Starting phenix.real_space_refine
on Fri Aug 22 15:10:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b23_44095/08_2025/9b23_44095.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b23_44095/08_2025/9b23_44095.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b23_44095/08_2025/9b23_44095.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b23_44095/08_2025/9b23_44095.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b23_44095/08_2025/9b23_44095.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b23_44095/08_2025/9b23_44095.cif"
  }
  resolution = 3.2
  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=   0.009
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      10      5.16       5
     C    2975      2.51       5
     N     748      2.21       5
     O     937      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  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: 4670
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "D"
      Number of atoms: 2342
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2342
          Classifications: {'peptide': 285}
          Link IDs: {'PTRANS': 12, 'TRANS': 272}
    Chain: "E"
      Number of atoms: 2328
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2328
          Classifications: {'peptide': 283}
          Link IDs: {'PTRANS': 12, 'TRANS': 270}
  Time building chain proxies: 1.21, per 1000 atoms: 0.26
  Number of scatterers: 4670
  At special positions: 0
  Unit cell: (69.72, 86.32, 123.67, 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      10     16.00
     O     937      8.00
     N     748      7.00
     C    2975      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: 0.28
  Conformation dependent library (CDL) restraints added in 134.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1080

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 4 sheets defined
      56.9% alpha, 14.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'D' and resid 81 through 88
    Processing helix  chain 'D' and resid 89 through 141
      Proline residue:  D 130  - end of helix
    Processing helix  chain 'D' and resid 146 through 159
    Processing helix  chain 'D' and resid 162 through 166
    Processing helix  chain 'D' and resid 168 through 173
    Processing helix  chain 'D' and resid 175 through 180
    Processing helix  chain 'D' and resid 187 through 196
    Processing helix  chain 'D' and resid 196 through 201
      removed outlier: 4.021A  pdb=" N   ASP D 201 " --> pdb=" O   PRO D 197 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 204 through 212
      removed outlier: 3.804A  pdb=" N   VAL D 210 " --> pdb=" O   ARG D 206 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 311 through 316
    Processing helix  chain 'D' and resid 322 through 352
      removed outlier: 4.070A  pdb=" N   GLU D 328 " --> pdb=" O   GLU D 324 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   GLU D 331 " --> pdb=" O   ASP D 327 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   GLU D 332 " --> pdb=" O   GLU D 328 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LEU D 338 " --> pdb=" O   LEU D 334 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   ALA D 339 " --> pdb=" O   GLU D 335 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 355 through 362
    Processing helix  chain 'E' and resid 84 through 88
    Processing helix  chain 'E' and resid 89 through 140
      removed outlier: 3.576A  pdb=" N   LYS E 127 " --> pdb=" O   LYS E 123 " (cutoff:3.500A)
      Proline residue:  E 130  - end of helix
    Processing helix  chain 'E' and resid 146 through 161
    Processing helix  chain 'E' and resid 162 through 166
      removed outlier: 3.543A  pdb=" N   LEU E 165 " --> pdb=" O   GLU E 162 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 168 through 173
    Processing helix  chain 'E' and resid 175 through 180
    Processing helix  chain 'E' and resid 187 through 196
    Processing helix  chain 'E' and resid 198 through 203
      removed outlier: 3.936A  pdb=" N   THR E 202 " --> pdb=" O   ILE E 198 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ILE E 203 " --> pdb=" O   VAL E 199 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 198 through 203'
    Processing helix  chain 'E' and resid 204 through 212
    Processing helix  chain 'E' and resid 259 through 263
      removed outlier: 4.253A  pdb=" N   ASP E 263 " --> pdb=" O   TYR E 260 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 311 through 316
    Processing helix  chain 'E' and resid 324 through 326
      No H-bonds generated for 'chain 'E' and resid 324 through 326'
    Processing helix  chain 'E' and resid 327 through 351
      removed outlier: 4.337A  pdb=" N   ASP E 333 " --> pdb=" O   GLU E 329 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 356 through 362
    Processing sheet with id=AA1, first strand: chain 'D' and resid 216 through 221
      removed outlier: 4.429A  pdb=" N   ASP D 216 " --> pdb=" O   ARG D 234 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ARG D 234 " --> pdb=" O   ASP D 216 " (cutoff:3.500A)
      removed outlier: 8.082A  pdb=" N   CYS D 249 " --> pdb=" O   GLY D 271 " (cutoff:3.500A)
      removed outlier: 5.833A  pdb=" N   GLY D 271 " --> pdb=" O   CYS D 249 " (cutoff:3.500A)
      removed outlier: 7.470A  pdb=" N   THR D 251 " --> pdb=" O   ALA D 269 " (cutoff:3.500A)
      removed outlier: 5.425A  pdb=" N   ALA D 269 " --> pdb=" O   THR D 251 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   PHE D 253 " --> pdb=" O   ASP D 267 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 285 through 294
    Processing sheet with id=AA3, first strand: chain 'E' and resid 214 through 222
      removed outlier: 3.993A  pdb=" N   GLY E 228 " --> pdb=" O   LEU E 222 " (cutoff:3.500A)
      removed outlier: 7.447A  pdb=" N   CYS E 249 " --> pdb=" O   GLY E 271 " (cutoff:3.500A)
      removed outlier: 5.108A  pdb=" N   GLY E 271 " --> pdb=" O   CYS E 249 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   THR E 251 " --> pdb=" O   ALA E 269 " (cutoff:3.500A)
      removed outlier: 4.821A  pdb=" N   ALA E 269 " --> pdb=" O   THR E 251 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   PHE E 253 " --> pdb=" O   ASP E 267 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 285 through 293
      removed outlier: 3.533A  pdb=" N   GLU E 288 " --> pdb=" O   LYS E 305 " (cutoff:3.500A)

    248 hydrogen bonds defined for protein.
    711 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: 0.53

  Time building geometry restraints manager: 0.38 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1451
        1.33 -     1.45: 616
        1.45 -     1.57: 2683
        1.57 -     1.69: 0
        1.69 -     1.81: 14
  Bond restraints: 4764
  Sorted by residual:
  bond pdb=" N   THR D 163 "
       pdb=" CA  THR D 163 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.032 1.29e-02 6.01e+03 6.32e+00
  bond pdb=" N   GLU D 162 "
       pdb=" CA  GLU D 162 "
    ideal  model  delta    sigma   weight residual
    1.458  1.486 -0.029 1.25e-02 6.40e+03 5.21e+00
  bond pdb=" N   LEU D 160 "
       pdb=" CA  LEU D 160 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.028 1.29e-02 6.01e+03 4.80e+00
  bond pdb=" N   LEU D 165 "
       pdb=" CA  LEU D 165 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.029 1.33e-02 5.65e+03 4.73e+00
  bond pdb=" N   GLU D 164 "
       pdb=" CA  GLU D 164 "
    ideal  model  delta    sigma   weight residual
    1.458  1.485 -0.026 1.27e-02 6.20e+03 4.25e+00
  ... (remaining 4759 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.04: 5994
        1.04 -     2.08: 337
        2.08 -     3.12: 72
        3.12 -     4.15: 26
        4.15 -     5.19: 4
  Bond angle restraints: 6433
  Sorted by residual:
  angle pdb=" C   PRO E 308 "
        pdb=" CA  PRO E 308 "
        pdb=" CB  PRO E 308 "
      ideal   model   delta    sigma   weight residual
     111.23  107.44    3.79 1.28e+00 6.10e-01 8.76e+00
  angle pdb=" N   GLU D 164 "
        pdb=" CA  GLU D 164 "
        pdb=" C   GLU D 164 "
      ideal   model   delta    sigma   weight residual
     111.75  107.99    3.76 1.28e+00 6.10e-01 8.64e+00
  angle pdb=" CA  PRO E 308 "
        pdb=" C   PRO E 308 "
        pdb=" O   PRO E 308 "
      ideal   model   delta    sigma   weight residual
     121.56  118.19    3.37 1.16e+00 7.43e-01 8.46e+00
  angle pdb=" C   PHE E 316 "
        pdb=" N   ASP E 317 "
        pdb=" CA  ASP E 317 "
      ideal   model   delta    sigma   weight residual
     123.10  120.45    2.65 9.60e-01 1.09e+00 7.65e+00
  angle pdb=" CA  GLU D 162 "
        pdb=" C   GLU D 162 "
        pdb=" O   GLU D 162 "
      ideal   model   delta    sigma   weight residual
     120.32  117.50    2.82 1.02e+00 9.61e-01 7.62e+00
  ... (remaining 6428 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 2629
       17.89 -    35.78: 211
       35.78 -    53.67: 44
       53.67 -    71.57: 15
       71.57 -    89.46: 6
  Dihedral angle restraints: 2905
    sinusoidal: 1241
      harmonic: 1664
  Sorted by residual:
  dihedral pdb=" CA  ILE D 265 "
           pdb=" C   ILE D 265 "
           pdb=" N   TYR D 266 "
           pdb=" CA  TYR D 266 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.97  -24.03     0      5.00e+00 4.00e-02 2.31e+01
  dihedral pdb=" CA  TYR E 266 "
           pdb=" C   TYR E 266 "
           pdb=" N   ASP E 267 "
           pdb=" CA  ASP E 267 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.83   22.17     0      5.00e+00 4.00e-02 1.97e+01
  dihedral pdb=" CA  GLN D 322 "
           pdb=" C   GLN D 322 "
           pdb=" N   ASN D 323 "
           pdb=" CA  ASN D 323 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.09  -20.91     0      5.00e+00 4.00e-02 1.75e+01
  ... (remaining 2902 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 467
       0.031 -    0.062: 136
       0.062 -    0.092: 52
       0.092 -    0.123: 29
       0.123 -    0.154: 6
  Chirality restraints: 690
  Sorted by residual:
  chirality pdb=" CA  LEU D 160 "
            pdb=" N   LEU D 160 "
            pdb=" C   LEU D 160 "
            pdb=" CB  LEU D 160 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.90e-01
  chirality pdb=" CA  GLU D 164 "
            pdb=" N   GLU D 164 "
            pdb=" C   GLU D 164 "
            pdb=" CB  GLU D 164 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 5.16e-01
  chirality pdb=" CA  PRO E 197 "
            pdb=" N   PRO E 197 "
            pdb=" C   PRO E 197 "
            pdb=" CB  PRO E 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 5.03e-01
  ... (remaining 687 not shown)

  Planarity restraints: 851
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU E 348 "   -0.009 2.00e-02 2.50e+03   1.85e-02 3.43e+00
        pdb=" C   LEU E 348 "    0.032 2.00e-02 2.50e+03
        pdb=" O   LEU E 348 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   LYS E 349 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN D 240 "   -0.030 5.00e-02 4.00e+02   4.60e-02 3.38e+00
        pdb=" N   PRO D 241 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO D 241 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO D 241 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D  88 "   -0.027 5.00e-02 4.00e+02   4.11e-02 2.70e+00
        pdb=" N   PRO D  89 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO D  89 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO D  89 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 848 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.57: 65
        2.57 -     3.15: 4141
        3.15 -     3.73: 7324
        3.73 -     4.32: 10238
        4.32 -     4.90: 16541
  Nonbonded interactions: 38309
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E 252 "
            pdb=" OD1 ASP E 341 "
     model   vdw
     1.981 3.040
  nonbonded pdb=" OH  TYR D 252 "
            pdb=" OD1 ASP D 341 "
     model   vdw
     1.998 3.040
  nonbonded pdb=" OH  TYR D 260 "
            pdb=" OD2 ASP E 358 "
     model   vdw
     2.022 3.040
  nonbonded pdb=" O   LEU E 160 "
            pdb=" ND2 ASN E 161 "
     model   vdw
     2.061 3.120
  nonbonded pdb=" O   TYR E 260 "
            pdb=" OG  SER E 261 "
     model   vdw
     2.128 3.040
  ... (remaining 38304 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 'D' and resid 83 through 365)
  selection = chain 'E'
}

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 individual isotropic
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:             1.270
  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:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.420
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6860
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   0.032   4764  Z= 0.159
  Angle     :  0.592   5.193   6433  Z= 0.341
  Chirality :  0.040   0.154    690
  Planarity :  0.005   0.058    851
  Dihedral  : 14.698  89.457   1825
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  0.39 %
    Favored  : 99.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.35), residues: 564
  helix:  1.50 (0.33), residues: 243
  sheet:  0.82 (0.47), residues: 94
  loop : -0.31 (0.43), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 135 
 TYR   0.014   0.002   TYR E 266 
 PHE   0.020   0.002   PHE E 188 
 TRP   0.006   0.001   TRP D 189 
 HIS   0.003   0.001   HIS D 268 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 4764)
  covalent geometry    : angle       0.59195 ( 6433)
  hydrogen bonds       : bond        0.18456 (  248)
  hydrogen bonds       : angle       7.34237 (  711)

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

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

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 57
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 58
  average time/residue: 0.0911
  time to fit residues: 6.5077
Evaluate side-chains
  40 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  160 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 53 optimal weight:    0.6980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
D 294 ASN
E 161 ASN
** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.104661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.081785 restraints weight = 17740.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.3848 rms_B_bonded: 6.28
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7139
moved from start:          0.1746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4764  Z= 0.179
  Angle     :  0.662   6.284   6433  Z= 0.360
  Chirality :  0.044   0.151    690
  Planarity :  0.005   0.048    851
  Dihedral  :  6.204  25.936    606
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  7.14 %
    Favored  : 92.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.35), residues: 564
  helix:  1.13 (0.30), residues: 255
  sheet:  1.37 (0.46), residues: 92
  loop : -0.21 (0.47), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 135 
 TYR   0.020   0.002   TYR D  84 
 PHE   0.027   0.003   PHE E 188 
 TRP   0.011   0.002   TRP D 189 
 HIS   0.002   0.001   HIS E 268 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 4764)
  covalent geometry    : angle       0.66249 ( 6433)
  hydrogen bonds       : bond        0.05830 (  248)
  hydrogen bonds       : angle       6.06339 (  711)

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

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

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
REVERT: D  290 ARG cc_start: 0.8745 (mpp-170) cc_final: 0.8398 (mtm-85)
REVERT: D  335 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8421 (mm-30)
REVERT: D  346 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7235 (mp0)
REVERT: E  349 LYS cc_start: 0.7889 (tttt) cc_final: 0.7535 (tttp)
  outliers start: 4
  outliers final: 3
  residues processed: 48
  average time/residue: 0.0794
  time to fit residues: 4.7852
Evaluate side-chains
  40 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 37
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  160 LEU
Chi-restraints excluded: chain E residue  274 ILE
Chi-restraints excluded: chain E residue  352 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 19 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 52 optimal weight:    0.1980
   chunk 25 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 28 optimal weight:   10.0000
   chunk 44 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
E 268 HIS
** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.104210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.081910 restraints weight = 17232.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.3853 rms_B_bonded: 6.06
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7144
moved from start:          0.2326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4764  Z= 0.162
  Angle     :  0.621   6.352   6433  Z= 0.334
  Chirality :  0.044   0.168    690
  Planarity :  0.005   0.047    851
  Dihedral  :  6.065  27.605    606
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  :  8.69 %
    Favored  : 89.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.35), residues: 564
  helix:  1.07 (0.30), residues: 262
  sheet:  1.43 (0.49), residues: 92
  loop : -0.09 (0.48), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 290 
 TYR   0.022   0.002   TYR D  84 
 PHE   0.018   0.002   PHE D 233 
 TRP   0.009   0.001   TRP D 189 
 HIS   0.002   0.001   HIS E 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 4764)
  covalent geometry    : angle       0.62113 ( 6433)
  hydrogen bonds       : bond        0.05306 (  248)
  hydrogen bonds       : angle       5.82010 (  711)

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

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

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  335 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8525 (mm-30)
REVERT: D  346 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7180 (mp0)
  outliers start: 8
  outliers final: 5
  residues processed: 50
  average time/residue: 0.1060
  time to fit residues: 6.4697
Evaluate side-chains
  43 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  160 LEU
Chi-restraints excluded: chain D residue  248 LEU
Chi-restraints excluded: chain D residue  307 THR
Chi-restraints excluded: chain E residue  118 PHE
Chi-restraints excluded: chain E residue  274 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 22 optimal weight:    7.9990
   chunk 10 optimal weight:    0.0270
   chunk 47 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 25 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0870
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.105725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.082680 restraints weight = 17513.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.3873 rms_B_bonded: 6.32
r_work (final): 0.3873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7115
moved from start:          0.2644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4764  Z= 0.134
  Angle     :  0.599   7.731   6433  Z= 0.320
  Chirality :  0.043   0.160    690
  Planarity :  0.004   0.038    851
  Dihedral  :  5.848  27.046    606
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  :  9.65 %
    Favored  : 88.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.27 (0.36), residues: 564
  helix:  1.46 (0.31), residues: 251
  sheet:  1.31 (0.49), residues: 92
  loop :  0.03 (0.47), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 290 
 TYR   0.015   0.001   TYR D  84 
 PHE   0.016   0.002   PHE D 124 
 TRP   0.008   0.001   TRP E 359 
 HIS   0.002   0.001   HIS E 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 4764)
  covalent geometry    : angle       0.59949 ( 6433)
  hydrogen bonds       : bond        0.04989 (  248)
  hydrogen bonds       : angle       5.63349 (  711)

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

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

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  335 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8599 (mm-30)
REVERT: E  266 TYR cc_start: 0.7996 (p90) cc_final: 0.7741 (p90)
REVERT: E  346 GLU cc_start: 0.8794 (tp30) cc_final: 0.8470 (tp30)
  outliers start: 8
  outliers final: 5
  residues processed: 49
  average time/residue: 0.0720
  time to fit residues: 4.5253
Evaluate side-chains
  43 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  160 LEU
Chi-restraints excluded: chain D residue  248 LEU
Chi-restraints excluded: chain E residue  118 PHE
Chi-restraints excluded: chain E residue  274 ILE
Chi-restraints excluded: chain E residue  348 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0040
   chunk 25 optimal weight:    3.9990
   chunk 52 optimal weight:   10.0000
   chunk 55 optimal weight:    0.7980
   chunk 35 optimal weight:    9.9990
   chunk 51 optimal weight:    0.6980
   chunk 24 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    1.0996

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

Flipped N/Q/H residues before XYZ refinement:
** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 326 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.104253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.081179 restraints weight = 17731.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.3843 rms_B_bonded: 6.37
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7164
moved from start:          0.2922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4764  Z= 0.150
  Angle     :  0.589   7.372   6433  Z= 0.313
  Chirality :  0.042   0.156    690
  Planarity :  0.004   0.038    851
  Dihedral  :  5.736  26.766    606
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 11.39 %
    Favored  : 86.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.31 (0.36), residues: 564
  helix:  1.53 (0.32), residues: 251
  sheet:  0.78 (0.49), residues: 100
  loop :  0.25 (0.48), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 135 
 TYR   0.013   0.001   TYR D  84 
 PHE   0.014   0.002   PHE D 233 
 TRP   0.009   0.001   TRP D 189 
 HIS   0.002   0.001   HIS E 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 4764)
  covalent geometry    : angle       0.58949 ( 6433)
  hydrogen bonds       : bond        0.04945 (  248)
  hydrogen bonds       : angle       5.59382 (  711)

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

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

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  289 MET cc_start: 0.8942 (mmm) cc_final: 0.8623 (mmm)
REVERT: D  305 LYS cc_start: 0.9310 (pptt) cc_final: 0.8867 (pttt)
REVERT: D  335 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8654 (mm-30)
REVERT: E  249 CYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8624 (p)
REVERT: E  266 TYR cc_start: 0.8090 (p90) cc_final: 0.7816 (p90)
REVERT: E  346 GLU cc_start: 0.8810 (tp30) cc_final: 0.8480 (tp30)
  outliers start: 9
  outliers final: 5
  residues processed: 47
  average time/residue: 0.0704
  time to fit residues: 4.2866
Evaluate side-chains
  45 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  160 LEU
Chi-restraints excluded: chain E residue   85 VAL
Chi-restraints excluded: chain E residue  118 PHE
Chi-restraints excluded: chain E residue  249 CYS
Chi-restraints excluded: chain E residue  274 ILE
Chi-restraints excluded: chain E residue  348 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 21 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9980
   chunk 35 optimal weight:    9.9990
   chunk 43 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 50 optimal weight:    9.9990
   chunk 29 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0980
   chunk 23 optimal weight:    0.0020
   overall best weight:    0.5788

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

Flipped N/Q/H residues before XYZ refinement:
** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.105068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.083228 restraints weight = 17404.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.3896 rms_B_bonded: 6.05
r_work (final): 0.3896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7097
moved from start:          0.3156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4764  Z= 0.124
  Angle     :  0.568   8.111   6433  Z= 0.298
  Chirality :  0.041   0.150    690
  Planarity :  0.004   0.036    851
  Dihedral  :  5.542  26.922    606
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 11.20 %
    Favored  : 87.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.36), residues: 564
  helix:  1.56 (0.31), residues: 251
  sheet:  0.79 (0.51), residues: 100
  loop :  0.29 (0.48), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 301 
 TYR   0.011   0.001   TYR D  84 
 PHE   0.014   0.002   PHE D 124 
 TRP   0.006   0.001   TRP E 359 
 HIS   0.001   0.000   HIS D 268 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 4764)
  covalent geometry    : angle       0.56762 ( 6433)
  hydrogen bonds       : bond        0.04767 (  248)
  hydrogen bonds       : angle       5.43116 (  711)

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

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

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
REVERT: D  289 MET cc_start: 0.8808 (mmm) cc_final: 0.8501 (mmm)
REVERT: D  305 LYS cc_start: 0.9295 (pptt) cc_final: 0.8943 (pttt)
REVERT: D  335 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8733 (mm-30)
REVERT: E  249 CYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8554 (p)
REVERT: E  266 TYR cc_start: 0.8076 (p90) cc_final: 0.7839 (p90)
REVERT: E  346 GLU cc_start: 0.8848 (tp30) cc_final: 0.8534 (tp30)
  outliers start: 9
  outliers final: 5
  residues processed: 49
  average time/residue: 0.0800
  time to fit residues: 4.9244
Evaluate side-chains
  42 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  343 SER
Chi-restraints excluded: chain E residue   85 VAL
Chi-restraints excluded: chain E residue  118 PHE
Chi-restraints excluded: chain E residue  249 CYS
Chi-restraints excluded: chain E residue  274 ILE
Chi-restraints excluded: chain E residue  348 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0670
   chunk 42 optimal weight:    3.9990
   chunk 14 optimal weight:    0.5980
   chunk 32 optimal weight:    0.5980
   chunk 35 optimal weight:   10.0000
   chunk 48 optimal weight:    0.7980
   chunk 22 optimal weight:    6.9990
   chunk 16 optimal weight:    0.4980
   chunk 53 optimal weight:    0.4980
   overall best weight:    0.4518

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

Flipped N/Q/H residues before XYZ refinement:
E 292 GLN
** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.105304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.083005 restraints weight = 16997.985|
|-----------------------------------------------------------------------------|
r_work (start): 0.3900 rms_B_bonded: 6.22
r_work (final): 0.3900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7086
moved from start:          0.3331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   4764  Z= 0.120
  Angle     :  0.599   8.255   6433  Z= 0.305
  Chirality :  0.041   0.145    690
  Planarity :  0.004   0.037    851
  Dihedral  :  5.373  26.753    604
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 12.36 %
    Favored  : 86.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.40 (0.36), residues: 564
  helix:  1.62 (0.32), residues: 248
  sheet:  0.80 (0.52), residues: 99
  loop :  0.31 (0.47), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 301 
 TYR   0.011   0.001   TYR D  84 
 PHE   0.014   0.001   PHE D 124 
 TRP   0.005   0.001   TRP E 359 
 HIS   0.001   0.000   HIS D 268 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 4764)
  covalent geometry    : angle       0.59882 ( 6433)
  hydrogen bonds       : bond        0.04679 (  248)
  hydrogen bonds       : angle       5.33079 (  711)

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

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

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
REVERT: D  289 MET cc_start: 0.8855 (mmm) cc_final: 0.8568 (mmm)
REVERT: D  305 LYS cc_start: 0.9317 (pptt) cc_final: 0.8990 (pttt)
REVERT: D  335 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8753 (mm-30)
REVERT: E  117 MET cc_start: 0.8676 (ppp) cc_final: 0.8235 (ppp)
REVERT: E  249 CYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8541 (p)
REVERT: E  266 TYR cc_start: 0.8056 (p90) cc_final: 0.7849 (p90)
REVERT: E  346 GLU cc_start: 0.8901 (tp30) cc_final: 0.8607 (tp30)
  outliers start: 8
  outliers final: 5
  residues processed: 49
  average time/residue: 0.0597
  time to fit residues: 3.9137
Evaluate side-chains
  42 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  343 SER
Chi-restraints excluded: chain E residue   85 VAL
Chi-restraints excluded: chain E residue  118 PHE
Chi-restraints excluded: chain E residue  249 CYS
Chi-restraints excluded: chain E residue  274 ILE
Chi-restraints excluded: chain E residue  348 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 20 optimal weight:    0.4980
   chunk 31 optimal weight:    0.8980
   chunk 36 optimal weight:    7.9990
   chunk 33 optimal weight:    0.7980
   chunk 21 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   chunk 37 optimal weight:    6.9990
   chunk 46 optimal weight:    7.9990
   chunk 41 optimal weight:    4.9990
   chunk 18 optimal weight:    0.1980
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.103734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.081486 restraints weight = 17689.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3864 rms_B_bonded: 6.27
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7152
moved from start:          0.3431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4764  Z= 0.144
  Angle     :  0.599  11.626   6433  Z= 0.307
  Chirality :  0.041   0.144    690
  Planarity :  0.004   0.034    851
  Dihedral  :  5.368  26.802    604
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 13.13 %
    Favored  : 85.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.37), residues: 564
  helix:  1.65 (0.32), residues: 248
  sheet:  0.67 (0.53), residues: 101
  loop :  0.45 (0.48), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 301 
 TYR   0.023   0.002   TYR D 266 
 PHE   0.014   0.002   PHE D 233 
 TRP   0.009   0.001   TRP D 189 
 HIS   0.002   0.001   HIS E 268 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 4764)
  covalent geometry    : angle       0.59863 ( 6433)
  hydrogen bonds       : bond        0.04771 (  248)
  hydrogen bonds       : angle       5.37127 (  711)

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

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

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
REVERT: D  289 MET cc_start: 0.8838 (mmm) cc_final: 0.8586 (mmm)
REVERT: D  305 LYS cc_start: 0.9313 (pptt) cc_final: 0.9029 (pttt)
REVERT: D  335 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8753 (mm-30)
REVERT: E  117 MET cc_start: 0.8602 (ppp) cc_final: 0.8177 (ppp)
REVERT: E  249 CYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8579 (p)
REVERT: E  266 TYR cc_start: 0.8092 (p90) cc_final: 0.7889 (p90)
  outliers start: 7
  outliers final: 4
  residues processed: 45
  average time/residue: 0.0612
  time to fit residues: 3.6245
Evaluate side-chains
  40 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   85 VAL
Chi-restraints excluded: chain E residue  118 PHE
Chi-restraints excluded: chain E residue  249 CYS
Chi-restraints excluded: chain E residue  274 ILE
Chi-restraints excluded: chain E residue  348 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 18 optimal weight:    6.9990
   chunk 50 optimal weight:    9.9990
   chunk 36 optimal weight:    8.9990
   chunk 29 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0770
   overall best weight:    1.3944

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

Flipped N/Q/H residues before XYZ refinement:
** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.102603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.081016 restraints weight = 17483.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3846 rms_B_bonded: 6.02
r_work (final): 0.3846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7184
moved from start:          0.3544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4764  Z= 0.166
  Angle     :  0.651  10.477   6433  Z= 0.333
  Chirality :  0.044   0.234    690
  Planarity :  0.004   0.035    851
  Dihedral  :  5.450  26.775    604
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 14.29 %
    Favored  : 84.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.28 (0.37), residues: 564
  helix:  1.55 (0.31), residues: 248
  sheet:  0.40 (0.53), residues: 104
  loop :  0.41 (0.48), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D 135 
 TYR   0.021   0.002   TYR D 266 
 PHE   0.017   0.002   PHE D 233 
 TRP   0.010   0.001   TRP D 189 
 HIS   0.002   0.001   HIS E 268 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 4764)
  covalent geometry    : angle       0.65057 ( 6433)
  hydrogen bonds       : bond        0.04876 (  248)
  hydrogen bonds       : angle       5.42713 (  711)

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

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

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.141 
Fit side-chains
REVERT: D  289 MET cc_start: 0.8769 (mmm) cc_final: 0.8505 (mmm)
REVERT: D  305 LYS cc_start: 0.9312 (pptt) cc_final: 0.9031 (pttt)
REVERT: D  335 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8746 (mm-30)
REVERT: E  117 MET cc_start: 0.8542 (ppp) cc_final: 0.8102 (ppp)
REVERT: E  249 CYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8625 (p)
  outliers start: 6
  outliers final: 4
  residues processed: 41
  average time/residue: 0.0634
  time to fit residues: 3.4240
Evaluate side-chains
  37 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   85 VAL
Chi-restraints excluded: chain E residue  118 PHE
Chi-restraints excluded: chain E residue  249 CYS
Chi-restraints excluded: chain E residue  274 ILE
Chi-restraints excluded: chain E residue  348 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 12 optimal weight:    0.0570
   chunk 19 optimal weight:    1.9990
   chunk 37 optimal weight:    6.9990
   chunk 4 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0010
   chunk 11 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0370
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.3182

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

Flipped N/Q/H residues before XYZ refinement:
E 299 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.105317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.083126 restraints weight = 17452.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3895 rms_B_bonded: 6.21
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7107
moved from start:          0.3710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   4764  Z= 0.125
  Angle     :  0.650  10.326   6433  Z= 0.322
  Chirality :  0.042   0.215    690
  Planarity :  0.004   0.040    851
  Dihedral  :  5.385  26.864    604
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 14.48 %
    Favored  : 84.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.36 (0.37), residues: 564
  helix:  1.62 (0.32), residues: 248
  sheet:  0.49 (0.53), residues: 102
  loop :  0.40 (0.48), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E 293 
 TYR   0.016   0.002   TYR D 266 
 PHE   0.015   0.001   PHE D 124 
 TRP   0.009   0.001   TRP E 359 
 HIS   0.001   0.000   HIS D 268 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 4764)
  covalent geometry    : angle       0.65005 ( 6433)
  hydrogen bonds       : bond        0.04630 (  248)
  hydrogen bonds       : angle       5.30639 (  711)

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

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

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  289 MET cc_start: 0.8861 (mmm) cc_final: 0.8625 (mmm)
REVERT: D  305 LYS cc_start: 0.9322 (pptt) cc_final: 0.9097 (pttt)
REVERT: D  335 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8763 (mm-30)
REVERT: E  117 MET cc_start: 0.8563 (ppp) cc_final: 0.8142 (ppp)
REVERT: E  214 LEU cc_start: 0.8806 (tt) cc_final: 0.8587 (tt)
REVERT: E  249 CYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8528 (p)
  outliers start: 5
  outliers final: 3
  residues processed: 47
  average time/residue: 0.0676
  time to fit residues: 4.1177
Evaluate side-chains
  41 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  118 PHE
Chi-restraints excluded: chain E residue  249 CYS
Chi-restraints excluded: chain E residue  274 ILE
Chi-restraints excluded: chain E residue  348 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 55 optimal weight:    0.5980
   chunk 52 optimal weight:    0.0870
   chunk 4 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 8 optimal weight:   10.0000
   chunk 2 optimal weight:    0.7980
   chunk 30 optimal weight:    5.9990
   chunk 25 optimal weight:    8.9990
   chunk 36 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.6758

-------------------------------------------------------------------------------
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 = 0.4317 r_free = 0.4317 target = 0.104870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.082915 restraints weight = 17341.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3893 rms_B_bonded: 6.14
r_work (final): 0.3893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7100
moved from start:          0.3927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   4764  Z= 0.130
  Angle     :  0.643  10.257   6433  Z= 0.321
  Chirality :  0.042   0.224    690
  Planarity :  0.004   0.036    851
  Dihedral  :  5.334  26.703    604
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  : 15.06 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.39 (0.37), residues: 564
  helix:  1.64 (0.31), residues: 248
  sheet:  0.44 (0.54), residues: 103
  loop :  0.48 (0.48), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 293 
 TYR   0.020   0.002   TYR D 266 
 PHE   0.016   0.002   PHE E 188 
 TRP   0.024   0.002   TRP E 189 
 HIS   0.001   0.000   HIS E 268 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 4764)
  covalent geometry    : angle       0.64329 ( 6433)
  hydrogen bonds       : bond        0.04598 (  248)
  hydrogen bonds       : angle       5.25615 (  711)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1232.88 seconds
wall clock time: 21 minutes 41.85 seconds (1301.85 seconds total)