Starting phenix.real_space_refine
on Tue Feb 11 16:46:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gyx_34379/02_2025/8gyx_34379.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gyx_34379/02_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_34379/02_2025/8gyx_34379.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gyx_34379/02_2025/8gyx_34379.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gyx_34379/02_2025/8gyx_34379.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gyx_34379/02_2025/8gyx_34379.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6118
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      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: "A"
      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:
    B
  Time building chain proxies: 5.08, per 1000 atoms: 0.83
  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: 1.56
  Conformation dependent library (CDL) restraints added in 873.3 milliseconds
  

  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: 0.50
  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: 1.81

  Time building geometry restraints manager: 1.78 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             0.600
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     18.750
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.840
-------------------------------------------------------------------------------
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= 0.447
  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 : 6.07
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.022   0.003   TRP B  74 
 HIS   0.031   0.004   HIS A  46 
 PHE   0.056   0.003   PHE B 260 
 TYR   0.046   0.005   TYR B 387 
 ARG   0.014   0.003   ARG A  50 

*********************** 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  : 0.735 
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: 0.2238
  time to fit residues: 47.0665
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  : 0.685 
-------------------------------------------------------------------------------
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 64 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 38 optimal weight:    9.9990
   chunk 30 optimal weight:    0.6980
   chunk 59 optimal weight:    8.9990
   chunk 23 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   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 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 = 0.172880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.135138 restraints weight = 7301.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.140846 restraints weight = 3638.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.144731 restraints weight = 2382.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.1911

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= 0.218
  Angle     :  0.642  10.180   8544  Z= 0.335
  Chirality :  0.043   0.151    978
  Planarity :  0.005   0.061   1040
  Dihedral  : 10.963  87.806    898
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 18.13 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.010   0.001   TRP B  74 
 HIS   0.006   0.001   HIS B  46 
 PHE   0.019   0.002   PHE A 358 
 TYR   0.015   0.002   TYR A 362 
 ARG   0.005   0.001   ARG B  50 

*********************** 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
  218 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 193
  time to evaluate  : 0.653 
Fit side-chains
   revert: symmetry clash
REVERT: B   69 GLN cc_start: 0.8631 (tp40) cc_final: 0.8415 (tp40)
REVERT: B  219 PHE cc_start: 0.7431 (t80) cc_final: 0.6953 (m-10)
REVERT: B  267 ARG cc_start: 0.8002 (ptm160) cc_final: 0.7629 (ptm160)
REVERT: B  347 HIS cc_start: 0.8144 (p90) cc_final: 0.7578 (p90)
REVERT: B  360 ASP cc_start: 0.9034 (t70) cc_final: 0.8639 (t0)
REVERT: B  362 TYR cc_start: 0.9067 (t80) cc_final: 0.8613 (t80)
REVERT: A   50 ARG cc_start: 0.7845 (ttm110) cc_final: 0.7621 (ttp-110)
REVERT: A   69 GLN cc_start: 0.8610 (tp40) cc_final: 0.8391 (tp40)
REVERT: A  119 TYR cc_start: 0.8749 (m-10) cc_final: 0.8425 (m-10)
REVERT: A  219 PHE cc_start: 0.7453 (t80) cc_final: 0.6953 (m-10)
REVERT: A  347 HIS cc_start: 0.8161 (p90) cc_final: 0.7398 (p-80)
REVERT: A  360 ASP cc_start: 0.9049 (t70) cc_final: 0.8672 (t0)
REVERT: A  362 TYR cc_start: 0.9066 (t80) cc_final: 0.8630 (t80)
  outliers start: 25
  outliers final: 19
  residues processed: 209
  average time/residue: 0.1923
  time to fit residues: 51.4632
Evaluate side-chains
  205 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 186
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
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  162 THR
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  162 THR
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 37 optimal weight:    5.9990
   chunk 23 optimal weight:    6.9990
   chunk 38 optimal weight:   10.0000
   chunk 54 optimal weight:    2.9990
   chunk 48 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 58 optimal weight:    6.9990
   chunk 68 optimal weight:    0.6980
   chunk 52 optimal weight:    0.4980
   chunk 44 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   overall best weight:    1.4384

-------------------------------------------------------------------------------
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
B 224 HIS
A 224 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.172842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.134268 restraints weight = 7764.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.140104 restraints weight = 3959.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.143868 restraints weight = 2618.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.2925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6286  Z= 0.267
  Angle     :  0.616   8.626   8544  Z= 0.326
  Chirality :  0.044   0.144    978
  Planarity :  0.005   0.047   1040
  Dihedral  : 10.506  82.435    898
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 21.15 %
    Favored  : 73.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.75 (0.30), residues: 756
  helix:  2.17 (0.20), residues: 568
  sheet:  None (None), residues: 0
  loop :  0.89 (0.48), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 235 
 HIS   0.005   0.001   HIS A 315 
 PHE   0.029   0.002   PHE B 234 
 TYR   0.017   0.002   TYR A 201 
 ARG   0.003   0.000   ARG B  50 

*********************** 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
  246 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 210
  time to evaluate  : 0.681 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8514 (tp40) cc_final: 0.8297 (tp40)
REVERT: B   74 TRP cc_start: 0.7987 (t60) cc_final: 0.7781 (t60)
REVERT: B   78 ARG cc_start: 0.8642 (mmm160) cc_final: 0.8126 (mmm-85)
REVERT: B  119 TYR cc_start: 0.8851 (m-10) cc_final: 0.8614 (m-10)
REVERT: B  199 GLN cc_start: 0.8729 (tm-30) cc_final: 0.8371 (tm-30)
REVERT: B  252 LEU cc_start: 0.8870 (mt) cc_final: 0.8569 (mt)
REVERT: B  360 ASP cc_start: 0.8825 (t70) cc_final: 0.8357 (t0)
REVERT: B  362 TYR cc_start: 0.9087 (t80) cc_final: 0.8704 (t80)
REVERT: A   69 GLN cc_start: 0.8502 (tp40) cc_final: 0.8284 (tp40)
REVERT: A   74 TRP cc_start: 0.8061 (t60) cc_final: 0.7843 (t60)
REVERT: A  119 TYR cc_start: 0.8858 (m-10) cc_final: 0.8628 (m-10)
REVERT: A  252 LEU cc_start: 0.8818 (mt) cc_final: 0.8517 (mt)
REVERT: A  329 LYS cc_start: 0.8198 (tttp) cc_final: 0.7991 (tttm)
REVERT: A  339 MET cc_start: 0.8823 (mmm) cc_final: 0.8466 (mmm)
REVERT: A  360 ASP cc_start: 0.8849 (t70) cc_final: 0.8417 (t0)
REVERT: A  362 TYR cc_start: 0.9096 (t80) cc_final: 0.8790 (t80)
  outliers start: 36
  outliers final: 30
  residues processed: 227
  average time/residue: 0.1929
  time to fit residues: 55.9938
Evaluate side-chains
  231 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 201
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
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   90 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  162 THR
Chi-restraints excluded: chain B residue  163 VAL
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  253 CYS
Chi-restraints excluded: chain B residue  254 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  111 THR
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  163 VAL
Chi-restraints excluded: chain A residue  173 VAL
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  254 THR
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 65 optimal weight:    0.6980
   chunk 38 optimal weight:   10.0000
   chunk 41 optimal weight:    5.9990
   chunk 46 optimal weight:    0.8980
   chunk 31 optimal weight:    7.9990
   chunk 6 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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**
B 217 GLN
A  46 HIS
A 217 GLN
A 224 HIS
** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.163232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.124546 restraints weight = 7690.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.130000 restraints weight = 3957.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.133584 restraints weight = 2635.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.3268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6286  Z= 0.251
  Angle     :  0.611  11.712   8544  Z= 0.318
  Chirality :  0.043   0.167    978
  Planarity :  0.005   0.042   1040
  Dihedral  : 10.069  80.741    898
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  5.74 %
    Allowed  : 23.41 %
    Favored  : 70.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.67 (0.30), residues: 756
  helix:  2.15 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop :  0.70 (0.48), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 117 
 HIS   0.004   0.001   HIS A 315 
 PHE   0.015   0.002   PHE A 358 
 TYR   0.018   0.002   TYR B 304 
 ARG   0.006   0.000   ARG A  50 

*********************** 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
  241 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 203
  time to evaluate  : 0.657 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8462 (tp40) cc_final: 0.8210 (tp40)
REVERT: B   74 TRP cc_start: 0.8008 (t60) cc_final: 0.7716 (t60)
REVERT: B   78 ARG cc_start: 0.8615 (mmm160) cc_final: 0.8139 (mmm-85)
REVERT: B  149 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8656 (tt)
REVERT: B  252 LEU cc_start: 0.8886 (mt) cc_final: 0.8610 (mt)
REVERT: B  267 ARG cc_start: 0.8119 (ptp-110) cc_final: 0.7878 (ptm160)
REVERT: B  305 LYS cc_start: 0.8932 (mmtt) cc_final: 0.8693 (mmmt)
REVERT: B  360 ASP cc_start: 0.8843 (t70) cc_final: 0.8398 (t0)
REVERT: B  362 TYR cc_start: 0.9067 (t80) cc_final: 0.8711 (t80)
REVERT: A   69 GLN cc_start: 0.8536 (tp40) cc_final: 0.8293 (tp40)
REVERT: A   74 TRP cc_start: 0.8020 (t60) cc_final: 0.7771 (t60)
REVERT: A  119 TYR cc_start: 0.8829 (m-10) cc_final: 0.8611 (m-10)
REVERT: A  149 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8639 (tt)
REVERT: A  199 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8267 (tm-30)
REVERT: A  252 LEU cc_start: 0.8893 (mt) cc_final: 0.8604 (mt)
REVERT: A  305 LYS cc_start: 0.8937 (mmtt) cc_final: 0.8705 (mmmt)
REVERT: A  360 ASP cc_start: 0.8848 (t70) cc_final: 0.8419 (t0)
REVERT: A  362 TYR cc_start: 0.9068 (t80) cc_final: 0.8733 (t80)
  outliers start: 38
  outliers final: 31
  residues processed: 226
  average time/residue: 0.2079
  time to fit residues: 59.7916
Evaluate side-chains
  217 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 184
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
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  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  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  274 VAL
Chi-restraints excluded: chain A residue  309 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0020
   chunk 25 optimal weight:    0.3980
   chunk 69 optimal weight:    0.0060
   overall best weight:    0.4406

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

Flipped N/Q/H residues before XYZ refinement:
A 398 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.172762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.135508 restraints weight = 7591.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.141088 restraints weight = 3822.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.144683 restraints weight = 2516.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.3547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6286  Z= 0.161
  Angle     :  0.579  11.731   8544  Z= 0.297
  Chirality :  0.041   0.178    978
  Planarity :  0.005   0.039   1040
  Dihedral  :  9.603  80.656    898
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 27.34 %
    Favored  : 68.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.73 (0.30), residues: 756
  helix:  2.23 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop :  0.53 (0.49), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 117 
 HIS   0.004   0.001   HIS B 315 
 PHE   0.032   0.001   PHE B 234 
 TYR   0.014   0.001   TYR A 201 
 ARG   0.006   0.001   ARG B  50 

*********************** 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
  215 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 190
  time to evaluate  : 0.669 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8159 (tp40) cc_final: 0.7914 (tp40)
REVERT: B   74 TRP cc_start: 0.7999 (t60) cc_final: 0.7671 (t60)
REVERT: B   95 ILE cc_start: 0.8595 (tp) cc_final: 0.8376 (mt)
REVERT: B  199 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8347 (tm-30)
REVERT: B  219 PHE cc_start: 0.7577 (t80) cc_final: 0.7057 (m-10)
REVERT: B  252 LEU cc_start: 0.8948 (mt) cc_final: 0.8622 (mt)
REVERT: B  360 ASP cc_start: 0.8803 (t70) cc_final: 0.8343 (t0)
REVERT: B  362 TYR cc_start: 0.9007 (t80) cc_final: 0.8563 (t80)
REVERT: A   69 GLN cc_start: 0.8161 (tp40) cc_final: 0.7915 (tp40)
REVERT: A   74 TRP cc_start: 0.8011 (t60) cc_final: 0.7745 (t60)
REVERT: A  149 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8811 (tt)
REVERT: A  219 PHE cc_start: 0.7663 (t80) cc_final: 0.7083 (m-10)
REVERT: A  252 LEU cc_start: 0.8891 (mt) cc_final: 0.8556 (mt)
REVERT: A  360 ASP cc_start: 0.8836 (t70) cc_final: 0.8383 (t0)
REVERT: A  362 TYR cc_start: 0.8981 (t80) cc_final: 0.8711 (t80)
  outliers start: 25
  outliers final: 19
  residues processed: 205
  average time/residue: 0.1622
  time to fit residues: 44.6487
Evaluate side-chains
  200 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 180
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
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  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 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  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  383 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 62 optimal weight:    9.9990
   chunk 15 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0370
   chunk 44 optimal weight:    0.0980
   chunk 26 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.4258

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

Flipped N/Q/H residues before XYZ refinement:
B 174 GLN
A  46 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.174432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.136356 restraints weight = 7700.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.142101 restraints weight = 3953.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.145734 restraints weight = 2642.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.3749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6286  Z= 0.163
  Angle     :  0.560   6.612   8544  Z= 0.291
  Chirality :  0.041   0.180    978
  Planarity :  0.005   0.040   1040
  Dihedral  :  9.384  81.908    896
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 27.34 %
    Favored  : 69.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.80 (0.30), residues: 756
  helix:  2.27 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop :  0.58 (0.49), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 235 
 HIS   0.003   0.001   HIS B 315 
 PHE   0.022   0.001   PHE B 234 
 TYR   0.017   0.001   TYR A 387 
 ARG   0.007   0.001   ARG A  45 

*********************** 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
  218 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 197
  time to evaluate  : 0.638 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8133 (tp40) cc_final: 0.7886 (tp40)
REVERT: B   74 TRP cc_start: 0.7951 (t60) cc_final: 0.7644 (t60)
REVERT: B  199 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8415 (tm-30)
REVERT: B  219 PHE cc_start: 0.7545 (t80) cc_final: 0.7097 (m-10)
REVERT: B  244 ILE cc_start: 0.7852 (tp) cc_final: 0.7419 (mm)
REVERT: B  252 LEU cc_start: 0.8954 (mt) cc_final: 0.8634 (mt)
REVERT: B  360 ASP cc_start: 0.8791 (t70) cc_final: 0.8313 (t0)
REVERT: B  362 TYR cc_start: 0.9002 (t80) cc_final: 0.8644 (t80)
REVERT: B  369 GLU cc_start: 0.7368 (mp0) cc_final: 0.7045 (mp0)
REVERT: A   45 ARG cc_start: 0.8703 (ttp-110) cc_final: 0.8317 (ttp-110)
REVERT: A   69 GLN cc_start: 0.8251 (tp40) cc_final: 0.8005 (tp40)
REVERT: A   74 TRP cc_start: 0.7948 (t60) cc_final: 0.7694 (t60)
REVERT: A  182 MET cc_start: 0.8075 (ttt) cc_final: 0.7829 (ttt)
REVERT: A  199 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8271 (tm-30)
REVERT: A  244 ILE cc_start: 0.7845 (tp) cc_final: 0.7408 (mm)
REVERT: A  252 LEU cc_start: 0.8897 (mt) cc_final: 0.8591 (mt)
REVERT: A  360 ASP cc_start: 0.8830 (t70) cc_final: 0.8382 (t0)
REVERT: A  362 TYR cc_start: 0.8991 (t80) cc_final: 0.8670 (t80)
  outliers start: 21
  outliers final: 17
  residues processed: 212
  average time/residue: 0.1854
  time to fit residues: 51.0112
Evaluate side-chains
  200 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 183
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  161 SER
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  383 ASP
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  157 CYS
Chi-restraints excluded: chain A residue  161 SER
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  390 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0980
   chunk 53 optimal weight:    0.7980
   chunk 62 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 23 optimal weight:    5.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B  46 HIS
B 174 GLN
** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  46 HIS
A 224 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.175207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.137399 restraints weight = 7714.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.143212 restraints weight = 3852.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.146985 restraints weight = 2529.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.3890

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= 0.190
  Angle     :  0.603   8.933   8544  Z= 0.304
  Chirality :  0.041   0.172    978
  Planarity :  0.005   0.041   1040
  Dihedral  :  9.215  81.777    894
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 27.04 %
    Favored  : 69.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.79 (0.30), residues: 756
  helix:  2.29 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop :  0.45 (0.48), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A  46 
 PHE   0.015   0.001   PHE A 187 
 TYR   0.018   0.001   TYR A 387 
 ARG   0.007   0.001   ARG B  50 

*********************** 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
  217 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 194
  time to evaluate  : 0.688 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8125 (tp40) cc_final: 0.7885 (tp40)
REVERT: B  199 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8452 (tm-30)
REVERT: B  219 PHE cc_start: 0.7696 (t80) cc_final: 0.7128 (m-10)
REVERT: B  244 ILE cc_start: 0.7877 (tp) cc_final: 0.7446 (mm)
REVERT: B  252 LEU cc_start: 0.8994 (mt) cc_final: 0.8664 (mt)
REVERT: B  360 ASP cc_start: 0.8808 (t70) cc_final: 0.8585 (t0)
REVERT: B  362 TYR cc_start: 0.8985 (t80) cc_final: 0.8667 (t80)
REVERT: B  369 GLU cc_start: 0.7458 (mp0) cc_final: 0.7077 (mt-10)
REVERT: A   69 GLN cc_start: 0.8229 (tp40) cc_final: 0.7975 (tp40)
REVERT: A   74 TRP cc_start: 0.7986 (t60) cc_final: 0.7696 (t60)
REVERT: A  182 MET cc_start: 0.8061 (ttt) cc_final: 0.7828 (ttt)
REVERT: A  199 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8396 (tm-30)
REVERT: A  244 ILE cc_start: 0.8108 (tp) cc_final: 0.7661 (mm)
REVERT: A  252 LEU cc_start: 0.9010 (mt) cc_final: 0.8687 (mt)
REVERT: A  329 LYS cc_start: 0.8202 (tttp) cc_final: 0.7966 (tttm)
REVERT: A  339 MET cc_start: 0.8747 (mmm) cc_final: 0.8505 (mmm)
REVERT: A  360 ASP cc_start: 0.8839 (t70) cc_final: 0.8365 (t0)
REVERT: A  362 TYR cc_start: 0.8944 (t80) cc_final: 0.8659 (t80)
REVERT: A  369 GLU cc_start: 0.7410 (mp0) cc_final: 0.7132 (mt-10)
  outliers start: 23
  outliers final: 22
  residues processed: 209
  average time/residue: 0.1540
  time to fit residues: 43.7493
Evaluate side-chains
  209 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 187
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
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  157 CYS
Chi-restraints excluded: chain B residue  161 SER
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  343 GLU
Chi-restraints excluded: chain B residue  365 SER
Chi-restraints excluded: chain B residue  383 ASP
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  157 CYS
Chi-restraints excluded: chain A residue  161 SER
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  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 68 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 16 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 71 optimal weight:    0.0570
   chunk 29 optimal weight:    0.5980
   chunk 48 optimal weight:    0.4980
   chunk 52 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 38 optimal weight:   10.0000
   overall best weight:    0.5700

-------------------------------------------------------------------------------
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 224 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.174145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.135355 restraints weight = 7790.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.141267 restraints weight = 3891.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.145022 restraints weight = 2566.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.4000

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= 0.179
  Angle     :  0.600   8.434   8544  Z= 0.305
  Chirality :  0.041   0.179    978
  Planarity :  0.005   0.042   1040
  Dihedral  :  9.099  81.343    894
  Min Nonbonded Distance : 1.880

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 28.25 %
    Favored  : 68.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.75 (0.30), residues: 756
  helix:  2.30 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop :  0.30 (0.47), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 235 
 HIS   0.005   0.001   HIS A  46 
 PHE   0.043   0.001   PHE B 234 
 TYR   0.019   0.001   TYR A 387 
 ARG   0.008   0.001   ARG A  45 

*********************** 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
  217 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 197
  time to evaluate  : 0.651 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8057 (tp40) cc_final: 0.7793 (tp40)
REVERT: B  199 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8448 (tm-30)
REVERT: B  244 ILE cc_start: 0.7888 (tp) cc_final: 0.7460 (mm)
REVERT: B  252 LEU cc_start: 0.9011 (mt) cc_final: 0.8672 (mt)
REVERT: B  360 ASP cc_start: 0.8787 (t70) cc_final: 0.8300 (t0)
REVERT: B  362 TYR cc_start: 0.8949 (t80) cc_final: 0.8609 (t80)
REVERT: B  369 GLU cc_start: 0.7349 (mp0) cc_final: 0.7142 (mt-10)
REVERT: A   49 LYS cc_start: 0.8632 (tttt) cc_final: 0.8219 (ttmt)
REVERT: A   69 GLN cc_start: 0.8084 (tp40) cc_final: 0.7843 (tp40)
REVERT: A   74 TRP cc_start: 0.8006 (t60) cc_final: 0.7662 (t60)
REVERT: A  182 MET cc_start: 0.8019 (ttt) cc_final: 0.7800 (ttt)
REVERT: A  199 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8406 (tm-30)
REVERT: A  244 ILE cc_start: 0.8194 (tp) cc_final: 0.7759 (mm)
REVERT: A  252 LEU cc_start: 0.9023 (mt) cc_final: 0.8688 (mt)
REVERT: A  360 ASP cc_start: 0.8792 (t70) cc_final: 0.8306 (t0)
REVERT: A  362 TYR cc_start: 0.8925 (t80) cc_final: 0.8616 (t80)
  outliers start: 20
  outliers final: 20
  residues processed: 211
  average time/residue: 0.1795
  time to fit residues: 49.1615
Evaluate side-chains
  208 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 188
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   88 ILE
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  383 ASP
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  157 CYS
Chi-restraints excluded: chain A residue  161 SER
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  365 SER
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 30 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   chunk 73 optimal weight:    0.6980
   overall best weight:    1.0786

-------------------------------------------------------------------------------
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  47 GLN
A 224 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.171304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.132920 restraints weight = 7835.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.138559 restraints weight = 3927.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.142368 restraints weight = 2598.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.4082

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= 0.235
  Angle     :  0.646  12.425   8544  Z= 0.325
  Chirality :  0.042   0.184    978
  Planarity :  0.005   0.042   1040
  Dihedral  :  9.058  79.964    894
  Min Nonbonded Distance : 1.795

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 27.49 %
    Favored  : 68.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.69 (0.30), residues: 756
  helix:  2.29 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop :  0.15 (0.46), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B  74 
 HIS   0.004   0.001   HIS B 315 
 PHE   0.037   0.002   PHE B 234 
 TYR   0.018   0.002   TYR B 387 
 ARG   0.009   0.001   ARG A  45 

*********************** 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
  215 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 190
  time to evaluate  : 0.635 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8141 (tp40) cc_final: 0.7878 (tp40)
REVERT: B   98 CYS cc_start: 0.8500 (m) cc_final: 0.7854 (m)
REVERT: B  199 GLN cc_start: 0.8887 (tm-30) cc_final: 0.8502 (tm-30)
REVERT: B  244 ILE cc_start: 0.7934 (tp) cc_final: 0.7506 (mm)
REVERT: B  252 LEU cc_start: 0.8986 (mt) cc_final: 0.8672 (mt)
REVERT: B  360 ASP cc_start: 0.8815 (t70) cc_final: 0.8329 (t0)
REVERT: B  362 TYR cc_start: 0.8977 (t80) cc_final: 0.8671 (t80)
REVERT: B  369 GLU cc_start: 0.7412 (mp0) cc_final: 0.7140 (mt-10)
REVERT: B  381 PHE cc_start: 0.8145 (t80) cc_final: 0.7608 (t80)
REVERT: A   49 LYS cc_start: 0.8623 (tttt) cc_final: 0.8245 (ttmt)
REVERT: A   74 TRP cc_start: 0.7968 (t60) cc_final: 0.7705 (t60)
REVERT: A  199 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8437 (tm-30)
REVERT: A  244 ILE cc_start: 0.8248 (tp) cc_final: 0.7750 (mm)
REVERT: A  252 LEU cc_start: 0.8999 (mt) cc_final: 0.8686 (mt)
REVERT: A  360 ASP cc_start: 0.8820 (t70) cc_final: 0.8611 (t0)
REVERT: A  362 TYR cc_start: 0.8941 (t80) cc_final: 0.8663 (t80)
REVERT: A  381 PHE cc_start: 0.8160 (t80) cc_final: 0.7614 (t80)
  outliers start: 25
  outliers final: 24
  residues processed: 206
  average time/residue: 0.1671
  time to fit residues: 45.3841
Evaluate side-chains
  207 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 183
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
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  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  343 GLU
Chi-restraints excluded: chain B residue  365 SER
Chi-restraints excluded: chain B residue  383 ASP
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  157 CYS
Chi-restraints excluded: chain A residue  161 SER
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  390 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 74 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 24 optimal weight:    8.9990
   chunk 32 optimal weight:    0.0070
   chunk 66 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   overall best weight:    0.6998

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.171956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.133181 restraints weight = 7891.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.139165 restraints weight = 3933.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.142960 restraints weight = 2586.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.4149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6286  Z= 0.198
  Angle     :  0.642  12.293   8544  Z= 0.319
  Chirality :  0.042   0.202    978
  Planarity :  0.005   0.041   1040
  Dihedral  :  9.004  80.656    894
  Min Nonbonded Distance : 1.726

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 27.79 %
    Favored  : 68.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.69 (0.30), residues: 756
  helix:  2.30 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop :  0.11 (0.46), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B  74 
 HIS   0.005   0.001   HIS A  46 
 PHE   0.037   0.001   PHE B 234 
 TYR   0.020   0.001   TYR A 387 
 ARG   0.007   0.000   ARG B  50 

********************** 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
  206 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 179
  time to evaluate  : 0.745 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8109 (tp40) cc_final: 0.7845 (tp40)
REVERT: B  199 GLN cc_start: 0.8868 (tm-30) cc_final: 0.8471 (tm-30)
REVERT: B  252 LEU cc_start: 0.8983 (mt) cc_final: 0.8664 (mt)
REVERT: B  362 TYR cc_start: 0.8939 (t80) cc_final: 0.8602 (t80)
REVERT: B  381 PHE cc_start: 0.8173 (t80) cc_final: 0.7626 (t80)
REVERT: A   49 LYS cc_start: 0.8650 (tttt) cc_final: 0.8236 (ttmt)
REVERT: A   74 TRP cc_start: 0.7950 (t60) cc_final: 0.7585 (t60)
REVERT: A  182 MET cc_start: 0.8040 (ttt) cc_final: 0.7815 (ttt)
REVERT: A  199 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8443 (tm-30)
REVERT: A  244 ILE cc_start: 0.8196 (tp) cc_final: 0.7811 (mm)
REVERT: A  252 LEU cc_start: 0.9012 (mt) cc_final: 0.8685 (mt)
REVERT: A  362 TYR cc_start: 0.8932 (t80) cc_final: 0.8637 (t80)
REVERT: A  387 TYR cc_start: 0.8480 (t80) cc_final: 0.8226 (t80)
  outliers start: 27
  outliers final: 24
  residues processed: 196
  average time/residue: 0.2037
  time to fit residues: 52.3025
Evaluate side-chains
  197 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 173
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
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  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  365 SER
Chi-restraints excluded: chain B residue  383 ASP
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain A residue   88 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  390 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 10 optimal weight:    0.1980
   chunk 55 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 70 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 67 optimal weight:    0.5980
   chunk 8 optimal weight:    0.0970
   chunk 52 optimal weight:    4.9990
   chunk 59 optimal weight:   10.0000
   chunk 30 optimal weight:    0.4980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.172057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.133585 restraints weight = 7854.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.139466 restraints weight = 3912.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.143393 restraints weight = 2574.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.4215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6286  Z= 0.199
  Angle     :  0.646  12.656   8544  Z= 0.318
  Chirality :  0.042   0.201    978
  Planarity :  0.005   0.041   1040
  Dihedral  :  8.950  80.732    894
  Min Nonbonded Distance : 1.669

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 27.19 %
    Favored  : 68.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.69 (0.30), residues: 756
  helix:  2.31 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop :  0.05 (0.46), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  74 
 HIS   0.004   0.001   HIS B 315 
 PHE   0.034   0.001   PHE B 234 
 TYR   0.019   0.001   TYR B 387 
 ARG   0.008   0.000   ARG B  50 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2136.23 seconds
wall clock time: 39 minutes 13.07 seconds (2353.07 seconds total)