Starting phenix.real_space_refine
on Fri Aug 22 17:00:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qjy_18454/08_2025/8qjy_18454.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qjy_18454/08_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_18454/08_2025/8qjy_18454.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qjy_18454/08_2025/8qjy_18454.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qjy_18454/08_2025/8qjy_18454.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qjy_18454/08_2025/8qjy_18454.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.61, per 1000 atoms: 0.26
  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: 0.35
  Conformation dependent library (CDL) restraints added in 362.4 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.23
  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: 0.97

  Time building geometry restraints manager: 0.48 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:             0.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.340
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.320
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.009   0.001   ARG C 249 
 TYR   0.012   0.002   TYR C 174 
 PHE   0.022   0.002   PHE D 301 
 TRP   0.013   0.002   TRP C 296 
 HIS   0.005   0.001   HIS B 218 

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

*********************** 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  : 0.171 
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: 0.7619 (mm110)
REVERT: A  236 MET cc_start: 0.8374 (mmp) cc_final: 0.7799 (mmt)
REVERT: B  252 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7448 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 213
  average time/residue: 0.1004
  time to fit residues: 26.2842
Evaluate side-chains
  137 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    7.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:   10.0000
   chunk 74 optimal weight:    2.9990
   overall best weight:    2.1186

-------------------------------------------------------------------------------
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 = 0.3290 r_free = 0.3290 target = 0.062997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.048071 restraints weight = 23566.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.049922 restraints weight = 11349.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.051159 restraints weight = 7216.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.052039 restraints weight = 5341.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.052658 restraints weight = 4326.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.3193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6414  Z= 0.184
  Angle     :  0.633   5.376   8740  Z= 0.334
  Chirality :  0.047   0.139   1021
  Planarity :  0.005   0.046   1123
  Dihedral  :  4.848  16.712    860
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 17.44 %
    Favored  : 79.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.10 (0.32), residues: 786
  helix: -1.17 (1.16), residues: 18
  sheet:  0.02 (0.30), residues: 291
  loop :  0.03 (0.32), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 249 
 TYR   0.015   0.002   TYR A 260 
 PHE   0.019   0.002   PHE D 247 
 TRP   0.014   0.002   TRP C 296 
 HIS   0.005   0.001   HIS B 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 6414)
  covalent geometry    : angle       0.63308 ( 8740)
  hydrogen bonds       : bond        0.03540 (  196)
  hydrogen bonds       : angle       6.05505 (  489)

*********************** 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
  157 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 132
  time to evaluate  : 0.238 
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: 0.9340 (OUTLIER) cc_final: 0.9139 (tp)
REVERT: D  170 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8842 (pt0)
REVERT: D  185 SER cc_start: 0.9213 (OUTLIER) cc_final: 0.8927 (m)
REVERT: D  208 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7429 (tm-30)
REVERT: D  293 TYR cc_start: 0.6147 (t80) cc_final: 0.5766 (t80)
REVERT: D  301 PHE cc_start: 0.9117 (p90) cc_final: 0.8844 (p90)
REVERT: C  157 LYS cc_start: 0.8825 (mtpt) cc_final: 0.8399 (mtpp)
REVERT: C  224 MET cc_start: 0.8460 (mtm) cc_final: 0.8138 (mtp)
REVERT: C  284 ASP cc_start: 0.8912 (p0) cc_final: 0.8624 (p0)
REVERT: C  300 ASP cc_start: 0.8962 (t0) cc_final: 0.8680 (t0)
REVERT: C  323 GLU cc_start: 0.8842 (tp30) cc_final: 0.8497 (tp30)
REVERT: A  134 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8963 (mp)
REVERT: A  184 MET cc_start: 0.8451 (tmm) cc_final: 0.8163 (tmm)
REVERT: A  222 GLN cc_start: 0.8921 (mm110) cc_final: 0.8650 (mm110)
REVERT: A  236 MET cc_start: 0.9294 (mmp) cc_final: 0.9059 (mmp)
REVERT: A  319 TYR cc_start: 0.8640 (m-80) cc_final: 0.8406 (m-80)
REVERT: B  158 LEU cc_start: 0.9362 (tp) cc_final: 0.9111 (tp)
REVERT: B  233 LYS cc_start: 0.9268 (ttpt) cc_final: 0.8735 (ttpp)
REVERT: B  246 ASP cc_start: 0.8598 (t0) cc_final: 0.8348 (t0)
REVERT: B  249 ARG cc_start: 0.8555 (mtp85) cc_final: 0.7824 (mtp-110)
REVERT: B  252 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8026 (mt-10)
REVERT: B  319 TYR cc_start: 0.8159 (m-80) cc_final: 0.7555 (m-80)
REVERT: B  324 ASP cc_start: 0.8812 (m-30) cc_final: 0.8515 (m-30)
  outliers start: 25
  outliers final: 14
  residues processed: 151
  average time/residue: 0.0828
  time to fit residues: 16.0327
Evaluate side-chains
  142 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
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  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  250 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 7 optimal weight:    8.9990
   chunk 44 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 1 optimal weight:    8.9990
   chunk 67 optimal weight:   10.0000
   chunk 12 optimal weight:    9.9990
   chunk 73 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 4 optimal weight:    8.9990
   overall best weight:    2.3786

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.062479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.047608 restraints weight = 23440.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.049363 restraints weight = 11458.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.050541 restraints weight = 7314.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.051344 restraints weight = 5459.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.051826 restraints weight = 4475.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.3764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6414  Z= 0.189
  Angle     :  0.591   6.120   8740  Z= 0.312
  Chirality :  0.045   0.134   1021
  Planarity :  0.004   0.035   1123
  Dihedral  :  4.722  16.101    860
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 17.72 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.08 (0.32), residues: 786
  helix: -0.77 (1.28), residues: 18
  sheet: -0.01 (0.30), residues: 297
  loop :  0.07 (0.33), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 208 
 TYR   0.017   0.002   TYR A 260 
 PHE   0.016   0.002   PHE B 172 
 TRP   0.013   0.002   TRP C 296 
 HIS   0.007   0.001   HIS D 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 6414)
  covalent geometry    : angle       0.59139 ( 8740)
  hydrogen bonds       : bond        0.03367 (  196)
  hydrogen bonds       : angle       5.95080 (  489)

*********************** 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
  137 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  172 TYR cc_start: 0.8351 (m-80) cc_final: 0.7920 (m-80)
REVERT: D  185 SER cc_start: 0.9214 (OUTLIER) cc_final: 0.8894 (m)
REVERT: D  293 TYR cc_start: 0.5852 (t80) cc_final: 0.5526 (t80)
REVERT: D  301 PHE cc_start: 0.9223 (p90) cc_final: 0.8886 (p90)
REVERT: C  157 LYS cc_start: 0.8973 (mtpt) cc_final: 0.8574 (mtpp)
REVERT: C  224 MET cc_start: 0.8364 (mtm) cc_final: 0.8081 (mtp)
REVERT: C  284 ASP cc_start: 0.8742 (p0) cc_final: 0.8512 (p0)
REVERT: C  300 ASP cc_start: 0.8989 (t0) cc_final: 0.8624 (t0)
REVERT: C  323 GLU cc_start: 0.8980 (tp30) cc_final: 0.8661 (tp30)
REVERT: A  184 MET cc_start: 0.8410 (tmm) cc_final: 0.8020 (tmm)
REVERT: A  236 MET cc_start: 0.9252 (mmp) cc_final: 0.9033 (mmp)
REVERT: A  305 GLN cc_start: 0.8970 (pm20) cc_final: 0.8695 (pm20)
REVERT: B  246 ASP cc_start: 0.8476 (t0) cc_final: 0.8025 (t0)
  outliers start: 19
  outliers final: 14
  residues processed: 134
  average time/residue: 0.0816
  time to fit residues: 14.2142
Evaluate side-chains
  126 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  109 VAL
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  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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 75 optimal weight:    0.0370
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 63 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 69 optimal weight:    5.9990
   chunk 30 optimal weight:    0.8980
   chunk 73 optimal weight:    0.5980
   overall best weight:    0.6658

-------------------------------------------------------------------------------
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 = 0.3362 r_free = 0.3362 target = 0.064340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.049230 restraints weight = 23090.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.051069 restraints weight = 11116.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.052309 restraints weight = 7108.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.053123 restraints weight = 5297.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.053695 restraints weight = 4361.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.4132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6414  Z= 0.105
  Angle     :  0.564   6.024   8740  Z= 0.297
  Chirality :  0.044   0.133   1021
  Planarity :  0.003   0.028   1123
  Dihedral  :  4.382  16.053    860
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 16.60 %
    Favored  : 80.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.09 (0.31), residues: 786
  helix: -0.31 (1.40), residues: 18
  sheet:  0.06 (0.30), residues: 299
  loop : -0.03 (0.32), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 208 
 TYR   0.018   0.001   TYR D 172 
 PHE   0.018   0.002   PHE C 193 
 TRP   0.014   0.001   TRP C 296 
 HIS   0.002   0.001   HIS D 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 6414)
  covalent geometry    : angle       0.56434 ( 8740)
  hydrogen bonds       : bond        0.03046 (  196)
  hydrogen bonds       : angle       5.72460 (  489)

*********************** 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
  156 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 132
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  172 TYR cc_start: 0.8229 (m-80) cc_final: 0.7976 (m-80)
REVERT: D  185 SER cc_start: 0.9225 (OUTLIER) cc_final: 0.8853 (m)
REVERT: D  208 GLN cc_start: 0.8384 (tm-30) cc_final: 0.8149 (tm-30)
REVERT: D  293 TYR cc_start: 0.5986 (t80) cc_final: 0.5620 (t80)
REVERT: D  301 PHE cc_start: 0.9259 (p90) cc_final: 0.8987 (p90)
REVERT: C  157 LYS cc_start: 0.8885 (mtpt) cc_final: 0.8458 (mtpp)
REVERT: C  182 PHE cc_start: 0.9245 (t80) cc_final: 0.8889 (t80)
REVERT: C  193 PHE cc_start: 0.8988 (p90) cc_final: 0.8777 (p90)
REVERT: C  224 MET cc_start: 0.8334 (mtm) cc_final: 0.8038 (mtp)
REVERT: C  246 ASP cc_start: 0.8774 (t0) cc_final: 0.8571 (t0)
REVERT: C  250 GLU cc_start: 0.8878 (pm20) cc_final: 0.8292 (pm20)
REVERT: C  300 ASP cc_start: 0.9008 (t0) cc_final: 0.8542 (t0)
REVERT: C  319 TYR cc_start: 0.8048 (m-80) cc_final: 0.7702 (m-80)
REVERT: C  323 GLU cc_start: 0.8920 (tp30) cc_final: 0.8550 (tp30)
REVERT: A  184 MET cc_start: 0.8492 (tmm) cc_final: 0.8278 (tmm)
REVERT: A  224 MET cc_start: 0.8209 (mtp) cc_final: 0.7788 (mtp)
REVERT: A  236 MET cc_start: 0.9173 (mmp) cc_final: 0.8691 (mmt)
REVERT: A  323 GLU cc_start: 0.9240 (tp30) cc_final: 0.8635 (tp30)
REVERT: B  164 LYS cc_start: 0.8800 (ttmm) cc_final: 0.8339 (tppp)
REVERT: B  196 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7667 (mt-10)
REVERT: B  246 ASP cc_start: 0.8480 (t0) cc_final: 0.7948 (t0)
REVERT: B  256 TYR cc_start: 0.9027 (m-80) cc_final: 0.8571 (m-80)
REVERT: B  259 CYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7445 (m)
REVERT: B  320 TYR cc_start: 0.9007 (p90) cc_final: 0.8775 (p90)
  outliers start: 24
  outliers final: 16
  residues processed: 151
  average time/residue: 0.0755
  time to fit residues: 14.9538
Evaluate side-chains
  134 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
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 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  161 THR
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  250 GLU
Chi-restraints excluded: chain B residue  259 CYS
Chi-restraints excluded: chain B residue  300 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 10 optimal weight:   20.0000
   chunk 7 optimal weight:   10.0000
   chunk 73 optimal weight:    8.9990
   chunk 72 optimal weight:    8.9990
   chunk 60 optimal weight:    9.9990
   chunk 1 optimal weight:   10.0000
   chunk 68 optimal weight:    9.9990
   chunk 13 optimal weight:   10.0000
   chunk 53 optimal weight:    5.9990
   chunk 59 optimal weight:    9.9990
   chunk 56 optimal weight:    0.3980
   overall best weight:    6.8788

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.058440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.043994 restraints weight = 25249.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.045590 restraints weight = 12776.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.046740 restraints weight = 8426.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.047458 restraints weight = 6388.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.047883 restraints weight = 5313.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.4547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.106   6414  Z= 0.486
  Angle     :  0.778   7.081   8740  Z= 0.414
  Chirality :  0.049   0.190   1021
  Planarity :  0.005   0.039   1123
  Dihedral  :  5.506  21.131    860
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 13.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 18.28 %
    Favored  : 76.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.57 (0.31), residues: 786
  helix: -1.08 (1.25), residues: 18
  sheet: -0.39 (0.28), residues: 312
  loop : -0.22 (0.32), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 291 
 TYR   0.023   0.003   TYR A 260 
 PHE   0.026   0.003   PHE B 172 
 TRP   0.018   0.003   TRP B 296 
 HIS   0.005   0.002   HIS D 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.01054 ( 6414)
  covalent geometry    : angle       0.77847 ( 8740)
  hydrogen bonds       : bond        0.04296 (  196)
  hydrogen bonds       : angle       6.34446 (  489)

*********************** 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
  140 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 102
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  185 SER cc_start: 0.9200 (OUTLIER) cc_final: 0.8941 (m)
REVERT: D  293 TYR cc_start: 0.6216 (t80) cc_final: 0.5787 (t80)
REVERT: D  301 PHE cc_start: 0.9305 (p90) cc_final: 0.8544 (p90)
REVERT: C  157 LYS cc_start: 0.9204 (mtpt) cc_final: 0.8842 (mtpp)
REVERT: C  196 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8204 (mt-10)
REVERT: C  224 MET cc_start: 0.8441 (mtm) cc_final: 0.8149 (mtp)
REVERT: C  250 GLU cc_start: 0.8941 (pm20) cc_final: 0.8729 (pm20)
REVERT: C  300 ASP cc_start: 0.9024 (t0) cc_final: 0.8605 (t0)
REVERT: C  323 GLU cc_start: 0.8913 (tp30) cc_final: 0.8569 (tp30)
REVERT: A  184 MET cc_start: 0.8425 (tmm) cc_final: 0.7986 (tmm)
REVERT: B  246 ASP cc_start: 0.8938 (t0) cc_final: 0.8529 (t0)
REVERT: B  303 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7967 (mp0)
REVERT: B  323 GLU cc_start: 0.8687 (tp30) cc_final: 0.8229 (tp30)
  outliers start: 38
  outliers final: 28
  residues processed: 128
  average time/residue: 0.0821
  time to fit residues: 13.8066
Evaluate side-chains
  131 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 101
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
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  231 MET
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  163 VAL
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  173 VAL
Chi-restraints excluded: chain C residue  196 GLU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  192 ASN
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  272 ASP
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  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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 39 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 17 optimal weight:    7.9990
   chunk 64 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 69 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 35 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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 = 0.3319 r_free = 0.3319 target = 0.062546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.047555 restraints weight = 23786.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.049318 restraints weight = 11536.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.050516 restraints weight = 7448.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.051335 restraints weight = 5586.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.051881 restraints weight = 4595.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.4598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6414  Z= 0.120
  Angle     :  0.605   7.373   8740  Z= 0.313
  Chirality :  0.045   0.143   1021
  Planarity :  0.003   0.024   1123
  Dihedral  :  4.648  16.753    860
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 20.53 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.46 (0.31), residues: 786
  helix: -1.94 (0.86), residues: 36
  sheet: -0.07 (0.29), residues: 298
  loop : -0.23 (0.32), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 208 
 TYR   0.018   0.001   TYR D 172 
 PHE   0.014   0.002   PHE A 318 
 TRP   0.013   0.002   TRP C 296 
 HIS   0.003   0.001   HIS B 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 6414)
  covalent geometry    : angle       0.60538 ( 8740)
  hydrogen bonds       : bond        0.03165 (  196)
  hydrogen bonds       : angle       5.81601 (  489)

*********************** 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
  140 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  172 TYR cc_start: 0.8396 (m-80) cc_final: 0.8091 (m-80)
REVERT: D  185 SER cc_start: 0.9201 (OUTLIER) cc_final: 0.8846 (m)
REVERT: D  293 TYR cc_start: 0.6273 (t80) cc_final: 0.5942 (t80)
REVERT: D  301 PHE cc_start: 0.9226 (p90) cc_final: 0.8746 (p90)
REVERT: C  157 LYS cc_start: 0.8951 (mtpt) cc_final: 0.8578 (mtpp)
REVERT: C  182 PHE cc_start: 0.9319 (t80) cc_final: 0.9013 (t80)
REVERT: C  196 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8016 (mt-10)
REVERT: C  224 MET cc_start: 0.8383 (mtm) cc_final: 0.8083 (mtp)
REVERT: C  233 LYS cc_start: 0.9279 (tttt) cc_final: 0.9054 (tttp)
REVERT: C  250 GLU cc_start: 0.8961 (pm20) cc_final: 0.8412 (pm20)
REVERT: C  300 ASP cc_start: 0.9028 (t0) cc_final: 0.8549 (t0)
REVERT: C  323 GLU cc_start: 0.8979 (tp30) cc_final: 0.8599 (tp30)
REVERT: A  134 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9088 (mp)
REVERT: A  184 MET cc_start: 0.8589 (tmm) cc_final: 0.8342 (tmm)
REVERT: A  224 MET cc_start: 0.8294 (mtp) cc_final: 0.7950 (mtp)
REVERT: A  319 TYR cc_start: 0.8656 (m-80) cc_final: 0.8421 (m-80)
REVERT: B  164 LYS cc_start: 0.8879 (ttmm) cc_final: 0.8623 (tppp)
REVERT: B  196 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7594 (mt-10)
REVERT: B  246 ASP cc_start: 0.8746 (t0) cc_final: 0.8224 (t0)
REVERT: B  256 TYR cc_start: 0.9032 (m-80) cc_final: 0.8492 (m-80)
REVERT: B  320 TYR cc_start: 0.8972 (p90) cc_final: 0.8625 (p90)
REVERT: B  323 GLU cc_start: 0.8754 (tp30) cc_final: 0.8402 (tp30)
  outliers start: 25
  outliers final: 19
  residues processed: 135
  average time/residue: 0.0794
  time to fit residues: 14.0133
Evaluate side-chains
  134 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
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  272 PHE
Chi-restraints excluded: chain D residue  322 THR
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  196 GLU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain A residue  134 LEU
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  317 THR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  259 CYS
Chi-restraints excluded: chain B residue  311 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   chunk 74 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 66 optimal weight:    7.9990
   chunk 27 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   chunk 71 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
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 = 0.3263 r_free = 0.3263 target = 0.059973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.045177 restraints weight = 24316.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.046830 restraints weight = 12174.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.047973 restraints weight = 8008.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.048707 restraints weight = 6069.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.049231 restraints weight = 5068.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.4645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   6414  Z= 0.262
  Angle     :  0.635   6.997   8740  Z= 0.333
  Chirality :  0.045   0.142   1021
  Planarity :  0.004   0.030   1123
  Dihedral  :  4.910  17.847    860
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 20.25 %
    Favored  : 75.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.45 (0.31), residues: 786
  helix: -0.24 (1.35), residues: 18
  sheet: -0.23 (0.28), residues: 313
  loop : -0.25 (0.32), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 279 
 TYR   0.019   0.002   TYR A 260 
 PHE   0.027   0.002   PHE C 193 
 TRP   0.016   0.002   TRP B 296 
 HIS   0.003   0.001   HIS D 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00570 ( 6414)
  covalent geometry    : angle       0.63490 ( 8740)
  hydrogen bonds       : bond        0.03502 (  196)
  hydrogen bonds       : angle       5.96021 (  489)

*********************** 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
  142 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 112
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  172 TYR cc_start: 0.8394 (m-80) cc_final: 0.8129 (m-80)
REVERT: D  185 SER cc_start: 0.9198 (OUTLIER) cc_final: 0.8878 (m)
REVERT: D  208 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7938 (tm-30)
REVERT: D  293 TYR cc_start: 0.6497 (t80) cc_final: 0.6108 (t80)
REVERT: D  301 PHE cc_start: 0.9224 (p90) cc_final: 0.8656 (p90)
REVERT: C  157 LYS cc_start: 0.9154 (mtpt) cc_final: 0.8815 (mtpp)
REVERT: C  182 PHE cc_start: 0.9408 (t80) cc_final: 0.9065 (t80)
REVERT: C  196 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8150 (mt-10)
REVERT: C  233 LYS cc_start: 0.9293 (tttt) cc_final: 0.9072 (tttp)
REVERT: C  250 GLU cc_start: 0.8859 (pm20) cc_final: 0.8282 (pm20)
REVERT: C  300 ASP cc_start: 0.8976 (t0) cc_final: 0.8517 (t0)
REVERT: C  323 GLU cc_start: 0.8854 (tp30) cc_final: 0.8423 (tp30)
REVERT: A  146 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7845 (tp40)
REVERT: A  184 MET cc_start: 0.8479 (tmm) cc_final: 0.7890 (tmm)
REVERT: A  191 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8710 (mm)
REVERT: B  164 LYS cc_start: 0.8960 (ttmm) cc_final: 0.8563 (ttmt)
REVERT: B  246 ASP cc_start: 0.8876 (t0) cc_final: 0.8411 (t0)
REVERT: B  319 TYR cc_start: 0.8877 (m-80) cc_final: 0.8487 (m-80)
REVERT: B  323 GLU cc_start: 0.8720 (tp30) cc_final: 0.8417 (tp30)
  outliers start: 30
  outliers final: 23
  residues processed: 137
  average time/residue: 0.0795
  time to fit residues: 14.1580
Evaluate side-chains
  135 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 108
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
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 C residue  216 LEU
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  146 GLN
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  192 ASN
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  250 GLU
Chi-restraints excluded: chain B residue  259 CYS
Chi-restraints excluded: chain B residue  311 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 48 optimal weight:    9.9990
   chunk 7 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 39 optimal weight:    0.0980
   chunk 29 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 4 optimal weight:    9.9990
   chunk 37 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.6186

-------------------------------------------------------------------------------
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 = 0.3304 r_free = 0.3304 target = 0.061771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.047019 restraints weight = 23750.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.048772 restraints weight = 11771.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.049984 restraints weight = 7659.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.050767 restraints weight = 5752.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.051337 restraints weight = 4764.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.4767

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= 0.153
  Angle     :  0.614   5.852   8740  Z= 0.319
  Chirality :  0.044   0.134   1021
  Planarity :  0.003   0.027   1123
  Dihedral  :  4.738  18.726    860
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 21.38 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.59 (0.31), residues: 786
  helix: -1.83 (0.88), residues: 36
  sheet: -0.19 (0.28), residues: 313
  loop : -0.31 (0.33), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 208 
 TYR   0.015   0.001   TYR A 260 
 PHE   0.014   0.002   PHE B 172 
 TRP   0.014   0.002   TRP C 296 
 HIS   0.003   0.001   HIS B 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 6414)
  covalent geometry    : angle       0.61440 ( 8740)
  hydrogen bonds       : bond        0.03167 (  196)
  hydrogen bonds       : angle       5.86121 (  489)

*********************** 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
  142 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 114
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  172 TYR cc_start: 0.8356 (m-80) cc_final: 0.7934 (m-80)
REVERT: D  185 SER cc_start: 0.9199 (OUTLIER) cc_final: 0.8868 (m)
REVERT: D  208 GLN cc_start: 0.8290 (tm-30) cc_final: 0.7952 (tm-30)
REVERT: D  293 TYR cc_start: 0.6264 (t80) cc_final: 0.6003 (t80)
REVERT: D  301 PHE cc_start: 0.9177 (p90) cc_final: 0.8616 (p90)
REVERT: C  157 LYS cc_start: 0.9060 (mtpt) cc_final: 0.8749 (mtpp)
REVERT: C  182 PHE cc_start: 0.9313 (t80) cc_final: 0.9005 (t80)
REVERT: C  196 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8049 (mt-10)
REVERT: C  224 MET cc_start: 0.8510 (mtm) cc_final: 0.8192 (mtp)
REVERT: C  233 LYS cc_start: 0.9281 (tttt) cc_final: 0.9059 (tttp)
REVERT: C  250 GLU cc_start: 0.8821 (pm20) cc_final: 0.8289 (pm20)
REVERT: C  300 ASP cc_start: 0.8976 (t0) cc_final: 0.8546 (t0)
REVERT: C  323 GLU cc_start: 0.8948 (tp30) cc_final: 0.8213 (tp30)
REVERT: A  134 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9084 (mp)
REVERT: A  146 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7919 (tt0)
REVERT: A  184 MET cc_start: 0.8558 (tmm) cc_final: 0.8240 (tmm)
REVERT: A  323 GLU cc_start: 0.9230 (tp30) cc_final: 0.8657 (tp30)
REVERT: B  164 LYS cc_start: 0.8845 (ttmm) cc_final: 0.8570 (tppp)
REVERT: B  196 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7834 (mt-10)
REVERT: B  246 ASP cc_start: 0.8841 (t0) cc_final: 0.8347 (t0)
REVERT: B  256 TYR cc_start: 0.9008 (m-80) cc_final: 0.8747 (m-80)
REVERT: B  319 TYR cc_start: 0.8612 (m-80) cc_final: 0.7901 (m-80)
REVERT: B  320 TYR cc_start: 0.9028 (p90) cc_final: 0.8822 (p90)
REVERT: B  323 GLU cc_start: 0.8718 (tp30) cc_final: 0.8383 (tp30)
  outliers start: 28
  outliers final: 21
  residues processed: 135
  average time/residue: 0.0691
  time to fit residues: 12.4682
Evaluate side-chains
  136 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
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  173 VAL
Chi-restraints excluded: chain C residue  196 GLU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  146 GLN
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  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
Chi-restraints excluded: chain B residue  311 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 63 optimal weight:    0.3980
   chunk 45 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 17 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9980
   chunk 40 optimal weight:   10.0000
   chunk 59 optimal weight:    0.0050
   chunk 75 optimal weight:    0.0770
   chunk 2 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.4954

-------------------------------------------------------------------------------
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 = 0.3378 r_free = 0.3378 target = 0.064996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.050426 restraints weight = 23651.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.052296 restraints weight = 11205.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.053607 restraints weight = 7075.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.054354 restraints weight = 5201.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.055026 restraints weight = 4296.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.4967

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= 0.112
  Angle     :  0.632   7.937   8740  Z= 0.328
  Chirality :  0.045   0.139   1021
  Planarity :  0.003   0.036   1123
  Dihedral  :  4.613  21.584    860
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 21.94 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.46 (0.31), residues: 786
  helix: -1.68 (0.91), residues: 36
  sheet: -0.00 (0.29), residues: 299
  loop : -0.32 (0.32), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 208 
 TYR   0.017   0.001   TYR D 172 
 PHE   0.013   0.002   PHE C 172 
 TRP   0.014   0.002   TRP C 296 
 HIS   0.003   0.001   HIS B 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 6414)
  covalent geometry    : angle       0.63214 ( 8740)
  hydrogen bonds       : bond        0.02914 (  196)
  hydrogen bonds       : angle       5.85619 (  489)

*********************** 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
  141 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  172 TYR cc_start: 0.8285 (m-80) cc_final: 0.8046 (m-80)
REVERT: D  208 GLN cc_start: 0.8242 (tm-30) cc_final: 0.7914 (tm-30)
REVERT: D  301 PHE cc_start: 0.9181 (p90) cc_final: 0.8753 (p90)
REVERT: C  157 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8551 (mtpp)
REVERT: C  182 PHE cc_start: 0.9272 (t80) cc_final: 0.8984 (t80)
REVERT: C  196 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8035 (mt-10)
REVERT: C  224 MET cc_start: 0.8561 (mtm) cc_final: 0.8358 (mtp)
REVERT: C  233 LYS cc_start: 0.9237 (tttt) cc_final: 0.9018 (tttp)
REVERT: C  250 GLU cc_start: 0.9081 (pm20) cc_final: 0.8555 (pm20)
REVERT: C  300 ASP cc_start: 0.9004 (t0) cc_final: 0.8645 (t0)
REVERT: C  323 GLU cc_start: 0.8771 (tp30) cc_final: 0.7991 (tp30)
REVERT: C  324 ASP cc_start: 0.7605 (m-30) cc_final: 0.7351 (m-30)
REVERT: A  184 MET cc_start: 0.8629 (tmm) cc_final: 0.8273 (tmm)
REVERT: A  191 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8555 (mm)
REVERT: A  236 MET cc_start: 0.8921 (mmt) cc_final: 0.8719 (mmt)
REVERT: A  323 GLU cc_start: 0.9286 (tp30) cc_final: 0.8586 (tp30)
REVERT: B  164 LYS cc_start: 0.8738 (ttmm) cc_final: 0.8514 (ttmt)
REVERT: B  196 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7891 (mm-30)
REVERT: B  233 LYS cc_start: 0.9140 (ttpt) cc_final: 0.8716 (ttpp)
REVERT: B  246 ASP cc_start: 0.8818 (t0) cc_final: 0.8416 (t0)
REVERT: B  249 ARG cc_start: 0.8624 (mtp85) cc_final: 0.8399 (mtp85)
REVERT: B  252 GLU cc_start: 0.8523 (pt0) cc_final: 0.8022 (pt0)
REVERT: B  319 TYR cc_start: 0.8511 (m-80) cc_final: 0.8279 (m-80)
REVERT: B  320 TYR cc_start: 0.8841 (p90) cc_final: 0.8409 (p90)
REVERT: B  323 GLU cc_start: 0.8803 (tp30) cc_final: 0.8554 (tp30)
REVERT: B  324 ASP cc_start: 0.8531 (m-30) cc_final: 0.8225 (m-30)
  outliers start: 22
  outliers final: 20
  residues processed: 138
  average time/residue: 0.0804
  time to fit residues: 14.4175
Evaluate side-chains
  136 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
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  220 ILE
Chi-restraints excluded: chain D residue  322 THR
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  196 GLU
Chi-restraints excluded: chain C residue  216 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  191 ILE
Chi-restraints excluded: chain A residue  192 ASN
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  250 GLU
Chi-restraints excluded: chain B residue  259 CYS
Chi-restraints excluded: chain B residue  311 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 17 optimal weight:    6.9990
   chunk 19 optimal weight:    0.0980
   chunk 11 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 65 optimal weight:    0.0010
   chunk 2 optimal weight:    6.9990
   chunk 28 optimal weight:    0.0570
   chunk 75 optimal weight:    0.9990
   chunk 22 optimal weight:   10.0000
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.4306

-------------------------------------------------------------------------------
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 = 0.3401 r_free = 0.3401 target = 0.066073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.051468 restraints weight = 23085.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.053375 restraints weight = 11132.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.054685 restraints weight = 7042.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.055543 restraints weight = 5186.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.056182 restraints weight = 4209.050|
|-----------------------------------------------------------------------------|
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.5110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6414  Z= 0.111
  Angle     :  0.632   8.656   8740  Z= 0.326
  Chirality :  0.045   0.155   1021
  Planarity :  0.003   0.029   1123
  Dihedral  :  4.432  23.772    860
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 22.08 %
    Favored  : 74.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.42 (0.31), residues: 786
  helix: -1.65 (0.92), residues: 36
  sheet:  0.05 (0.29), residues: 299
  loop : -0.31 (0.32), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 208 
 TYR   0.023   0.002   TYR C 174 
 PHE   0.013   0.001   PHE C 172 
 TRP   0.014   0.002   TRP C 296 
 HIS   0.003   0.001   HIS B 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 6414)
  covalent geometry    : angle       0.63220 ( 8740)
  hydrogen bonds       : bond        0.02792 (  196)
  hydrogen bonds       : angle       5.68953 (  489)

********************** 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
  140 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  185 SER cc_start: 0.9204 (OUTLIER) cc_final: 0.8825 (m)
REVERT: D  208 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7938 (tm-30)
REVERT: D  301 PHE cc_start: 0.9169 (p90) cc_final: 0.8713 (p90)
REVERT: C  157 LYS cc_start: 0.8946 (mtpt) cc_final: 0.8572 (mtpp)
REVERT: C  182 PHE cc_start: 0.9261 (t80) cc_final: 0.8981 (t80)
REVERT: C  196 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8032 (mt-10)
REVERT: C  300 ASP cc_start: 0.9022 (t0) cc_final: 0.8669 (t0)
REVERT: C  323 GLU cc_start: 0.8908 (tp30) cc_final: 0.8496 (mm-30)
REVERT: A  184 MET cc_start: 0.8603 (tmm) cc_final: 0.8238 (tmm)
REVERT: A  191 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8562 (mm)
REVERT: A  319 TYR cc_start: 0.8268 (m-80) cc_final: 0.7969 (m-80)
REVERT: A  323 GLU cc_start: 0.9106 (tp30) cc_final: 0.8572 (tp30)
REVERT: B  164 LYS cc_start: 0.8698 (ttmm) cc_final: 0.8495 (ttmt)
REVERT: B  196 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7582 (mm-30)
REVERT: B  246 ASP cc_start: 0.8764 (t0) cc_final: 0.8359 (t0)
REVERT: B  249 ARG cc_start: 0.8511 (mtp85) cc_final: 0.8290 (mtp85)
REVERT: B  252 GLU cc_start: 0.8669 (pt0) cc_final: 0.8171 (pt0)
REVERT: B  319 TYR cc_start: 0.8624 (m-80) cc_final: 0.8366 (m-80)
REVERT: B  323 GLU cc_start: 0.8755 (tp30) cc_final: 0.8511 (tp30)
  outliers start: 22
  outliers final: 17
  residues processed: 137
  average time/residue: 0.0682
  time to fit residues: 12.1803
Evaluate side-chains
  133 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 C residue  216 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  191 ILE
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  259 CYS
Chi-restraints excluded: chain B residue  311 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 8 optimal weight:    8.9990
   chunk 50 optimal weight:    7.9990
   chunk 54 optimal weight:    4.9990
   chunk 37 optimal weight:    0.1980
   chunk 1 optimal weight:    4.9990
   chunk 22 optimal weight:    0.7980
   chunk 21 optimal weight:    8.9990
   chunk 49 optimal weight:    0.6980
   chunk 72 optimal weight:    0.8980
   chunk 5 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.5182

-------------------------------------------------------------------------------
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 = 0.3342 r_free = 0.3342 target = 0.063112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.048396 restraints weight = 23828.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.050198 restraints weight = 11604.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.051414 restraints weight = 7442.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.052229 restraints weight = 5570.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.052761 restraints weight = 4562.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.5102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6414  Z= 0.152
  Angle     :  0.647   8.339   8740  Z= 0.338
  Chirality :  0.045   0.192   1021
  Planarity :  0.003   0.036   1123
  Dihedral  :  4.516  23.376    860
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 22.36 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.54 (0.31), residues: 786
  helix: -1.67 (0.92), residues: 36
  sheet: -0.09 (0.28), residues: 314
  loop : -0.34 (0.32), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 208 
 TYR   0.020   0.002   TYR C 174 
 PHE   0.014   0.002   PHE B 172 
 TRP   0.014   0.002   TRP C 296 
 HIS   0.002   0.001   HIS B 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 6414)
  covalent geometry    : angle       0.64706 ( 8740)
  hydrogen bonds       : bond        0.03018 (  196)
  hydrogen bonds       : angle       5.75826 (  489)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1064.03 seconds
wall clock time: 19 minutes 11.55 seconds (1151.55 seconds total)