Starting phenix.real_space_refine
on Thu Jul  2 03:22:16 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8gyx_34379/07_2026/8gyx_34379.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gyx_34379/07_2026/8gyx_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_34379/07_2026/8gyx_34379.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gyx_34379/07_2026/8gyx_34379.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gyx_34379/07_2026/8gyx_34379.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gyx_34379/07_2026/8gyx_34379.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8gyx_34379/07_2026/8gyx_34379.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8gyx_34379/07_2026/8gyx_34379.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.108
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     Mg      4      5.21       5
     S      48      5.16       5
     C    4050      2.51       5
     N     978      2.21       5
     O    1036      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6118
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 3005
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 380, 3005
          Classifications: {'peptide': 380}
          Link IDs: {'PTRANS': 17, 'TRANS': 362}
    Chain: "B"
      Number of atoms: 54
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 54
          Unusual residues: {' MG': 2, 'POV': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Restraints were copied for chains:
    A
  Time building chain proxies: 2.18, per 1000 atoms: 0.36
  Number of scatterers: 6118
  At special positions: 0
  Unit cell: (108.07, 90.95, 72.76, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      48     16.00
     P       2     15.00
     Mg      4     11.99
     O    1036      8.00
     N     978      7.00
     C    4050      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.50
  Conformation dependent library (CDL) restraints added in 297.8 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: 0.12
  Creating SS restraints...
    Processing helix  chain 'B' and resid 28 through 36
    Processing helix  chain 'B' and resid 44 through 53
      removed outlier: 3.808A  pdb=" N   GLU B  53 " --> pdb=" O   LYS B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 64 through 79
      removed outlier: 3.966A  pdb=" N   GLY B  70 " --> pdb=" O   PRO B  66 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   TYR B  71 " --> pdb=" O   LEU B  67 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ARG B  77 " --> pdb=" O   GLU B  73 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ARG B  78 " --> pdb=" O   TRP B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 107
    Processing helix  chain 'B' and resid 115 through 143
      removed outlier: 3.922A  pdb=" N   TYR B 119 " --> pdb=" O   PRO B 115 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ILE B 135 " --> pdb=" O   SER B 131 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ASP B 136 " --> pdb=" O   LEU B 132 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   GLY B 137 " --> pdb=" O   ASP B 133 " (cutoff:3.500A)
      removed outlier: 4.845A  pdb=" N   LYS B 138 " --> pdb=" O   ALA B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 174
      removed outlier: 3.595A  pdb=" N   LEU B 160 " --> pdb=" O   GLY B 156 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   VAL B 163 " --> pdb=" O   SER B 159 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   PHE B 164 " --> pdb=" O   LEU B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 177
      No H-bonds generated for 'chain 'B' and resid 175 through 177'
    Processing helix  chain 'B' and resid 178 through 204
    Processing helix  chain 'B' and resid 212 through 237
      removed outlier: 3.540A  pdb=" N   LEU B 225 " --> pdb=" O   ILE B 221 " (cutoff:3.500A)
      Proline residue:  B 232  - end of helix
    Processing helix  chain 'B' and resid 245 through 247
      No H-bonds generated for 'chain 'B' and resid 245 through 247'
    Processing helix  chain 'B' and resid 248 through 272
      removed outlier: 3.702A  pdb=" N   VAL B 268 " --> pdb=" O   ASN B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 279
    Processing helix  chain 'B' and resid 287 through 307
      removed outlier: 3.884A  pdb=" N   LEU B 291 " --> pdb=" O   LEU B 287 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   HIS B 292 " --> pdb=" O   SER B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 315
    Processing helix  chain 'B' and resid 315 through 341
    Processing helix  chain 'B' and resid 348 through 350
      No H-bonds generated for 'chain 'B' and resid 348 through 350'
    Processing helix  chain 'B' and resid 351 through 363
    Processing helix  chain 'B' and resid 368 through 400
    Processing helix  chain 'A' and resid 29 through 36
    Processing helix  chain 'A' and resid 44 through 53
      removed outlier: 3.808A  pdb=" N   GLU A  53 " --> pdb=" O   LYS A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 79
      removed outlier: 3.967A  pdb=" N   GLY A  70 " --> pdb=" O   PRO A  66 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   TYR A  71 " --> pdb=" O   LEU A  67 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ARG A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ARG A  78 " --> pdb=" O   TRP A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 107
    Processing helix  chain 'A' and resid 115 through 143
      removed outlier: 3.922A  pdb=" N   TYR A 119 " --> pdb=" O   PRO A 115 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ILE A 135 " --> pdb=" O   SER A 131 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ASP A 136 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   GLY A 137 " --> pdb=" O   ASP A 133 " (cutoff:3.500A)
      removed outlier: 4.846A  pdb=" N   LYS A 138 " --> pdb=" O   ALA A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 174
      removed outlier: 3.596A  pdb=" N   LEU A 160 " --> pdb=" O   GLY A 156 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   VAL A 163 " --> pdb=" O   SER A 159 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   PHE A 164 " --> pdb=" O   LEU A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 177
      No H-bonds generated for 'chain 'A' and resid 175 through 177'
    Processing helix  chain 'A' and resid 178 through 204
    Processing helix  chain 'A' and resid 212 through 237
      removed outlier: 3.540A  pdb=" N   LEU A 225 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      Proline residue:  A 232  - end of helix
    Processing helix  chain 'A' and resid 245 through 247
      No H-bonds generated for 'chain 'A' and resid 245 through 247'
    Processing helix  chain 'A' and resid 248 through 272
      removed outlier: 3.703A  pdb=" N   VAL A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 287 through 307
      removed outlier: 3.885A  pdb=" N   LEU A 291 " --> pdb=" O   LEU A 287 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   HIS A 292 " --> pdb=" O   SER A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 315
    Processing helix  chain 'A' and resid 315 through 341
    Processing helix  chain 'A' and resid 348 through 350
      No H-bonds generated for 'chain 'A' and resid 348 through 350'
    Processing helix  chain 'A' and resid 351 through 363
    Processing helix  chain 'A' and resid 368 through 400

    439 hydrogen bonds defined for protein.
    1305 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.75

  Time building geometry restraints manager: 0.66 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: 3223
       18.09 -    36.17: 305
       36.17 -    54.26: 90
       54.26 -    72.34: 18
       72.34 -    90.43: 6
  Dihedral angle restraints: 3642
    sinusoidal: 1434
      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 3639 not shown)

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

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

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

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.760
  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:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.460
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.060   6286  Z= 0.356
  Angle     :  1.358  18.179   8544  Z= 0.780
  Chirality :  0.072   0.409    978
  Planarity :  0.014   0.238   1040
  Dihedral  : 15.990  90.426   2218
  Min Nonbonded Distance : 2.208

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

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

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



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00683 /  0.36 ( 6286)
  covalent geometry    : angle       1.35818 /  0.78 ( 8544)
  hydrogen bonds       : bond        0.20796 / 14.07 (  439)
  hydrogen bonds       : angle       6.77726 /  4.97 ( 1305)

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

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 163
  time to evaluate  : 0.237 
Fit side-chains
REVERT: B  131 SER cc_start: 0.8853 (m) cc_final: 0.8614 (m)
REVERT: B  267 ARG cc_start: 0.7785 (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: 0.0835
  time to fit residues: 17.6519
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  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain A residue  149 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    9.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.4054 r_free = 0.4054 target = 0.177217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.140649 restraints weight = 7354.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.146359 restraints weight = 3624.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.150219 restraints weight = 2348.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.152624 restraints weight = 1793.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.154104 restraints weight = 1516.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6286  Z= 0.158
  Angle     :  0.637  10.178   8544  Z= 0.333
  Chirality :  0.043   0.152    978
  Planarity :  0.005   0.060   1040
  Dihedral  : 10.223  83.827    886
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 18.13 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.65 (0.29), residues: 756
  helix:  2.10 (0.20), residues: 570
  sheet:  None (None), residues: 0
  loop :  0.84 (0.49), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  50 
 TYR   0.015   0.002   TYR A 362 
 PHE   0.019   0.002   PHE A 358 
 TRP   0.010   0.001   TRP A  74 
 HIS   0.004   0.001   HIS B 315 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.16 ( 6286)
  covalent geometry    : angle       0.63744 /  0.33 ( 8544)
  hydrogen bonds       : bond        0.06128 /  4.13 (  439)
  hydrogen bonds       : angle       4.62470 /  3.36 ( 1305)

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

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 194
  time to evaluate  : 0.237 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8664 (tp40) cc_final: 0.8434 (tp40)
REVERT: B  131 SER cc_start: 0.8931 (m) cc_final: 0.8725 (m)
REVERT: B  219 PHE cc_start: 0.7395 (t80) cc_final: 0.6968 (m-10)
REVERT: B  267 ARG cc_start: 0.7962 (ptm160) cc_final: 0.7602 (ptm160)
REVERT: B  347 HIS cc_start: 0.8125 (p90) cc_final: 0.7553 (p90)
REVERT: B  360 ASP cc_start: 0.9039 (t70) cc_final: 0.8638 (t0)
REVERT: B  362 TYR cc_start: 0.9068 (t80) cc_final: 0.8612 (t80)
REVERT: A   50 ARG cc_start: 0.7801 (ttm110) cc_final: 0.7580 (ttp-110)
REVERT: A   69 GLN cc_start: 0.8661 (tp40) cc_final: 0.8444 (tp40)
REVERT: A  119 TYR cc_start: 0.8718 (m-10) cc_final: 0.8411 (m-10)
REVERT: A  219 PHE cc_start: 0.7425 (t80) cc_final: 0.6967 (m-10)
REVERT: A  347 HIS cc_start: 0.8146 (p90) cc_final: 0.7394 (p-80)
REVERT: A  360 ASP cc_start: 0.9049 (t70) cc_final: 0.8668 (t0)
REVERT: A  362 TYR cc_start: 0.9079 (t80) cc_final: 0.8713 (t80)
  outliers start: 24
  outliers final: 18
  residues processed: 209
  average time/residue: 0.0782
  time to fit residues: 21.2479
Evaluate side-chains
  206 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 188
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
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  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 24 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 41 optimal weight:    8.9990
   chunk 71 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   chunk 18 optimal weight:    8.9990
   chunk 5 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 4 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  47 GLN
B  57 GLN
** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.169578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.128140 restraints weight = 7561.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.134066 restraints weight = 3944.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.138080 restraints weight = 2654.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.140676 restraints weight = 2071.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.142318 restraints weight = 1773.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.2608

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= 0.144
  Angle     :  0.593   9.914   8544  Z= 0.309
  Chirality :  0.042   0.143    978
  Planarity :  0.005   0.043   1040
  Dihedral  :  9.262  74.997    886
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 22.21 %
    Favored  : 73.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.86 (0.30), residues: 756
  helix:  2.26 (0.21), residues: 568
  sheet:  None (None), residues: 0
  loop :  0.89 (0.48), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  50 
 TYR   0.015   0.002   TYR A 201 
 PHE   0.028   0.002   PHE A 234 
 TRP   0.006   0.001   TRP A 181 
 HIS   0.005   0.001   HIS A 315 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.14 ( 6286)
  covalent geometry    : angle       0.59254 /  0.31 ( 8544)
  hydrogen bonds       : bond        0.05544 /  3.70 (  439)
  hydrogen bonds       : angle       4.41100 /  3.20 ( 1305)

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

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 193
  time to evaluate  : 0.214 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8437 (tp40) cc_final: 0.8191 (tp40)
REVERT: B   74 TRP cc_start: 0.7988 (t60) cc_final: 0.7771 (t60)
REVERT: B  119 TYR cc_start: 0.8875 (m-10) cc_final: 0.8601 (m-10)
REVERT: B  201 TYR cc_start: 0.8823 (t80) cc_final: 0.8547 (t80)
REVERT: B  219 PHE cc_start: 0.7548 (t80) cc_final: 0.7027 (m-10)
REVERT: B  252 LEU cc_start: 0.8825 (mt) cc_final: 0.8507 (mt)
REVERT: B  305 LYS cc_start: 0.8785 (mmtt) cc_final: 0.8565 (mmmt)
REVERT: B  313 GLU cc_start: 0.7820 (mp0) cc_final: 0.7478 (mp0)
REVERT: B  347 HIS cc_start: 0.8292 (p90) cc_final: 0.7750 (p90)
REVERT: B  360 ASP cc_start: 0.8895 (t70) cc_final: 0.8449 (t0)
REVERT: B  362 TYR cc_start: 0.8961 (t80) cc_final: 0.8615 (t80)
REVERT: A   69 GLN cc_start: 0.8426 (tp40) cc_final: 0.8200 (tp40)
REVERT: A   74 TRP cc_start: 0.8147 (t60) cc_final: 0.7889 (t60)
REVERT: A  119 TYR cc_start: 0.8868 (m-10) cc_final: 0.8647 (m-10)
REVERT: A  201 TYR cc_start: 0.8831 (t80) cc_final: 0.8567 (t80)
REVERT: A  219 PHE cc_start: 0.7530 (t80) cc_final: 0.7026 (m-10)
REVERT: A  252 LEU cc_start: 0.8783 (mt) cc_final: 0.8458 (mt)
REVERT: A  305 LYS cc_start: 0.8771 (mmtt) cc_final: 0.8540 (mmmt)
REVERT: A  339 MET cc_start: 0.8723 (mmm) cc_final: 0.8488 (mmm)
REVERT: A  347 HIS cc_start: 0.8300 (p90) cc_final: 0.7539 (p90)
REVERT: A  360 ASP cc_start: 0.8929 (t70) cc_final: 0.8521 (t0)
REVERT: A  362 TYR cc_start: 0.8979 (t80) cc_final: 0.8610 (t80)
REVERT: A  381 PHE cc_start: 0.8420 (t80) cc_final: 0.7872 (t80)
  outliers start: 27
  outliers final: 21
  residues processed: 206
  average time/residue: 0.0824
  time to fit residues: 21.7428
Evaluate side-chains
  212 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 191
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   47 GLN
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  365 SER
Chi-restraints excluded: chain B residue  385 ILE
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  173 VAL
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  365 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 14 optimal weight:    4.9990
   chunk 10 optimal weight:    8.9990
   chunk 5 optimal weight:    4.9990
   chunk 41 optimal weight:    9.9990
   chunk 24 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   overall best weight:    1.5386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 217 GLN
B 224 HIS
A 217 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.171328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.134311 restraints weight = 7703.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.140017 restraints weight = 3820.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.143574 restraints weight = 2491.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.145817 restraints weight = 1922.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.147125 restraints weight = 1637.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.3083

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= 0.192
  Angle     :  0.614  11.061   8544  Z= 0.321
  Chirality :  0.044   0.174    978
  Planarity :  0.005   0.040   1040
  Dihedral  :  8.761  72.065    886
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  5.89 %
    Allowed  : 21.75 %
    Favored  : 72.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.82 (0.30), residues: 756
  helix:  2.21 (0.21), residues: 568
  sheet:  None (None), residues: 0
  loop :  0.96 (0.48), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  50 
 TYR   0.015   0.002   TYR B 304 
 PHE   0.016   0.002   PHE B 358 
 TRP   0.006   0.001   TRP A 117 
 HIS   0.004   0.001   HIS B 315 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00427 /  0.19 ( 6286)
  covalent geometry    : angle       0.61378 /  0.32 ( 8544)
  hydrogen bonds       : bond        0.05698 /  3.78 (  439)
  hydrogen bonds       : angle       4.46362 /  3.22 ( 1305)

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

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 200
  time to evaluate  : 0.201 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8581 (tp40) cc_final: 0.8343 (tp40)
REVERT: B   74 TRP cc_start: 0.7912 (t60) cc_final: 0.7698 (t60)
REVERT: B   78 ARG cc_start: 0.8515 (mmm160) cc_final: 0.8033 (mmm-85)
REVERT: B  252 LEU cc_start: 0.8864 (mt) cc_final: 0.8586 (mt)
REVERT: B  267 ARG cc_start: 0.8067 (ptp-110) cc_final: 0.7835 (ptm160)
REVERT: B  360 ASP cc_start: 0.8890 (t70) cc_final: 0.8481 (t0)
REVERT: B  362 TYR cc_start: 0.9060 (t80) cc_final: 0.8640 (t80)
REVERT: A   69 GLN cc_start: 0.8584 (tp40) cc_final: 0.8364 (tp40)
REVERT: A  119 TYR cc_start: 0.8880 (m-10) cc_final: 0.8646 (m-10)
REVERT: A  149 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8666 (tt)
REVERT: A  252 LEU cc_start: 0.8866 (mt) cc_final: 0.8572 (mt)
REVERT: A  360 ASP cc_start: 0.8916 (t70) cc_final: 0.8517 (t0)
REVERT: A  362 TYR cc_start: 0.9063 (t80) cc_final: 0.8633 (t80)
  outliers start: 39
  outliers final: 36
  residues processed: 222
  average time/residue: 0.0815
  time to fit residues: 23.4697
Evaluate side-chains
  233 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 196
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
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   90 ILE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  248 ILE
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  309 VAL
Chi-restraints excluded: chain B residue  365 SER
Chi-restraints excluded: chain B residue  383 ASP
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  157 CYS
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  365 SER
Chi-restraints excluded: chain A residue  383 ASP
Chi-restraints excluded: chain A residue  390 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 8 optimal weight:    5.9990
   chunk 46 optimal weight:    5.9990
   chunk 54 optimal weight:    0.7980
   chunk 1 optimal weight:    0.1980
   chunk 52 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  46 HIS
B  47 GLN
** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.170191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.132284 restraints weight = 7685.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.137866 restraints weight = 3906.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.141444 restraints weight = 2580.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.143397 restraints weight = 2006.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.144966 restraints weight = 1739.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.3352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6286  Z= 0.146
  Angle     :  0.589  11.641   8544  Z= 0.306
  Chirality :  0.042   0.162    978
  Planarity :  0.005   0.040   1040
  Dihedral  :  8.168  67.316    886
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 24.77 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.82 (0.30), residues: 756
  helix:  2.27 (0.21), residues: 570
  sheet:  None (None), residues: 0
  loop :  0.70 (0.47), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  50 
 TYR   0.017   0.001   TYR B 201 
 PHE   0.032   0.002   PHE A 234 
 TRP   0.006   0.001   TRP A 235 
 HIS   0.004   0.001   HIS B  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.15 ( 6286)
  covalent geometry    : angle       0.58891 /  0.31 ( 8544)
  hydrogen bonds       : bond        0.05309 /  3.51 (  439)
  hydrogen bonds       : angle       4.29228 /  3.10 ( 1305)

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

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 197
  time to evaluate  : 0.213 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8305 (tp40) cc_final: 0.8051 (tp40)
REVERT: B   74 TRP cc_start: 0.7972 (t60) cc_final: 0.7664 (t60)
REVERT: B   78 ARG cc_start: 0.8550 (mmm160) cc_final: 0.8077 (mmm-85)
REVERT: B  149 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8726 (tt)
REVERT: B  199 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8280 (tm-30)
REVERT: B  219 PHE cc_start: 0.7695 (t80) cc_final: 0.7099 (m-10)
REVERT: B  252 LEU cc_start: 0.8923 (mt) cc_final: 0.8632 (mt)
REVERT: B  305 LYS cc_start: 0.9027 (mmtt) cc_final: 0.8748 (mmmt)
REVERT: B  329 LYS cc_start: 0.8076 (tttp) cc_final: 0.7842 (tttm)
REVERT: B  362 TYR cc_start: 0.8996 (t80) cc_final: 0.8512 (t80)
REVERT: B  381 PHE cc_start: 0.8404 (t80) cc_final: 0.7866 (t80)
REVERT: A   69 GLN cc_start: 0.8464 (tp40) cc_final: 0.8185 (tp40)
REVERT: A  149 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8730 (tt)
REVERT: A  199 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8273 (tm-30)
REVERT: A  252 LEU cc_start: 0.8920 (mt) cc_final: 0.8605 (mt)
REVERT: A  329 LYS cc_start: 0.8079 (tttp) cc_final: 0.7863 (tttm)
REVERT: A  360 ASP cc_start: 0.8876 (t70) cc_final: 0.8466 (t0)
REVERT: A  362 TYR cc_start: 0.9014 (t80) cc_final: 0.8603 (t80)
REVERT: A  381 PHE cc_start: 0.8406 (t80) cc_final: 0.7880 (t80)
  outliers start: 34
  outliers final: 25
  residues processed: 217
  average time/residue: 0.0854
  time to fit residues: 23.7443
Evaluate side-chains
  218 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 191
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
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  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   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  161 SER
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  365 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 52 optimal weight:    0.7980
   chunk 3 optimal weight:   10.0000
   chunk 2 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0570
   chunk 53 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 75 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.6498

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  46 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.173381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.135788 restraints weight = 7628.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.141458 restraints weight = 3763.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.145144 restraints weight = 2457.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.147369 restraints weight = 1899.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.148900 restraints weight = 1628.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.3586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6286  Z= 0.135
  Angle     :  0.612  13.651   8544  Z= 0.309
  Chirality :  0.042   0.173    978
  Planarity :  0.005   0.040   1040
  Dihedral  :  7.688  63.244    886
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 27.49 %
    Favored  : 68.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.82 (0.30), residues: 756
  helix:  2.26 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop :  0.71 (0.49), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  50 
 TYR   0.014   0.001   TYR A 201 
 PHE   0.015   0.001   PHE B 187 
 TRP   0.007   0.001   TRP A 235 
 HIS   0.004   0.001   HIS B 315 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.14 ( 6286)
  covalent geometry    : angle       0.61241 /  0.31 ( 8544)
  hydrogen bonds       : bond        0.05131 /  3.40 (  439)
  hydrogen bonds       : angle       4.21597 /  3.05 ( 1305)

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

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 195
  time to evaluate  : 0.184 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8293 (tp40) cc_final: 0.8040 (tp40)
REVERT: B   74 TRP cc_start: 0.7896 (t60) cc_final: 0.7640 (t60)
REVERT: B   95 ILE cc_start: 0.8644 (tp) cc_final: 0.8426 (mt)
REVERT: B  199 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8381 (tm-30)
REVERT: B  244 ILE cc_start: 0.7854 (tp) cc_final: 0.7432 (mm)
REVERT: B  252 LEU cc_start: 0.8921 (mt) cc_final: 0.8618 (mt)
REVERT: B  329 LYS cc_start: 0.8162 (tttp) cc_final: 0.7956 (tttm)
REVERT: B  362 TYR cc_start: 0.9011 (t80) cc_final: 0.8486 (t80)
REVERT: A   69 GLN cc_start: 0.8332 (tp40) cc_final: 0.8066 (tp40)
REVERT: A  199 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8375 (tm-30)
REVERT: A  219 PHE cc_start: 0.7708 (t80) cc_final: 0.7407 (t80)
REVERT: A  247 LYS cc_start: 0.7695 (tttt) cc_final: 0.7457 (tttt)
REVERT: A  252 LEU cc_start: 0.8907 (mt) cc_final: 0.8619 (mt)
REVERT: A  329 LYS cc_start: 0.8144 (tttp) cc_final: 0.7938 (tttm)
REVERT: A  339 MET cc_start: 0.8582 (mmm) cc_final: 0.8379 (mmm)
REVERT: A  360 ASP cc_start: 0.8865 (t70) cc_final: 0.8453 (t0)
REVERT: A  362 TYR cc_start: 0.8991 (t80) cc_final: 0.8480 (t80)
REVERT: A  381 PHE cc_start: 0.8371 (t80) cc_final: 0.7830 (t80)
  outliers start: 26
  outliers final: 23
  residues processed: 214
  average time/residue: 0.0745
  time to fit residues: 21.0981
Evaluate side-chains
  209 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 186
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
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  190 THR
Chi-restraints excluded: chain B residue  210 ILE
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  111 THR
Chi-restraints excluded: chain A residue  157 CYS
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain A residue  365 SER
Chi-restraints excluded: chain A residue  390 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0170
   chunk 9 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 69 optimal weight:    3.9990
   chunk 43 optimal weight:    0.0970
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    0.7618

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 224 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.170998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.132569 restraints weight = 7764.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.138406 restraints weight = 3874.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.142220 restraints weight = 2548.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.144587 restraints weight = 1971.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.145868 restraints weight = 1679.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.3793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6286  Z= 0.140
  Angle     :  0.600   9.193   8544  Z= 0.306
  Chirality :  0.041   0.171    978
  Planarity :  0.005   0.041   1040
  Dihedral  :  7.192  59.979    882
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 27.04 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.85 (0.30), residues: 756
  helix:  2.30 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop :  0.67 (0.49), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  50 
 TYR   0.016   0.001   TYR A 304 
 PHE   0.031   0.001   PHE A 234 
 TRP   0.005   0.001   TRP B 235 
 HIS   0.004   0.001   HIS B 315 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.14 ( 6286)
  covalent geometry    : angle       0.59983 /  0.31 ( 8544)
  hydrogen bonds       : bond        0.05124 /  3.40 (  439)
  hydrogen bonds       : angle       4.18231 /  3.03 ( 1305)

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

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 195
  time to evaluate  : 0.189 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8140 (tp40) cc_final: 0.7894 (tp40)
REVERT: B  199 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8407 (tm-30)
REVERT: B  244 ILE cc_start: 0.7916 (tp) cc_final: 0.7504 (mm)
REVERT: B  252 LEU cc_start: 0.8953 (mt) cc_final: 0.8641 (mt)
REVERT: B  362 TYR cc_start: 0.8970 (t80) cc_final: 0.8524 (t80)
REVERT: A  199 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8428 (tm-30)
REVERT: A  252 LEU cc_start: 0.8978 (mt) cc_final: 0.8656 (mt)
REVERT: A  329 LYS cc_start: 0.8029 (tttp) cc_final: 0.7818 (tttm)
REVERT: A  360 ASP cc_start: 0.8874 (t70) cc_final: 0.8430 (t0)
REVERT: A  362 TYR cc_start: 0.8947 (t80) cc_final: 0.8545 (t80)
REVERT: A  369 GLU cc_start: 0.7406 (mp0) cc_final: 0.7134 (mt-10)
REVERT: A  381 PHE cc_start: 0.8419 (t80) cc_final: 0.7947 (t80)
  outliers start: 27
  outliers final: 24
  residues processed: 214
  average time/residue: 0.0748
  time to fit residues: 21.2482
Evaluate side-chains
  203 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 179
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  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  162 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  365 SER
Chi-restraints excluded: chain A residue  390 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 70 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 74 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 18 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0030
   chunk 51 optimal weight:    0.9980
   chunk 71 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.6390

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3989 r_free = 0.3989 target = 0.172039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.133561 restraints weight = 7837.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.139439 restraints weight = 3898.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.143228 restraints weight = 2557.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.145504 restraints weight = 1982.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.146730 restraints weight = 1702.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.3906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6286  Z= 0.135
  Angle     :  0.623  11.743   8544  Z= 0.313
  Chirality :  0.041   0.159    978
  Planarity :  0.005   0.042   1040
  Dihedral  :  6.958  57.019    882
  Min Nonbonded Distance : 1.879

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 27.49 %
    Favored  : 68.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.69 (0.30), residues: 756
  helix:  2.24 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop :  0.32 (0.48), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  50 
 TYR   0.015   0.001   TYR B 304 
 PHE   0.044   0.001   PHE B 234 
 TRP   0.008   0.001   TRP B 235 
 HIS   0.004   0.001   HIS A  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.13 ( 6286)
  covalent geometry    : angle       0.62331 /  0.31 ( 8544)
  hydrogen bonds       : bond        0.04991 /  3.30 (  439)
  hydrogen bonds       : angle       4.14156 /  3.01 ( 1305)

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

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 187
  time to evaluate  : 0.146 
Fit side-chains
REVERT: B   69 GLN cc_start: 0.8145 (tp40) cc_final: 0.7894 (tp40)
REVERT: B  199 GLN cc_start: 0.8761 (tm-30) cc_final: 0.8396 (tm-30)
REVERT: B  244 ILE cc_start: 0.7850 (tp) cc_final: 0.7410 (mm)
REVERT: B  252 LEU cc_start: 0.8962 (mt) cc_final: 0.8630 (mt)
REVERT: B  313 GLU cc_start: 0.7619 (mp0) cc_final: 0.7329 (mp0)
REVERT: B  362 TYR cc_start: 0.8956 (t80) cc_final: 0.8430 (t80)
REVERT: A  199 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8425 (tm-30)
REVERT: A  252 LEU cc_start: 0.8989 (mt) cc_final: 0.8662 (mt)
REVERT: A  281 ILE cc_start: 0.8165 (tt) cc_final: 0.7949 (tp)
REVERT: A  329 LYS cc_start: 0.8032 (tttp) cc_final: 0.7805 (tttm)
REVERT: A  360 ASP cc_start: 0.8834 (t70) cc_final: 0.8384 (t0)
REVERT: A  362 TYR cc_start: 0.8948 (t80) cc_final: 0.8502 (t80)
REVERT: A  381 PHE cc_start: 0.8402 (t80) cc_final: 0.7922 (t80)
  outliers start: 26
  outliers final: 25
  residues processed: 205
  average time/residue: 0.0617
  time to fit residues: 17.5025
Evaluate side-chains
  207 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 182
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  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  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  253 CYS
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  343 GLU
Chi-restraints excluded: chain A residue  365 SER
Chi-restraints excluded: chain A residue  390 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 50 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.0986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 174 GLN
A 174 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.168906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.131196 restraints weight = 7720.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.136700 restraints weight = 3820.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.140307 restraints weight = 2502.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.142630 restraints weight = 1938.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.143963 restraints weight = 1652.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.4024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6286  Z= 0.162
  Angle     :  0.660  10.635   8544  Z= 0.330
  Chirality :  0.042   0.174    978
  Planarity :  0.005   0.043   1040
  Dihedral  :  6.957  55.525    882
  Min Nonbonded Distance : 1.766

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 26.74 %
    Favored  : 68.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.64 (0.30), residues: 756
  helix:  2.23 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop :  0.30 (0.46), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  45 
 TYR   0.016   0.001   TYR B 304 
 PHE   0.037   0.002   PHE A 234 
 TRP   0.024   0.001   TRP B  74 
 HIS   0.005   0.001   HIS A  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00357 /  0.16 ( 6286)
  covalent geometry    : angle       0.65957 /  0.33 ( 8544)
  hydrogen bonds       : bond        0.05315 /  3.50 (  439)
  hydrogen bonds       : angle       4.23383 /  3.08 ( 1305)

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

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 192
  time to evaluate  : 0.141 
Fit side-chains
REVERT: B   50 ARG cc_start: 0.8318 (ttm110) cc_final: 0.7490 (ttt180)
REVERT: B   69 GLN cc_start: 0.8173 (tp40) cc_final: 0.7902 (tp40)
REVERT: B   98 CYS cc_start: 0.8479 (m) cc_final: 0.7820 (m)
REVERT: B  199 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8459 (tm-30)
REVERT: B  244 ILE cc_start: 0.7952 (tp) cc_final: 0.7541 (mm)
REVERT: B  252 LEU cc_start: 0.8941 (mt) cc_final: 0.8630 (mt)
REVERT: B  313 GLU cc_start: 0.7735 (mp0) cc_final: 0.7471 (mp0)
REVERT: B  362 TYR cc_start: 0.8964 (t80) cc_final: 0.8507 (t80)
REVERT: B  381 PHE cc_start: 0.8209 (t80) cc_final: 0.7684 (t80)
REVERT: A   74 TRP cc_start: 0.7956 (t60) cc_final: 0.7688 (t60)
REVERT: A  199 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8439 (tm-30)
REVERT: A  247 LYS cc_start: 0.7666 (tttt) cc_final: 0.7456 (tttm)
REVERT: A  252 LEU cc_start: 0.8965 (mt) cc_final: 0.8668 (mt)
REVERT: A  360 ASP cc_start: 0.8879 (t70) cc_final: 0.8431 (t0)
REVERT: A  362 TYR cc_start: 0.8954 (t80) cc_final: 0.8552 (t80)
REVERT: A  381 PHE cc_start: 0.8437 (t80) cc_final: 0.7965 (t80)
  outliers start: 31
  outliers final: 27
  residues processed: 211
  average time/residue: 0.0675
  time to fit residues: 19.0696
Evaluate side-chains
  209 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 182
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  248 ILE
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  365 SER
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  157 CYS
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 73 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 61 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 75 optimal weight:    0.9990
   chunk 56 optimal weight:    0.6980
   chunk 66 optimal weight:    0.7980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 174 GLN
A  46 HIS
A 174 GLN
A 217 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.171348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.133564 restraints weight = 7795.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.139110 restraints weight = 3815.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.142702 restraints weight = 2502.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.144877 restraints weight = 1948.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.146293 restraints weight = 1673.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.4088

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= 0.146
  Angle     :  0.663  12.103   8544  Z= 0.329
  Chirality :  0.042   0.191    978
  Planarity :  0.005   0.042   1040
  Dihedral  :  6.906  56.370    882
  Min Nonbonded Distance : 1.689

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 27.95 %
    Favored  : 67.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.59 (0.30), residues: 756
  helix:  2.21 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop :  0.20 (0.46), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  45 
 TYR   0.016   0.001   TYR B 304 
 PHE   0.039   0.002   PHE A 234 
 TRP   0.021   0.001   TRP B  74 
 HIS   0.006   0.001   HIS A  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.15 ( 6286)
  covalent geometry    : angle       0.66326 /  0.33 ( 8544)
  hydrogen bonds       : bond        0.05140 /  3.39 (  439)
  hydrogen bonds       : angle       4.17286 /  3.04 ( 1305)

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

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 182
  time to evaluate  : 0.135 
Fit side-chains
REVERT: B   50 ARG cc_start: 0.8355 (ttm110) cc_final: 0.7522 (ttt180)
REVERT: B   69 GLN cc_start: 0.8180 (tp40) cc_final: 0.7917 (tp40)
REVERT: B   95 ILE cc_start: 0.8569 (tp) cc_final: 0.8354 (mt)
REVERT: B  199 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8430 (tm-30)
REVERT: B  252 LEU cc_start: 0.8948 (mt) cc_final: 0.8625 (mt)
REVERT: B  281 ILE cc_start: 0.8406 (tt) cc_final: 0.7957 (tp)
REVERT: B  313 GLU cc_start: 0.7674 (mp0) cc_final: 0.7428 (mp0)
REVERT: B  362 TYR cc_start: 0.8949 (t80) cc_final: 0.8420 (t80)
REVERT: A   74 TRP cc_start: 0.7924 (t60) cc_final: 0.7686 (t60)
REVERT: A  199 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8439 (tm-30)
REVERT: A  252 LEU cc_start: 0.8975 (mt) cc_final: 0.8662 (mt)
REVERT: A  360 ASP cc_start: 0.8839 (t70) cc_final: 0.8381 (t0)
REVERT: A  362 TYR cc_start: 0.8956 (t80) cc_final: 0.8495 (t80)
REVERT: A  381 PHE cc_start: 0.8409 (t80) cc_final: 0.7931 (t80)
  outliers start: 28
  outliers final: 25
  residues processed: 200
  average time/residue: 0.0578
  time to fit residues: 15.5289
Evaluate side-chains
  201 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 176
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 CYS
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  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  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  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 9 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0050
   chunk 3 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0470
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.5492

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  47 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.170174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.132944 restraints weight = 7656.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.138386 restraints weight = 3841.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.141999 restraints weight = 2539.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.144259 restraints weight = 1974.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.145721 restraints weight = 1688.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.4158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6286  Z= 0.135
  Angle     :  0.651  10.503   8544  Z= 0.321
  Chirality :  0.042   0.196    978
  Planarity :  0.005   0.042   1040
  Dihedral  :  6.765  55.228    882
  Min Nonbonded Distance : 1.643

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 28.55 %
    Favored  : 67.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.65 (0.30), residues: 756
  helix:  2.26 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop :  0.20 (0.46), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  45 
 TYR   0.013   0.001   TYR A 201 
 PHE   0.044   0.001   PHE A 234 
 TRP   0.021   0.001   TRP B  74 
 HIS   0.004   0.001   HIS A 315 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.14 ( 6286)
  covalent geometry    : angle       0.65134 /  0.32 ( 8544)
  hydrogen bonds       : bond        0.04942 /  3.25 (  439)
  hydrogen bonds       : angle       4.14373 /  3.02 ( 1305)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1119.57 seconds
wall clock time: 20 minutes 4.09 seconds (1204.09 seconds total)