Starting phenix.real_space_refine
on Tue Mar 11 16:18:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gyx_34379/03_2025/8gyx_34379.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gyx_34379/03_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_34379/03_2025/8gyx_34379.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gyx_34379/03_2025/8gyx_34379.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gyx_34379/03_2025/8gyx_34379.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gyx_34379/03_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.88, per 1000 atoms: 0.80
  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: 1.73
  Conformation dependent library (CDL) restraints added in 760.2 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: 0.73
  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: 1.66

  Time building geometry restraints manager: 1.90 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:             0.370
  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:         0.040
  Set scattering table:                    0.050
  Process input model:                     18.540
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.900
-------------------------------------------------------------------------------
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  : 0.692 
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: 0.2059
  time to fit residues: 43.0603
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  : 0.704 
-------------------------------------------------------------------------------
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 = 0.135137 restraints weight = 7301.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.140827 restraints weight = 3639.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.144737 restraints weight = 2382.522|
|-----------------------------------------------------------------------------|
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  : 0.643 
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: 0.6954 (m-10)
REVERT: B  267 ARG cc_start: 0.8002 (ptm160) cc_final: 0.7628 (ptm160)
REVERT: B  347 HIS cc_start: 0.8146 (p90) cc_final: 0.7579 (p90)
REVERT: B  360 ASP cc_start: 0.9035 (t70) cc_final: 0.8639 (t0)
REVERT: B  362 TYR cc_start: 0.9066 (t80) cc_final: 0.8612 (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: 0.8160 (p90) cc_final: 0.7398 (p-80)
REVERT: A  360 ASP cc_start: 0.9050 (t70) cc_final: 0.8673 (t0)
REVERT: A  362 TYR cc_start: 0.9065 (t80) cc_final: 0.8629 (t80)
  outliers start: 25
  outliers final: 19
  residues processed: 209
  average time/residue: 0.1887
  time to fit residues: 50.4929
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  : 0.607 
-------------------------------------------------------------------------------
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:    0.0770
   chunk 44 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   overall best weight:    1.3342

-------------------------------------------------------------------------------
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 = 0.4002 r_free = 0.4002 target = 0.172385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.133681 restraints weight = 7741.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.139530 restraints weight = 3946.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.143292 restraints weight = 2611.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.2935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   6286  Z= 0.255
  Angle     :  0.607   8.446   8544  Z= 0.322
  Chirality :  0.044   0.143    978
  Planarity :  0.005   0.047   1040
  Dihedral  : 10.436  81.887    898
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 20.54 %
    Favored  : 74.17 %
  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:  2.78 (0.30), residues: 756
  helix:  2.19 (0.20), residues: 568
  sheet:  None (None), residues: 0
  loop :  0.91 (0.48), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 181 
 HIS   0.005   0.001   HIS A 315 
 PHE   0.029   0.002   PHE B 234 
 TYR   0.016   0.002   TYR A 201 
 ARG   0.002   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
  242 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 207
  time to evaluate  : 0.661 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8504 (tp40) cc_final: 0.8289 (tp40)
REVERT: B   74 TRP cc_start: 0.7988 (t60) cc_final: 0.7781 (t60)
REVERT: B   78 ARG cc_start: 0.8602 (mmm160) cc_final: 0.8127 (mmm-85)
REVERT: B  119 TYR cc_start: 0.8847 (m-10) cc_final: 0.8607 (m-10)
REVERT: B  199 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8381 (tm-30)
REVERT: B  252 LEU cc_start: 0.8894 (mt) cc_final: 0.8595 (mt)
REVERT: B  360 ASP cc_start: 0.8810 (t70) cc_final: 0.8338 (t0)
REVERT: B  362 TYR cc_start: 0.9089 (t80) cc_final: 0.8777 (t80)
REVERT: B  387 TYR cc_start: 0.8527 (t80) cc_final: 0.8325 (t80)
REVERT: A   69 GLN cc_start: 0.8492 (tp40) cc_final: 0.8275 (tp40)
REVERT: A   74 TRP cc_start: 0.8063 (t60) cc_final: 0.7844 (t60)
REVERT: A  119 TYR cc_start: 0.8853 (m-10) cc_final: 0.8630 (m-10)
REVERT: A  252 LEU cc_start: 0.8841 (mt) cc_final: 0.8549 (mt)
REVERT: A  305 LYS cc_start: 0.8837 (mmtt) cc_final: 0.8624 (mmmt)
REVERT: A  339 MET cc_start: 0.8818 (mmm) cc_final: 0.8468 (mmm)
REVERT: A  360 ASP cc_start: 0.8851 (t70) cc_final: 0.8395 (t0)
REVERT: A  362 TYR cc_start: 0.9090 (t80) cc_final: 0.8778 (t80)
REVERT: A  387 TYR cc_start: 0.8516 (t80) cc_final: 0.8259 (t80)
  outliers start: 35
  outliers final: 29
  residues processed: 224
  average time/residue: 0.1952
  time to fit residues: 56.4105
Evaluate side-chains
  225 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 196
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
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  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:    0.9990
   chunk 38 optimal weight:   10.0000
   chunk 41 optimal weight:    9.9990
   chunk 46 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 34 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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**
B 217 GLN
A 217 GLN
A 224 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.168756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.129403 restraints weight = 7862.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.135227 restraints weight = 3940.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.138963 restraints weight = 2607.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.3240

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= 0.232
  Angle     :  0.598  11.769   8544  Z= 0.310
  Chirality :  0.043   0.176    978
  Planarity :  0.005   0.041   1040
  Dihedral  :  9.966  80.063    898
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 23.41 %
    Favored  : 71.45 %
  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:  2.74 (0.30), residues: 756
  helix:  2.20 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop :  0.71 (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   0.001   PHE A 358 
 TYR   0.017   0.002   TYR B 304 
 ARG   0.004   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
  235 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 201
  time to evaluate  : 0.658 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8385 (tp40) cc_final: 0.8127 (tp40)
REVERT: B   74 TRP cc_start: 0.8059 (t60) cc_final: 0.7729 (t60)
REVERT: B   78 ARG cc_start: 0.8658 (mmm160) cc_final: 0.8191 (mmm-85)
REVERT: B  149 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8737 (tt)
REVERT: B  219 PHE cc_start: 0.7689 (t80) cc_final: 0.7063 (m-10)
REVERT: B  252 LEU cc_start: 0.8928 (mt) cc_final: 0.8618 (mt)
REVERT: B  267 ARG cc_start: 0.8149 (ptp-110) cc_final: 0.7912 (ptm160)
REVERT: B  360 ASP cc_start: 0.8832 (t70) cc_final: 0.8383 (t0)
REVERT: B  362 TYR cc_start: 0.9064 (t80) cc_final: 0.8695 (t80)
REVERT: B  381 PHE cc_start: 0.8377 (t80) cc_final: 0.7887 (t80)
REVERT: A   69 GLN cc_start: 0.8478 (tp40) cc_final: 0.8230 (tp40)
REVERT: A   74 TRP cc_start: 0.8068 (t60) cc_final: 0.7783 (t60)
REVERT: A  119 TYR cc_start: 0.8850 (m-10) cc_final: 0.8644 (m-10)
REVERT: A  149 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8710 (tt)
REVERT: A  199 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8255 (tm-30)
REVERT: A  252 LEU cc_start: 0.8914 (mt) cc_final: 0.8599 (mt)
REVERT: A  360 ASP cc_start: 0.8833 (t70) cc_final: 0.8399 (t0)
REVERT: A  362 TYR cc_start: 0.9052 (t80) cc_final: 0.8700 (t80)
  outliers start: 34
  outliers final: 27
  residues processed: 221
  average time/residue: 0.1971
  time to fit residues: 55.6676
Evaluate side-chains
  222 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 193
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
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  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 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  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  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:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 50 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 23 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0000
   chunk 20 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0570
   chunk 69 optimal weight:    4.9990
   overall best weight:    0.4502

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

Flipped N/Q/H residues before XYZ refinement:
B  46 HIS
A 398 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.173426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.134288 restraints weight = 7736.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.140189 restraints weight = 3889.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.143988 restraints weight = 2569.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.3482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6286  Z= 0.166
  Angle     :  0.590  12.180   8544  Z= 0.299
  Chirality :  0.041   0.167    978
  Planarity :  0.005   0.039   1040
  Dihedral  :  9.669  80.722    898
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 28.40 %
    Favored  : 68.28 %
  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:  2.72 (0.30), residues: 756
  helix:  2.23 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop :  0.51 (0.48), 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   0.034   0.001   PHE B 234 
 TYR   0.014   0.001   TYR A 201 
 ARG   0.008   0.000   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
  212 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 190
  time to evaluate  : 0.656 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8210 (tp40) cc_final: 0.7963 (tp40)
REVERT: B   74 TRP cc_start: 0.7976 (t60) cc_final: 0.7656 (t60)
REVERT: B   78 ARG cc_start: 0.8595 (mmm160) cc_final: 0.8142 (mmm-85)
REVERT: B  149 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8840 (tt)
REVERT: B  199 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8269 (tm-30)
REVERT: B  219 PHE cc_start: 0.7638 (t80) cc_final: 0.7093 (m-10)
REVERT: B  252 LEU cc_start: 0.8923 (mt) cc_final: 0.8601 (mt)
REVERT: B  313 GLU cc_start: 0.7664 (mp0) cc_final: 0.7408 (mp0)
REVERT: B  360 ASP cc_start: 0.8804 (t70) cc_final: 0.8322 (t0)
REVERT: B  362 TYR cc_start: 0.9029 (t80) cc_final: 0.8575 (t80)
REVERT: B  369 GLU cc_start: 0.7400 (mp0) cc_final: 0.7142 (mt-10)
REVERT: A   69 GLN cc_start: 0.8174 (tp40) cc_final: 0.7926 (tp40)
REVERT: A   74 TRP cc_start: 0.8002 (t60) cc_final: 0.7741 (t60)
REVERT: A  149 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8721 (tt)
REVERT: A  219 PHE cc_start: 0.7668 (t80) cc_final: 0.7101 (m-10)
REVERT: A  252 LEU cc_start: 0.8863 (mt) cc_final: 0.8544 (mt)
REVERT: A  305 LYS cc_start: 0.8939 (mmtt) cc_final: 0.8688 (mmmt)
REVERT: A  339 MET cc_start: 0.8846 (mmm) cc_final: 0.8635 (mmm)
REVERT: A  360 ASP cc_start: 0.8816 (t70) cc_final: 0.8343 (t0)
REVERT: A  362 TYR cc_start: 0.9004 (t80) cc_final: 0.8666 (t80)
  outliers start: 22
  outliers final: 17
  residues processed: 205
  average time/residue: 0.1685
  time to fit residues: 45.5296
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  : 0.646 
-------------------------------------------------------------------------------
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  149 LEU
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  241 VAL
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  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  190 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  241 VAL
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:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 44 optimal weight:    0.0980
   chunk 26 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 174 GLN
A 224 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.172485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.133127 restraints weight = 7704.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.139005 restraints weight = 3894.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.142813 restraints weight = 2584.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.3682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6286  Z= 0.178
  Angle     :  0.568   9.342   8544  Z= 0.294
  Chirality :  0.041   0.164    978
  Planarity :  0.005   0.039   1040
  Dihedral  :  9.481  80.996    898
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 26.74 %
    Favored  : 70.09 %
  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:  2.91 (0.30), residues: 756
  helix:  2.33 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop :  0.71 (0.49), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 117 
 HIS   0.004   0.001   HIS B 315 
 PHE   0.015   0.001   PHE A 187 
 TYR   0.016   0.001   TYR A 387 
 ARG   0.007   0.000   ARG B  50 

*********************** 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
  220 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 199
  time to evaluate  : 0.676 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8248 (tp40) cc_final: 0.7994 (tp40)
REVERT: B   78 ARG cc_start: 0.8599 (mmm160) cc_final: 0.8118 (mmm-85)
REVERT: B  199 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8404 (tm-30)
REVERT: B  244 ILE cc_start: 0.7843 (tp) cc_final: 0.7382 (mm)
REVERT: B  247 LYS cc_start: 0.7651 (tttt) cc_final: 0.7390 (tttt)
REVERT: B  252 LEU cc_start: 0.8967 (mt) cc_final: 0.8654 (mt)
REVERT: B  313 GLU cc_start: 0.7540 (mp0) cc_final: 0.7288 (mp0)
REVERT: B  360 ASP cc_start: 0.8815 (t70) cc_final: 0.8338 (t0)
REVERT: B  362 TYR cc_start: 0.9010 (t80) cc_final: 0.8564 (t80)
REVERT: B  369 GLU cc_start: 0.7339 (mp0) cc_final: 0.7118 (mt-10)
REVERT: B  381 PHE cc_start: 0.8430 (t80) cc_final: 0.7945 (t80)
REVERT: A   69 GLN cc_start: 0.8241 (tp40) cc_final: 0.8001 (tp40)
REVERT: A   74 TRP cc_start: 0.8000 (t60) cc_final: 0.7729 (t60)
REVERT: A  182 MET cc_start: 0.8089 (ttt) cc_final: 0.7846 (ttt)
REVERT: A  199 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8285 (tm-30)
REVERT: A  247 LYS cc_start: 0.7658 (tttt) cc_final: 0.7382 (tttt)
REVERT: A  252 LEU cc_start: 0.8908 (mt) cc_final: 0.8593 (mt)
REVERT: A  305 LYS cc_start: 0.8981 (mmtt) cc_final: 0.8744 (mmmt)
REVERT: A  360 ASP cc_start: 0.8822 (t70) cc_final: 0.8337 (t0)
REVERT: A  362 TYR cc_start: 0.9013 (t80) cc_final: 0.8663 (t80)
  outliers start: 21
  outliers final: 17
  residues processed: 215
  average time/residue: 0.1851
  time to fit residues: 51.5702
Evaluate side-chains
  202 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 185
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
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  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  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  190 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  365 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0470
   chunk 53 optimal weight:    0.8980
   chunk 62 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 23 optimal weight:    5.9990
   overall best weight:    0.7678

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

Flipped N/Q/H residues before XYZ refinement:
B 174 GLN
A 224 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.172810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.134664 restraints weight = 7709.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.140488 restraints weight = 3871.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.144243 restraints weight = 2552.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.3862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6286  Z= 0.193
  Angle     :  0.603   8.964   8544  Z= 0.304
  Chirality :  0.041   0.158    978
  Planarity :  0.005   0.040   1040
  Dihedral  :  9.241  80.839    894
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 26.74 %
    Favored  : 69.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.86 (0.30), residues: 756
  helix:  2.34 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop :  0.54 (0.47), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  74 
 HIS   0.004   0.001   HIS B 315 
 PHE   0.015   0.001   PHE A 187 
 TYR   0.017   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
  215 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 191
  time to evaluate  : 0.679 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8217 (tp40) cc_final: 0.7970 (tp40)
REVERT: B  199 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8408 (tm-30)
REVERT: B  244 ILE cc_start: 0.8214 (tp) cc_final: 0.7786 (mm)
REVERT: B  252 LEU cc_start: 0.8982 (mt) cc_final: 0.8669 (mt)
REVERT: B  313 GLU cc_start: 0.7561 (mp0) cc_final: 0.7179 (mp0)
REVERT: B  360 ASP cc_start: 0.8814 (t70) cc_final: 0.8334 (t0)
REVERT: B  362 TYR cc_start: 0.8976 (t80) cc_final: 0.8630 (t80)
REVERT: B  369 GLU cc_start: 0.7371 (mp0) cc_final: 0.7142 (mt-10)
REVERT: B  381 PHE cc_start: 0.8433 (t80) cc_final: 0.7980 (t80)
REVERT: A   69 GLN cc_start: 0.8230 (tp40) cc_final: 0.7975 (tp40)
REVERT: A   74 TRP cc_start: 0.7996 (t60) cc_final: 0.7708 (t60)
REVERT: A  244 ILE cc_start: 0.8206 (tp) cc_final: 0.7779 (mm)
REVERT: A  252 LEU cc_start: 0.8989 (mt) cc_final: 0.8671 (mt)
REVERT: A  305 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8754 (mmmt)
REVERT: A  360 ASP cc_start: 0.8833 (t70) cc_final: 0.8348 (t0)
REVERT: A  362 TYR cc_start: 0.8990 (t80) cc_final: 0.8683 (t80)
REVERT: A  381 PHE cc_start: 0.8198 (t80) cc_final: 0.7685 (t80)
  outliers start: 24
  outliers final: 21
  residues processed: 206
  average time/residue: 0.1472
  time to fit residues: 41.3058
Evaluate side-chains
  205 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 184
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
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  253 CYS
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  157 CYS
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain A residue  343 GLU
Chi-restraints excluded: chain A residue  365 SER
Chi-restraints excluded: chain A residue  390 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 16 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 71 optimal weight:    0.0670
   chunk 29 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 28 optimal weight:    0.1980
   chunk 12 optimal weight:    3.9990
   chunk 38 optimal weight:   10.0000
   overall best weight:    0.7520

-------------------------------------------------------------------------------
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
A 174 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 = 0.3991 r_free = 0.3991 target = 0.171707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.133329 restraints weight = 7834.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.139018 restraints weight = 4030.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.142591 restraints weight = 2698.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.3993

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= 0.195
  Angle     :  0.615  12.160   8544  Z= 0.309
  Chirality :  0.041   0.163    978
  Planarity :  0.005   0.041   1040
  Dihedral  :  9.130  80.166    894
  Min Nonbonded Distance : 1.862

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 26.89 %
    Favored  : 69.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.78 (0.30), residues: 756
  helix:  2.30 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop :  0.43 (0.46), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B  74 
 HIS   0.004   0.001   HIS B 315 
 PHE   0.044   0.002   PHE A 234 
 TYR   0.017   0.001   TYR A 387 
 ARG   0.008   0.001   ARG A  50 

*********************** 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
  215 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 188
  time to evaluate  : 0.679 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8093 (tp40) cc_final: 0.7853 (tp40)
REVERT: B  199 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8403 (tm-30)
REVERT: B  244 ILE cc_start: 0.8246 (tp) cc_final: 0.7811 (mm)
REVERT: B  252 LEU cc_start: 0.8993 (mt) cc_final: 0.8672 (mt)
REVERT: B  313 GLU cc_start: 0.7531 (mp0) cc_final: 0.7162 (mp0)
REVERT: B  360 ASP cc_start: 0.8791 (t70) cc_final: 0.8310 (t0)
REVERT: B  362 TYR cc_start: 0.8974 (t80) cc_final: 0.8606 (t80)
REVERT: B  381 PHE cc_start: 0.8464 (t80) cc_final: 0.8016 (t80)
REVERT: A   69 GLN cc_start: 0.8220 (tp40) cc_final: 0.7968 (tp40)
REVERT: A   74 TRP cc_start: 0.8007 (t60) cc_final: 0.7693 (t60)
REVERT: A  199 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8351 (tm-30)
REVERT: A  244 ILE cc_start: 0.8234 (tp) cc_final: 0.7717 (mm)
REVERT: A  252 LEU cc_start: 0.9005 (mt) cc_final: 0.8677 (mt)
REVERT: A  305 LYS cc_start: 0.8990 (mmtt) cc_final: 0.8743 (mmmt)
REVERT: A  360 ASP cc_start: 0.8819 (t70) cc_final: 0.8320 (t0)
REVERT: A  362 TYR cc_start: 0.8964 (t80) cc_final: 0.8619 (t80)
REVERT: A  381 PHE cc_start: 0.8335 (t80) cc_final: 0.7791 (t80)
  outliers start: 27
  outliers final: 24
  residues processed: 207
  average time/residue: 0.1692
  time to fit residues: 47.9981
Evaluate side-chains
  202 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 178
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  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  343 GLU
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  157 CYS
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  253 CYS
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 52 optimal weight:    0.0770
   chunk 64 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 51 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   chunk 2 optimal weight:    7.9990
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.5938

-------------------------------------------------------------------------------
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
A 174 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.173655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.135371 restraints weight = 7849.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.141238 restraints weight = 3925.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.145048 restraints weight = 2581.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.4107

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= 0.191
  Angle     :  0.639  10.897   8544  Z= 0.318
  Chirality :  0.041   0.160    978
  Planarity :  0.005   0.041   1040
  Dihedral  :  9.078  80.164    894
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 27.04 %
    Favored  : 68.43 %
  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:  2.32 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop :  0.42 (0.46), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  74 
 HIS   0.004   0.001   HIS B 315 
 PHE   0.027   0.001   PHE B 234 
 TYR   0.017   0.001   TYR A 387 
 ARG   0.008   0.001   ARG B  50 

*********************** 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
  220 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 190
  time to evaluate  : 0.642 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8116 (tp40) cc_final: 0.7863 (tp40)
REVERT: B  199 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8406 (tm-30)
REVERT: B  244 ILE cc_start: 0.8283 (tp) cc_final: 0.7787 (mm)
REVERT: B  246 MET cc_start: 0.6641 (tmm) cc_final: 0.6399 (ttp)
REVERT: B  252 LEU cc_start: 0.8973 (mt) cc_final: 0.8647 (mt)
REVERT: B  313 GLU cc_start: 0.7489 (mp0) cc_final: 0.7083 (mp0)
REVERT: B  360 ASP cc_start: 0.8806 (t70) cc_final: 0.8327 (t0)
REVERT: B  362 TYR cc_start: 0.8951 (t80) cc_final: 0.8590 (t80)
REVERT: B  381 PHE cc_start: 0.8407 (t80) cc_final: 0.7974 (t80)
REVERT: A   74 TRP cc_start: 0.8004 (t60) cc_final: 0.7702 (t60)
REVERT: A  182 MET cc_start: 0.8063 (ttt) cc_final: 0.7825 (ttt)
REVERT: A  199 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8286 (tm-30)
REVERT: A  244 ILE cc_start: 0.8128 (tp) cc_final: 0.7711 (mm)
REVERT: A  246 MET cc_start: 0.6664 (tmm) cc_final: 0.6418 (ttp)
REVERT: A  252 LEU cc_start: 0.8987 (mt) cc_final: 0.8665 (mt)
REVERT: A  281 ILE cc_start: 0.8340 (tt) cc_final: 0.7948 (tp)
REVERT: A  305 LYS cc_start: 0.8970 (mmtt) cc_final: 0.8739 (mmmt)
REVERT: A  360 ASP cc_start: 0.8808 (t70) cc_final: 0.8315 (t0)
REVERT: A  362 TYR cc_start: 0.8946 (t80) cc_final: 0.8675 (t80)
REVERT: A  381 PHE cc_start: 0.8246 (t80) cc_final: 0.7708 (t80)
  outliers start: 30
  outliers final: 26
  residues processed: 208
  average time/residue: 0.1519
  time to fit residues: 43.8388
Evaluate side-chains
  207 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 181
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  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  253 CYS
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  111 THR
Chi-restraints excluded: chain A residue  157 CYS
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain A residue  365 SER
Chi-restraints excluded: chain A residue  383 ASP
Chi-restraints excluded: chain A residue  390 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 24 optimal weight:   10.0000
   chunk 32 optimal weight:    0.6980
   chunk 66 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    1.0984

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.168817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.130149 restraints weight = 7969.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.135884 restraints weight = 4006.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.139567 restraints weight = 2656.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.4162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6286  Z= 0.239
  Angle     :  0.667  10.481   8544  Z= 0.333
  Chirality :  0.043   0.188    978
  Planarity :  0.005   0.041   1040
  Dihedral  :  9.045  81.940    894
  Min Nonbonded Distance : 1.702

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 27.19 %
    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:  2.70 (0.30), residues: 756
  helix:  2.28 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop :  0.27 (0.46), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  74 
 HIS   0.004   0.001   HIS B 315 
 PHE   0.026   0.002   PHE A 234 
 TYR   0.017   0.002   TYR A 387 
 ARG   0.009   0.001   ARG A  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: 26
    poor density    : 180
  time to evaluate  : 0.617 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8172 (tp40) cc_final: 0.7911 (tp40)
REVERT: B   98 CYS cc_start: 0.8498 (m) cc_final: 0.7850 (m)
REVERT: B  199 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8475 (tm-30)
REVERT: B  244 ILE cc_start: 0.8201 (tp) cc_final: 0.7812 (mm)
REVERT: B  252 LEU cc_start: 0.8959 (mt) cc_final: 0.8632 (mt)
REVERT: B  313 GLU cc_start: 0.7581 (mp0) cc_final: 0.7215 (mp0)
REVERT: B  360 ASP cc_start: 0.8830 (t70) cc_final: 0.8342 (t0)
REVERT: B  362 TYR cc_start: 0.8986 (t80) cc_final: 0.8636 (t80)
REVERT: A   74 TRP cc_start: 0.7958 (t60) cc_final: 0.7684 (t60)
REVERT: A  252 LEU cc_start: 0.8971 (mt) cc_final: 0.8660 (mt)
REVERT: A  281 ILE cc_start: 0.8405 (tt) cc_final: 0.7999 (tp)
REVERT: A  305 LYS cc_start: 0.8977 (mmtt) cc_final: 0.8753 (mmmt)
REVERT: A  360 ASP cc_start: 0.8827 (t70) cc_final: 0.8320 (t0)
REVERT: A  362 TYR cc_start: 0.8976 (t80) cc_final: 0.8654 (t80)
REVERT: A  381 PHE cc_start: 0.8343 (t80) cc_final: 0.7796 (t80)
  outliers start: 26
  outliers final: 25
  residues processed: 197
  average time/residue: 0.1398
  time to fit residues: 38.1122
Evaluate side-chains
  203 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 178
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  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  253 CYS
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  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  242 LEU
Chi-restraints excluded: chain A residue  253 CYS
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:    0.0060
   chunk 55 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 70 optimal weight:    0.0370
   chunk 16 optimal weight:    2.9990
   chunk 67 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 59 optimal weight:    6.9990
   chunk 30 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.5876

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.172139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.133121 restraints weight = 7882.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.139036 restraints weight = 3927.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.142928 restraints weight = 2585.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.4250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6286  Z= 0.190
  Angle     :  0.640  10.258   8544  Z= 0.317
  Chirality :  0.042   0.208    978
  Planarity :  0.005   0.041   1040
  Dihedral  :  9.003  81.469    894
  Min Nonbonded Distance : 1.652

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  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:  2.76 (0.30), residues: 756
  helix:  2.35 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop :  0.22 (0.45), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  74 
 HIS   0.004   0.001   HIS B 315 
 PHE   0.026   0.001   PHE A 234 
 TYR   0.017   0.001   TYR A 387 
 ARG   0.009   0.001   ARG A  50 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2162.91 seconds
wall clock time: 38 minutes 12.31 seconds (2292.31 seconds total)