Starting phenix.real_space_refine
on Thu Jun  5 12:41:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qjy_18454/06_2025/8qjy_18454.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qjy_18454/06_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_18454/06_2025/8qjy_18454.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qjy_18454/06_2025/8qjy_18454.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qjy_18454/06_2025/8qjy_18454.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qjy_18454/06_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-5710/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: 4.17, per 1000 atoms: 0.66
  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: 1.48
  Conformation dependent library (CDL) restraints added in 981.8 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: 0.85
  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: 1.57

  Time building geometry restraints manager: 1.72 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:             0.210
  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:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     17.810
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.860
-------------------------------------------------------------------------------
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  : 0.955 
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: 0.2544
  time to fit residues: 66.3500
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  : 0.750 
-------------------------------------------------------------------------------
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 = 33)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.050512 restraints weight = 22471.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.052385 restraints weight = 10652.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.053644 restraints weight = 6728.149|
|-----------------------------------------------------------------------------|
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  : 0.689 
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: 0.7770 (tm-30) cc_final: 0.7415 (tm-30)
REVERT: D  293 TYR cc_start: 0.6107 (t80) cc_final: 0.5683 (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: 0.9054 (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: 0.7930 (m-80) cc_final: 0.7584 (m-80)
REVERT: C  323 GLU cc_start: 0.8831 (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: 0.8858 (mm110) cc_final: 0.8468 (mm110)
REVERT: A  236 MET cc_start: 0.9257 (mmp) cc_final: 0.9041 (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: 0.8497 (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: 0.2178
  time to fit residues: 42.9080
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  : 0.730 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 4 optimal weight:    2.9990
   chunk 10 optimal weight:    9.9990
   chunk 54 optimal weight:   10.0000
   chunk 75 optimal weight:    8.9990
   chunk 72 optimal weight:    5.9990
   chunk 74 optimal weight:    0.7980
   chunk 35 optimal weight:   10.0000
   chunk 50 optimal weight:    3.9990
   chunk 6 optimal weight:    9.9990
   chunk 45 optimal weight:   10.0000
   overall best weight:    4.3588

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.060207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.045261 restraints weight = 24314.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.046941 restraints weight = 12071.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.048092 restraints weight = 7893.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8520
moved from start:          0.3901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.075   6414  Z= 0.321
  Angle     :  0.668   6.783   8740  Z= 0.356
  Chirality :  0.046   0.135   1021
  Planarity :  0.004   0.036   1123
  Dihedral  :  5.144  17.271    860
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 16.60 %
    Favored  : 79.18 %
  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: -0.26 (0.32), residues: 786
  helix: -1.12 (1.22), residues: 18
  sheet: -0.18 (0.29), residues: 298
  loop : -0.01 (0.32), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 296 
 HIS   0.009   0.002   HIS D 183 
 PHE   0.019   0.002   PHE B 172 
 TYR   0.020   0.002   TYR A 260 
 ARG   0.007   0.001   ARG B 291 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03935 (  196)
  hydrogen bonds       : angle       6.20543 (  489)
  covalent geometry    : bond        0.00703 ( 6414)
  covalent geometry    : angle       0.66840 ( 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: 30
    poor density    : 114
  time to evaluate  : 0.679 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  130 MET cc_start: 0.8823 (ppp) cc_final: 0.8609 (ppp)
REVERT: D  185 SER cc_start: 0.9199 (OUTLIER) cc_final: 0.8917 (m)
REVERT: D  293 TYR cc_start: 0.6081 (t80) cc_final: 0.5618 (t80)
REVERT: D  301 PHE cc_start: 0.9279 (p90) cc_final: 0.8792 (p90)
REVERT: C  157 LYS cc_start: 0.9089 (mtpt) cc_final: 0.8731 (mtpp)
REVERT: C  182 PHE cc_start: 0.9510 (t80) cc_final: 0.9289 (t80)
REVERT: C  193 PHE cc_start: 0.9164 (p90) cc_final: 0.8921 (p90)
REVERT: C  200 ASP cc_start: 0.8795 (p0) cc_final: 0.8562 (p0)
REVERT: C  300 ASP cc_start: 0.9008 (t0) cc_final: 0.8658 (t0)
REVERT: C  323 GLU cc_start: 0.8952 (tp30) cc_final: 0.8583 (tp30)
REVERT: A  184 MET cc_start: 0.8383 (tmm) cc_final: 0.8006 (tmm)
REVERT: A  319 TYR cc_start: 0.8707 (m-80) cc_final: 0.8466 (m-80)
REVERT: B  164 LYS cc_start: 0.8741 (ttmt) cc_final: 0.8535 (ttmm)
REVERT: B  246 ASP cc_start: 0.8717 (t0) cc_final: 0.8335 (t0)
  outliers start: 30
  outliers final: 19
  residues processed: 135
  average time/residue: 0.1833
  time to fit residues: 32.7601
Evaluate side-chains
  129 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
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  163 VAL
Chi-restraints excluded: chain A residue  164 LYS
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:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   chunk 2 optimal weight:    9.9990
   chunk 5 optimal weight:    4.9990
   chunk 67 optimal weight:   10.0000
   chunk 15 optimal weight:   10.0000
   chunk 60 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0870
   chunk 6 optimal weight:    9.9990
   overall best weight:    2.4166

-------------------------------------------------------------------------------
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
A 222 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.061102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.046134 restraints weight = 24199.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.047917 restraints weight = 11847.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.049108 restraints weight = 7604.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.4122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6414  Z= 0.190
  Angle     :  0.591   5.934   8740  Z= 0.314
  Chirality :  0.045   0.135   1021
  Planarity :  0.004   0.027   1123
  Dihedral  :  4.858  16.085    860
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 17.86 %
    Favored  : 78.48 %
  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: -0.23 (0.31), residues: 786
  helix: -0.76 (1.30), residues: 18
  sheet: -0.15 (0.29), residues: 297
  loop : -0.01 (0.32), residues: 471

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   0.015   0.002   PHE B 172 
 TYR   0.017   0.002   TYR A 260 
 ARG   0.006   0.001   ARG B 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03461 (  196)
  hydrogen bonds       : angle       5.98207 (  489)
  covalent geometry    : bond        0.00416 ( 6414)
  covalent geometry    : angle       0.59081 ( 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
  143 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 117
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  185 SER cc_start: 0.9216 (OUTLIER) cc_final: 0.8878 (m)
REVERT: D  293 TYR cc_start: 0.5935 (t80) cc_final: 0.5596 (t80)
REVERT: D  301 PHE cc_start: 0.9289 (p90) cc_final: 0.8801 (p90)
REVERT: C  157 LYS cc_start: 0.9034 (mtpt) cc_final: 0.8632 (mtpp)
REVERT: C  193 PHE cc_start: 0.9092 (p90) cc_final: 0.8858 (p90)
REVERT: C  200 ASP cc_start: 0.8715 (p0) cc_final: 0.8490 (p0)
REVERT: C  222 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7988 (mm-40)
REVERT: C  300 ASP cc_start: 0.9062 (t0) cc_final: 0.8621 (t0)
REVERT: C  323 GLU cc_start: 0.8962 (tp30) cc_final: 0.8577 (tp30)
REVERT: A  184 MET cc_start: 0.8495 (tmm) cc_final: 0.8050 (tmm)
REVERT: A  236 MET cc_start: 0.9051 (mmp) cc_final: 0.8826 (mmp)
REVERT: B  164 LYS cc_start: 0.8848 (ttmt) cc_final: 0.8629 (ttmt)
REVERT: B  246 ASP cc_start: 0.8722 (t0) cc_final: 0.8246 (t0)
REVERT: B  319 TYR cc_start: 0.8431 (m-80) cc_final: 0.7992 (m-80)
REVERT: B  323 GLU cc_start: 0.8794 (tp30) cc_final: 0.8451 (tp30)
  outliers start: 26
  outliers final: 20
  residues processed: 136
  average time/residue: 0.1930
  time to fit residues: 34.6933
Evaluate side-chains
  130 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 109
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
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  167 ASP
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  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  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  240 THR
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:    8.9990
   chunk 69 optimal weight:    0.0770
   chunk 20 optimal weight:    0.8980
   chunk 44 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 43 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 45 optimal weight:    7.9990
   chunk 37 optimal weight:    6.9990
   overall best weight:    1.0940

-------------------------------------------------------------------------------
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 = 0.062894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.047792 restraints weight = 23494.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.049568 restraints weight = 11532.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.050733 restraints weight = 7474.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.4343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6414  Z= 0.120
  Angle     :  0.557   5.156   8740  Z= 0.295
  Chirality :  0.044   0.132   1021
  Planarity :  0.003   0.034   1123
  Dihedral  :  4.554  17.474    860
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 20.11 %
    Favored  : 76.79 %
  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: -0.26 (1.41), residues: 18
  sheet: -0.10 (0.29), residues: 299
  loop : -0.00 (0.32), residues: 469

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   0.014   0.001   TYR A 260 
 ARG   0.006   0.001   ARG B 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03102 (  196)
  hydrogen bonds       : angle       5.77223 (  489)
  covalent geometry    : bond        0.00271 ( 6414)
  covalent geometry    : angle       0.55651 ( 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
  141 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  172 TYR cc_start: 0.8337 (m-80) cc_final: 0.8097 (m-80)
REVERT: D  185 SER cc_start: 0.9238 (OUTLIER) cc_final: 0.8890 (m)
REVERT: D  293 TYR cc_start: 0.6242 (t80) cc_final: 0.5963 (t80)
REVERT: D  299 LEU cc_start: 0.8783 (mt) cc_final: 0.8517 (mp)
REVERT: D  301 PHE cc_start: 0.9272 (p90) cc_final: 0.8811 (p90)
REVERT: C  157 LYS cc_start: 0.8990 (mtpt) cc_final: 0.8640 (mtpp)
REVERT: C  182 PHE cc_start: 0.9254 (t80) cc_final: 0.8893 (t80)
REVERT: C  196 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8058 (mt-10)
REVERT: C  233 LYS cc_start: 0.9275 (tttt) cc_final: 0.9047 (tttp)
REVERT: C  250 GLU cc_start: 0.8860 (pm20) cc_final: 0.8279 (pm20)
REVERT: C  300 ASP cc_start: 0.9074 (t0) cc_final: 0.8593 (t0)
REVERT: C  323 GLU cc_start: 0.8916 (tp30) cc_final: 0.8512 (tp30)
REVERT: A  184 MET cc_start: 0.8516 (tmm) cc_final: 0.8291 (tmm)
REVERT: A  236 MET cc_start: 0.9107 (mmp) cc_final: 0.8420 (mmt)
REVERT: A  320 TYR cc_start: 0.9039 (p90) cc_final: 0.8570 (p90)
REVERT: A  323 GLU cc_start: 0.9225 (tp30) cc_final: 0.8639 (tp30)
REVERT: B  164 LYS cc_start: 0.8833 (ttmt) cc_final: 0.8558 (ttmt)
REVERT: B  246 ASP cc_start: 0.8734 (t0) cc_final: 0.8228 (t0)
REVERT: B  256 TYR cc_start: 0.9008 (m-80) cc_final: 0.8553 (m-80)
REVERT: B  276 MET cc_start: 0.7929 (mtm) cc_final: 0.7717 (ttm)
REVERT: B  279 ARG cc_start: 0.8604 (tmm-80) cc_final: 0.7665 (tmm-80)
REVERT: B  303 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7424 (mt-10)
REVERT: B  323 GLU cc_start: 0.8777 (tp30) cc_final: 0.8400 (tp30)
  outliers start: 22
  outliers final: 15
  residues processed: 138
  average time/residue: 0.1865
  time to fit residues: 33.8176
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  : 0.711 
-------------------------------------------------------------------------------
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 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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 34 optimal weight:    8.9990
   chunk 47 optimal weight:    1.9990
   chunk 16 optimal weight:    7.9990
   chunk 44 optimal weight:    0.5980
   chunk 37 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 13 optimal weight:    9.9990
   chunk 11 optimal weight:    6.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
C 231 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.062308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.047408 restraints weight = 23445.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.049141 restraints weight = 11557.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.050312 restraints weight = 7517.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.4457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6414  Z= 0.151
  Angle     :  0.572   7.538   8740  Z= 0.301
  Chirality :  0.044   0.136   1021
  Planarity :  0.003   0.026   1123
  Dihedral  :  4.506  16.752    860
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 20.11 %
    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: -0.25 (0.31), residues: 786
  helix: -0.05 (1.41), residues: 18
  sheet: -0.18 (0.28), residues: 315
  loop : -0.05 (0.32), residues: 453

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   0.018   0.002   PHE C 193 
 TYR   0.015   0.001   TYR A 260 
 ARG   0.007   0.001   ARG B 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03123 (  196)
  hydrogen bonds       : angle       5.76468 (  489)
  covalent geometry    : bond        0.00340 ( 6414)
  covalent geometry    : angle       0.57222 ( 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
  135 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 109
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  172 TYR cc_start: 0.8352 (m-80) cc_final: 0.8106 (m-80)
REVERT: D  185 SER cc_start: 0.9223 (OUTLIER) cc_final: 0.8871 (m)
REVERT: D  293 TYR cc_start: 0.6343 (t80) cc_final: 0.6015 (t80)
REVERT: D  299 LEU cc_start: 0.8888 (mt) cc_final: 0.8630 (mp)
REVERT: D  301 PHE cc_start: 0.9321 (p90) cc_final: 0.8832 (p90)
REVERT: C  157 LYS cc_start: 0.8996 (mtpt) cc_final: 0.8616 (mtpp)
REVERT: C  182 PHE cc_start: 0.9321 (t80) cc_final: 0.8952 (t80)
REVERT: C  196 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8183 (mt-10)
REVERT: C  300 ASP cc_start: 0.9021 (t0) cc_final: 0.8544 (t0)
REVERT: C  323 GLU cc_start: 0.8939 (tp30) cc_final: 0.8420 (tp30)
REVERT: A  184 MET cc_start: 0.8553 (tmm) cc_final: 0.8295 (tmm)
REVERT: A  236 MET cc_start: 0.9135 (mmp) cc_final: 0.8884 (mmp)
REVERT: A  319 TYR cc_start: 0.8606 (m-80) cc_final: 0.8169 (m-80)
REVERT: A  323 GLU cc_start: 0.9231 (tp30) cc_final: 0.8763 (tp30)
REVERT: B  196 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7525 (mt-10)
REVERT: B  246 ASP cc_start: 0.8785 (t0) cc_final: 0.8246 (t0)
REVERT: B  256 TYR cc_start: 0.9029 (m-80) cc_final: 0.8531 (m-80)
REVERT: B  303 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7409 (mt-10)
REVERT: B  323 GLU cc_start: 0.8756 (tp30) cc_final: 0.8401 (tp30)
  outliers start: 26
  outliers final: 22
  residues processed: 132
  average time/residue: 0.1799
  time to fit residues: 31.3501
Evaluate side-chains
  131 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 107
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
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  167 ASP
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  141 THR
Chi-restraints excluded: chain A residue  150 SER
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  309 THR
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  147 ILE
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:    0.9990
   chunk 49 optimal weight:    9.9990
   chunk 74 optimal weight:    6.9990
   chunk 25 optimal weight:    0.0970
   chunk 22 optimal weight:    8.9990
   chunk 8 optimal weight:   10.0000
   chunk 70 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 40 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 75 optimal weight:    6.9990
   overall best weight:    1.7984

-------------------------------------------------------------------------------
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 = 0.3315 r_free = 0.3315 target = 0.062075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.047305 restraints weight = 23804.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.049065 restraints weight = 11783.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.050268 restraints weight = 7617.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.4601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6414  Z= 0.157
  Angle     :  0.589   6.798   8740  Z= 0.310
  Chirality :  0.044   0.135   1021
  Planarity :  0.003   0.028   1123
  Dihedral  :  4.568  16.907    860
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 21.10 %
    Favored  : 74.96 %
  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 (0.31), residues: 786
  helix:  0.06 (1.43), residues: 18
  sheet: -0.13 (0.28), residues: 313
  loop : -0.04 (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 B 218 
 PHE   0.015   0.002   PHE B 172 
 TYR   0.016   0.001   TYR A 260 
 ARG   0.008   0.001   ARG B 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03092 (  196)
  hydrogen bonds       : angle       5.74976 (  489)
  covalent geometry    : bond        0.00352 ( 6414)
  covalent geometry    : angle       0.58914 ( 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
  140 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 112
  time to evaluate  : 0.740 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  172 TYR cc_start: 0.8340 (m-80) cc_final: 0.8005 (m-80)
REVERT: D  185 SER cc_start: 0.9217 (OUTLIER) cc_final: 0.8887 (m)
REVERT: D  293 TYR cc_start: 0.6328 (t80) cc_final: 0.6038 (t80)
REVERT: D  299 LEU cc_start: 0.8874 (mt) cc_final: 0.8605 (mp)
REVERT: D  301 PHE cc_start: 0.9305 (p90) cc_final: 0.8798 (p90)
REVERT: C  157 LYS cc_start: 0.9024 (mtpt) cc_final: 0.8673 (mtpp)
REVERT: C  182 PHE cc_start: 0.9299 (t80) cc_final: 0.8953 (t80)
REVERT: C  196 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8150 (mt-10)
REVERT: C  300 ASP cc_start: 0.9019 (t0) cc_final: 0.8553 (t0)
REVERT: C  323 GLU cc_start: 0.8909 (tp30) cc_final: 0.8495 (tp30)
REVERT: A  184 MET cc_start: 0.8578 (tmm) cc_final: 0.8276 (tmm)
REVERT: A  236 MET cc_start: 0.9113 (mmp) cc_final: 0.8851 (mmp)
REVERT: B  196 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7611 (mt-10)
REVERT: B  246 ASP cc_start: 0.8779 (t0) cc_final: 0.8239 (t0)
REVERT: B  256 TYR cc_start: 0.8995 (m-80) cc_final: 0.8507 (m-80)
REVERT: B  303 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7403 (mt-10)
REVERT: B  319 TYR cc_start: 0.8467 (m-80) cc_final: 0.8054 (m-80)
REVERT: B  323 GLU cc_start: 0.8741 (tp30) cc_final: 0.8259 (tp30)
  outliers start: 28
  outliers final: 22
  residues processed: 136
  average time/residue: 0.1897
  time to fit residues: 33.7304
Evaluate side-chains
  134 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
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  167 ASP
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  141 THR
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  173 VAL
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  147 ILE
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  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:    0.7980
   chunk 69 optimal weight:    0.9980
   chunk 3 optimal weight:   10.0000
   chunk 61 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   chunk 76 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3355 r_free = 0.3355 target = 0.063820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.048864 restraints weight = 23662.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.050686 restraints weight = 11671.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.051929 restraints weight = 7553.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.4746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6414  Z= 0.114
  Angle     :  0.600   9.166   8740  Z= 0.314
  Chirality :  0.044   0.144   1021
  Planarity :  0.003   0.037   1123
  Dihedral  :  4.406  16.841    860
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 21.52 %
    Favored  : 74.96 %
  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: -0.26 (0.31), residues: 786
  helix:  0.16 (1.45), residues: 18
  sheet: -0.12 (0.28), residues: 314
  loop : -0.11 (0.32), residues: 454

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   0.014   0.001   PHE C 172 
 TYR   0.015   0.001   TYR C 320 
 ARG   0.008   0.001   ARG B 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03021 (  196)
  hydrogen bonds       : angle       5.67703 (  489)
  covalent geometry    : bond        0.00264 ( 6414)
  covalent geometry    : angle       0.60014 ( 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
  146 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 121
  time to evaluate  : 0.672 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  185 SER cc_start: 0.9210 (OUTLIER) cc_final: 0.8866 (m)
REVERT: D  293 TYR cc_start: 0.6362 (t80) cc_final: 0.6122 (t80)
REVERT: D  299 LEU cc_start: 0.8883 (mt) cc_final: 0.8603 (mp)
REVERT: D  301 PHE cc_start: 0.9249 (p90) cc_final: 0.8767 (p90)
REVERT: C  157 LYS cc_start: 0.9018 (mtpt) cc_final: 0.8649 (mtpp)
REVERT: C  182 PHE cc_start: 0.9258 (t80) cc_final: 0.8949 (t80)
REVERT: C  196 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8061 (mt-10)
REVERT: C  300 ASP cc_start: 0.8977 (t0) cc_final: 0.8557 (t0)
REVERT: C  323 GLU cc_start: 0.8932 (tp30) cc_final: 0.8461 (tp30)
REVERT: A  134 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9112 (mp)
REVERT: A  184 MET cc_start: 0.8568 (tmm) cc_final: 0.8249 (tmm)
REVERT: A  191 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8640 (mm)
REVERT: A  236 MET cc_start: 0.9105 (mmp) cc_final: 0.8362 (mmt)
REVERT: A  319 TYR cc_start: 0.8314 (m-80) cc_final: 0.7950 (m-80)
REVERT: A  323 GLU cc_start: 0.9203 (tp30) cc_final: 0.8767 (tp30)
REVERT: B  196 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7541 (mt-10)
REVERT: B  246 ASP cc_start: 0.8820 (t0) cc_final: 0.8573 (t0)
REVERT: B  249 ARG cc_start: 0.8724 (mtp85) cc_final: 0.8376 (mtp180)
REVERT: B  256 TYR cc_start: 0.8928 (m-80) cc_final: 0.8495 (m-80)
REVERT: B  276 MET cc_start: 0.7899 (ttm) cc_final: 0.7577 (ttm)
REVERT: B  303 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7621 (mt-10)
REVERT: B  319 TYR cc_start: 0.8490 (m-80) cc_final: 0.8223 (m-80)
REVERT: B  323 GLU cc_start: 0.8773 (tp30) cc_final: 0.8429 (tp30)
  outliers start: 25
  outliers final: 20
  residues processed: 142
  average time/residue: 0.2214
  time to fit residues: 41.2683
Evaluate side-chains
  138 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 114
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
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 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  150 SER
Chi-restraints excluded: chain A residue  153 SER
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  163 VAL
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
Chi-restraints excluded: chain B residue  279 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 64 optimal weight:    8.9990
   chunk 72 optimal weight:   10.0000
   chunk 41 optimal weight:    9.9990
   chunk 51 optimal weight:    6.9990
   chunk 27 optimal weight:    0.0030
   chunk 32 optimal weight:    6.9990
   chunk 16 optimal weight:    0.1980
   chunk 37 optimal weight:    0.0970
   chunk 60 optimal weight:    4.9990
   chunk 13 optimal weight:    9.9990
   overall best weight:    2.2592

-------------------------------------------------------------------------------
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 = 0.3310 r_free = 0.3310 target = 0.061798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.046951 restraints weight = 24097.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.048674 restraints weight = 11866.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.049858 restraints weight = 7701.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.4750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6414  Z= 0.189
  Angle     :  0.635   7.333   8740  Z= 0.333
  Chirality :  0.045   0.163   1021
  Planarity :  0.004   0.034   1123
  Dihedral  :  4.606  15.938    860
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 22.22 %
    Favored  : 74.40 %
  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: -0.24 (0.31), residues: 786
  helix:  0.10 (1.42), residues: 18
  sheet: -0.14 (0.28), residues: 313
  loop : -0.07 (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   0.018   0.002   PHE D 247 
 TYR   0.015   0.002   TYR A 260 
 ARG   0.009   0.001   ARG B 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03278 (  196)
  hydrogen bonds       : angle       5.81622 (  489)
  covalent geometry    : bond        0.00420 ( 6414)
  covalent geometry    : angle       0.63472 ( 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
  138 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 114
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  293 TYR cc_start: 0.6501 (t80) cc_final: 0.6213 (t80)
REVERT: D  301 PHE cc_start: 0.9322 (p90) cc_final: 0.8788 (p90)
REVERT: C  157 LYS cc_start: 0.9096 (mtpt) cc_final: 0.8726 (mtpp)
REVERT: C  182 PHE cc_start: 0.9328 (t80) cc_final: 0.9027 (t80)
REVERT: C  196 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8154 (mt-10)
REVERT: C  250 GLU cc_start: 0.8864 (pm20) cc_final: 0.8197 (pm20)
REVERT: C  300 ASP cc_start: 0.8970 (t0) cc_final: 0.8557 (t0)
REVERT: C  323 GLU cc_start: 0.8846 (tp30) cc_final: 0.8421 (tp30)
REVERT: A  134 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9084 (mp)
REVERT: A  184 MET cc_start: 0.8588 (tmm) cc_final: 0.8254 (tmm)
REVERT: A  191 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8652 (mm)
REVERT: A  236 MET cc_start: 0.9114 (mmp) cc_final: 0.8835 (mmp)
REVERT: B  246 ASP cc_start: 0.8836 (t0) cc_final: 0.8341 (t0)
REVERT: B  256 TYR cc_start: 0.8972 (m-80) cc_final: 0.8479 (m-80)
REVERT: B  276 MET cc_start: 0.7857 (ttm) cc_final: 0.7498 (ttm)
REVERT: B  323 GLU cc_start: 0.8811 (tp30) cc_final: 0.8536 (tp30)
  outliers start: 24
  outliers final: 21
  residues processed: 135
  average time/residue: 0.2401
  time to fit residues: 42.1061
Evaluate side-chains
  135 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 111
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
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 A residue  134 LEU
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  153 SER
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  147 ILE
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  240 THR
Chi-restraints excluded: chain B residue  250 GLU
Chi-restraints excluded: chain B residue  259 CYS
Chi-restraints excluded: chain B residue  279 ARG
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:   10.0000
   chunk 66 optimal weight:    6.9990
   chunk 54 optimal weight:    6.9990
   chunk 16 optimal weight:    0.8980
   chunk 63 optimal weight:    0.0570
   chunk 39 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   chunk 71 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    1.3302

-------------------------------------------------------------------------------
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 = 0.3337 r_free = 0.3337 target = 0.062994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.048046 restraints weight = 23950.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.049823 restraints weight = 11808.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.051040 restraints weight = 7637.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.4858

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= 0.139
  Angle     :  0.646   8.072   8740  Z= 0.335
  Chirality :  0.045   0.165   1021
  Planarity :  0.003   0.037   1123
  Dihedral  :  4.542  15.999    860
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 22.64 %
    Favored  : 73.98 %
  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: -1.70 (0.90), residues: 36
  sheet: -0.14 (0.28), residues: 313
  loop : -0.17 (0.33), residues: 437

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   0.017   0.002   PHE D 247 
 TYR   0.014   0.001   TYR A 260 
 ARG   0.010   0.001   ARG B 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03149 (  196)
  hydrogen bonds       : angle       5.74295 (  489)
  covalent geometry    : bond        0.00321 ( 6414)
  covalent geometry    : angle       0.64575 ( 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
  141 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 117
  time to evaluate  : 0.773 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  301 PHE cc_start: 0.9298 (p90) cc_final: 0.8779 (p90)
REVERT: C  157 LYS cc_start: 0.9089 (mtpt) cc_final: 0.8732 (mtpp)
REVERT: C  182 PHE cc_start: 0.9317 (t80) cc_final: 0.9027 (t80)
REVERT: C  196 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8163 (mt-10)
REVERT: C  250 GLU cc_start: 0.8946 (pm20) cc_final: 0.8226 (pm20)
REVERT: C  300 ASP cc_start: 0.8963 (t0) cc_final: 0.8584 (t0)
REVERT: C  323 GLU cc_start: 0.8873 (tp30) cc_final: 0.8350 (tp30)
REVERT: A  134 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9088 (mp)
REVERT: A  184 MET cc_start: 0.8574 (tmm) cc_final: 0.8237 (tmm)
REVERT: A  191 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8626 (mm)
REVERT: A  236 MET cc_start: 0.9108 (mmp) cc_final: 0.8849 (mmp)
REVERT: B  246 ASP cc_start: 0.8800 (t0) cc_final: 0.8293 (t0)
REVERT: B  256 TYR cc_start: 0.8944 (m-80) cc_final: 0.8488 (m-80)
REVERT: B  276 MET cc_start: 0.7880 (ttm) cc_final: 0.7402 (tmm)
REVERT: B  323 GLU cc_start: 0.8837 (tp30) cc_final: 0.8608 (tp30)
  outliers start: 24
  outliers final: 20
  residues processed: 138
  average time/residue: 0.1945
  time to fit residues: 34.8958
Evaluate side-chains
  135 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 112
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 A residue  134 LEU
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  153 SER
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  147 ILE
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  240 THR
Chi-restraints excluded: chain B residue  250 GLU
Chi-restraints excluded: chain B residue  259 CYS
Chi-restraints excluded: chain B residue  279 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 15 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 64 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   chunk 9 optimal weight:    0.3980
   chunk 27 optimal weight:    0.3980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.7184

-------------------------------------------------------------------------------
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 = 0.3365 r_free = 0.3365 target = 0.064132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.049143 restraints weight = 23808.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.050949 restraints weight = 11627.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.052180 restraints weight = 7508.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.5029

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= 0.118
  Angle     :  0.631   7.308   8740  Z= 0.327
  Chirality :  0.045   0.156   1021
  Planarity :  0.003   0.035   1123
  Dihedral  :  4.397  15.903    860
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 23.35 %
    Favored  : 73.56 %
  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: -0.49 (0.31), residues: 786
  helix: -1.68 (0.90), residues: 36
  sheet: -0.10 (0.28), residues: 314
  loop : -0.26 (0.33), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 296 
 HIS   0.003   0.001   HIS B 218 
 PHE   0.014   0.001   PHE C 172 
 TYR   0.015   0.001   TYR C 174 
 ARG   0.010   0.001   ARG B 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03000 (  196)
  hydrogen bonds       : angle       5.63690 (  489)
  covalent geometry    : bond        0.00280 ( 6414)
  covalent geometry    : angle       0.63060 ( 8740)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2349.81 seconds
wall clock time: 42 minutes 33.79 seconds (2553.79 seconds total)