.7937 (tp40)
REVERT: B  149 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8764 (tt)
REVERT: B  199 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8479 (tm-30)
REVERT: B  219 PHE cc_start: 0.7436 (t80) cc_final: 0.7017 (m-10)
REVERT: B  252 LEU cc_start: 0.8958 (mt) cc_final: 0.8645 (mt)
REVERT: B  266 PHE cc_start: 0.8345 (m-80) cc_final: 0.8140 (m-80)
REVERT: B  360 ASP cc_start: 0.8830 (t70) cc_final: 0.8395 (t0)
REVERT: B  381 PHE cc_start: 0.8399 (t80) cc_final: 0.7865 (t80)
REVERT: A   69 GLN cc_start: 0.8246 (tp40) cc_final: 0.7980 (tp40)
REVERT: A  149 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8751 (tt)
REVERT: A  199 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8451 (tm-30)
REVERT: A  252 LEU cc_start: 0.8959 (mt) cc_final: 0.8647 (mt)
REVERT: A  305 LYS cc_start: 0.9041 (mmtt) cc_final: 0.8791 (mmmt)
REVERT: A  360 ASP cc_start: 0.8877 (t70) cc_final: 0.8445 (t0)
REVERT: A  362 TYR cc_start: 0.8982 (t80) cc_final: 0.8550 (t80)
REVERT: A  381 PHE cc_start: 0.8410 (t80) cc_final: 0.7871 (t80)
  outliers start: 27
  outliers final: 18
  residues processed: 207
  average time/residue: 0.0552
  time to fit residues: 15.9404
Evaluate side-chains
  203 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 183
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  157 CYS
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  383 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 52 optimal weight:    0.4980
   chunk 3 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0970
   chunk 4 optimal weight:    5.9990
   chunk 44 optimal weight:    0.0870
   chunk 53 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 224 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.170341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.133422 restraints weight = 7737.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.138989 restraints weight = 3748.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.142628 restraints weight = 2442.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.144895 restraints weight = 1886.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.146172 restraints weight = 1613.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.3812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6286  Z= 0.137
  Angle     :  0.573   7.354   8544  Z= 0.300
  Chirality :  0.042   0.184    978
  Planarity :  0.005   0.040   1040
  Dihedral  :  9.332  80.889    898
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 29.15 %
    Favored  : 67.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.72 (0.30), residues: 756
  helix:  2.20 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop :  0.64 (0.49), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  50 
 TYR   0.019   0.002   TYR B 387 
 PHE   0.017   0.001   PHE A 358 
 TRP   0.007   0.001   TRP B  74 
 HIS   0.003   0.001   HIS B 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 6286)
  covalent geometry    : angle       0.57275 ( 8544)
  hydrogen bonds       : bond        0.05146 (  439)
  hydrogen bonds       : angle       4.19902 ( 1305)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 192
  time to evaluate  : 0.213 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8159 (tp40) cc_final: 0.7911 (tp40)
REVERT: B   74 TRP cc_start: 0.7992 (t60) cc_final: 0.7686 (t60)
REVERT: B   95 ILE cc_start: 0.8604 (tp) cc_final: 0.8393 (mt)
REVERT: B  219 PHE cc_start: 0.7391 (t80) cc_final: 0.6946 (m-10)
REVERT: B  252 LEU cc_start: 0.8974 (mt) cc_final: 0.8643 (mt)
REVERT: B  360 ASP cc_start: 0.8827 (t70) cc_final: 0.8399 (t0)
REVERT: B  362 TYR cc_start: 0.8944 (t80) cc_final: 0.8531 (t80)
REVERT: B  381 PHE cc_start: 0.8415 (t80) cc_final: 0.7879 (t80)
REVERT: A   50 ARG cc_start: 0.8292 (ttm110) cc_final: 0.7619 (ttt180)
REVERT: A  199 GLN cc_start: 0.8851 (tm-30) cc_final: 0.8444 (tm-30)
REVERT: A  252 LEU cc_start: 0.8962 (mt) cc_final: 0.8638 (mt)
REVERT: A  305 LYS cc_start: 0.9030 (mmtt) cc_final: 0.8800 (mmmt)
REVERT: A  360 ASP cc_start: 0.8869 (t70) cc_final: 0.8428 (t0)
REVERT: A  362 TYR cc_start: 0.9024 (t80) cc_final: 0.8593 (t80)
REVERT: A  369 GLU cc_start: 0.7495 (mp0) cc_final: 0.7258 (mt-10)
REVERT: A  381 PHE cc_start: 0.8431 (t80) cc_final: 0.7892 (t80)
  outliers start: 22
  outliers final: 19
  residues processed: 207
  average time/residue: 0.0556
  time to fit residues: 15.9986
Evaluate side-chains
  207 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 188
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  365 SER
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  157 CYS
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  365 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0980
   chunk 69 optimal weight:    0.8980
   chunk 43 optimal weight:    0.6980
   chunk 50 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.169604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.131710 restraints weight = 7854.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.137438 restraints weight = 3946.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.141229 restraints weight = 2602.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.143593 restraints weight = 2015.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.144903 restraints weight = 1718.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.3935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6286  Z= 0.148
  Angle     :  0.613   9.039   8544  Z= 0.312
  Chirality :  0.042   0.171    978
  Planarity :  0.005   0.040   1040
  Dihedral  :  9.127  80.707    894
  Min Nonbonded Distance : 1.874

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 27.64 %
    Favored  : 67.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.76 (0.30), residues: 756
  helix:  2.25 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop :  0.60 (0.49), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  50 
 TYR   0.016   0.002   TYR A 387 
 PHE   0.015   0.001   PHE B 187 
 TRP   0.009   0.001   TRP B 235 
 HIS   0.004   0.001   HIS B 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 6286)
  covalent geometry    : angle       0.61279 ( 8544)
  hydrogen bonds       : bond        0.05224 (  439)
  hydrogen bonds       : angle       4.22874 ( 1305)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 192
  time to evaluate  : 0.234 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8184 (tp40) cc_final: 0.7949 (tp40)
REVERT: B   74 TRP cc_start: 0.7954 (t60) cc_final: 0.7659 (t60)
REVERT: B   95 ILE cc_start: 0.8602 (tp) cc_final: 0.8393 (mt)
REVERT: B  219 PHE cc_start: 0.7442 (t80) cc_final: 0.7173 (t80)
REVERT: B  244 ILE cc_start: 0.7988 (tp) cc_final: 0.7575 (mm)
REVERT: B  252 LEU cc_start: 0.8966 (mt) cc_final: 0.8661 (mt)
REVERT: B  360 ASP cc_start: 0.8821 (t70) cc_final: 0.8368 (t0)
REVERT: B  381 PHE cc_start: 0.8388 (t80) cc_final: 0.7870 (t80)
REVERT: A   49 LYS cc_start: 0.8594 (tttt) cc_final: 0.8175 (ttmt)
REVERT: A   50 ARG cc_start: 0.8333 (ttm110) cc_final: 0.7652 (ttt180)
REVERT: A  199 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8434 (tm-30)
REVERT: A  244 ILE cc_start: 0.7944 (tp) cc_final: 0.7519 (mm)
REVERT: A  252 LEU cc_start: 0.8976 (mt) cc_final: 0.8657 (mt)
REVERT: A  305 LYS cc_start: 0.9031 (mmtt) cc_final: 0.8797 (mmmt)
REVERT: A  360 ASP cc_start: 0.8866 (t70) cc_final: 0.8413 (t0)
REVERT: A  362 TYR cc_start: 0.9020 (t80) cc_final: 0.8677 (t80)
REVERT: A  369 GLU cc_start: 0.7420 (mp0) cc_final: 0.7150 (mt-10)
REVERT: A  381 PHE cc_start: 0.8466 (t80) cc_final: 0.7929 (t80)
  outliers start: 30
  outliers final: 27
  residues processed: 208
  average time/residue: 0.0603
  time to fit residues: 17.2271
Evaluate side-chains
  212 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 185
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  180 ASP
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  248 ILE
Chi-restraints excluded: chain B residue  365 SER
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  157 CYS
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  343 GLU
Chi-restraints excluded: chain A residue  365 SER
Chi-restraints excluded: chain A residue  390 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 71 optimal weight:    0.6980
   chunk 9 optimal weight:    6.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  46 HIS
** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.169785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.131513 restraints weight = 7920.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.137325 restraints weight = 3924.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.141134 restraints weight = 2587.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.143454 restraints weight = 2009.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.144785 restraints weight = 1721.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.4020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6286  Z= 0.146
  Angle     :  0.616   8.623   8544  Z= 0.317
  Chirality :  0.042   0.182    978
  Planarity :  0.005   0.041   1040
  Dihedral  :  9.082  80.589    894
  Min Nonbonded Distance : 1.793

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 28.40 %
    Favored  : 67.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.72 (0.30), residues: 756
  helix:  2.24 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop :  0.50 (0.47), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  50 
 TYR   0.017   0.002   TYR A 387 
 PHE   0.040   0.002   PHE B 234 
 TRP   0.013   0.001   TRP B 235 
 HIS   0.004   0.001   HIS A  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 6286)
  covalent geometry    : angle       0.61627 ( 8544)
  hydrogen bonds       : bond        0.05173 (  439)
  hydrogen bonds       : angle       4.17613 ( 1305)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 191
  time to evaluate  : 0.198 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8142 (tp40) cc_final: 0.7900 (tp40)
REVERT: B   74 TRP cc_start: 0.7993 (t60) cc_final: 0.7654 (t60)
REVERT: B   95 ILE cc_start: 0.8542 (tp) cc_final: 0.8334 (mt)
REVERT: B  244 ILE cc_start: 0.7952 (tp) cc_final: 0.7525 (mm)
REVERT: B  252 LEU cc_start: 0.8985 (mt) cc_final: 0.8667 (mt)
REVERT: B  369 GLU cc_start: 0.7480 (mp0) cc_final: 0.7253 (mt-10)
REVERT: B  381 PHE cc_start: 0.8363 (t80) cc_final: 0.7817 (t80)
REVERT: A  199 GLN cc_start: 0.8835 (tm-30) cc_final: 0.8429 (tm-30)
REVERT: A  252 LEU cc_start: 0.8979 (mt) cc_final: 0.8663 (mt)
REVERT: A  305 LYS cc_start: 0.9015 (mmtt) cc_final: 0.8768 (mmmt)
REVERT: A  360 ASP cc_start: 0.8944 (t70) cc_final: 0.8530 (t0)
REVERT: A  362 TYR cc_start: 0.9079 (t80) cc_final: 0.8653 (t80)
REVERT: A  369 GLU cc_start: 0.7471 (mp0) cc_final: 0.7249 (mt-10)
REVERT: A  381 PHE cc_start: 0.8375 (t80) cc_final: 0.7826 (t80)
  outliers start: 28
  outliers final: 28
  residues processed: 208
  average time/residue: 0.0564
  time to fit residues: 16.2969
Evaluate side-chains
  212 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 184
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  180 ASP
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  248 ILE
Chi-restraints excluded: chain B residue  365 SER
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  157 CYS
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  343 GLU
Chi-restraints excluded: chain A residue  365 SER
Chi-restraints excluded: chain A residue  383 ASP
Chi-restraints excluded: chain A residue  390 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 69 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   chunk 8 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 174 GLN
** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  46 HIS
A 174 GLN
** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.169666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.131693 restraints weight = 7876.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.137342 restraints weight = 3943.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.140988 restraints weight = 2612.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.143335 restraints weight = 2038.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.144266 restraints weight = 1743.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.4095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6286  Z= 0.146
  Angle     :  0.637   8.485   8544  Z= 0.324
  Chirality :  0.042   0.188    978
  Planarity :  0.005   0.042   1040
  Dihedral  :  9.031  80.663    894
  Min Nonbonded Distance : 1.719

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 27.95 %
    Favored  : 67.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.71 (0.30), residues: 756
  helix:  2.23 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop :  0.51 (0.47), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  50 
 TYR   0.018   0.002   TYR A 387 
 PHE   0.019   0.001   PHE A 358 
 TRP   0.016   0.001   TRP B 235 
 HIS   0.004   0.001   HIS A  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6286)
  covalent geometry    : angle       0.63741 ( 8544)
  hydrogen bonds       : bond        0.05155 (  439)
  hydrogen bonds       : angle       4.17696 ( 1305)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 187
  time to evaluate  : 0.136 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8177 (tp40) cc_final: 0.7929 (tp40)
REVERT: B   95 ILE cc_start: 0.8585 (tp) cc_final: 0.8369 (mt)
REVERT: B  252 LEU cc_start: 0.8961 (mt) cc_final: 0.8644 (mt)
REVERT: B  360 ASP cc_start: 0.8773 (t70) cc_final: 0.8244 (t0)
REVERT: B  369 GLU cc_start: 0.7406 (mp0) cc_final: 0.7130 (mt-10)
REVERT: B  381 PHE cc_start: 0.8443 (t80) cc_final: 0.7868 (t80)
REVERT: A  199 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8439 (tm-30)
REVERT: A  252 LEU cc_start: 0.8961 (mt) cc_final: 0.8647 (mt)
REVERT: A  305 LYS cc_start: 0.8983 (mmtt) cc_final: 0.8659 (mmmt)
REVERT: A  360 ASP cc_start: 0.8873 (t70) cc_final: 0.8419 (t0)
REVERT: A  362 TYR cc_start: 0.9045 (t80) cc_final: 0.8726 (t80)
REVERT: A  381 PHE cc_start: 0.8404 (t80) cc_final: 0.7847 (t80)
  outliers start: 30
  outliers final: 30
  residues processed: 206
  average time/residue: 0.0660
  time to fit residues: 18.2119
Evaluate side-chains
  209 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 179
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  180 ASP
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  200 THR
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  248 ILE
Chi-restraints excluded: chain B residue  365 SER
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  157 CYS
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  343 GLU
Chi-restraints excluded: chain A residue  365 SER
Chi-restraints excluded: chain A residue  383 ASP
Chi-restraints excluded: chain A residue  390 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 73 optimal weight:    0.6980
   chunk 58 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 75 optimal weight:    6.9990
   chunk 56 optimal weight:    4.9990
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
B  46 HIS
** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  46 HIS
** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 217 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.168601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.130358 restraints weight = 7940.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.135937 restraints weight = 4012.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.139618 restraints weight = 2664.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.141911 restraints weight = 2085.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.143243 restraints weight = 1791.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.4155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6286  Z= 0.155
  Angle     :  0.645   8.738   8544  Z= 0.329
  Chirality :  0.043   0.193    978
  Planarity :  0.005   0.042   1040
  Dihedral  :  9.062  79.419    894
  Min Nonbonded Distance : 1.633

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 27.95 %
    Favored  : 67.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.66 (0.30), residues: 756
  helix:  2.20 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop :  0.44 (0.47), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  50 
 TYR   0.018   0.002   TYR A 387 
 PHE   0.015   0.001   PHE B 187 
 TRP   0.025   0.001   TRP B  74 
 HIS   0.005   0.001   HIS A  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 6286)
  covalent geometry    : angle       0.64535 ( 8544)
  hydrogen bonds       : bond        0.05258 (  439)
  hydrogen bonds       : angle       4.19813 ( 1305)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 181
  time to evaluate  : 0.192 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8147 (tp40) cc_final: 0.7892 (tp40)
REVERT: B   95 ILE cc_start: 0.8573 (tp) cc_final: 0.8370 (mt)
REVERT: B  246 MET cc_start: 0.7125 (ttp) cc_final: 0.6795 (ttp)
REVERT: B  252 LEU cc_start: 0.8982 (mt) cc_final: 0.8668 (mt)
REVERT: B  369 GLU cc_start: 0.7448 (mp0) cc_final: 0.7227 (mt-10)
REVERT: B  381 PHE cc_start: 0.8400 (t80) cc_final: 0.7847 (t80)
REVERT: A  199 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8439 (tm-30)
REVERT: A  252 LEU cc_start: 0.8985 (mt) cc_final: 0.8666 (mt)
REVERT: A  305 LYS cc_start: 0.9008 (mmtt) cc_final: 0.8688 (mmmt)
REVERT: A  360 ASP cc_start: 0.8882 (t70) cc_final: 0.8403 (t0)
REVERT: A  362 TYR cc_start: 0.9030 (t80) cc_final: 0.8728 (t80)
REVERT: A  381 PHE cc_start: 0.8418 (t80) cc_final: 0.7860 (t80)
  outliers start: 32
  outliers final: 29
  residues processed: 200
  average time/residue: 0.0618
  time to fit residues: 16.5702
Evaluate side-chains
  206 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 177
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  200 THR
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  248 ILE
Chi-restraints excluded: chain B residue  365 SER
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  157 CYS
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  365 SER
Chi-restraints excluded: chain A residue  383 ASP
Chi-restraints excluded: chain A residue  390 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 53 optimal weight:    0.3980
   chunk 39 optimal weight:    0.0170
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.6418

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

Flipped N/Q/H residues before XYZ refinement:
** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  46 HIS
** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.171234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.133926 restraints weight = 7774.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.139538 restraints weight = 3830.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.143195 restraints weight = 2510.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.145467 restraints weight = 1943.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.146668 restraints weight = 1660.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.4209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6286  Z= 0.137
  Angle     :  0.628   8.716   8544  Z= 0.318
  Chirality :  0.042   0.201    978
  Planarity :  0.005   0.042   1040
  Dihedral  :  9.081  81.225    894
  Min Nonbonded Distance : 1.582

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 28.85 %
    Favored  : 67.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.70 (0.30), residues: 756
  helix:  2.25 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop :  0.40 (0.47), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  50 
 TYR   0.019   0.001   TYR A 387 
 PHE   0.024   0.001   PHE B 234 
 TRP   0.023   0.001   TRP B  74 
 HIS   0.004   0.001   HIS A  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6286)
  covalent geometry    : angle       0.62786 ( 8544)
  hydrogen bonds       : bond        0.05056 (  439)
  hydrogen bonds       : angle       4.11933 ( 1305)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1028.77 seconds
wall clock time: 18 minutes 28.61 seconds (1108.61 seconds total)