Starting phenix.real_space_refine
on Tue Mar  3 13:36:36 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6zlv_11275/03_2026/6zlv_11275.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6zlv_11275/03_2026/6zlv_11275.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6zlv_11275/03_2026/6zlv_11275.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6zlv_11275/03_2026/6zlv_11275.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6zlv_11275/03_2026/6zlv_11275.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6zlv_11275/03_2026/6zlv_11275.map"
  }
  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
-------------------------------------------------------------------------------
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=   0.010
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      16      5.16       5
     C    3380      2.51       5
     N     944      2.21       5
     O    1012      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5352
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1338
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 176, 1338
          Classifications: {'peptide': 176}
          Link IDs: {'PTRANS': 10, 'TRANS': 165}
    Chain: "B"
      Number of atoms: 1338
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 176, 1338
          Classifications: {'peptide': 176}
          Link IDs: {'PTRANS': 10, 'TRANS': 165}
    Chain: "C"
      Number of atoms: 1338
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 176, 1338
          Classifications: {'peptide': 176}
          Link IDs: {'PTRANS': 10, 'TRANS': 165}
    Chain: "D"
      Number of atoms: 1338
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 176, 1338
          Classifications: {'peptide': 176}
          Link IDs: {'PTRANS': 10, 'TRANS': 165}
  Time building chain proxies: 1.10, per 1000 atoms: 0.21
  Number of scatterers: 5352
  At special positions: 0
  Unit cell: (75.978, 79.596, 121.806, 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      16     16.00
     O    1012      8.00
     N     944      7.00
     C    3380      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: 0.33
  Conformation dependent library (CDL) restraints added in 294.1 milliseconds
  

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1296

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 8 sheets defined
      14.3% alpha, 39.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 79 through 94
      removed outlier: 3.586A  pdb=" N   GLU A  83 " --> pdb=" O   ALA A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 128
    Processing helix  chain 'A' and resid 243 through 247
    Processing helix  chain 'B' and resid 80 through 94
    Processing helix  chain 'B' and resid 124 through 128
    Processing helix  chain 'B' and resid 243 through 247
    Processing helix  chain 'C' and resid 80 through 94
    Processing helix  chain 'C' and resid 124 through 128
    Processing helix  chain 'C' and resid 243 through 247
    Processing helix  chain 'D' and resid 80 through 94
    Processing helix  chain 'D' and resid 124 through 128
    Processing helix  chain 'D' and resid 243 through 247
    Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 110
      removed outlier: 4.218A  pdb=" N   GLY A 109 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
      removed outlier: 5.934A  pdb=" N   LEU A 156 " --> pdb=" O   VAL A 145 " (cutoff:3.500A)
      removed outlier: 5.510A  pdb=" N   VAL A 145 " --> pdb=" O   LEU A 156 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   VAL A 135 " --> pdb=" O   MET A 142 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 169
      removed outlier: 4.222A  pdb=" N   VAL A 236 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
      removed outlier: 5.912A  pdb=" N   VAL A 239 " --> pdb=" O   VAL A 222 " (cutoff:3.500A)
      removed outlier: 5.715A  pdb=" N   VAL A 222 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
      removed outlier: 5.692A  pdb=" N   SER A 206 " --> pdb=" O   PRO A 218 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 110
      removed outlier: 4.248A  pdb=" N   GLY B 109 " --> pdb=" O   MET B 120 " (cutoff:3.500A)
      removed outlier: 5.935A  pdb=" N   LEU B 156 " --> pdb=" O   VAL B 145 " (cutoff:3.500A)
      removed outlier: 5.516A  pdb=" N   VAL B 145 " --> pdb=" O   LEU B 156 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   VAL B 135 " --> pdb=" O   MET B 142 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 164 through 169
      removed outlier: 4.209A  pdb=" N   VAL B 236 " --> pdb=" O   LEU B 189 " (cutoff:3.500A)
      removed outlier: 5.900A  pdb=" N   VAL B 239 " --> pdb=" O   VAL B 222 " (cutoff:3.500A)
      removed outlier: 5.704A  pdb=" N   VAL B 222 " --> pdb=" O   VAL B 239 " (cutoff:3.500A)
      removed outlier: 5.703A  pdb=" N   SER B 206 " --> pdb=" O   PRO B 218 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 102 through 110
      removed outlier: 4.238A  pdb=" N   GLY C 109 " --> pdb=" O   MET C 120 " (cutoff:3.500A)
      removed outlier: 5.941A  pdb=" N   LEU C 156 " --> pdb=" O   VAL C 145 " (cutoff:3.500A)
      removed outlier: 5.514A  pdb=" N   VAL C 145 " --> pdb=" O   LEU C 156 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   VAL C 135 " --> pdb=" O   MET C 142 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 164 through 169
      removed outlier: 4.241A  pdb=" N   VAL C 236 " --> pdb=" O   LEU C 189 " (cutoff:3.500A)
      removed outlier: 5.913A  pdb=" N   VAL C 239 " --> pdb=" O   VAL C 222 " (cutoff:3.500A)
      removed outlier: 5.711A  pdb=" N   VAL C 222 " --> pdb=" O   VAL C 239 " (cutoff:3.500A)
      removed outlier: 5.693A  pdb=" N   SER C 206 " --> pdb=" O   PRO C 218 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 102 through 110
      removed outlier: 4.209A  pdb=" N   GLY D 109 " --> pdb=" O   MET D 120 " (cutoff:3.500A)
      removed outlier: 5.942A  pdb=" N   LEU D 156 " --> pdb=" O   VAL D 145 " (cutoff:3.500A)
      removed outlier: 5.515A  pdb=" N   VAL D 145 " --> pdb=" O   LEU D 156 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   VAL D 135 " --> pdb=" O   MET D 142 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 164 through 169
      removed outlier: 4.244A  pdb=" N   VAL D 236 " --> pdb=" O   LEU D 189 " (cutoff:3.500A)
      removed outlier: 5.906A  pdb=" N   VAL D 239 " --> pdb=" O   VAL D 222 " (cutoff:3.500A)
      removed outlier: 5.706A  pdb=" N   VAL D 222 " --> pdb=" O   VAL D 239 " (cutoff:3.500A)
      removed outlier: 5.695A  pdb=" N   SER D 206 " --> pdb=" O   PRO D 218 " (cutoff:3.500A)

    196 hydrogen bonds defined for protein.
    504 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: 0.65

  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:
        1.20 -     1.33: 1121
        1.33 -     1.45: 1188
        1.45 -     1.57: 3088
        1.57 -     1.70: 3
        1.70 -     1.82: 32
  Bond restraints: 5432
  Sorted by residual:
  bond pdb=" C   ILE B 108 "
       pdb=" N   GLY B 109 "
    ideal  model  delta    sigma   weight residual
    1.332  1.354 -0.022 6.60e-03 2.30e+04 1.16e+01
  bond pdb=" C   ILE C 108 "
       pdb=" N   GLY C 109 "
    ideal  model  delta    sigma   weight residual
    1.332  1.354 -0.022 6.60e-03 2.30e+04 1.08e+01
  bond pdb=" C   ILE D 108 "
       pdb=" N   GLY D 109 "
    ideal  model  delta    sigma   weight residual
    1.332  1.352 -0.020 6.60e-03 2.30e+04 9.55e+00
  bond pdb=" C   ILE A 108 "
       pdb=" N   GLY A 109 "
    ideal  model  delta    sigma   weight residual
    1.332  1.352 -0.020 6.60e-03 2.30e+04 9.09e+00
  bond pdb=" C   VAL A 236 "
       pdb=" O   VAL A 236 "
    ideal  model  delta    sigma   weight residual
    1.237  1.205  0.032 1.09e-02 8.42e+03 8.70e+00
  ... (remaining 5427 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.34: 6140
        2.34 -     4.68: 1056
        4.68 -     7.02: 174
        7.02 -     9.35: 20
        9.35 -    11.69: 6
  Bond angle restraints: 7396
  Sorted by residual:
  angle pdb=" C   THR A  82 "
        pdb=" N   GLU A  83 "
        pdb=" CA  GLU A  83 "
      ideal   model   delta    sigma   weight residual
     120.54  128.15   -7.61 1.35e+00 5.49e-01 3.18e+01
  angle pdb=" C   THR C  82 "
        pdb=" N   GLU C  83 "
        pdb=" CA  GLU C  83 "
      ideal   model   delta    sigma   weight residual
     120.54  128.11   -7.57 1.35e+00 5.49e-01 3.14e+01
  angle pdb=" C   THR D  82 "
        pdb=" N   GLU D  83 "
        pdb=" CA  GLU D  83 "
      ideal   model   delta    sigma   weight residual
     120.54  128.06   -7.52 1.35e+00 5.49e-01 3.10e+01
  angle pdb=" C   THR B  82 "
        pdb=" N   GLU B  83 "
        pdb=" CA  GLU B  83 "
      ideal   model   delta    sigma   weight residual
     120.54  127.97   -7.43 1.35e+00 5.49e-01 3.03e+01
  angle pdb=" CB  ARG D 175 "
        pdb=" CG  ARG D 175 "
        pdb=" CD  ARG D 175 "
      ideal   model   delta    sigma   weight residual
     111.30  122.99  -11.69 2.30e+00 1.89e-01 2.58e+01
  ... (remaining 7391 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.79: 3103
       15.79 -    31.57: 139
       31.57 -    47.35: 60
       47.35 -    63.14: 14
       63.14 -    78.92: 4
  Dihedral angle restraints: 3320
    sinusoidal: 1308
      harmonic: 2012
  Sorted by residual:
  dihedral pdb=" C   THR C 241 "
           pdb=" N   THR C 241 "
           pdb=" CA  THR C 241 "
           pdb=" CB  THR C 241 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -132.49   10.49     0      2.50e+00 1.60e-01 1.76e+01
  dihedral pdb=" C   THR A 241 "
           pdb=" N   THR A 241 "
           pdb=" CA  THR A 241 "
           pdb=" CB  THR A 241 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -132.16   10.16     0      2.50e+00 1.60e-01 1.65e+01
  dihedral pdb=" C   THR B 241 "
           pdb=" N   THR B 241 "
           pdb=" CA  THR B 241 "
           pdb=" CB  THR B 241 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -131.88    9.88     0      2.50e+00 1.60e-01 1.56e+01
  ... (remaining 3317 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 451
       0.079 -    0.158: 276
       0.158 -    0.237: 128
       0.237 -    0.316: 27
       0.316 -    0.395: 14
  Chirality restraints: 896
  Sorted by residual:
  chirality pdb=" CA  SER D 139 "
            pdb=" N   SER D 139 "
            pdb=" C   SER D 139 "
            pdb=" CB  SER D 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.40 2.00e-01 2.50e+01 3.91e+00
  chirality pdb=" CG  LEU B 204 "
            pdb=" CB  LEU B 204 "
            pdb=" CD1 LEU B 204 "
            pdb=" CD2 LEU B 204 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.20   -0.39 2.00e-01 2.50e+01 3.88e+00
  chirality pdb=" CA  SER A 139 "
            pdb=" N   SER A 139 "
            pdb=" C   SER A 139 "
            pdb=" CB  SER A 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.64e+00
  ... (remaining 893 not shown)

  Planarity restraints: 972
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE D 108 "   -0.022 2.00e-02 2.50e+03   4.36e-02 1.90e+01
        pdb=" C   ILE D 108 "    0.075 2.00e-02 2.50e+03
        pdb=" O   ILE D 108 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   GLY D 109 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 108 "   -0.021 2.00e-02 2.50e+03   4.16e-02 1.73e+01
        pdb=" C   ILE B 108 "    0.072 2.00e-02 2.50e+03
        pdb=" O   ILE B 108 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   GLY B 109 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE C 108 "   -0.020 2.00e-02 2.50e+03   4.07e-02 1.66e+01
        pdb=" C   ILE C 108 "    0.070 2.00e-02 2.50e+03
        pdb=" O   ILE C 108 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   GLY C 109 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 969 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 663
        2.76 -     3.29: 5020
        3.29 -     3.83: 8521
        3.83 -     4.36: 10848
        4.36 -     4.90: 18243
  Nonbonded interactions: 43295
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU C 188 "
            pdb=" NH2 ARG D 190 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" NH2 ARG C 190 "
            pdb=" OE1 GLU D 188 "
     model   vdw
     2.230 3.120
  nonbonded pdb=" OE1 GLN D 117 "
            pdb=" OG1 THR D 159 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" OE1 GLU A 188 "
            pdb=" NH2 ARG B 190 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" OE1 GLN B 117 "
            pdb=" OG1 THR B 159 "
     model   vdw
     2.240 3.040
  ... (remaining 43290 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

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:             3.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.910
  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:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
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      :  0.011   0.058   5432  Z= 0.667
  Angle     :  1.856  11.693   7396  Z= 1.212
  Chirality :  0.120   0.395    896
  Planarity :  0.010   0.049    972
  Dihedral  : 12.218  78.921   2024
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 19.37
  Ramachandran Plot:
    Outliers :  0.57 %
    Allowed  :  3.74 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  :  4.25 %
    Favored  : 93.03 %
  Cbeta Deviations :  0.62 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.53 (0.30), residues: 696
  helix: -3.69 (0.38), residues: 64
  sheet: -0.88 (0.30), residues: 256
  loop : -0.47 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.003   ARG C 190 
 TYR   0.054   0.013   TYR D 191 
 PHE   0.041   0.009   PHE A 115 
 HIS   0.012   0.004   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.01060 ( 5432)
  covalent geometry    : angle       1.85575 ( 7396)
  hydrogen bonds       : bond        0.19404 (  196)
  hydrogen bonds       : angle       8.48021 (  504)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 163
  time to evaluate  : 0.129 
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: A   89 ARG cc_start: 0.6101 (tpt90) cc_final: 0.5707 (mmp-170)
REVERT: A   97 LEU cc_start: 0.3451 (OUTLIER) cc_final: 0.1244 (tp)
REVERT: A  125 GLU cc_start: 0.7596 (tp30) cc_final: 0.6680 (pt0)
REVERT: A  133 GLN cc_start: 0.8409 (tt0) cc_final: 0.8189 (tt0)
REVERT: A  147 GLU cc_start: 0.8762 (tt0) cc_final: 0.8471 (pt0)
REVERT: A  152 THR cc_start: 0.8739 (p) cc_final: 0.8538 (t)
REVERT: A  184 PRO cc_start: 0.9107 (Cg_exo) cc_final: 0.8879 (Cg_endo)
REVERT: A  185 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7922 (tm-30)
REVERT: B   83 GLU cc_start: 0.5305 (mm-30) cc_final: 0.4393 (pt0)
REVERT: B   89 ARG cc_start: 0.6500 (tpt90) cc_final: 0.6070 (mmp-170)
REVERT: B   97 LEU cc_start: 0.3480 (OUTLIER) cc_final: 0.1993 (tp)
REVERT: B  125 GLU cc_start: 0.8238 (tp30) cc_final: 0.7563 (mt-10)
REVERT: B  133 GLN cc_start: 0.8833 (tt0) cc_final: 0.8624 (tt0)
REVERT: B  154 ARG cc_start: 0.8854 (mtt180) cc_final: 0.8626 (ttm110)
REVERT: C   89 ARG cc_start: 0.6160 (tpt90) cc_final: 0.5871 (mmp-170)
REVERT: C   90 GLU cc_start: 0.7320 (tp30) cc_final: 0.7024 (tt0)
REVERT: C   97 LEU cc_start: 0.3264 (OUTLIER) cc_final: 0.2134 (tp)
REVERT: C  125 GLU cc_start: 0.7516 (tp30) cc_final: 0.6734 (pt0)
REVERT: C  152 THR cc_start: 0.8683 (p) cc_final: 0.8443 (t)
REVERT: C  154 ARG cc_start: 0.8709 (mtt180) cc_final: 0.8401 (ttm-80)
REVERT: D   89 ARG cc_start: 0.6474 (tpt90) cc_final: 0.5986 (mmp-170)
REVERT: D   97 LEU cc_start: 0.3550 (OUTLIER) cc_final: 0.1669 (tp)
REVERT: D  125 GLU cc_start: 0.8017 (tp30) cc_final: 0.7334 (pt0)
REVERT: D  126 ASN cc_start: 0.7178 (m110) cc_final: 0.6535 (m110)
REVERT: D  170 ASN cc_start: 0.6916 (t0) cc_final: 0.6026 (p0)
REVERT: D  223 LYS cc_start: 0.9032 (tptt) cc_final: 0.8788 (tttm)
  outliers start: 16
  outliers final: 0
  residues processed: 174
  average time/residue: 0.0916
  time to fit residues: 19.4949
Evaluate side-chains
  113 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 109
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   97 LEU
Chi-restraints excluded: chain D residue   97 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 144 GLN
A 168 GLN
** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 144 GLN
B 168 GLN
C 113 ASN
** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 126 ASN
C 144 GLN
C 168 GLN
** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 144 GLN
D 168 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.082762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.067997 restraints weight = 10924.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.070492 restraints weight = 6371.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.072195 restraints weight = 4402.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.073438 restraints weight = 3385.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.074312 restraints weight = 2775.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.3531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5432  Z= 0.170
  Angle     :  0.699   5.798   7396  Z= 0.361
  Chirality :  0.051   0.154    896
  Planarity :  0.005   0.036    972
  Dihedral  :  5.476  36.004    772
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  :  7.65 %
    Favored  : 89.80 %
  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 are not related in a simple way.
  whole: -0.21 (0.30), residues: 696
  helix:  0.38 (0.52), residues: 64
  sheet: -0.37 (0.31), residues: 284
  loop :  0.16 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 186 
 TYR   0.012   0.002   TYR C 249 
 PHE   0.016   0.001   PHE A 115 
 HIS   0.003   0.001   HIS B 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 5432)
  covalent geometry    : angle       0.69897 ( 7396)
  hydrogen bonds       : bond        0.04494 (  196)
  hydrogen bonds       : angle       5.35248 (  504)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 GLU cc_start: 0.6080 (mm-30) cc_final: 0.5601 (pt0)
REVERT: A  101 LYS cc_start: 0.7430 (tptp) cc_final: 0.7195 (tptp)
REVERT: A  126 ASN cc_start: 0.6877 (m110) cc_final: 0.6318 (m-40)
REVERT: B   83 GLU cc_start: 0.6622 (mm-30) cc_final: 0.5490 (pt0)
REVERT: B  170 ASN cc_start: 0.7452 (t0) cc_final: 0.6977 (p0)
REVERT: C  149 MET cc_start: 0.7747 (mpp) cc_final: 0.7041 (mpp)
REVERT: C  152 THR cc_start: 0.8590 (p) cc_final: 0.8347 (p)
REVERT: D  149 MET cc_start: 0.7879 (mpt) cc_final: 0.7434 (mpp)
REVERT: D  170 ASN cc_start: 0.6635 (t0) cc_final: 0.6247 (p0)
REVERT: D  195 THR cc_start: 0.8015 (p) cc_final: 0.7746 (t)
  outliers start: 15
  outliers final: 2
  residues processed: 121
  average time/residue: 0.0958
  time to fit residues: 14.0806
Evaluate side-chains
  84 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 82
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain C residue   92 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 17 optimal weight:   20.0000
   chunk 59 optimal weight:   10.0000
   chunk 44 optimal weight:    7.9990
   chunk 64 optimal weight:    5.9990
   chunk 16 optimal weight:    9.9990
   chunk 8 optimal weight:    0.0370
   chunk 58 optimal weight:    7.9990
   chunk 51 optimal weight:   20.0000
   chunk 61 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    3.2066

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

Flipped N/Q/H residues before XYZ refinement:
A  84 GLN
A 117 GLN
A 133 GLN
B 117 GLN
C 117 GLN
D  84 GLN
D 117 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.076698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.063322 restraints weight = 12195.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.065414 restraints weight = 7304.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.066891 restraints weight = 5156.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.067900 restraints weight = 4005.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.068650 restraints weight = 3339.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.5002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5432  Z= 0.163
  Angle     :  0.707   7.481   7396  Z= 0.347
  Chirality :  0.050   0.134    896
  Planarity :  0.005   0.032    972
  Dihedral  :  4.587  15.145    764
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  :  9.69 %
    Favored  : 87.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.32), residues: 696
  helix:  2.28 (0.59), residues: 64
  sheet: -0.48 (0.30), residues: 288
  loop :  0.50 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 154 
 TYR   0.009   0.002   TYR A 249 
 PHE   0.007   0.001   PHE A 254 
 HIS   0.003   0.001   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 5432)
  covalent geometry    : angle       0.70699 ( 7396)
  hydrogen bonds       : bond        0.03968 (  196)
  hydrogen bonds       : angle       5.36419 (  504)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 GLU cc_start: 0.6539 (mm-30) cc_final: 0.5524 (pt0)
REVERT: A  126 ASN cc_start: 0.7154 (m110) cc_final: 0.6889 (m-40)
REVERT: B   83 GLU cc_start: 0.6912 (mm-30) cc_final: 0.5518 (pt0)
REVERT: C   83 GLU cc_start: 0.6757 (mm-30) cc_final: 0.5531 (pt0)
REVERT: C  123 LYS cc_start: 0.8078 (mmtt) cc_final: 0.7773 (mtpp)
REVERT: C  149 MET cc_start: 0.7574 (mpp) cc_final: 0.6844 (mpp)
REVERT: D   83 GLU cc_start: 0.6872 (mm-30) cc_final: 0.5764 (pt0)
REVERT: D  126 ASN cc_start: 0.8270 (m110) cc_final: 0.7778 (m-40)
REVERT: D  149 MET cc_start: 0.7856 (mpt) cc_final: 0.7219 (mpp)
REVERT: D  195 THR cc_start: 0.7890 (p) cc_final: 0.7664 (t)
  outliers start: 17
  outliers final: 10
  residues processed: 101
  average time/residue: 0.0817
  time to fit residues: 10.4070
Evaluate side-chains
  86 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  162 THR
Chi-restraints excluded: chain C residue  221 THR
Chi-restraints excluded: chain D residue  221 THR
Chi-restraints excluded: chain D residue  226 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 8 optimal weight:    9.9990
   chunk 3 optimal weight:    0.2980
   chunk 0 optimal weight:   20.0000
   chunk 41 optimal weight:    5.9990
   chunk 46 optimal weight:    0.5980
   chunk 27 optimal weight:    7.9990
   chunk 60 optimal weight:    9.9990
   chunk 9 optimal weight:    7.9990
   chunk 25 optimal weight:    5.9990
   chunk 39 optimal weight:    0.1980
   overall best weight:    2.4184

-------------------------------------------------------------------------------
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 = 0.3500 r_free = 0.3500 target = 0.079132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.065008 restraints weight = 11394.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.067316 restraints weight = 6671.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.068924 restraints weight = 4647.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.070028 restraints weight = 3589.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.070869 restraints weight = 2977.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.5407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5432  Z= 0.136
  Angle     :  0.661   7.985   7396  Z= 0.325
  Chirality :  0.048   0.129    896
  Planarity :  0.005   0.029    972
  Dihedral  :  4.357  14.938    764
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 10.71 %
    Favored  : 86.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.32), residues: 696
  helix:  2.88 (0.59), residues: 64
  sheet: -0.65 (0.30), residues: 288
  loop :  0.61 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 186 
 TYR   0.013   0.002   TYR D 249 
 PHE   0.007   0.001   PHE A 115 
 HIS   0.002   0.001   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 5432)
  covalent geometry    : angle       0.66081 ( 7396)
  hydrogen bonds       : bond        0.03411 (  196)
  hydrogen bonds       : angle       5.31925 (  504)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 GLU cc_start: 0.6572 (mm-30) cc_final: 0.5205 (pt0)
REVERT: A  142 MET cc_start: 0.7504 (mmm) cc_final: 0.7116 (ttt)
REVERT: B   83 GLU cc_start: 0.6942 (mm-30) cc_final: 0.5466 (pt0)
REVERT: B  223 LYS cc_start: 0.8239 (tttt) cc_final: 0.7624 (tttp)
REVERT: C   83 GLU cc_start: 0.6761 (mm-30) cc_final: 0.5531 (pt0)
REVERT: C  123 LYS cc_start: 0.8134 (mmtt) cc_final: 0.7848 (mmtm)
REVERT: C  149 MET cc_start: 0.7536 (mpp) cc_final: 0.7007 (mpp)
REVERT: D   83 GLU cc_start: 0.6916 (mm-30) cc_final: 0.5712 (pt0)
REVERT: D  126 ASN cc_start: 0.8408 (m110) cc_final: 0.7895 (m-40)
REVERT: D  149 MET cc_start: 0.7880 (mpt) cc_final: 0.7157 (mpp)
REVERT: D  195 THR cc_start: 0.7996 (p) cc_final: 0.7743 (t)
  outliers start: 17
  outliers final: 10
  residues processed: 94
  average time/residue: 0.0805
  time to fit residues: 9.7508
Evaluate side-chains
  79 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain B residue  123 LYS
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  139 SER
Chi-restraints excluded: chain C residue  162 THR
Chi-restraints excluded: chain C residue  221 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 13 optimal weight:    0.1980
   chunk 2 optimal weight:    4.9990
   chunk 12 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   chunk 22 optimal weight:   20.0000
   chunk 6 optimal weight:    8.9990
   chunk 28 optimal weight:    5.9990
   chunk 65 optimal weight:   10.0000
   chunk 58 optimal weight:   10.0000
   chunk 7 optimal weight:    6.9990
   overall best weight:    4.0388

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

Flipped N/Q/H residues before XYZ refinement:
C  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.075718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.061482 restraints weight = 12031.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.063570 restraints weight = 7291.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.065042 restraints weight = 5190.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.066045 restraints weight = 4079.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.066801 restraints weight = 3432.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.5967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5432  Z= 0.187
  Angle     :  0.725   8.844   7396  Z= 0.356
  Chirality :  0.050   0.136    896
  Planarity :  0.005   0.032    972
  Dihedral  :  4.654  15.194    764
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 11.90 %
    Favored  : 85.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.32), residues: 696
  helix:  2.87 (0.58), residues: 64
  sheet: -0.96 (0.29), residues: 284
  loop :  0.50 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 186 
 TYR   0.010   0.002   TYR C 249 
 PHE   0.009   0.001   PHE A 115 
 HIS   0.004   0.001   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 5432)
  covalent geometry    : angle       0.72488 ( 7396)
  hydrogen bonds       : bond        0.03670 (  196)
  hydrogen bonds       : angle       5.65269 (  504)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 GLU cc_start: 0.7010 (mm-30) cc_final: 0.5399 (pt0)
REVERT: A  126 ASN cc_start: 0.7764 (m110) cc_final: 0.7546 (m-40)
REVERT: A  142 MET cc_start: 0.7423 (mmm) cc_final: 0.7068 (ttt)
REVERT: B   83 GLU cc_start: 0.7304 (mm-30) cc_final: 0.5605 (pt0)
REVERT: C   83 GLU cc_start: 0.7205 (mm-30) cc_final: 0.5540 (pt0)
REVERT: C  123 LYS cc_start: 0.8349 (mmtt) cc_final: 0.8001 (mmmt)
REVERT: C  224 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7763 (pm20)
REVERT: D   83 GLU cc_start: 0.7123 (mm-30) cc_final: 0.5722 (pt0)
REVERT: D  126 ASN cc_start: 0.8493 (m110) cc_final: 0.7880 (m-40)
REVERT: D  149 MET cc_start: 0.7844 (mpt) cc_final: 0.7039 (mpp)
  outliers start: 16
  outliers final: 11
  residues processed: 96
  average time/residue: 0.0731
  time to fit residues: 9.0611
Evaluate side-chains
  89 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  123 LYS
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  162 THR
Chi-restraints excluded: chain C residue  221 THR
Chi-restraints excluded: chain C residue  224 GLU
Chi-restraints excluded: chain D residue  247 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 30 optimal weight:   10.0000
   chunk 10 optimal weight:    8.9990
   chunk 42 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0000
   chunk 67 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9980
   chunk 55 optimal weight:    9.9990
   chunk 56 optimal weight:    4.9990
   chunk 36 optimal weight:    6.9990
   overall best weight:    2.1990

-------------------------------------------------------------------------------
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 = 0.3479 r_free = 0.3479 target = 0.078460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.064068 restraints weight = 11657.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.066377 restraints weight = 6749.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.067991 restraints weight = 4674.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.069082 restraints weight = 3597.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.069902 restraints weight = 2991.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.6148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5432  Z= 0.127
  Angle     :  0.635   8.077   7396  Z= 0.313
  Chirality :  0.048   0.129    896
  Planarity :  0.004   0.030    972
  Dihedral  :  4.314  15.913    764
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 11.90 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.32), residues: 696
  helix:  3.32 (0.58), residues: 64
  sheet: -1.13 (0.29), residues: 292
  loop :  0.56 (0.35), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 186 
 TYR   0.009   0.001   TYR D 249 
 PHE   0.006   0.001   PHE A 115 
 HIS   0.002   0.001   HIS A 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 5432)
  covalent geometry    : angle       0.63539 ( 7396)
  hydrogen bonds       : bond        0.03148 (  196)
  hydrogen bonds       : angle       5.38581 (  504)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 GLU cc_start: 0.7045 (mm-30) cc_final: 0.5478 (pt0)
REVERT: A  126 ASN cc_start: 0.7842 (m110) cc_final: 0.7422 (m-40)
REVERT: A  142 MET cc_start: 0.7465 (mmm) cc_final: 0.7124 (ttt)
REVERT: A  223 LYS cc_start: 0.8295 (tttt) cc_final: 0.8091 (ttpt)
REVERT: B   83 GLU cc_start: 0.7222 (mm-30) cc_final: 0.5536 (pt0)
REVERT: B  223 LYS cc_start: 0.8396 (tttp) cc_final: 0.8107 (tttm)
REVERT: C   83 GLU cc_start: 0.7171 (mm-30) cc_final: 0.5592 (pt0)
REVERT: C  123 LYS cc_start: 0.8354 (mmtt) cc_final: 0.7984 (mmmt)
REVERT: C  149 MET cc_start: 0.7343 (mpp) cc_final: 0.6805 (mtm)
REVERT: C  224 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7847 (pm20)
REVERT: D   83 GLU cc_start: 0.7241 (mm-30) cc_final: 0.5839 (pt0)
REVERT: D  126 ASN cc_start: 0.8534 (m110) cc_final: 0.7795 (m-40)
REVERT: D  149 MET cc_start: 0.7839 (mpt) cc_final: 0.7388 (mpp)
REVERT: D  151 TYR cc_start: 0.7676 (m-80) cc_final: 0.7365 (m-80)
  outliers start: 14
  outliers final: 11
  residues processed: 95
  average time/residue: 0.0907
  time to fit residues: 10.7644
Evaluate side-chains
  88 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain B residue  123 LYS
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  162 THR
Chi-restraints excluded: chain C residue  221 THR
Chi-restraints excluded: chain C residue  224 GLU
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain D residue  226 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 35 optimal weight:   10.0000
   chunk 40 optimal weight:    8.9990
   chunk 24 optimal weight:   10.0000
   chunk 66 optimal weight:    8.9990
   chunk 48 optimal weight:    9.9990
   chunk 64 optimal weight:    5.9990
   chunk 11 optimal weight:    0.1980
   chunk 55 optimal weight:    9.9990
   chunk 29 optimal weight:    6.9990
   chunk 4 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   overall best weight:    4.2388

-------------------------------------------------------------------------------
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 = 0.3427 r_free = 0.3427 target = 0.075669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.061503 restraints weight = 11802.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.063662 restraints weight = 6894.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.065196 restraints weight = 4835.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.066284 restraints weight = 3759.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.067029 restraints weight = 3125.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.6402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   5432  Z= 0.189
  Angle     :  0.723   8.649   7396  Z= 0.350
  Chirality :  0.050   0.151    896
  Planarity :  0.005   0.033    972
  Dihedral  :  4.563  17.149    764
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 13.78 %
    Favored  : 83.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.32), residues: 696
  helix:  3.10 (0.58), residues: 64
  sheet: -1.28 (0.28), residues: 292
  loop :  0.60 (0.35), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 186 
 TYR   0.010   0.002   TYR C 249 
 PHE   0.007   0.001   PHE B 115 
 HIS   0.003   0.001   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 5432)
  covalent geometry    : angle       0.72251 ( 7396)
  hydrogen bonds       : bond        0.03620 (  196)
  hydrogen bonds       : angle       5.70116 (  504)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 ASN cc_start: 0.8073 (m110) cc_final: 0.7607 (m110)
REVERT: A  142 MET cc_start: 0.7516 (mmm) cc_final: 0.7279 (ttm)
REVERT: A  223 LYS cc_start: 0.8365 (tttt) cc_final: 0.8161 (ttpt)
REVERT: C   83 GLU cc_start: 0.7402 (mm-30) cc_final: 0.5772 (pt0)
REVERT: C  123 LYS cc_start: 0.8587 (mmtt) cc_final: 0.8174 (mmmt)
REVERT: C  149 MET cc_start: 0.7200 (mpp) cc_final: 0.6979 (mtm)
REVERT: C  224 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7869 (pm20)
REVERT: D   83 GLU cc_start: 0.7299 (mm-30) cc_final: 0.5873 (pt0)
REVERT: D  126 ASN cc_start: 0.8551 (m110) cc_final: 0.7824 (m-40)
  outliers start: 15
  outliers final: 11
  residues processed: 91
  average time/residue: 0.0775
  time to fit residues: 8.9920
Evaluate side-chains
  86 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain B residue  123 LYS
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  162 THR
Chi-restraints excluded: chain C residue  221 THR
Chi-restraints excluded: chain C residue  224 GLU
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain D residue  226 ILE
Chi-restraints excluded: chain D residue  247 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 28 optimal weight:    9.9990
   chunk 55 optimal weight:    7.9990
   chunk 36 optimal weight:    5.9990
   chunk 56 optimal weight:    8.9990
   chunk 59 optimal weight:   10.0000
   chunk 14 optimal weight:    0.6980
   chunk 62 optimal weight:    5.9990
   chunk 48 optimal weight:    6.9990
   chunk 11 optimal weight:    8.9990
   chunk 43 optimal weight:    7.9990
   overall best weight:    5.1388

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

Flipped N/Q/H residues before XYZ refinement:
B 126 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.074372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.060372 restraints weight = 11787.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.062563 restraints weight = 6993.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.064070 restraints weight = 4899.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.065148 restraints weight = 3817.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.065886 restraints weight = 3177.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.6702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   5432  Z= 0.220
  Angle     :  0.792  11.426   7396  Z= 0.380
  Chirality :  0.051   0.156    896
  Planarity :  0.005   0.035    972
  Dihedral  :  4.796  22.406    764
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 14.12 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.34 (0.32), residues: 696
  helix:  2.40 (0.59), residues: 64
  sheet: -1.42 (0.28), residues: 292
  loop :  0.66 (0.36), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 186 
 TYR   0.011   0.002   TYR C 249 
 PHE   0.009   0.001   PHE B 115 
 HIS   0.004   0.001   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 ( 5432)
  covalent geometry    : angle       0.79177 ( 7396)
  hydrogen bonds       : bond        0.03805 (  196)
  hydrogen bonds       : angle       5.90109 (  504)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 MET cc_start: 0.7572 (mmm) cc_final: 0.7349 (ttm)
REVERT: C  123 LYS cc_start: 0.8602 (mmtt) cc_final: 0.8156 (mmmt)
REVERT: C  224 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7869 (pm20)
REVERT: D   83 GLU cc_start: 0.7405 (mm-30) cc_final: 0.5689 (pt0)
REVERT: D  126 ASN cc_start: 0.8574 (m110) cc_final: 0.7947 (m-40)
  outliers start: 16
  outliers final: 12
  residues processed: 86
  average time/residue: 0.0764
  time to fit residues: 8.5205
Evaluate side-chains
  82 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain B residue  123 LYS
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  162 THR
Chi-restraints excluded: chain C residue  221 THR
Chi-restraints excluded: chain C residue  224 GLU
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain D residue  226 ILE
Chi-restraints excluded: chain D residue  247 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 51 optimal weight:   20.0000
   chunk 58 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   chunk 52 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   chunk 4 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 35 optimal weight:    6.9990
   chunk 29 optimal weight:   10.0000
   chunk 57 optimal weight:    7.9990
   chunk 46 optimal weight:    6.9990
   overall best weight:    4.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 126 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.074345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.060229 restraints weight = 11982.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.062481 restraints weight = 7050.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.064023 restraints weight = 4912.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.065098 restraints weight = 3812.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.065885 restraints weight = 3167.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.6817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   5432  Z= 0.205
  Angle     :  0.780   9.550   7396  Z= 0.376
  Chirality :  0.050   0.144    896
  Planarity :  0.005   0.036    972
  Dihedral  :  4.857  19.929    764
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 14.97 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.33), residues: 696
  helix:  2.23 (0.58), residues: 64
  sheet: -1.31 (0.29), residues: 296
  loop :  0.68 (0.36), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 186 
 TYR   0.010   0.002   TYR C 249 
 PHE   0.009   0.001   PHE B 115 
 HIS   0.003   0.001   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 ( 5432)
  covalent geometry    : angle       0.77970 ( 7396)
  hydrogen bonds       : bond        0.03688 (  196)
  hydrogen bonds       : angle       5.87487 (  504)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 GLU cc_start: 0.7300 (tp30) cc_final: 0.6790 (tt0)
REVERT: A  126 ASN cc_start: 0.8218 (m-40) cc_final: 0.7816 (m-40)
REVERT: A  223 LYS cc_start: 0.8455 (tttt) cc_final: 0.8203 (ttpt)
REVERT: C  123 LYS cc_start: 0.8564 (mmtt) cc_final: 0.8130 (mmmt)
REVERT: C  224 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7851 (pm20)
REVERT: D   83 GLU cc_start: 0.7308 (mm-30) cc_final: 0.5669 (pt0)
REVERT: D  126 ASN cc_start: 0.8618 (m110) cc_final: 0.8049 (m-40)
  outliers start: 14
  outliers final: 9
  residues processed: 85
  average time/residue: 0.0781
  time to fit residues: 8.4517
Evaluate side-chains
  81 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain B residue  123 LYS
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  162 THR
Chi-restraints excluded: chain C residue  221 THR
Chi-restraints excluded: chain C residue  224 GLU
Chi-restraints excluded: chain D residue  247 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 53 optimal weight:    0.8980
   chunk 24 optimal weight:    6.9990
   chunk 12 optimal weight:    0.0970
   chunk 29 optimal weight:    0.7980
   chunk 65 optimal weight:   10.0000
   chunk 5 optimal weight:   20.0000
   chunk 54 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 62 optimal weight:    7.9990
   chunk 20 optimal weight:    8.9990
   overall best weight:    1.9582

-------------------------------------------------------------------------------
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 = 0.3447 r_free = 0.3447 target = 0.076601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.062786 restraints weight = 11652.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.065098 restraints weight = 6778.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.066636 restraints weight = 4672.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.067772 restraints weight = 3606.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.068601 restraints weight = 2971.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.6845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5432  Z= 0.138
  Angle     :  0.730   9.445   7396  Z= 0.354
  Chirality :  0.049   0.141    896
  Planarity :  0.004   0.033    972
  Dihedral  :  4.566  21.015    764
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 15.48 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.32 (0.33), residues: 696
  helix:  2.50 (0.57), residues: 64
  sheet: -1.43 (0.29), residues: 300
  loop :  0.73 (0.36), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 186 
 TYR   0.007   0.001   TYR C 249 
 PHE   0.008   0.001   PHE A 115 
 HIS   0.001   0.001   HIS A 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 5432)
  covalent geometry    : angle       0.72995 ( 7396)
  hydrogen bonds       : bond        0.03177 (  196)
  hydrogen bonds       : angle       5.58949 (  504)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  223 LYS cc_start: 0.8399 (tttt) cc_final: 0.8192 (ttpt)
REVERT: C  123 LYS cc_start: 0.8501 (mmtt) cc_final: 0.8076 (mmmt)
REVERT: C  224 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7785 (pm20)
REVERT: D   83 GLU cc_start: 0.7256 (mm-30) cc_final: 0.5845 (pt0)
REVERT: D  126 ASN cc_start: 0.8574 (m110) cc_final: 0.8022 (m-40)
  outliers start: 11
  outliers final: 9
  residues processed: 88
  average time/residue: 0.0805
  time to fit residues: 9.0455
Evaluate side-chains
  85 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain B residue  123 LYS
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  162 THR
Chi-restraints excluded: chain C residue  221 THR
Chi-restraints excluded: chain C residue  224 GLU
Chi-restraints excluded: chain D residue  247 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    4.9990
   chunk 57 optimal weight:    9.9990
   chunk 38 optimal weight:    8.9990
   chunk 44 optimal weight:    0.9990
   chunk 53 optimal weight:    9.9990
   chunk 3 optimal weight:    3.9990
   chunk 14 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   overall best weight:    2.3188

-------------------------------------------------------------------------------
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 = 0.3443 r_free = 0.3443 target = 0.076466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.062642 restraints weight = 11612.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.064966 restraints weight = 6695.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.066575 restraints weight = 4610.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.067700 restraints weight = 3531.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.068522 restraints weight = 2907.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.6927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5432  Z= 0.145
  Angle     :  0.734   9.112   7396  Z= 0.356
  Chirality :  0.049   0.138    896
  Planarity :  0.004   0.035    972
  Dihedral  :  4.517  20.001    764
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 16.16 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.30 (0.33), residues: 696
  helix:  2.64 (0.57), residues: 64
  sheet: -1.43 (0.29), residues: 300
  loop :  0.73 (0.36), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 186 
 TYR   0.008   0.001   TYR C 249 
 PHE   0.009   0.001   PHE A 115 
 HIS   0.002   0.001   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 5432)
  covalent geometry    : angle       0.73404 ( 7396)
  hydrogen bonds       : bond        0.03205 (  196)
  hydrogen bonds       : angle       5.50714 (  504)

===============================================================================
Job complete
usr+sys time: 1087.93 seconds
wall clock time: 19 minutes 23.16 seconds (1163.16 seconds total)