Starting phenix.real_space_refine
on Tue Feb 11 07:52:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pkd_17735/02_2025/8pkd_17735.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pkd_17735/02_2025/8pkd_17735.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.33
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pkd_17735/02_2025/8pkd_17735.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pkd_17735/02_2025/8pkd_17735.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pkd_17735/02_2025/8pkd_17735.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pkd_17735/02_2025/8pkd_17735.cif"
  }
  resolution = 2.33
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.083
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       8      5.16       5
     C    3048      2.51       5
     N     872      2.21       5
     O     916      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4844
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1207
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 150, 1207
          Classifications: {'peptide': 150}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 144}
    Chain: "B"
      Number of atoms: 1207
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 150, 1207
          Classifications: {'peptide': 150}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 144}
    Chain: "C"
      Number of atoms: 1207
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 150, 1207
          Classifications: {'peptide': 150}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 144}
    Chain: "D"
      Number of atoms: 1207
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 150, 1207
          Classifications: {'peptide': 150}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 144}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Classifications: {'water': 5}
          Link IDs: {None: 4}
    Chain: "C"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "D"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 3.55, per 1000 atoms: 0.73
  Number of scatterers: 4844
  At special positions: 0
  Unit cell: (72.927, 79.497, 77.526, 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       8     16.00
     O     916      8.00
     N     872      7.00
     C    3048      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: 1.24
  Conformation dependent library (CDL) restraints added in 593.0 milliseconds
  

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1128

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 4 sheets defined
      59.5% alpha, 13.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 12
    Processing helix  chain 'A' and resid 18 through 33
    Processing helix  chain 'A' and resid 34 through 53
    Processing helix  chain 'A' and resid 60 through 74
      removed outlier: 3.848A  pdb=" N   THR A  74 " --> pdb=" O   GLY A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 103
    Processing helix  chain 'A' and resid 106 through 111
      removed outlier: 3.592A  pdb=" N   ALA A 111 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 125
      removed outlier: 3.764A  pdb=" N   GLU A 119 " --> pdb=" O   GLU A 115 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLN A 120 " --> pdb=" O   GLY A 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 12
    Processing helix  chain 'B' and resid 18 through 33
    Processing helix  chain 'B' and resid 34 through 53
    Processing helix  chain 'B' and resid 60 through 74
      removed outlier: 3.859A  pdb=" N   THR B  74 " --> pdb=" O   GLY B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 103
    Processing helix  chain 'B' and resid 106 through 111
      removed outlier: 3.605A  pdb=" N   ALA B 111 " --> pdb=" O   LEU B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 125
      removed outlier: 3.766A  pdb=" N   GLU B 119 " --> pdb=" O   GLU B 115 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   GLN B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 3 through 12
    Processing helix  chain 'C' and resid 18 through 33
    Processing helix  chain 'C' and resid 34 through 53
    Processing helix  chain 'C' and resid 60 through 74
      removed outlier: 3.845A  pdb=" N   THR C  74 " --> pdb=" O   GLY C  70 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 97 through 103
    Processing helix  chain 'C' and resid 106 through 111
      removed outlier: 3.556A  pdb=" N   ALA C 111 " --> pdb=" O   LEU C 107 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 111 through 125
      removed outlier: 3.750A  pdb=" N   GLU C 119 " --> pdb=" O   GLU C 115 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLN C 120 " --> pdb=" O   GLY C 116 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 12
    Processing helix  chain 'D' and resid 18 through 33
    Processing helix  chain 'D' and resid 34 through 53
    Processing helix  chain 'D' and resid 60 through 74
      removed outlier: 3.827A  pdb=" N   THR D  74 " --> pdb=" O   GLY D  70 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 97 through 103
    Processing helix  chain 'D' and resid 106 through 111
      removed outlier: 3.574A  pdb=" N   ALA D 111 " --> pdb=" O   LEU D 107 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 111 through 125
      removed outlier: 3.743A  pdb=" N   GLU D 119 " --> pdb=" O   GLU D 115 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLN D 120 " --> pdb=" O   GLY D 116 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 85
      removed outlier: 3.725A  pdb=" N   LEU A  89 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 79 through 85
      removed outlier: 3.638A  pdb=" N   LEU B  89 " --> pdb=" O   LEU B 149 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 79 through 85
      removed outlier: 3.697A  pdb=" N   LEU C  89 " --> pdb=" O   LEU C 149 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 79 through 85
      removed outlier: 3.673A  pdb=" N   LEU D  89 " --> pdb=" O   LEU D 149 " (cutoff:3.500A)

    297 hydrogen bonds defined for protein.
    843 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: 1.33

  Time building geometry restraints manager: 1.42 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1656
        1.34 -     1.46: 1076
        1.46 -     1.57: 2212
        1.57 -     1.69: 0
        1.69 -     1.80: 16
  Bond restraints: 4960
  Sorted by residual:
  bond pdb=" C   ALA D  96 "
       pdb=" N   PRO D  97 "
    ideal  model  delta    sigma   weight residual
    1.334  1.328  0.006 8.40e-03 1.42e+04 4.32e-01
  bond pdb=" CA  ALA D 101 "
       pdb=" CB  ALA D 101 "
    ideal  model  delta    sigma   weight residual
    1.533  1.525  0.008 1.46e-02 4.69e+03 2.77e-01
  bond pdb=" CB  TRP C  18 "
       pdb=" CG  TRP C  18 "
    ideal  model  delta    sigma   weight residual
    1.498  1.482  0.016 3.10e-02 1.04e+03 2.74e-01
  bond pdb=" CB  TRP A  18 "
       pdb=" CG  TRP A  18 "
    ideal  model  delta    sigma   weight residual
    1.498  1.483  0.015 3.10e-02 1.04e+03 2.41e-01
  bond pdb=" CB  TRP D  18 "
       pdb=" CG  TRP D  18 "
    ideal  model  delta    sigma   weight residual
    1.498  1.483  0.015 3.10e-02 1.04e+03 2.39e-01
  ... (remaining 4955 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.02: 6543
        1.02 -     2.05: 159
        2.05 -     3.07: 46
        3.07 -     4.10: 4
        4.10 -     5.12: 4
  Bond angle restraints: 6756
  Sorted by residual:
  angle pdb=" CA  ASN B   3 "
        pdb=" C   ASN B   3 "
        pdb=" N   PRO B   4 "
      ideal   model   delta    sigma   weight residual
     118.44  121.26   -2.82 1.59e+00 3.96e-01 3.15e+00
  angle pdb=" N   GLU D  59 "
        pdb=" CA  GLU D  59 "
        pdb=" C   GLU D  59 "
      ideal   model   delta    sigma   weight residual
     113.18  111.07    2.11 1.33e+00 5.65e-01 2.53e+00
  angle pdb=" N   GLU C  59 "
        pdb=" CA  GLU C  59 "
        pdb=" C   GLU C  59 "
      ideal   model   delta    sigma   weight residual
     113.18  111.19    1.99 1.33e+00 5.65e-01 2.23e+00
  angle pdb=" N   GLU A  59 "
        pdb=" CA  GLU A  59 "
        pdb=" C   GLU A  59 "
      ideal   model   delta    sigma   weight residual
     113.18  111.40    1.78 1.33e+00 5.65e-01 1.78e+00
  angle pdb=" N   ASN B   3 "
        pdb=" CA  ASN B   3 "
        pdb=" C   ASN B   3 "
      ideal   model   delta    sigma   weight residual
     109.81  112.67   -2.86 2.21e+00 2.05e-01 1.68e+00
  ... (remaining 6751 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.71: 2578
       17.71 -    35.42: 229
       35.42 -    53.14: 39
       53.14 -    70.85: 13
       70.85 -    88.56: 9
  Dihedral angle restraints: 2868
    sinusoidal: 1128
      harmonic: 1740
  Sorted by residual:
  dihedral pdb=" CG  ARG D  19 "
           pdb=" CD  ARG D  19 "
           pdb=" NE  ARG D  19 "
           pdb=" CZ  ARG D  19 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.28  -44.28     2      1.50e+01 4.44e-03 1.04e+01
  dihedral pdb=" CG  ARG C  43 "
           pdb=" CD  ARG C  43 "
           pdb=" NE  ARG C  43 "
           pdb=" CZ  ARG C  43 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -128.71   38.71     2      1.50e+01 4.44e-03 8.34e+00
  dihedral pdb=" CG  ARG B  43 "
           pdb=" CD  ARG B  43 "
           pdb=" NE  ARG B  43 "
           pdb=" CZ  ARG B  43 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -128.40   38.40     2      1.50e+01 4.44e-03 8.23e+00
  ... (remaining 2865 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 383
       0.024 -    0.049: 188
       0.049 -    0.073: 86
       0.073 -    0.097: 27
       0.097 -    0.122: 20
  Chirality restraints: 704
  Sorted by residual:
  chirality pdb=" CA  PRO D  35 "
            pdb=" N   PRO D  35 "
            pdb=" C   PRO D  35 "
            pdb=" CB  PRO D  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.69e-01
  chirality pdb=" CA  PRO C  35 "
            pdb=" N   PRO C  35 "
            pdb=" C   PRO C  35 "
            pdb=" CB  PRO C  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.47e-01
  chirality pdb=" CA  PRO B  35 "
            pdb=" N   PRO B  35 "
            pdb=" C   PRO B  35 "
            pdb=" CB  PRO B  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.36e-01
  ... (remaining 701 not shown)

  Planarity restraints: 896
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D  34 "    0.023 5.00e-02 4.00e+02   3.45e-02 1.90e+00
        pdb=" N   PRO D  35 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO D  35 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO D  35 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B  34 "   -0.023 5.00e-02 4.00e+02   3.40e-02 1.85e+00
        pdb=" N   PRO B  35 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO B  35 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B  35 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  34 "    0.022 5.00e-02 4.00e+02   3.34e-02 1.79e+00
        pdb=" N   PRO A  35 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A  35 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A  35 "    0.019 5.00e-02 4.00e+02
  ... (remaining 893 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1000
        2.78 -     3.31: 4544
        3.31 -     3.84: 8294
        3.84 -     4.37: 9896
        4.37 -     4.90: 16647
  Nonbonded interactions: 40381
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS A  32 "
            pdb=" OE1 GLU D  44 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" O   PHE C 102 "
            pdb=" ND2 ASN C 106 "
     model   vdw
     2.339 3.120
  nonbonded pdb=" OE1 GLU A  44 "
            pdb=" NE2 HIS D  32 "
     model   vdw
     2.342 3.120
  nonbonded pdb=" OD1 ASP D   7 "
            pdb=" NH2 ARG D  10 "
     model   vdw
     2.345 3.120
  nonbonded pdb=" OD1 ASP C   7 "
            pdb=" NH2 ARG C  10 "
     model   vdw
     2.347 3.120
  ... (remaining 40376 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.220
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.410
  Find NCS groups from input model:        0.170
  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:             0.000
  Load rotamer database and sin/cos tables:12.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   4960  Z= 0.193
  Angle     :  0.441   5.120   6756  Z= 0.243
  Chirality :  0.038   0.122    704
  Planarity :  0.003   0.034    896
  Dihedral  : 15.001  88.562   1740
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  1.55 (0.34), residues: 592
  helix:  1.22 (0.28), residues: 352
  sheet:  2.88 (0.48), residues: 72
  loop : -0.10 (0.47), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 109 
 HIS   0.002   0.001   HIS C  32 
 PHE   0.006   0.001   PHE C 113 
 TYR   0.008   0.001   TYR D  94 
 ARG   0.003   0.000   ARG C  19 

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.558 
Fit side-chains
REVERT: A    3 ASN cc_start: 0.6793 (m-40) cc_final: 0.5790 (t0)
REVERT: A  148 ARG cc_start: 0.7506 (mtp180) cc_final: 0.7168 (mmt90)
REVERT: B    3 ASN cc_start: 0.6899 (m-40) cc_final: 0.5964 (t0)
REVERT: B   47 GLN cc_start: 0.7599 (mt0) cc_final: 0.7364 (mt0)
REVERT: B  148 ARG cc_start: 0.7348 (mtp180) cc_final: 0.7130 (mmt90)
REVERT: C    3 ASN cc_start: 0.6720 (m-40) cc_final: 0.5710 (t0)
REVERT: C   44 GLU cc_start: 0.8389 (tt0) cc_final: 0.8182 (tt0)
REVERT: C   47 GLN cc_start: 0.7751 (mt0) cc_final: 0.7420 (mt0)
REVERT: C   52 GLN cc_start: 0.8089 (mm110) cc_final: 0.7779 (mp10)
REVERT: C  148 ARG cc_start: 0.7471 (mtp180) cc_final: 0.7217 (mmt90)
REVERT: D    3 ASN cc_start: 0.6761 (m-40) cc_final: 0.5797 (t0)
REVERT: D   27 GLN cc_start: 0.8031 (tp-100) cc_final: 0.7820 (tp-100)
REVERT: D  148 ARG cc_start: 0.7461 (mtp180) cc_final: 0.7167 (mmt90)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 1.7061
  time to fit residues: 203.3493
Evaluate side-chains
  81 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 45 optimal weight:    0.6980
   chunk 25 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   chunk 30 optimal weight:    7.9990
   chunk 24 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 28 optimal weight:    0.3980
   chunk 35 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A  31 ASN
A 124 GLN
B  17 GLN
B  31 ASN
C  31 ASN
C 124 GLN
D  17 GLN
D 124 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.143763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.106167 restraints weight = 4294.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 1.71
r_work: 0.2856 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2715 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9002
moved from start:          0.2284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4960  Z= 0.206
  Angle     :  0.470   5.360   6756  Z= 0.263
  Chirality :  0.041   0.138    704
  Planarity :  0.004   0.035    896
  Dihedral  :  3.893  12.581    656
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  4.92 %
    Favored  : 94.67 %
  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:  1.75 (0.34), residues: 592
  helix:  1.45 (0.28), residues: 348
  sheet:  2.63 (0.50), residues: 72
  loop :  0.00 (0.46), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C  18 
 HIS   0.002   0.001   HIS A 132 
 PHE   0.009   0.001   PHE C 102 
 TYR   0.008   0.001   TYR C 118 
 ARG   0.004   0.000   ARG D  19 

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 87
  time to evaluate  : 0.527 
Fit side-chains
REVERT: A    3 ASN cc_start: 0.7407 (m-40) cc_final: 0.6592 (t0)
REVERT: A   75 GLN cc_start: 0.9232 (OUTLIER) cc_final: 0.8975 (mt0)
REVERT: A  148 ARG cc_start: 0.8515 (mtp180) cc_final: 0.7933 (mmt90)
REVERT: B    3 ASN cc_start: 0.7469 (m-40) cc_final: 0.6578 (t0)
REVERT: B  148 ARG cc_start: 0.8493 (mtp180) cc_final: 0.7951 (mmt90)
REVERT: C    3 ASN cc_start: 0.7376 (m-40) cc_final: 0.6525 (t0)
REVERT: C  148 ARG cc_start: 0.8513 (mtp180) cc_final: 0.7964 (mmt90)
REVERT: D    3 ASN cc_start: 0.7356 (m-40) cc_final: 0.6533 (t0)
REVERT: D  148 ARG cc_start: 0.8511 (mtp180) cc_final: 0.7973 (mmt90)
  outliers start: 2
  outliers final: 0
  residues processed: 89
  average time/residue: 1.7442
  time to fit residues: 159.6968
Evaluate side-chains
  79 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 41 optimal weight:    7.9990
   chunk 47 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    1.5788

-------------------------------------------------------------------------------
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 = 0.3579 r_free = 0.3579 target = 0.141830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.103802 restraints weight = 4306.534|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 1.72
r_work: 0.2837 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2698 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9018
moved from start:          0.2602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4960  Z= 0.219
  Angle     :  0.476   5.340   6756  Z= 0.268
  Chirality :  0.041   0.142    704
  Planarity :  0.004   0.037    896
  Dihedral  :  4.203  16.131    656
  Min Nonbonded Distance : 2.678

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  5.94 %
    Favored  : 93.44 %
  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:  1.89 (0.34), residues: 592
  helix:  1.57 (0.28), residues: 344
  sheet:  2.38 (0.49), residues: 72
  loop :  0.27 (0.47), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D  18 
 HIS   0.002   0.001   HIS A  32 
 PHE   0.007   0.001   PHE A  33 
 TYR   0.009   0.001   TYR C 118 
 ARG   0.003   0.000   ARG D  19 

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 86
  time to evaluate  : 0.502 
Fit side-chains
REVERT: A    3 ASN cc_start: 0.7338 (m-40) cc_final: 0.6497 (t0)
REVERT: A  148 ARG cc_start: 0.8521 (mtp180) cc_final: 0.7936 (mmt90)
REVERT: B    3 ASN cc_start: 0.7369 (m-40) cc_final: 0.6443 (t0)
REVERT: B  148 ARG cc_start: 0.8491 (mtp180) cc_final: 0.7965 (mmt90)
REVERT: C    3 ASN cc_start: 0.7354 (m-40) cc_final: 0.6443 (t0)
REVERT: C  148 ARG cc_start: 0.8508 (mtp180) cc_final: 0.7954 (mmt90)
REVERT: D    3 ASN cc_start: 0.7293 (m-40) cc_final: 0.6418 (t0)
REVERT: D   75 GLN cc_start: 0.9286 (OUTLIER) cc_final: 0.9043 (mt0)
REVERT: D  148 ARG cc_start: 0.8511 (mtp180) cc_final: 0.7961 (mmt90)
  outliers start: 3
  outliers final: 0
  residues processed: 89
  average time/residue: 1.7357
  time to fit residues: 158.9890
Evaluate side-chains
  77 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   75 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 52 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 1 optimal weight:    0.7980
   chunk 50 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 37 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B  32 HIS
C  32 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.143664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.106207 restraints weight = 4371.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 1.73
r_work: 0.2893 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2759 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8984
moved from start:          0.2595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   4960  Z= 0.143
  Angle     :  0.420   5.286   6756  Z= 0.234
  Chirality :  0.038   0.131    704
  Planarity :  0.003   0.036    896
  Dihedral  :  4.010  14.939    656
  Min Nonbonded Distance : 2.671

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  6.97 %
    Favored  : 92.42 %
  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:  1.94 (0.34), residues: 592
  helix:  1.66 (0.28), residues: 348
  sheet:  2.34 (0.49), residues: 72
  loop :  0.13 (0.47), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D  18 
 HIS   0.002   0.000   HIS B  93 
 PHE   0.006   0.001   PHE D  88 
 TYR   0.009   0.001   TYR B 118 
 ARG   0.002   0.000   ARG D 123 

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 87
  time to evaluate  : 0.499 
Fit side-chains
REVERT: A    3 ASN cc_start: 0.7323 (m-40) cc_final: 0.6492 (t0)
REVERT: A  148 ARG cc_start: 0.8494 (mtp180) cc_final: 0.7938 (mmt90)
REVERT: B    3 ASN cc_start: 0.7381 (m-40) cc_final: 0.6447 (t0)
REVERT: B  148 ARG cc_start: 0.8469 (mtp180) cc_final: 0.7960 (mmt90)
REVERT: C    3 ASN cc_start: 0.7354 (m-40) cc_final: 0.6446 (t0)
REVERT: C  148 ARG cc_start: 0.8469 (mtp180) cc_final: 0.7950 (mmt90)
REVERT: D    3 ASN cc_start: 0.7324 (m-40) cc_final: 0.6438 (t0)
REVERT: D   75 GLN cc_start: 0.9269 (OUTLIER) cc_final: 0.9027 (mt0)
REVERT: D  148 ARG cc_start: 0.8493 (mtp180) cc_final: 0.7964 (mmt90)
  outliers start: 3
  outliers final: 0
  residues processed: 90
  average time/residue: 1.6697
  time to fit residues: 154.7356
Evaluate side-chains
  82 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   75 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 22 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0670
   chunk 53 optimal weight:    0.8980
   chunk 55 optimal weight:    0.5980
   chunk 28 optimal weight:    8.9990
   overall best weight:    0.6718

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

Flipped N/Q/H residues before XYZ refinement:
A  32 HIS
B  32 HIS
C  32 HIS
D  32 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.143996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.106567 restraints weight = 4347.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3107 rms_B_bonded: 1.73
r_work: 0.2897 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2765 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8969
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   4960  Z= 0.130
  Angle     :  0.407   5.266   6756  Z= 0.226
  Chirality :  0.038   0.126    704
  Planarity :  0.003   0.035    896
  Dihedral  :  3.926  13.785    656
  Min Nonbonded Distance : 2.667

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  6.97 %
    Favored  : 92.21 %
  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:  2.00 (0.34), residues: 592
  helix:  1.74 (0.29), residues: 348
  sheet:  2.31 (0.50), residues: 72
  loop :  0.14 (0.47), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D  18 
 HIS   0.001   0.000   HIS C  32 
 PHE   0.006   0.001   PHE B  88 
 TYR   0.008   0.001   TYR B 118 
 ARG   0.002   0.000   ARG C 123 

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 86
  time to evaluate  : 0.566 
Fit side-chains
REVERT: A    3 ASN cc_start: 0.7316 (m-40) cc_final: 0.6461 (t0)
REVERT: A  148 ARG cc_start: 0.8477 (mtp180) cc_final: 0.7942 (mmt90)
REVERT: B    3 ASN cc_start: 0.7331 (m-40) cc_final: 0.6410 (t0)
REVERT: B  148 ARG cc_start: 0.8457 (mtp180) cc_final: 0.7928 (mmt90)
REVERT: C    3 ASN cc_start: 0.7321 (m-40) cc_final: 0.6417 (t0)
REVERT: C  148 ARG cc_start: 0.8468 (mtp180) cc_final: 0.7900 (mmt90)
REVERT: D    3 ASN cc_start: 0.7303 (m-40) cc_final: 0.6387 (t0)
REVERT: D   75 GLN cc_start: 0.9256 (OUTLIER) cc_final: 0.9013 (mt0)
REVERT: D  148 ARG cc_start: 0.8469 (mtp180) cc_final: 0.7957 (mmt90)
  outliers start: 4
  outliers final: 3
  residues processed: 89
  average time/residue: 1.6739
  time to fit residues: 153.3502
Evaluate side-chains
  87 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain D residue   16 LEU
Chi-restraints excluded: chain D residue   75 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 15 optimal weight:    7.9990
   chunk 0 optimal weight:    8.9990
   chunk 48 optimal weight:    1.9990
   chunk 28 optimal weight:    0.1980
   chunk 17 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
A  32 HIS
B  32 HIS
C  32 HIS
D  32 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.141910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.104505 restraints weight = 4287.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3077 rms_B_bonded: 1.68
r_work: 0.2859 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2724 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.2724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9003
moved from start:          0.2712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4960  Z= 0.178
  Angle     :  0.446   5.287   6756  Z= 0.250
  Chirality :  0.039   0.136    704
  Planarity :  0.004   0.036    896
  Dihedral  :  4.163  17.370    656
  Min Nonbonded Distance : 2.668

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  6.56 %
    Favored  : 92.42 %
  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:  2.08 (0.35), residues: 592
  helix:  1.75 (0.29), residues: 344
  sheet:  2.30 (0.49), residues: 72
  loop :  0.36 (0.48), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP D  18 
 HIS   0.002   0.001   HIS B  93 
 PHE   0.006   0.001   PHE B  88 
 TYR   0.009   0.001   TYR C 118 
 ARG   0.002   0.000   ARG C 123 

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.523 
Fit side-chains
REVERT: A    3 ASN cc_start: 0.7321 (m-40) cc_final: 0.6463 (t0)
REVERT: A  148 ARG cc_start: 0.8508 (mtp180) cc_final: 0.7937 (mmt90)
REVERT: B    3 ASN cc_start: 0.7298 (m-40) cc_final: 0.6342 (t0)
REVERT: B  148 ARG cc_start: 0.8477 (mtp180) cc_final: 0.7979 (mmt90)
REVERT: C    3 ASN cc_start: 0.7345 (m-40) cc_final: 0.6415 (t0)
REVERT: C  148 ARG cc_start: 0.8492 (mtp180) cc_final: 0.7962 (mmt90)
REVERT: D    3 ASN cc_start: 0.7335 (m-40) cc_final: 0.6401 (t0)
REVERT: D   75 GLN cc_start: 0.9274 (OUTLIER) cc_final: 0.9033 (mt0)
REVERT: D  148 ARG cc_start: 0.8495 (mtp180) cc_final: 0.7974 (mmt90)
  outliers start: 5
  outliers final: 4
  residues processed: 88
  average time/residue: 1.6719
  time to fit residues: 151.4938
Evaluate side-chains
  85 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain C residue  134 ARG
Chi-restraints excluded: chain D residue   16 LEU
Chi-restraints excluded: chain D residue   75 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A  32 HIS
B  32 HIS
C  32 HIS
D  32 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.141118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.103170 restraints weight = 4222.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 1.70
r_work: 0.2837 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2700 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9008
moved from start:          0.2844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4960  Z= 0.211
  Angle     :  0.471   5.290   6756  Z= 0.265
  Chirality :  0.040   0.140    704
  Planarity :  0.004   0.036    896
  Dihedral  :  4.369  21.353    656
  Min Nonbonded Distance : 2.669

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  6.56 %
    Favored  : 91.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.05 (0.35), residues: 592
  helix:  1.71 (0.29), residues: 344
  sheet:  2.26 (0.48), residues: 72
  loop :  0.39 (0.48), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP D  18 
 HIS   0.002   0.001   HIS B  93 
 PHE   0.007   0.001   PHE B  88 
 TYR   0.009   0.001   TYR C 118 
 ARG   0.002   0.000   ARG D  19 

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.560 
Fit side-chains
REVERT: A    3 ASN cc_start: 0.7314 (m-40) cc_final: 0.6454 (t0)
REVERT: A  148 ARG cc_start: 0.8507 (mtp180) cc_final: 0.7922 (mmt90)
REVERT: B    3 ASN cc_start: 0.7275 (m-40) cc_final: 0.6324 (t0)
REVERT: B  148 ARG cc_start: 0.8476 (mtp180) cc_final: 0.7950 (mmt90)
REVERT: C    3 ASN cc_start: 0.7283 (m-40) cc_final: 0.6390 (t0)
REVERT: C  148 ARG cc_start: 0.8493 (mtp180) cc_final: 0.7936 (mmt90)
REVERT: D    3 ASN cc_start: 0.7293 (m-40) cc_final: 0.6341 (t0)
REVERT: D   75 GLN cc_start: 0.9282 (OUTLIER) cc_final: 0.9037 (mt0)
REVERT: D  148 ARG cc_start: 0.8503 (mtp180) cc_final: 0.7951 (mmt90)
  outliers start: 8
  outliers final: 4
  residues processed: 90
  average time/residue: 1.6677
  time to fit residues: 154.4215
Evaluate side-chains
  85 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain D residue   16 LEU
Chi-restraints excluded: chain D residue   75 GLN
Chi-restraints excluded: chain D residue   77 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 15 optimal weight:    7.9990
   chunk 28 optimal weight:    9.9990
   chunk 17 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 8 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0970
   chunk 32 optimal weight:    3.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A  32 HIS
B  32 HIS
C  32 HIS
D  32 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.146015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.109550 restraints weight = 4320.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 1.65
r_work: 0.2879 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2741 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9010
moved from start:          0.2836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4960  Z= 0.174
  Angle     :  0.443   5.262   6756  Z= 0.250
  Chirality :  0.039   0.136    704
  Planarity :  0.004   0.036    896
  Dihedral  :  4.242  19.867    656
  Min Nonbonded Distance : 2.668

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  7.38 %
    Favored  : 91.60 %
  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:  2.05 (0.34), residues: 592
  helix:  1.72 (0.29), residues: 344
  sheet:  2.26 (0.49), residues: 72
  loop :  0.38 (0.48), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP D  18 
 HIS   0.002   0.001   HIS B  93 
 PHE   0.007   0.001   PHE B  88 
 TYR   0.009   0.001   TYR C 118 
 ARG   0.002   0.000   ARG C 123 

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.544 
Fit side-chains
REVERT: A    3 ASN cc_start: 0.7358 (m-40) cc_final: 0.6520 (t0)
REVERT: A  148 ARG cc_start: 0.8475 (mtp180) cc_final: 0.7977 (mmt90)
REVERT: B    3 ASN cc_start: 0.7310 (m-40) cc_final: 0.6873 (t0)
REVERT: B  148 ARG cc_start: 0.8441 (mtp180) cc_final: 0.7989 (mmt90)
REVERT: C    3 ASN cc_start: 0.7314 (m-40) cc_final: 0.6426 (t0)
REVERT: C  148 ARG cc_start: 0.8456 (mtp180) cc_final: 0.8010 (mmt90)
REVERT: D    3 ASN cc_start: 0.7323 (m-40) cc_final: 0.6389 (t0)
REVERT: D   75 GLN cc_start: 0.9278 (OUTLIER) cc_final: 0.9038 (mt0)
REVERT: D  148 ARG cc_start: 0.8459 (mtp180) cc_final: 0.7978 (mmt90)
  outliers start: 5
  outliers final: 4
  residues processed: 90
  average time/residue: 1.6942
  time to fit residues: 157.0222
Evaluate side-chains
  86 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain D residue   16 LEU
Chi-restraints excluded: chain D residue   75 GLN
Chi-restraints excluded: chain D residue   77 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0000
   chunk 14 optimal weight:    4.9990
   chunk 49 optimal weight:    9.9990
   chunk 12 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9980
   chunk 50 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
A  32 HIS
B  32 HIS
C  32 HIS
D  32 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.142850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.105526 restraints weight = 4201.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 1.65
r_work: 0.2866 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2727 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9018
moved from start:          0.2914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4960  Z= 0.197
  Angle     :  0.463   5.291   6756  Z= 0.261
  Chirality :  0.040   0.139    704
  Planarity :  0.004   0.037    896
  Dihedral  :  4.364  21.683    656
  Min Nonbonded Distance : 2.669

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  7.38 %
    Favored  : 91.60 %
  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:  2.04 (0.35), residues: 592
  helix:  1.69 (0.29), residues: 344
  sheet:  2.31 (0.49), residues: 72
  loop :  0.39 (0.48), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP D  18 
 HIS   0.002   0.001   HIS B  93 
 PHE   0.007   0.001   PHE B  88 
 TYR   0.009   0.001   TYR A 118 
 ARG   0.002   0.000   ARG D  19 

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.601 
Fit side-chains
REVERT: A    3 ASN cc_start: 0.7365 (m-40) cc_final: 0.6506 (t0)
REVERT: A  148 ARG cc_start: 0.8484 (mtp180) cc_final: 0.7974 (mmt90)
REVERT: B    3 ASN cc_start: 0.7310 (m-40) cc_final: 0.6873 (t0)
REVERT: B  148 ARG cc_start: 0.8457 (mtp180) cc_final: 0.7997 (mmt90)
REVERT: C    3 ASN cc_start: 0.7323 (m-40) cc_final: 0.6423 (t0)
REVERT: C  148 ARG cc_start: 0.8457 (mtp180) cc_final: 0.7998 (mmt90)
REVERT: D    3 ASN cc_start: 0.7304 (m-40) cc_final: 0.6381 (t0)
REVERT: D   75 GLN cc_start: 0.9288 (OUTLIER) cc_final: 0.9045 (mt0)
REVERT: D  148 ARG cc_start: 0.8478 (mtp180) cc_final: 0.7990 (mmt90)
  outliers start: 5
  outliers final: 4
  residues processed: 90
  average time/residue: 1.7007
  time to fit residues: 157.6524
Evaluate side-chains
  85 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain D residue   16 LEU
Chi-restraints excluded: chain D residue   75 GLN
Chi-restraints excluded: chain D residue   77 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 5 optimal weight:    6.9990
   chunk 20 optimal weight:    7.9990
   chunk 2 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 42 optimal weight:    0.1980
   chunk 54 optimal weight:    0.9980
   chunk 33 optimal weight:    4.9990
   chunk 3 optimal weight:    0.6980
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A  32 HIS
B  32 HIS
C  32 HIS
D  32 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.143771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.106459 restraints weight = 4299.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3096 rms_B_bonded: 1.67
r_work: 0.2876 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2740 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9010
moved from start:          0.2885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4960  Z= 0.176
  Angle     :  0.447   5.273   6756  Z= 0.252
  Chirality :  0.039   0.137    704
  Planarity :  0.004   0.036    896
  Dihedral  :  4.266  20.596    656
  Min Nonbonded Distance : 2.668

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  7.17 %
    Favored  : 91.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.96 (0.34), residues: 592
  helix:  1.65 (0.29), residues: 348
  sheet:  2.34 (0.50), residues: 72
  loop :  0.21 (0.48), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP D  18 
 HIS   0.002   0.001   HIS B  93 
 PHE   0.007   0.001   PHE B  88 
 TYR   0.009   0.001   TYR C 118 
 ARG   0.002   0.000   ARG C 123 

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 84
  time to evaluate  : 0.528 
Fit side-chains
REVERT: A    3 ASN cc_start: 0.7357 (m-40) cc_final: 0.6517 (t0)
REVERT: A  148 ARG cc_start: 0.8482 (mtp180) cc_final: 0.7977 (mmt90)
REVERT: B    3 ASN cc_start: 0.7304 (m-40) cc_final: 0.6883 (t0)
REVERT: B  148 ARG cc_start: 0.8458 (mtp180) cc_final: 0.8008 (mmt90)
REVERT: C    3 ASN cc_start: 0.7319 (m-40) cc_final: 0.6433 (t0)
REVERT: C  148 ARG cc_start: 0.8451 (mtp180) cc_final: 0.8013 (mmt90)
REVERT: D    3 ASN cc_start: 0.7338 (m-40) cc_final: 0.6397 (t0)
REVERT: D   75 GLN cc_start: 0.9279 (OUTLIER) cc_final: 0.9039 (mt0)
REVERT: D  148 ARG cc_start: 0.8472 (mtp180) cc_final: 0.7994 (mmt90)
  outliers start: 5
  outliers final: 4
  residues processed: 89
  average time/residue: 1.6780
  time to fit residues: 153.6692
Evaluate side-chains
  86 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain D residue   16 LEU
Chi-restraints excluded: chain D residue   75 GLN
Chi-restraints excluded: chain D residue   77 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 16 optimal weight:    0.0670
   chunk 39 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0770
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.5076

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

Flipped N/Q/H residues before XYZ refinement:
A  32 HIS
B  32 HIS
C  32 HIS
D  32 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.146858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.110371 restraints weight = 4318.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 1.67
r_work: 0.2956 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2820 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8969
moved from start:          0.2859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   4960  Z= 0.116
  Angle     :  0.403   5.217   6756  Z= 0.224
  Chirality :  0.037   0.123    704
  Planarity :  0.003   0.036    896
  Dihedral  :  3.985  16.949    656
  Min Nonbonded Distance : 2.665

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  7.79 %
    Favored  : 91.60 %
  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:  2.07 (0.34), residues: 592
  helix:  1.78 (0.28), residues: 348
  sheet:  2.37 (0.51), residues: 72
  loop :  0.19 (0.48), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP D  18 
 HIS   0.002   0.000   HIS D  32 
 PHE   0.006   0.001   PHE B  88 
 TYR   0.009   0.001   TYR C 118 
 ARG   0.002   0.000   ARG C 123 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4574.25 seconds
wall clock time: 81 minutes 7.22 seconds (4867.22 seconds total)