Starting phenix.real_space_refine
on Thu Mar  6 07:23:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6zlv_11275/03_2025/6zlv_11275.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6zlv_11275/03_2025/6zlv_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6zlv_11275/03_2025/6zlv_11275.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6zlv_11275/03_2025/6zlv_11275.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6zlv_11275/03_2025/6zlv_11275.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6zlv_11275/03_2025/6zlv_11275.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.43, per 1000 atoms: 0.83
  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: 1.35
  Conformation dependent library (CDL) restraints added in 712.2 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: 0.83
  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: 1.57

  Time building geometry restraints manager: 1.62 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  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:             1.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     18.280
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.310
-------------------------------------------------------------------------------
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= 0.689
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 HIS   0.012   0.004   HIS A 163 
 PHE   0.041   0.009   PHE A 115 
 TYR   0.054   0.013   TYR D 191 
 ARG   0.021   0.003   ARG C 190 

*********************** 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  : 0.643 
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: 0.2287
  time to fit residues: 48.2769
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  : 0.643 
-------------------------------------------------------------------------------
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 57 optimal weight:    6.9990
   chunk 51 optimal weight:    9.9990
   chunk 28 optimal weight:    4.9990
   chunk 17 optimal weight:   20.0000
   chunk 34 optimal weight:   20.0000
   chunk 27 optimal weight:    8.9990
   chunk 53 optimal weight:    1.9990
   chunk 20 optimal weight:    8.9990
   chunk 32 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 61 optimal weight:    7.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 117 GLN
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
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: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.080015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.065483 restraints weight = 11095.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.067871 restraints weight = 6545.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.069488 restraints weight = 4577.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.3971

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= 0.320
  Angle     :  0.760   7.346   7396  Z= 0.384
  Chirality :  0.052   0.148    896
  Planarity :  0.006   0.035    972
  Dihedral  :  5.717  38.713    772
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  :  6.97 %
    Favored  : 89.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.31), residues: 696
  helix:  0.51 (0.57), residues: 64
  sheet: -0.72 (0.30), residues: 304
  loop :  0.29 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B 227 
 PHE   0.014   0.001   PHE A 115 
 TYR   0.013   0.002   TYR C 249 
 ARG   0.007   0.001   ARG A 186 

*********************** 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: 18
    poor density    : 107
  time to evaluate  : 0.683 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 GLU cc_start: 0.6386 (mm-30) cc_final: 0.5540 (pt0)
REVERT: A  126 ASN cc_start: 0.7251 (m110) cc_final: 0.6892 (m-40)
REVERT: A  188 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6695 (mm-30)
REVERT: B   83 GLU cc_start: 0.6659 (mm-30) cc_final: 0.5396 (pt0)
REVERT: B  170 ASN cc_start: 0.7459 (t0) cc_final: 0.7195 (p0)
REVERT: D   83 GLU cc_start: 0.6713 (mm-30) cc_final: 0.5710 (pt0)
REVERT: D  170 ASN cc_start: 0.6712 (t0) cc_final: 0.6344 (p0)
REVERT: D  195 THR cc_start: 0.8111 (p) cc_final: 0.7855 (t)
  outliers start: 18
  outliers final: 5
  residues processed: 121
  average time/residue: 0.2537
  time to fit residues: 37.4047
Evaluate side-chains
  90 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain B residue  123 LYS
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  162 THR
Chi-restraints excluded: chain D residue  221 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 55 optimal weight:    6.9990
   chunk 17 optimal weight:   20.0000
   chunk 1 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9990
   chunk 63 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0980
   chunk 15 optimal weight:    8.9990
   chunk 20 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    2.4188

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.077166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.063551 restraints weight = 11981.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.065623 restraints weight = 7236.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.067079 restraints weight = 5127.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.4960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5432  Z= 0.211
  Angle     :  0.661   7.822   7396  Z= 0.324
  Chirality :  0.049   0.134    896
  Planarity :  0.005   0.034    972
  Dihedral  :  4.427  14.806    764
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 13.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 10.54 %
    Favored  : 87.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.32), residues: 696
  helix:  2.48 (0.61), residues: 64
  sheet: -0.56 (0.30), residues: 288
  loop :  0.46 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 163 
 PHE   0.007   0.001   PHE A 115 
 TYR   0.011   0.002   TYR A 249 
 ARG   0.005   0.001   ARG B 186 

*********************** 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
  111 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.675 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 GLU cc_start: 0.6702 (mm-30) cc_final: 0.5529 (pt0)
REVERT: B   83 GLU cc_start: 0.6884 (mm-30) cc_final: 0.5485 (pt0)
REVERT: C   83 GLU cc_start: 0.6726 (mm-30) cc_final: 0.5594 (pt0)
REVERT: C  123 LYS cc_start: 0.7979 (mmtt) cc_final: 0.7723 (mtpp)
REVERT: C  149 MET cc_start: 0.7767 (mpp) cc_final: 0.7058 (mpp)
REVERT: C  249 TYR cc_start: 0.7015 (m-80) cc_final: 0.6782 (m-80)
REVERT: D   83 GLU cc_start: 0.6918 (mm-30) cc_final: 0.5751 (pt0)
REVERT: D  126 ASN cc_start: 0.8338 (m110) cc_final: 0.7815 (m-40)
REVERT: D  195 THR cc_start: 0.7992 (p) cc_final: 0.7743 (t)
  outliers start: 13
  outliers final: 8
  residues processed: 105
  average time/residue: 0.2285
  time to fit residues: 29.8112
Evaluate side-chains
  85 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
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  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  226 ILE
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 24 optimal weight:    9.9990
   chunk 60 optimal weight:    7.9990
   chunk 42 optimal weight:   10.0000
   chunk 32 optimal weight:    6.9990
   chunk 43 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   chunk 57 optimal weight:    0.0000
   chunk 31 optimal weight:    3.9990
   chunk 63 optimal weight:    8.9990
   chunk 17 optimal weight:   20.0000
   chunk 6 optimal weight:   20.0000
   overall best weight:    4.3992

-------------------------------------------------------------------------------
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 = 0.3446 r_free = 0.3446 target = 0.076597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.062212 restraints weight = 11869.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.064437 restraints weight = 7007.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.065947 restraints weight = 4921.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.5741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   5432  Z= 0.311
  Angle     :  0.734   8.491   7396  Z= 0.358
  Chirality :  0.051   0.139    896
  Planarity :  0.005   0.033    972
  Dihedral  :  4.641  16.161    764
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 11.73 %
    Favored  : 85.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.32), residues: 696
  helix:  2.73 (0.61), residues: 64
  sheet: -0.97 (0.29), residues: 288
  loop :  0.55 (0.35), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 163 
 PHE   0.010   0.001   PHE A 115 
 TYR   0.014   0.002   TYR D 249 
 ARG   0.005   0.001   ARG B 118 

*********************** 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
  104 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 86
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 GLU cc_start: 0.7005 (mm-30) cc_final: 0.5339 (pt0)
REVERT: A  126 ASN cc_start: 0.7783 (m-40) cc_final: 0.7508 (m-40)
REVERT: B   83 GLU cc_start: 0.7184 (mm-30) cc_final: 0.5494 (pt0)
REVERT: B  123 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7105 (mtmm)
REVERT: B  223 LYS cc_start: 0.8399 (tttt) cc_final: 0.7709 (tttp)
REVERT: C   83 GLU cc_start: 0.7213 (mm-30) cc_final: 0.5587 (pt0)
REVERT: C  123 LYS cc_start: 0.8230 (mmtt) cc_final: 0.7925 (mmtm)
REVERT: C  149 MET cc_start: 0.7647 (mpp) cc_final: 0.6793 (mpp)
REVERT: C  249 TYR cc_start: 0.6857 (m-80) cc_final: 0.6574 (m-80)
REVERT: D   83 GLU cc_start: 0.7290 (mm-30) cc_final: 0.5951 (pt0)
REVERT: D  126 ASN cc_start: 0.8488 (m110) cc_final: 0.7946 (m-40)
  outliers start: 18
  outliers final: 12
  residues processed: 97
  average time/residue: 0.1935
  time to fit residues: 24.1273
Evaluate side-chains
  90 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
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  194 ASP
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
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 6 optimal weight:   20.0000
   chunk 21 optimal weight:    3.9990
   chunk 18 optimal weight:    7.9990
   chunk 62 optimal weight:    6.9990
   chunk 20 optimal weight:    7.9990
   chunk 23 optimal weight:    5.9990
   chunk 65 optimal weight:    7.9990
   chunk 48 optimal weight:    3.9990
   chunk 2 optimal weight:    9.9990
   chunk 54 optimal weight:    3.9990
   chunk 15 optimal weight:    9.9990
   overall best weight:    4.9990

-------------------------------------------------------------------------------
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 = 0.3423 r_free = 0.3423 target = 0.075322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.061192 restraints weight = 11696.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.063347 restraints weight = 6988.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.064839 restraints weight = 4926.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.6172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   5432  Z= 0.334
  Angle     :  0.748   9.486   7396  Z= 0.362
  Chirality :  0.051   0.139    896
  Planarity :  0.005   0.031    972
  Dihedral  :  4.667  15.971    764
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 13.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.32), residues: 696
  helix:  2.74 (0.58), residues: 64
  sheet: -1.26 (0.28), residues: 288
  loop :  0.56 (0.35), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 163 
 PHE   0.006   0.001   PHE B 115 
 TYR   0.011   0.002   TYR B 249 
 ARG   0.006   0.001   ARG B 186 

*********************** 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
  102 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.649 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 ASN cc_start: 0.8125 (m-40) cc_final: 0.7667 (m-40)
REVERT: A  142 MET cc_start: 0.7448 (mmm) cc_final: 0.6991 (ttt)
REVERT: B   83 GLU cc_start: 0.7471 (mm-30) cc_final: 0.5645 (pt0)
REVERT: B  106 GLU cc_start: 0.6289 (tp30) cc_final: 0.5907 (mm-30)
REVERT: B  120 MET cc_start: 0.8534 (tpp) cc_final: 0.8310 (mmm)
REVERT: B  123 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7168 (mtmm)
REVERT: C   83 GLU cc_start: 0.7319 (mm-30) cc_final: 0.5743 (pt0)
REVERT: C  123 LYS cc_start: 0.8377 (mmtt) cc_final: 0.8014 (mmmt)
REVERT: C  249 TYR cc_start: 0.6898 (m-80) cc_final: 0.6618 (m-80)
REVERT: D   83 GLU cc_start: 0.7369 (mm-30) cc_final: 0.5672 (pt0)
REVERT: D  126 ASN cc_start: 0.8585 (m110) cc_final: 0.7984 (m-40)
  outliers start: 15
  outliers final: 12
  residues processed: 97
  average time/residue: 0.1958
  time to fit residues: 24.2511
Evaluate side-chains
  88 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
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  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  199 LYS
Chi-restraints excluded: chain C residue  221 THR
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 54 optimal weight:    0.0050
   chunk 66 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9990
   chunk 55 optimal weight:    7.9990
   chunk 24 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 50 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 40 optimal weight:   10.0000
   overall best weight:    0.9800

-------------------------------------------------------------------------------
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 = 0.3495 r_free = 0.3495 target = 0.079171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.064866 restraints weight = 11344.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.067175 restraints weight = 6632.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.068822 restraints weight = 4608.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.6290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5432  Z= 0.170
  Angle     :  0.644   9.628   7396  Z= 0.314
  Chirality :  0.048   0.161    896
  Planarity :  0.004   0.030    972
  Dihedral  :  4.168  15.743    764
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 16.33 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.32), residues: 696
  helix:  3.34 (0.57), residues: 64
  sheet: -1.42 (0.28), residues: 292
  loop :  0.58 (0.35), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A 227 
 PHE   0.007   0.001   PHE A 115 
 TYR   0.004   0.001   TYR B 249 
 ARG   0.004   0.000   ARG B 186 

*********************** 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
  103 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.668 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 GLU cc_start: 0.7041 (mm-30) cc_final: 0.5655 (pt0)
REVERT: A  126 ASN cc_start: 0.8150 (m-40) cc_final: 0.7710 (m-40)
REVERT: A  142 MET cc_start: 0.7430 (mmm) cc_final: 0.7077 (ttt)
REVERT: B   83 GLU cc_start: 0.7318 (mm-30) cc_final: 0.5574 (pt0)
REVERT: B  223 LYS cc_start: 0.8380 (tttp) cc_final: 0.7969 (tttt)
REVERT: C   83 GLU cc_start: 0.7335 (mm-30) cc_final: 0.5692 (pt0)
REVERT: C  123 LYS cc_start: 0.8347 (mmtt) cc_final: 0.7889 (mmmt)
REVERT: D   83 GLU cc_start: 0.7307 (mm-30) cc_final: 0.5829 (pt0)
REVERT: D   90 GLU cc_start: 0.7425 (tp30) cc_final: 0.7117 (tt0)
REVERT: D  126 ASN cc_start: 0.8581 (m110) cc_final: 0.7879 (m-40)
  outliers start: 10
  outliers final: 5
  residues processed: 98
  average time/residue: 0.1997
  time to fit residues: 24.7996
Evaluate side-chains
  85 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 SER
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 D residue  247 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 40 optimal weight:   20.0000
   chunk 53 optimal weight:    6.9990
   chunk 58 optimal weight:    0.6980
   chunk 46 optimal weight:    9.9990
   chunk 59 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 57 optimal weight:    8.9990
   chunk 43 optimal weight:    8.9990
   chunk 32 optimal weight:    9.9990
   chunk 37 optimal weight:    0.5980
   chunk 48 optimal weight:    6.9990
   overall best weight:    2.4584

-------------------------------------------------------------------------------
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 = 0.3471 r_free = 0.3471 target = 0.077748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.063331 restraints weight = 11336.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.065556 restraints weight = 6747.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.067091 restraints weight = 4736.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.6455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5432  Z= 0.222
  Angle     :  0.696   8.763   7396  Z= 0.338
  Chirality :  0.049   0.146    896
  Planarity :  0.004   0.029    972
  Dihedral  :  4.336  17.893    764
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 16.50 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.32), residues: 696
  helix:  3.39 (0.58), residues: 64
  sheet: -1.45 (0.28), residues: 292
  loop :  0.69 (0.35), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 227 
 PHE   0.007   0.001   PHE A 115 
 TYR   0.007   0.001   TYR C 249 
 ARG   0.007   0.000   ARG D 186 

*********************** 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
  97 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.673 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 ASN cc_start: 0.8307 (m-40) cc_final: 0.8036 (m-40)
REVERT: A  142 MET cc_start: 0.7424 (mmm) cc_final: 0.7108 (ttt)
REVERT: A  223 LYS cc_start: 0.8256 (ttpp) cc_final: 0.7885 (ttpt)
REVERT: B   83 GLU cc_start: 0.7427 (mm-30) cc_final: 0.5580 (pt0)
REVERT: C   83 GLU cc_start: 0.7278 (mm-30) cc_final: 0.5704 (pt0)
REVERT: C  123 LYS cc_start: 0.8365 (mmtt) cc_final: 0.8006 (mmmt)
REVERT: D   83 GLU cc_start: 0.7282 (mm-30) cc_final: 0.5863 (pt0)
REVERT: D   90 GLU cc_start: 0.7293 (tp30) cc_final: 0.6952 (tt0)
REVERT: D  126 ASN cc_start: 0.8718 (m110) cc_final: 0.8124 (m110)
  outliers start: 12
  outliers final: 10
  residues processed: 91
  average time/residue: 0.1954
  time to fit residues: 22.8828
Evaluate side-chains
  88 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
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  226 ILE
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  106 GLU
Chi-restraints excluded: chain C residue  162 THR
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 66 optimal weight:   10.0000
   chunk 8 optimal weight:   10.0000
   chunk 39 optimal weight:    7.9990
   chunk 53 optimal weight:    0.8980
   chunk 67 optimal weight:    0.0370
   chunk 10 optimal weight:    0.0970
   chunk 30 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 22 optimal weight:    0.2980
   chunk 59 optimal weight:    5.9990
   overall best weight:    0.6658

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.079605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.065299 restraints weight = 11325.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.067599 restraints weight = 6584.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.069243 restraints weight = 4560.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.6579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5432  Z= 0.178
  Angle     :  0.675   8.331   7396  Z= 0.329
  Chirality :  0.048   0.137    896
  Planarity :  0.004   0.028    972
  Dihedral  :  4.159  18.037    764
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 17.35 %
    Favored  : 81.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.32), residues: 696
  helix:  3.63 (0.58), residues: 64
  sheet: -1.34 (0.28), residues: 292
  loop :  0.74 (0.35), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS D 163 
 PHE   0.007   0.000   PHE A 115 
 TYR   0.009   0.001   TYR B 249 
 ARG   0.004   0.000   ARG D 186 

*********************** 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
  97 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.670 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 ASN cc_start: 0.8222 (m-40) cc_final: 0.7881 (m-40)
REVERT: A  142 MET cc_start: 0.7369 (mmm) cc_final: 0.6979 (ttt)
REVERT: A  223 LYS cc_start: 0.8199 (ttpp) cc_final: 0.7872 (ttpt)
REVERT: B   83 GLU cc_start: 0.7251 (mm-30) cc_final: 0.5358 (pt0)
REVERT: B  133 GLN cc_start: 0.8408 (tt0) cc_final: 0.8182 (tt0)
REVERT: B  197 ASP cc_start: 0.6886 (p0) cc_final: 0.6644 (p0)
REVERT: C   83 GLU cc_start: 0.7290 (mm-30) cc_final: 0.5721 (pt0)
REVERT: C  123 LYS cc_start: 0.8372 (mmtt) cc_final: 0.7991 (mmmt)
REVERT: D   83 GLU cc_start: 0.7195 (mm-30) cc_final: 0.5801 (pt0)
REVERT: D   90 GLU cc_start: 0.7202 (tp30) cc_final: 0.6919 (tt0)
REVERT: D  126 ASN cc_start: 0.8671 (m110) cc_final: 0.8002 (m-40)
REVERT: D  244 MET cc_start: 0.7361 (mmt) cc_final: 0.6676 (mmt)
  outliers start: 9
  outliers final: 7
  residues processed: 92
  average time/residue: 0.2006
  time to fit residues: 23.3850
Evaluate side-chains
  88 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
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  226 ILE
Chi-restraints excluded: chain C residue  106 GLU
Chi-restraints excluded: chain C residue  162 THR
Chi-restraints excluded: chain C residue  226 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 4 optimal weight:    8.9990
   chunk 20 optimal weight:    8.9990
   chunk 22 optimal weight:    0.0970
   chunk 28 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 6 optimal weight:    9.9990
   chunk 51 optimal weight:   20.0000
   chunk 27 optimal weight:    0.7980
   chunk 35 optimal weight:   10.0000
   chunk 19 optimal weight:    7.9990
   chunk 18 optimal weight:    8.9990
   overall best weight:    3.9784

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

Flipped N/Q/H residues before XYZ refinement:
A  84 GLN
B 126 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.075238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.060992 restraints weight = 11794.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.063093 restraints weight = 7105.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.064582 restraints weight = 5038.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.6682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5432  Z= 0.297
  Angle     :  0.779   8.671   7396  Z= 0.378
  Chirality :  0.050   0.146    896
  Planarity :  0.004   0.031    972
  Dihedral  :  4.560  20.501    764
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 17.86 %
    Favored  : 80.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.00 (0.33), residues: 696
  helix:  3.20 (0.57), residues: 64
  sheet: -1.31 (0.29), residues: 284
  loop :  0.81 (0.36), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 163 
 PHE   0.006   0.001   PHE A 115 
 TYR   0.010   0.002   TYR C 249 
 ARG   0.005   0.000   ARG C 186 

*********************** 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
  96 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 LYS cc_start: 0.7941 (tptt) cc_final: 0.7732 (tptt)
REVERT: A  126 ASN cc_start: 0.8413 (m-40) cc_final: 0.8152 (m-40)
REVERT: A  142 MET cc_start: 0.7473 (mmm) cc_final: 0.7231 (ttm)
REVERT: A  223 LYS cc_start: 0.8276 (ttpp) cc_final: 0.7924 (ttpt)
REVERT: B  197 ASP cc_start: 0.6777 (p0) cc_final: 0.6538 (p0)
REVERT: C  123 LYS cc_start: 0.8546 (mmtt) cc_final: 0.8139 (mmmt)
REVERT: C  224 GLU cc_start: 0.8278 (pm20) cc_final: 0.7969 (pm20)
REVERT: D   83 GLU cc_start: 0.7327 (mm-30) cc_final: 0.5780 (pt0)
REVERT: D  126 ASN cc_start: 0.8716 (m110) cc_final: 0.7999 (m110)
REVERT: D  244 MET cc_start: 0.7505 (mmt) cc_final: 0.6854 (mmt)
  outliers start: 11
  outliers final: 9
  residues processed: 90
  average time/residue: 0.2053
  time to fit residues: 23.6212
Evaluate side-chains
  89 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
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  226 ILE
Chi-restraints excluded: chain C residue  106 GLU
Chi-restraints excluded: chain C residue  162 THR
Chi-restraints excluded: chain C residue  221 THR
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain D residue  226 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 31 optimal weight:    7.9990
   chunk 46 optimal weight:   20.0000
   chunk 57 optimal weight:    9.9990
   chunk 15 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 12 optimal weight:    5.9990
   chunk 35 optimal weight:   10.0000
   chunk 2 optimal weight:    9.9990
   chunk 65 optimal weight:   20.0000
   chunk 39 optimal weight:    8.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  84 GLN
D 126 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.073812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.059753 restraints weight = 11877.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.061947 restraints weight = 7071.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.063465 restraints weight = 4942.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.6920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   5432  Z= 0.411
  Angle     :  0.866   9.419   7396  Z= 0.419
  Chirality :  0.052   0.152    896
  Planarity :  0.005   0.035    972
  Dihedral  :  5.004  21.832    764
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 13.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 17.18 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.33), residues: 696
  helix:  2.14 (0.58), residues: 64
  sheet: -1.52 (0.28), residues: 284
  loop :  0.71 (0.36), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 163 
 PHE   0.010   0.001   PHE B 115 
 TYR   0.012   0.002   TYR D 191 
 ARG   0.007   0.001   ARG B 186 

********************** 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
  96 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  223 LYS cc_start: 0.8329 (ttpp) cc_final: 0.8030 (ttpt)
REVERT: B  197 ASP cc_start: 0.6860 (p0) cc_final: 0.6585 (p0)
REVERT: C  123 LYS cc_start: 0.8578 (mmtt) cc_final: 0.8046 (mmmt)
REVERT: C  224 GLU cc_start: 0.8331 (pm20) cc_final: 0.8010 (pm20)
REVERT: D  126 ASN cc_start: 0.8692 (m-40) cc_final: 0.8041 (m-40)
  outliers start: 11
  outliers final: 11
  residues processed: 91
  average time/residue: 0.2148
  time to fit residues: 24.7948
Evaluate side-chains
  86 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
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  226 ILE
Chi-restraints excluded: chain C residue  106 GLU
Chi-restraints excluded: chain C residue  131 VAL
Chi-restraints excluded: chain C residue  162 THR
Chi-restraints excluded: chain C residue  221 THR
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 2 optimal weight:    7.9990
   chunk 12 optimal weight:    2.9990
   chunk 43 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9990
   chunk 63 optimal weight:   10.0000
   chunk 45 optimal weight:    0.7980
   chunk 0 optimal weight:   20.0000
   chunk 31 optimal weight:    3.9990
   chunk 52 optimal weight:   10.0000
   overall best weight:    1.5588

-------------------------------------------------------------------------------
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 = 0.3468 r_free = 0.3468 target = 0.077384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.063160 restraints weight = 11546.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.065490 restraints weight = 6689.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.067101 restraints weight = 4606.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.6962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5432  Z= 0.224
  Angle     :  0.748   8.348   7396  Z= 0.366
  Chirality :  0.049   0.144    896
  Planarity :  0.004   0.034    972
  Dihedral  :  4.514  20.946    764
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 17.35 %
    Favored  : 80.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.32), residues: 696
  helix:  2.32 (0.54), residues: 64
  sheet: -1.55 (0.28), residues: 292
  loop :  0.75 (0.36), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 227 
 PHE   0.008   0.001   PHE A 115 
 TYR   0.008   0.001   TYR A 249 
 ARG   0.004   0.000   ARG D 118 

===============================================================================
Job complete
usr+sys time: 2241.08 seconds
wall clock time: 39 minutes 28.49 seconds (2368.49 seconds total)