Starting phenix.real_space_refine
on Sat May 10 12:07:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qjy_18454/05_2025/8qjy_18454.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qjy_18454/05_2025/8qjy_18454.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qjy_18454/05_2025/8qjy_18454.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qjy_18454/05_2025/8qjy_18454.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qjy_18454/05_2025/8qjy_18454.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qjy_18454/05_2025/8qjy_18454.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    3961      2.51       5
     N    1044      2.21       5
     O    1252      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6287
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "D"
      Number of atoms: 1643
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 207, 1643
          Classifications: {'peptide': 207}
          Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 199}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 1548
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 1548
          Classifications: {'peptide': 197}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 189}
    Chain: "A"
      Number of atoms: 1548
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 1548
          Classifications: {'peptide': 197}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 189}
    Chain: "B"
      Number of atoms: 1548
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 1548
          Classifications: {'peptide': 197}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 189}
  Time building chain proxies: 4.02, per 1000 atoms: 0.64
  Number of scatterers: 6287
  At special positions: 0
  Unit cell: (94.9, 101.4, 98.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      30     16.00
     O    1252      8.00
     N    1044      7.00
     C    3961      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.43
  Conformation dependent library (CDL) restraints added in 902.4 milliseconds
  

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1526

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 13 sheets defined
      9.4% alpha, 33.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'C' and resid 129 through 131
      No H-bonds generated for 'chain 'C' and resid 129 through 131'
    Processing helix  chain 'C' and resid 179 through 184
    Processing helix  chain 'C' and resid 185 through 188
    Processing helix  chain 'C' and resid 231 through 236
    Processing helix  chain 'C' and resid 249 through 252
    Processing helix  chain 'A' and resid 129 through 131
      No H-bonds generated for 'chain 'A' and resid 129 through 131'
    Processing helix  chain 'A' and resid 179 through 184
    Processing helix  chain 'A' and resid 185 through 188
    Processing helix  chain 'A' and resid 231 through 236
      removed outlier: 3.922A  pdb=" N   PHE A 235 " --> pdb=" O   ASN A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 252
      removed outlier: 5.227A  pdb=" N   LYS A 251 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 131
      No H-bonds generated for 'chain 'B' and resid 129 through 131'
    Processing helix  chain 'B' and resid 179 through 184
    Processing helix  chain 'B' and resid 185 through 188
    Processing helix  chain 'B' and resid 231 through 236
    Processing helix  chain 'B' and resid 246 through 252
      removed outlier: 5.482A  pdb=" N   LYS B 251 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 114 through 120
      removed outlier: 6.537A  pdb=" N   PHE D 115 " --> pdb=" O   GLN D 210 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   ARG D 212 " --> pdb=" O   PHE D 115 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   GLY D 117 " --> pdb=" O   ARG D 212 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   LEU D 214 " --> pdb=" O   GLY D 117 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   VAL D 119 " --> pdb=" O   LEU D 214 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   GLU D 191 " --> pdb=" O   ILE D 151 " (cutoff:3.500A)
      removed outlier: 5.584A  pdb=" N   ILE D 151 " --> pdb=" O   GLU D 191 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 128 through 131
      removed outlier: 6.623A  pdb=" N   LEU D 128 " --> pdb=" O   THR D 173 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   THR D 173 " --> pdb=" O   LEU D 128 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 222 through 223
      removed outlier: 6.704A  pdb=" N   VAL D 285 " --> pdb=" O   VAL D 241 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   ARG D 243 " --> pdb=" O   GLY D 283 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   GLY D 283 " --> pdb=" O   ARG D 243 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 229 through 233
      removed outlier: 6.543A  pdb=" N   SER D 302 " --> pdb=" O   ALA D 264 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 133 through 135
    Processing sheet with id=AA6, first strand: chain 'C' and resid 190 through 199
      removed outlier: 5.780A  pdb=" N   ASN C 297 " --> pdb=" O   PRO C 270 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 218 through 220
      removed outlier: 4.574A  pdb=" N   HIS C 218 " --> pdb=" O   ALA C 225 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 133 through 135
    Processing sheet with id=AA9, first strand: chain 'A' and resid 190 through 199
      removed outlier: 6.389A  pdb=" N   ASN A 297 " --> pdb=" O   PRO A 270 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 218 through 220
      removed outlier: 4.584A  pdb=" N   HIS A 218 " --> pdb=" O   ALA A 225 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 133 through 135
    Processing sheet with id=AB3, first strand: chain 'B' and resid 190 through 199
      removed outlier: 6.417A  pdb=" N   ASN B 297 " --> pdb=" O   PRO B 270 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 218 through 220
      removed outlier: 4.414A  pdb=" N   HIS B 218 " --> pdb=" O   ALA B 225 " (cutoff:3.500A)

    196 hydrogen bonds defined for protein.
    489 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.68

  Time building geometry restraints manager: 1.70 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2054
        1.35 -     1.46: 1550
        1.46 -     1.58: 2762
        1.58 -     1.70: 0
        1.70 -     1.82: 48
  Bond restraints: 6414
  Sorted by residual:
  bond pdb=" N   MET C 276 "
       pdb=" CA  MET C 276 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.035 1.21e-02 6.83e+03 8.18e+00
  bond pdb=" N   ARG C 279 "
       pdb=" CA  ARG C 279 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.033 1.40e-02 5.10e+03 5.50e+00
  bond pdb=" N   ARG C 280 "
       pdb=" CA  ARG C 280 "
    ideal  model  delta    sigma   weight residual
    1.458  1.484 -0.027 1.16e-02 7.43e+03 5.40e+00
  bond pdb=" C   ARG C 280 "
       pdb=" O   ARG C 280 "
    ideal  model  delta    sigma   weight residual
    1.235  1.249 -0.014 1.25e-02 6.40e+03 1.26e+00
  bond pdb=" C   ASN A 278 "
       pdb=" O   ASN A 278 "
    ideal  model  delta    sigma   weight residual
    1.243  1.233  0.010 9.50e-03 1.11e+04 1.14e+00
  ... (remaining 6409 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 8623
        2.10 -     4.19: 108
        4.19 -     6.29: 7
        6.29 -     8.39: 1
        8.39 -    10.48: 1
  Bond angle restraints: 8740
  Sorted by residual:
  angle pdb=" C   MET C 276 "
        pdb=" N   LEU C 277 "
        pdb=" CA  LEU C 277 "
      ideal   model   delta    sigma   weight residual
     122.82  112.34   10.48 2.12e+00 2.22e-01 2.45e+01
  angle pdb=" C   ASN B 278 "
        pdb=" CA  ASN B 278 "
        pdb=" CB  ASN B 278 "
      ideal   model   delta    sigma   weight residual
     116.54  111.22    5.32 1.15e+00 7.56e-01 2.14e+01
  angle pdb=" N   ARG C 279 "
        pdb=" CA  ARG C 279 "
        pdb=" C   ARG C 279 "
      ideal   model   delta    sigma   weight residual
     113.89  107.05    6.84 1.58e+00 4.01e-01 1.87e+01
  angle pdb=" C   ASN A 278 "
        pdb=" CA  ASN A 278 "
        pdb=" CB  ASN A 278 "
      ideal   model   delta    sigma   weight residual
     117.23  111.43    5.80 1.36e+00 5.41e-01 1.82e+01
  angle pdb=" N   ARG B 279 "
        pdb=" CA  ARG B 279 "
        pdb=" CB  ARG B 279 "
      ideal   model   delta    sigma   weight residual
     114.17  109.44    4.73 1.14e+00 7.69e-01 1.72e+01
  ... (remaining 8735 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.38: 3469
       17.38 -    34.77: 287
       34.77 -    52.15: 50
       52.15 -    69.54: 6
       69.54 -    86.92: 7
  Dihedral angle restraints: 3819
    sinusoidal: 1466
      harmonic: 2353
  Sorted by residual:
  dihedral pdb=" CA  VAL A 138 "
           pdb=" C   VAL A 138 "
           pdb=" N   ASN A 139 "
           pdb=" CA  ASN A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.26  -17.74     0      5.00e+00 4.00e-02 1.26e+01
  dihedral pdb=" CA  LEU B 212 "
           pdb=" C   LEU B 212 "
           pdb=" N   LYS B 213 "
           pdb=" CA  LYS B 213 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.75  -16.25     0      5.00e+00 4.00e-02 1.06e+01
  dihedral pdb=" CB  GLU B 196 "
           pdb=" CG  GLU B 196 "
           pdb=" CD  GLU B 196 "
           pdb=" OE1 GLU B 196 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -86.92   86.92     1      3.00e+01 1.11e-03 1.01e+01
  ... (remaining 3816 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 662
       0.036 -    0.073: 253
       0.073 -    0.109: 62
       0.109 -    0.146: 42
       0.146 -    0.182: 2
  Chirality restraints: 1021
  Sorted by residual:
  chirality pdb=" CA  MET C 276 "
            pdb=" N   MET C 276 "
            pdb=" C   MET C 276 "
            pdb=" CB  MET C 276 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.28e-01
  chirality pdb=" CA  ILE C 255 "
            pdb=" N   ILE C 255 "
            pdb=" C   ILE C 255 "
            pdb=" CB  ILE C 255 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.68e-01
  chirality pdb=" CA  ILE B 176 "
            pdb=" N   ILE B 176 "
            pdb=" C   ILE B 176 "
            pdb=" CB  ILE B 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.09e-01
  ... (remaining 1018 not shown)

  Planarity restraints: 1123
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D 324 "    0.037 5.00e-02 4.00e+02   5.67e-02 5.15e+00
        pdb=" N   PRO D 325 "   -0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO D 325 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO D 325 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 139 "    0.035 5.00e-02 4.00e+02   5.37e-02 4.61e+00
        pdb=" N   PRO A 140 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 140 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 140 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 249 "   -0.143 9.50e-02 1.11e+02   6.45e-02 2.82e+00
        pdb=" NE  ARG C 249 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 249 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 249 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 249 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1120 not shown)

  Histogram of nonbonded interaction distances:
        1.68 -     2.33: 15
        2.33 -     2.97: 3327
        2.97 -     3.61: 8897
        3.61 -     4.26: 14822
        4.26 -     4.90: 24942
  Nonbonded interactions: 52003
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 254 "
            pdb=" NH2 ARG C 279 "
     model   vdw
     1.682 3.120
  nonbonded pdb=" O   ASN A 192 "
            pdb=" ND2 ASN A 192 "
     model   vdw
     1.908 3.120
  nonbonded pdb=" OH  TYR C 319 "
            pdb=" OH  TYR A 319 "
     model   vdw
     1.921 3.040
  nonbonded pdb=" OD1 ASN C 278 "
            pdb=" N   CYS C 289 "
     model   vdw
     1.988 3.120
  nonbonded pdb=" OH  TYR C 319 "
            pdb=" OH  TYR B 319 "
     model   vdw
     2.020 3.040
  ... (remaining 51998 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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:             0.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     17.930
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
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      :  0.003   0.035   6414  Z= 0.168
  Angle     :  0.607  10.483   8740  Z= 0.364
  Chirality :  0.046   0.182   1021
  Planarity :  0.004   0.064   1123
  Dihedral  : 13.674  86.923   2293
  Min Nonbonded Distance : 1.682

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  : 16.74 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.31), residues: 786
  helix: -0.85 (1.16), residues: 18
  sheet: -0.53 (0.27), residues: 322
  loop : -0.14 (0.32), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 296 
 HIS   0.005   0.001   HIS B 218 
 PHE   0.022   0.002   PHE D 301 
 TYR   0.012   0.002   TYR C 174 
 ARG   0.009   0.001   ARG C 249 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14753 (  196)
  hydrogen bonds       : angle       6.45170 (  489)
  covalent geometry    : bond        0.00323 ( 6414)
  covalent geometry    : angle       0.60736 ( 8740)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 212
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  299 LEU cc_start: 0.8127 (mt) cc_final: 0.7904 (mp)
REVERT: A  222 GLN cc_start: 0.7904 (mm110) cc_final: 0.7618 (mm110)
REVERT: A  236 MET cc_start: 0.8374 (mmp) cc_final: 0.7800 (mmt)
REVERT: B  252 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7424 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 213
  average time/residue: 0.2480
  time to fit residues: 64.3594
Evaluate side-chains
  136 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:    5.9990
   chunk 58 optimal weight:    6.9990
   chunk 32 optimal weight:    0.8980
   chunk 19 optimal weight:    4.9990
   chunk 39 optimal weight:   10.0000
   chunk 31 optimal weight:    0.0370
   chunk 60 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 69 optimal weight:    6.9990
   overall best weight:    1.5462

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

Flipped N/Q/H residues before XYZ refinement:
C 253 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.065411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.050515 restraints weight = 22471.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.052391 restraints weight = 10647.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.053649 restraints weight = 6723.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.3172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6414  Z= 0.154
  Angle     :  0.633   6.902   8740  Z= 0.333
  Chirality :  0.047   0.141   1021
  Planarity :  0.004   0.050   1123
  Dihedral  :  4.790  16.680    860
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 17.44 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.32), residues: 786
  helix: -1.11 (1.17), residues: 18
  sheet:  0.02 (0.30), residues: 291
  loop :  0.05 (0.32), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 296 
 HIS   0.005   0.001   HIS B 218 
 PHE   0.019   0.002   PHE D 247 
 TYR   0.015   0.002   TYR D 172 
 ARG   0.005   0.001   ARG C 249 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03395 (  196)
  hydrogen bonds       : angle       6.05762 (  489)
  covalent geometry    : bond        0.00344 ( 6414)
  covalent geometry    : angle       0.63341 ( 8740)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 138
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  128 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9173 (tp)
REVERT: D  185 SER cc_start: 0.9227 (OUTLIER) cc_final: 0.8949 (m)
REVERT: D  208 GLN cc_start: 0.7769 (tm-30) cc_final: 0.7414 (tm-30)
REVERT: D  293 TYR cc_start: 0.6106 (t80) cc_final: 0.5682 (t80)
REVERT: D  301 PHE cc_start: 0.9072 (p90) cc_final: 0.8857 (p90)
REVERT: C  157 LYS cc_start: 0.8839 (mtpt) cc_final: 0.8393 (mtpp)
REVERT: C  193 PHE cc_start: 0.9055 (p90) cc_final: 0.8777 (p90)
REVERT: C  284 ASP cc_start: 0.8899 (p0) cc_final: 0.8622 (p0)
REVERT: C  300 ASP cc_start: 0.8942 (t0) cc_final: 0.8661 (t0)
REVERT: C  319 TYR cc_start: 0.7933 (m-80) cc_final: 0.7587 (m-80)
REVERT: C  323 GLU cc_start: 0.8830 (tp30) cc_final: 0.8520 (tp30)
REVERT: A  134 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9089 (mp)
REVERT: A  184 MET cc_start: 0.8453 (tmm) cc_final: 0.8237 (tmm)
REVERT: A  222 GLN cc_start: 0.8859 (mm110) cc_final: 0.8468 (mm110)
REVERT: A  236 MET cc_start: 0.9256 (mmp) cc_final: 0.9040 (mmp)
REVERT: B  158 LEU cc_start: 0.9376 (tp) cc_final: 0.9146 (tp)
REVERT: B  233 LYS cc_start: 0.9278 (ttpt) cc_final: 0.8738 (ttpp)
REVERT: B  246 ASP cc_start: 0.8598 (t0) cc_final: 0.8357 (t0)
REVERT: B  249 ARG cc_start: 0.8581 (mtp85) cc_final: 0.7922 (mtp-110)
REVERT: B  252 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8020 (mt-10)
REVERT: B  324 ASP cc_start: 0.8860 (m-30) cc_final: 0.8604 (m-30)
  outliers start: 21
  outliers final: 12
  residues processed: 155
  average time/residue: 0.2071
  time to fit residues: 40.7873
Evaluate side-chains
  142 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  171 ILE
Chi-restraints excluded: chain D residue  185 SER
Chi-restraints excluded: chain D residue  272 PHE
Chi-restraints excluded: chain D residue  322 THR
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  192 ASN
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  250 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 37 optimal weight:    6.9990
   chunk 4 optimal weight:    2.9990
   chunk 10 optimal weight:    9.9990
   chunk 54 optimal weight:   10.0000
   chunk 75 optimal weight:    6.9990
   chunk 72 optimal weight:    5.9990
   chunk 74 optimal weight:    0.7980
   chunk 35 optimal weight:   10.0000
   chunk 50 optimal weight:    2.9990
   chunk 6 optimal weight:    9.9990
   chunk 45 optimal weight:   10.0000
   overall best weight:    3.9588

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

Flipped N/Q/H residues before XYZ refinement:
D 183 HIS
D 225 ASN
A 222 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.060524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.045554 restraints weight = 24155.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.047279 restraints weight = 12079.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.048419 restraints weight = 7830.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.3876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064   6414  Z= 0.297
  Angle     :  0.652   6.282   8740  Z= 0.346
  Chirality :  0.046   0.134   1021
  Planarity :  0.004   0.035   1123
  Dihedral  :  5.067  17.000    860
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 16.46 %
    Favored  : 79.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.32), residues: 786
  helix: -1.04 (1.22), residues: 18
  sheet: -0.14 (0.29), residues: 297
  loop :  0.00 (0.32), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 296 
 HIS   0.010   0.002   HIS D 183 
 PHE   0.018   0.002   PHE B 172 
 TYR   0.020   0.002   TYR A 260 
 ARG   0.006   0.001   ARG D 243 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03814 (  196)
  hydrogen bonds       : angle       6.16010 (  489)
  covalent geometry    : bond        0.00649 ( 6414)
  covalent geometry    : angle       0.65168 ( 8740)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 115
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  130 MET cc_start: 0.8774 (ppp) cc_final: 0.8558 (ppp)
REVERT: D  185 SER cc_start: 0.9202 (OUTLIER) cc_final: 0.8907 (m)
REVERT: D  293 TYR cc_start: 0.6046 (t80) cc_final: 0.5599 (t80)
REVERT: D  301 PHE cc_start: 0.9257 (p90) cc_final: 0.8769 (p90)
REVERT: C  157 LYS cc_start: 0.9074 (mtpt) cc_final: 0.8714 (mtpp)
REVERT: C  182 PHE cc_start: 0.9479 (t80) cc_final: 0.9252 (t80)
REVERT: C  193 PHE cc_start: 0.9148 (p90) cc_final: 0.8885 (p90)
REVERT: C  200 ASP cc_start: 0.8773 (p0) cc_final: 0.8554 (p0)
REVERT: C  300 ASP cc_start: 0.9009 (t0) cc_final: 0.8656 (t0)
REVERT: C  323 GLU cc_start: 0.8949 (tp30) cc_final: 0.8568 (tp30)
REVERT: A  184 MET cc_start: 0.8379 (tmm) cc_final: 0.7998 (tmm)
REVERT: A  305 GLN cc_start: 0.9097 (pm20) cc_final: 0.8861 (pm20)
REVERT: A  319 TYR cc_start: 0.8671 (m-80) cc_final: 0.8420 (m-80)
REVERT: B  164 LYS cc_start: 0.8737 (ttmt) cc_final: 0.8528 (ttmm)
REVERT: B  246 ASP cc_start: 0.8687 (t0) cc_final: 0.8293 (t0)
  outliers start: 29
  outliers final: 19
  residues processed: 136
  average time/residue: 0.1913
  time to fit residues: 34.0545
Evaluate side-chains
  130 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  171 ILE
Chi-restraints excluded: chain D residue  185 SER
Chi-restraints excluded: chain D residue  220 ILE
Chi-restraints excluded: chain D residue  272 PHE
Chi-restraints excluded: chain D residue  322 THR
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  173 VAL
Chi-restraints excluded: chain C residue  230 THR
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  192 ASN
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  309 THR
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  240 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 3 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9980
   chunk 45 optimal weight:    5.9990
   chunk 2 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9980
   chunk 67 optimal weight:   10.0000
   chunk 15 optimal weight:   10.0000
   chunk 60 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0010
   chunk 6 optimal weight:    9.9990
   overall best weight:    0.7588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.063713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.048588 restraints weight = 23616.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.050417 restraints weight = 11352.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.051651 restraints weight = 7264.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.4136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6414  Z= 0.108
  Angle     :  0.566   5.845   8740  Z= 0.298
  Chirality :  0.045   0.137   1021
  Planarity :  0.003   0.025   1123
  Dihedral  :  4.522  16.300    860
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 16.88 %
    Favored  : 80.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.31), residues: 786
  helix: -0.42 (1.38), residues: 18
  sheet:  0.02 (0.30), residues: 293
  loop : -0.05 (0.31), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 296 
 HIS   0.002   0.001   HIS B 218 
 PHE   0.013   0.002   PHE C 172 
 TYR   0.016   0.001   TYR C 320 
 ARG   0.006   0.001   ARG B 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03154 (  196)
  hydrogen bonds       : angle       5.80210 (  489)
  covalent geometry    : bond        0.00244 ( 6414)
  covalent geometry    : angle       0.56630 ( 8740)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 123
  time to evaluate  : 0.740 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  185 SER cc_start: 0.9226 (OUTLIER) cc_final: 0.8854 (m)
REVERT: D  208 GLN cc_start: 0.8261 (tm-30) cc_final: 0.8036 (tm-30)
REVERT: D  293 TYR cc_start: 0.6267 (t80) cc_final: 0.5953 (t80)
REVERT: D  301 PHE cc_start: 0.9242 (p90) cc_final: 0.8943 (p90)
REVERT: C  157 LYS cc_start: 0.8930 (mtpt) cc_final: 0.8552 (mtpp)
REVERT: C  182 PHE cc_start: 0.9317 (t80) cc_final: 0.9070 (t80)
REVERT: C  193 PHE cc_start: 0.8973 (p90) cc_final: 0.8769 (p90)
REVERT: C  200 ASP cc_start: 0.8585 (p0) cc_final: 0.8368 (p0)
REVERT: C  233 LYS cc_start: 0.9187 (tttt) cc_final: 0.8936 (tttp)
REVERT: C  300 ASP cc_start: 0.9053 (t0) cc_final: 0.8572 (t0)
REVERT: C  323 GLU cc_start: 0.8977 (tp30) cc_final: 0.8602 (tp30)
REVERT: A  184 MET cc_start: 0.8535 (tmm) cc_final: 0.8103 (tmm)
REVERT: A  236 MET cc_start: 0.9124 (mmp) cc_final: 0.8377 (mmt)
REVERT: A  305 GLN cc_start: 0.8974 (pm20) cc_final: 0.8768 (pm20)
REVERT: B  164 LYS cc_start: 0.8846 (ttmt) cc_final: 0.8631 (ttmt)
REVERT: B  246 ASP cc_start: 0.8596 (t0) cc_final: 0.8061 (t0)
REVERT: B  256 TYR cc_start: 0.8985 (m-80) cc_final: 0.8681 (m-80)
REVERT: B  319 TYR cc_start: 0.8385 (m-80) cc_final: 0.7880 (m-80)
  outliers start: 22
  outliers final: 15
  residues processed: 142
  average time/residue: 0.1810
  time to fit residues: 33.7742
Evaluate side-chains
  127 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  185 SER
Chi-restraints excluded: chain D residue  220 ILE
Chi-restraints excluded: chain D residue  322 THR
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  192 ASN
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  250 GLU
Chi-restraints excluded: chain B residue  259 CYS
Chi-restraints excluded: chain B residue  300 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 69 optimal weight:    0.1980
   chunk 20 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0970
   chunk 55 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 43 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 37 optimal weight:    7.9990
   overall best weight:    0.6584

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

Flipped N/Q/H residues before XYZ refinement:
D 217 ASN
D 307 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.064408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.049439 restraints weight = 23156.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.051234 restraints weight = 11261.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.052458 restraints weight = 7242.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.4393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6414  Z= 0.104
  Angle     :  0.550   7.887   8740  Z= 0.288
  Chirality :  0.044   0.133   1021
  Planarity :  0.003   0.034   1123
  Dihedral  :  4.302  16.646    860
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 19.69 %
    Favored  : 77.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.31), residues: 786
  helix: -0.13 (1.42), residues: 18
  sheet: -0.12 (0.29), residues: 314
  loop :  0.01 (0.32), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 296 
 HIS   0.002   0.000   HIS B 218 
 PHE   0.013   0.001   PHE C 172 
 TYR   0.012   0.001   TYR A 260 
 ARG   0.006   0.001   ARG B 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02962 (  196)
  hydrogen bonds       : angle       5.65221 (  489)
  covalent geometry    : bond        0.00236 ( 6414)
  covalent geometry    : angle       0.54993 ( 8740)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  172 TYR cc_start: 0.8274 (m-80) cc_final: 0.8017 (m-80)
REVERT: D  208 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7989 (tm-30)
REVERT: D  301 PHE cc_start: 0.9228 (p90) cc_final: 0.8905 (p90)
REVERT: C  157 LYS cc_start: 0.8965 (mtpt) cc_final: 0.8545 (mtpp)
REVERT: C  182 PHE cc_start: 0.9283 (t80) cc_final: 0.9039 (t80)
REVERT: C  196 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8086 (mt-10)
REVERT: C  300 ASP cc_start: 0.9049 (t0) cc_final: 0.8544 (t0)
REVERT: C  323 GLU cc_start: 0.8924 (tp30) cc_final: 0.8447 (tp30)
REVERT: A  184 MET cc_start: 0.8571 (tmm) cc_final: 0.8271 (tmm)
REVERT: A  236 MET cc_start: 0.9197 (mmp) cc_final: 0.8574 (mmt)
REVERT: A  320 TYR cc_start: 0.8916 (p90) cc_final: 0.8483 (p90)
REVERT: A  323 GLU cc_start: 0.9197 (tp30) cc_final: 0.8736 (tp30)
REVERT: B  164 LYS cc_start: 0.8796 (ttmt) cc_final: 0.8480 (ttmt)
REVERT: B  196 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7561 (mt-10)
REVERT: B  246 ASP cc_start: 0.8647 (t0) cc_final: 0.8075 (t0)
REVERT: B  256 TYR cc_start: 0.8915 (m-80) cc_final: 0.8624 (m-80)
REVERT: B  323 GLU cc_start: 0.8818 (tp30) cc_final: 0.8496 (tp30)
  outliers start: 19
  outliers final: 16
  residues processed: 134
  average time/residue: 0.1809
  time to fit residues: 31.7659
Evaluate side-chains
  128 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  220 ILE
Chi-restraints excluded: chain D residue  322 THR
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  196 GLU
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  192 ASN
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  250 GLU
Chi-restraints excluded: chain B residue  259 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 34 optimal weight:    4.9990
   chunk 47 optimal weight:    4.9990
   chunk 16 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9980
   chunk 37 optimal weight:    6.9990
   chunk 69 optimal weight:    0.8980
   chunk 27 optimal weight:    5.9990
   chunk 13 optimal weight:    6.9990
   chunk 11 optimal weight:    9.9990
   chunk 68 optimal weight:    0.8980
   overall best weight:    2.5584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.062229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.047794 restraints weight = 23742.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.049556 restraints weight = 11881.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.050751 restraints weight = 7598.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.4413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6414  Z= 0.202
  Angle     :  0.593   6.057   8740  Z= 0.310
  Chirality :  0.044   0.139   1021
  Planarity :  0.003   0.027   1123
  Dihedral  :  4.578  16.859    860
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 20.39 %
    Favored  : 76.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.31), residues: 786
  helix: -0.07 (1.38), residues: 18
  sheet: -0.12 (0.28), residues: 313
  loop :  0.02 (0.32), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 296 
 HIS   0.003   0.001   HIS D 312 
 PHE   0.018   0.002   PHE B 172 
 TYR   0.027   0.002   TYR D 293 
 ARG   0.007   0.001   ARG B 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03282 (  196)
  hydrogen bonds       : angle       5.75662 (  489)
  covalent geometry    : bond        0.00443 ( 6414)
  covalent geometry    : angle       0.59334 ( 8740)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 109
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  172 TYR cc_start: 0.8314 (m-80) cc_final: 0.8002 (m-80)
REVERT: D  185 SER cc_start: 0.9209 (OUTLIER) cc_final: 0.8876 (m)
REVERT: D  301 PHE cc_start: 0.9310 (p90) cc_final: 0.8780 (p90)
REVERT: C  157 LYS cc_start: 0.9020 (mtpt) cc_final: 0.8634 (mtpp)
REVERT: C  193 PHE cc_start: 0.9019 (p90) cc_final: 0.8803 (p90)
REVERT: C  196 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8185 (mt-10)
REVERT: C  233 LYS cc_start: 0.9304 (tttt) cc_final: 0.9068 (tttp)
REVERT: C  250 GLU cc_start: 0.8889 (pm20) cc_final: 0.8392 (pm20)
REVERT: C  300 ASP cc_start: 0.9021 (t0) cc_final: 0.8536 (t0)
REVERT: C  323 GLU cc_start: 0.8888 (tp30) cc_final: 0.8434 (tp30)
REVERT: A  184 MET cc_start: 0.8503 (tmm) cc_final: 0.7939 (tmm)
REVERT: A  236 MET cc_start: 0.9131 (mmp) cc_final: 0.8863 (mmp)
REVERT: A  319 TYR cc_start: 0.8481 (m-80) cc_final: 0.8193 (m-80)
REVERT: B  164 LYS cc_start: 0.8773 (ttmt) cc_final: 0.8506 (ttmt)
REVERT: B  246 ASP cc_start: 0.8788 (t0) cc_final: 0.8241 (t0)
REVERT: B  256 TYR cc_start: 0.8967 (m-80) cc_final: 0.8477 (m-80)
REVERT: B  323 GLU cc_start: 0.8792 (tp30) cc_final: 0.8503 (tp30)
  outliers start: 23
  outliers final: 18
  residues processed: 128
  average time/residue: 0.1829
  time to fit residues: 30.8397
Evaluate side-chains
  128 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  185 SER
Chi-restraints excluded: chain D residue  220 ILE
Chi-restraints excluded: chain D residue  272 PHE
Chi-restraints excluded: chain D residue  322 THR
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  173 VAL
Chi-restraints excluded: chain C residue  196 GLU
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  309 THR
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  250 GLU
Chi-restraints excluded: chain B residue  259 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   chunk 74 optimal weight:    6.9990
   chunk 25 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 8 optimal weight:    7.9990
   chunk 70 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 48 optimal weight:    9.9990
   chunk 75 optimal weight:    6.9990
   overall best weight:    1.9988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.061867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.046983 restraints weight = 23644.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.048723 restraints weight = 11533.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.049918 restraints weight = 7426.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.4522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6414  Z= 0.166
  Angle     :  0.586   6.048   8740  Z= 0.306
  Chirality :  0.044   0.134   1021
  Planarity :  0.003   0.027   1123
  Dihedral  :  4.516  16.018    860
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 20.82 %
    Favored  : 76.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.31), residues: 786
  helix: -0.04 (1.41), residues: 18
  sheet: -0.13 (0.28), residues: 313
  loop : -0.01 (0.32), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 296 
 HIS   0.002   0.001   HIS D 312 
 PHE   0.016   0.002   PHE B 172 
 TYR   0.027   0.002   TYR D 293 
 ARG   0.008   0.001   ARG B 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03205 (  196)
  hydrogen bonds       : angle       5.72037 (  489)
  covalent geometry    : bond        0.00370 ( 6414)
  covalent geometry    : angle       0.58553 ( 8740)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 0.718 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  172 TYR cc_start: 0.8329 (m-80) cc_final: 0.8021 (m-80)
REVERT: D  301 PHE cc_start: 0.9308 (p90) cc_final: 0.8759 (p90)
REVERT: C  157 LYS cc_start: 0.8999 (mtpt) cc_final: 0.8606 (mtpp)
REVERT: C  193 PHE cc_start: 0.9002 (p90) cc_final: 0.8765 (p90)
REVERT: C  196 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8165 (mt-10)
REVERT: C  250 GLU cc_start: 0.8988 (pm20) cc_final: 0.8541 (pm20)
REVERT: C  300 ASP cc_start: 0.9020 (t0) cc_final: 0.8531 (t0)
REVERT: C  323 GLU cc_start: 0.8969 (tp30) cc_final: 0.8502 (tp30)
REVERT: A  184 MET cc_start: 0.8609 (tmm) cc_final: 0.8306 (tmm)
REVERT: A  236 MET cc_start: 0.9141 (mmp) cc_final: 0.8866 (mmp)
REVERT: B  196 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7668 (mt-10)
REVERT: B  246 ASP cc_start: 0.8833 (t0) cc_final: 0.8284 (t0)
REVERT: B  256 TYR cc_start: 0.8957 (m-80) cc_final: 0.8473 (m-80)
REVERT: B  319 TYR cc_start: 0.8420 (m-80) cc_final: 0.7949 (m-80)
REVERT: B  323 GLU cc_start: 0.8862 (tp30) cc_final: 0.8576 (tp30)
  outliers start: 22
  outliers final: 18
  residues processed: 130
  average time/residue: 0.1753
  time to fit residues: 30.0349
Evaluate side-chains
  128 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  220 ILE
Chi-restraints excluded: chain D residue  272 PHE
Chi-restraints excluded: chain D residue  322 THR
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  196 GLU
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  192 ASN
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  250 GLU
Chi-restraints excluded: chain B residue  259 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 69 optimal weight:    1.9990
   chunk 3 optimal weight:   10.0000
   chunk 61 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 53 optimal weight:    6.9990
   chunk 76 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 73 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    1.7386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.062200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.047217 restraints weight = 23732.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.048968 restraints weight = 11640.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.050174 restraints weight = 7521.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.4624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6414  Z= 0.153
  Angle     :  0.596   6.022   8740  Z= 0.311
  Chirality :  0.044   0.135   1021
  Planarity :  0.003   0.029   1123
  Dihedral  :  4.495  15.430    860
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 20.96 %
    Favored  : 76.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.31), residues: 786
  helix: -1.84 (0.89), residues: 36
  sheet: -0.15 (0.28), residues: 315
  loop : -0.18 (0.33), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 296 
 HIS   0.002   0.001   HIS B 218 
 PHE   0.015   0.002   PHE B 172 
 TYR   0.034   0.002   TYR D 293 
 ARG   0.008   0.001   ARG B 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03123 (  196)
  hydrogen bonds       : angle       5.72607 (  489)
  covalent geometry    : bond        0.00345 ( 6414)
  covalent geometry    : angle       0.59650 ( 8740)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.801 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  172 TYR cc_start: 0.8317 (m-80) cc_final: 0.8078 (m-80)
REVERT: D  185 SER cc_start: 0.9199 (OUTLIER) cc_final: 0.8856 (m)
REVERT: D  301 PHE cc_start: 0.9315 (p90) cc_final: 0.8794 (p90)
REVERT: C  157 LYS cc_start: 0.9074 (mtpt) cc_final: 0.8702 (mtpp)
REVERT: C  193 PHE cc_start: 0.8984 (p90) cc_final: 0.8763 (p90)
REVERT: C  196 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8163 (mt-10)
REVERT: C  250 GLU cc_start: 0.8956 (pm20) cc_final: 0.8367 (pm20)
REVERT: C  300 ASP cc_start: 0.8981 (t0) cc_final: 0.8506 (t0)
REVERT: C  323 GLU cc_start: 0.8927 (tp30) cc_final: 0.8553 (mm-30)
REVERT: A  134 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9100 (mp)
REVERT: A  184 MET cc_start: 0.8609 (tmm) cc_final: 0.8293 (tmm)
REVERT: A  236 MET cc_start: 0.9140 (mmp) cc_final: 0.8871 (mmp)
REVERT: A  323 GLU cc_start: 0.9228 (tp30) cc_final: 0.8773 (tp30)
REVERT: B  164 LYS cc_start: 0.8754 (ttmt) cc_final: 0.8484 (tppt)
REVERT: B  246 ASP cc_start: 0.8884 (t0) cc_final: 0.8459 (t0)
REVERT: B  252 GLU cc_start: 0.8694 (pt0) cc_final: 0.8136 (pt0)
REVERT: B  256 TYR cc_start: 0.8926 (m-80) cc_final: 0.8449 (m-80)
REVERT: B  323 GLU cc_start: 0.8867 (tp30) cc_final: 0.8588 (tp30)
  outliers start: 20
  outliers final: 16
  residues processed: 128
  average time/residue: 0.1885
  time to fit residues: 31.6612
Evaluate side-chains
  127 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  185 SER
Chi-restraints excluded: chain D residue  220 ILE
Chi-restraints excluded: chain D residue  272 PHE
Chi-restraints excluded: chain D residue  322 THR
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  196 GLU
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  192 ASN
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  250 GLU
Chi-restraints excluded: chain B residue  259 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 64 optimal weight:    7.9990
   chunk 72 optimal weight:    0.8980
   chunk 41 optimal weight:   10.0000
   chunk 51 optimal weight:    6.9990
   chunk 27 optimal weight:    0.0170
   chunk 32 optimal weight:    6.9990
   chunk 16 optimal weight:    0.0670
   chunk 37 optimal weight:    0.0570
   chunk 60 optimal weight:   10.0000
   chunk 13 optimal weight:    9.9990
   overall best weight:    1.6076

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.062568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.047592 restraints weight = 23909.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.049372 restraints weight = 11813.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.050573 restraints weight = 7630.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.4766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6414  Z= 0.150
  Angle     :  0.614   6.209   8740  Z= 0.321
  Chirality :  0.044   0.134   1021
  Planarity :  0.003   0.031   1123
  Dihedral  :  4.508  15.219    860
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 21.94 %
    Favored  : 75.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.31), residues: 786
  helix: -2.17 (0.69), residues: 54
  sheet: -0.17 (0.28), residues: 315
  loop : -0.15 (0.34), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 296 
 HIS   0.002   0.001   HIS B 218 
 PHE   0.015   0.002   PHE B 172 
 TYR   0.033   0.002   TYR D 293 
 ARG   0.009   0.001   ARG B 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03154 (  196)
  hydrogen bonds       : angle       5.69459 (  489)
  covalent geometry    : bond        0.00339 ( 6414)
  covalent geometry    : angle       0.61351 ( 8740)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.764 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  185 SER cc_start: 0.9199 (OUTLIER) cc_final: 0.8859 (m)
REVERT: D  301 PHE cc_start: 0.9281 (p90) cc_final: 0.8757 (p90)
REVERT: C  157 LYS cc_start: 0.9091 (mtpt) cc_final: 0.8729 (mtpp)
REVERT: C  193 PHE cc_start: 0.8987 (p90) cc_final: 0.8786 (p90)
REVERT: C  196 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8159 (mt-10)
REVERT: C  250 GLU cc_start: 0.8899 (pm20) cc_final: 0.8377 (pm20)
REVERT: C  300 ASP cc_start: 0.8971 (t0) cc_final: 0.8536 (t0)
REVERT: C  324 ASP cc_start: 0.7403 (p0) cc_final: 0.7120 (p0)
REVERT: A  134 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9093 (mp)
REVERT: A  184 MET cc_start: 0.8570 (tmm) cc_final: 0.8163 (tmm)
REVERT: A  236 MET cc_start: 0.9107 (mmp) cc_final: 0.8846 (mmp)
REVERT: A  323 GLU cc_start: 0.9193 (tp30) cc_final: 0.8799 (tp30)
REVERT: B  164 LYS cc_start: 0.8761 (ttmt) cc_final: 0.8523 (ttmt)
REVERT: B  246 ASP cc_start: 0.8914 (t0) cc_final: 0.8408 (t0)
REVERT: B  256 TYR cc_start: 0.8905 (m-80) cc_final: 0.8433 (m-80)
REVERT: B  319 TYR cc_start: 0.8520 (m-80) cc_final: 0.8148 (m-80)
REVERT: B  323 GLU cc_start: 0.8869 (tp30) cc_final: 0.8605 (tp30)
  outliers start: 19
  outliers final: 15
  residues processed: 128
  average time/residue: 0.1884
  time to fit residues: 31.5677
Evaluate side-chains
  127 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  185 SER
Chi-restraints excluded: chain D residue  220 ILE
Chi-restraints excluded: chain D residue  272 PHE
Chi-restraints excluded: chain D residue  322 THR
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  196 GLU
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  192 ASN
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  250 GLU
Chi-restraints excluded: chain B residue  259 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 66 optimal weight:    0.6980
   chunk 54 optimal weight:    2.9990
   chunk 16 optimal weight:    9.9990
   chunk 63 optimal weight:    0.5980
   chunk 39 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9980
   chunk 71 optimal weight:    0.1980
   chunk 51 optimal weight:    5.9990
   chunk 69 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
D 225 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.065640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.050344 restraints weight = 23203.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.052215 restraints weight = 10940.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.053540 restraints weight = 6940.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.4931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6414  Z= 0.115
  Angle     :  0.633   7.536   8740  Z= 0.327
  Chirality :  0.044   0.146   1021
  Planarity :  0.004   0.042   1123
  Dihedral  :  4.381  15.848    860
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 22.36 %
    Favored  : 75.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.31), residues: 786
  helix: -1.69 (0.92), residues: 36
  sheet: -0.10 (0.28), residues: 314
  loop : -0.20 (0.33), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 296 
 HIS   0.003   0.001   HIS B 218 
 PHE   0.016   0.002   PHE C 182 
 TYR   0.021   0.001   TYR D 293 
 ARG   0.010   0.001   ARG B 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02947 (  196)
  hydrogen bonds       : angle       5.59996 (  489)
  covalent geometry    : bond        0.00273 ( 6414)
  covalent geometry    : angle       0.63278 ( 8740)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  185 SER cc_start: 0.9186 (OUTLIER) cc_final: 0.8792 (m)
REVERT: D  208 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7803 (tm-30)
REVERT: D  301 PHE cc_start: 0.9336 (p90) cc_final: 0.8833 (p90)
REVERT: C  157 LYS cc_start: 0.9071 (mtpt) cc_final: 0.8635 (mtpp)
REVERT: C  196 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8083 (mt-10)
REVERT: C  300 ASP cc_start: 0.9010 (t0) cc_final: 0.8706 (t0)
REVERT: C  323 GLU cc_start: 0.8779 (mm-30) cc_final: 0.7948 (mm-30)
REVERT: C  324 ASP cc_start: 0.7757 (p0) cc_final: 0.7068 (p0)
REVERT: A  134 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9012 (mp)
REVERT: A  184 MET cc_start: 0.8728 (tmm) cc_final: 0.8374 (tmm)
REVERT: A  191 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8478 (mm)
REVERT: A  236 MET cc_start: 0.9160 (mmp) cc_final: 0.8374 (mmt)
REVERT: A  319 TYR cc_start: 0.8086 (m-80) cc_final: 0.7730 (m-80)
REVERT: A  323 GLU cc_start: 0.9231 (tp30) cc_final: 0.8754 (tp30)
REVERT: B  164 LYS cc_start: 0.8624 (ttmt) cc_final: 0.8395 (ttmt)
REVERT: B  196 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7754 (mt-10)
REVERT: B  246 ASP cc_start: 0.8864 (t0) cc_final: 0.8320 (t0)
REVERT: B  256 TYR cc_start: 0.8916 (m-80) cc_final: 0.8425 (m-80)
REVERT: B  276 MET cc_start: 0.8089 (ttm) cc_final: 0.7701 (ttm)
REVERT: B  320 TYR cc_start: 0.8948 (p90) cc_final: 0.8741 (p90)
REVERT: B  323 GLU cc_start: 0.8958 (tp30) cc_final: 0.8688 (tp30)
  outliers start: 18
  outliers final: 13
  residues processed: 136
  average time/residue: 0.1912
  time to fit residues: 34.0060
Evaluate side-chains
  131 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  185 SER
Chi-restraints excluded: chain D residue  220 ILE
Chi-restraints excluded: chain D residue  322 THR
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  196 GLU
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  192 ASN
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  259 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 15 optimal weight:   10.0000
   chunk 34 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 64 optimal weight:    9.9990
   chunk 65 optimal weight:    2.9990
   chunk 68 optimal weight:    0.2980
   chunk 9 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   overall best weight:    1.5784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.064182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.048880 restraints weight = 23538.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.050754 restraints weight = 11121.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.052062 restraints weight = 7062.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.4930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6414  Z= 0.151
  Angle     :  0.628   6.703   8740  Z= 0.328
  Chirality :  0.044   0.161   1021
  Planarity :  0.003   0.029   1123
  Dihedral  :  4.466  14.912    860
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 22.50 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.31), residues: 786
  helix: -2.13 (0.69), residues: 54
  sheet: -0.12 (0.28), residues: 315
  loop : -0.19 (0.33), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 296 
 HIS   0.002   0.001   HIS B 218 
 PHE   0.029   0.002   PHE D 247 
 TYR   0.024   0.002   TYR D 293 
 ARG   0.009   0.001   ARG B 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03118 (  196)
  hydrogen bonds       : angle       5.62528 (  489)
  covalent geometry    : bond        0.00346 ( 6414)
  covalent geometry    : angle       0.62789 ( 8740)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2225.69 seconds
wall clock time: 39 minutes 55.26 seconds (2395.26 seconds total)