Starting phenix.real_space_refine
on Fri Aug 22 15:12:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pkd_17735/08_2025/8pkd_17735.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pkd_17735/08_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_17735/08_2025/8pkd_17735.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pkd_17735/08_2025/8pkd_17735.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pkd_17735/08_2025/8pkd_17735.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pkd_17735/08_2025/8pkd_17735.cif"
  }
  resolution = 2.33
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.083
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.14, per 1000 atoms: 0.24
  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: 0.25
  Conformation dependent library (CDL) restraints added in 133.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.11
  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: 0.58

  Time building geometry restraints manager: 0.34 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: 0.00
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:             2.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.540
  Find NCS groups from input model:        0.070
  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:9.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.550
-------------------------------------------------------------------------------
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= 0.139
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.55 (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
 ARG   0.003   0.000   ARG C  19 
 TYR   0.008   0.001   TYR D  94 
 PHE   0.006   0.001   PHE C 113 
 TRP   0.010   0.001   TRP D 109 
 HIS   0.002   0.001   HIS C  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 4960)
  covalent geometry    : angle       0.44140 ( 6756)
  hydrogen bonds       : bond        0.11432 (  297)
  hydrogen bonds       : angle       6.00509 (  843)

*********************** 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  : 0.222 
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: 0.6529
  time to fit residues: 77.7301
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  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9980
   chunk 56 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0000
   overall best weight:    0.6986

-------------------------------------------------------------------------------
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 = 0.3720 r_free = 0.3720 target = 0.152295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.117639 restraints weight = 4345.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 1.62
r_work: 0.2989 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2856 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8955
moved from start:          0.1946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   4960  Z= 0.108
  Angle     :  0.417   5.321   6756  Z= 0.229
  Chirality :  0.038   0.124    704
  Planarity :  0.003   0.034    896
  Dihedral  :  3.612  11.524    656
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  5.12 %
    Favored  : 94.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.69 (0.34), residues: 592
  helix:  1.45 (0.28), residues: 352
  sheet:  2.79 (0.49), residues: 72
  loop : -0.27 (0.46), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  19 
 TYR   0.009   0.001   TYR B 118 
 PHE   0.008   0.001   PHE C 102 
 TRP   0.013   0.002   TRP D  18 
 HIS   0.002   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 4960)
  covalent geometry    : angle       0.41654 ( 6756)
  hydrogen bonds       : bond        0.03977 (  297)
  hydrogen bonds       : angle       4.51681 (  843)

*********************** 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
  90 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 88
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A    3 ASN cc_start: 0.7511 (m-40) cc_final: 0.6724 (t0)
REVERT: A   75 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.8952 (mt0)
REVERT: A  148 ARG cc_start: 0.8449 (mtp180) cc_final: 0.7956 (mmt90)
REVERT: B    3 ASN cc_start: 0.7512 (m-40) cc_final: 0.6687 (t0)
REVERT: B  148 ARG cc_start: 0.8413 (mtp180) cc_final: 0.7939 (mmt90)
REVERT: C    3 ASN cc_start: 0.7460 (m-40) cc_final: 0.6703 (t0)
REVERT: C  148 ARG cc_start: 0.8433 (mtp180) cc_final: 0.7926 (mmt90)
REVERT: D    3 ASN cc_start: 0.7441 (m-40) cc_final: 0.6690 (t0)
REVERT: D  148 ARG cc_start: 0.8463 (mtp180) cc_final: 0.7998 (mmt90)
  outliers start: 2
  outliers final: 0
  residues processed: 90
  average time/residue: 0.6670
  time to fit residues: 61.6734
Evaluate side-chains
  85 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
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 25 optimal weight:    0.0970
   chunk 27 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 52 optimal weight:    5.9990
   chunk 54 optimal weight:    0.6980
   chunk 59 optimal weight:    2.9990
   chunk 43 optimal weight:    7.9990
   chunk 8 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
C  31 ASN
D  31 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.144083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.106606 restraints weight = 4339.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.3091 rms_B_bonded: 1.72
r_work: 0.2868 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2729 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8998
moved from start:          0.2425

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= 0.132
  Angle     :  0.443   5.366   6756  Z= 0.247
  Chirality :  0.039   0.134    704
  Planarity :  0.004   0.035    896
  Dihedral  :  3.928  11.908    656
  Min Nonbonded Distance : 2.675

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  5.94 %
    Favored  : 93.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.83 (0.34), residues: 592
  helix:  1.57 (0.28), residues: 348
  sheet:  2.58 (0.50), residues: 72
  loop : -0.05 (0.46), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 123 
 TYR   0.009   0.001   TYR B 118 
 PHE   0.006   0.001   PHE A  33 
 TRP   0.016   0.002   TRP C  18 
 HIS   0.002   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 4960)
  covalent geometry    : angle       0.44330 ( 6756)
  hydrogen bonds       : bond        0.04452 (  297)
  hydrogen bonds       : angle       4.53059 (  843)

*********************** 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
  90 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 89
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A    3 ASN cc_start: 0.7364 (m-40) cc_final: 0.6541 (t0)
REVERT: A  148 ARG cc_start: 0.8508 (mtp180) cc_final: 0.7933 (mmt90)
REVERT: B    3 ASN cc_start: 0.7402 (m-40) cc_final: 0.6459 (t0)
REVERT: B  148 ARG cc_start: 0.8497 (mtp180) cc_final: 0.7943 (mmt90)
REVERT: C    3 ASN cc_start: 0.7361 (m-40) cc_final: 0.6471 (t0)
REVERT: C  148 ARG cc_start: 0.8504 (mtp180) cc_final: 0.7951 (mmt90)
REVERT: D    3 ASN cc_start: 0.7310 (m-40) cc_final: 0.6457 (t0)
REVERT: D   75 GLN cc_start: 0.9274 (OUTLIER) cc_final: 0.9036 (mt0)
REVERT: D  148 ARG cc_start: 0.8507 (mtp180) cc_final: 0.7954 (mmt90)
  outliers start: 1
  outliers final: 0
  residues processed: 90
  average time/residue: 0.7577
  time to fit residues: 70.0220
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  : 0.164 
-------------------------------------------------------------------------------
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 56 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 13 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 42 optimal weight:    0.3980
   chunk 4 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
B  31 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.139799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.102232 restraints weight = 4239.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 1.68
r_work: 0.2821 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2682 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9028
moved from start:          0.2761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4960  Z= 0.190
  Angle     :  0.507   5.358   6756  Z= 0.286
  Chirality :  0.042   0.149    704
  Planarity :  0.004   0.037    896
  Dihedral  :  4.427  20.834    656
  Min Nonbonded Distance : 2.680

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  6.76 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.89 (0.34), residues: 592
  helix:  1.55 (0.29), residues: 344
  sheet:  2.43 (0.49), residues: 72
  loop :  0.29 (0.47), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D  19 
 TYR   0.009   0.002   TYR B 118 
 PHE   0.007   0.001   PHE D  88 
 TRP   0.019   0.002   TRP D  18 
 HIS   0.003   0.001   HIS D  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 4960)
  covalent geometry    : angle       0.50653 ( 6756)
  hydrogen bonds       : bond        0.05156 (  297)
  hydrogen bonds       : angle       4.66511 (  843)

*********************** 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: 4
    poor density    : 86
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A    3 ASN cc_start: 0.7339 (m-40) cc_final: 0.6485 (t0)
REVERT: A   75 GLN cc_start: 0.9277 (OUTLIER) cc_final: 0.9039 (mt0)
REVERT: A  148 ARG cc_start: 0.8534 (mtp180) cc_final: 0.7973 (mmt90)
REVERT: B    3 ASN cc_start: 0.7337 (m-40) cc_final: 0.6373 (t0)
REVERT: B  148 ARG cc_start: 0.8511 (mtp180) cc_final: 0.7997 (mmt90)
REVERT: C    3 ASN cc_start: 0.7330 (m-40) cc_final: 0.6406 (t0)
REVERT: C  148 ARG cc_start: 0.8513 (mtp180) cc_final: 0.7941 (mmt90)
REVERT: D    3 ASN cc_start: 0.7313 (m-40) cc_final: 0.6387 (t0)
REVERT: D   75 GLN cc_start: 0.9287 (OUTLIER) cc_final: 0.9046 (mt0)
REVERT: D  148 ARG cc_start: 0.8539 (mtp180) cc_final: 0.8010 (mmt90)
  outliers start: 4
  outliers final: 1
  residues processed: 89
  average time/residue: 0.6975
  time to fit residues: 63.8404
Evaluate side-chains
  81 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 78
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 GLN
Chi-restraints excluded: chain D residue   75 GLN
Chi-restraints excluded: chain D residue  134 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 28 optimal weight:    0.6980
   chunk 41 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 15 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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
B  37 GLN
C  32 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.146320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.109749 restraints weight = 4364.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 1.67
r_work: 0.2898 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2762 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8999
moved from start:          0.2688

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= 0.112
  Angle     :  0.424   5.253   6756  Z= 0.237
  Chirality :  0.038   0.132    704
  Planarity :  0.004   0.036    896
  Dihedral  :  4.097  17.283    656
  Min Nonbonded Distance : 2.672

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  6.56 %
    Favored  : 92.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.89 (0.34), residues: 592
  helix:  1.60 (0.28), residues: 348
  sheet:  2.38 (0.49), residues: 72
  loop :  0.13 (0.47), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  19 
 TYR   0.009   0.001   TYR B 118 
 PHE   0.006   0.001   PHE D  88 
 TRP   0.017   0.002   TRP B  18 
 HIS   0.001   0.000   HIS B  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 4960)
  covalent geometry    : angle       0.42417 ( 6756)
  hydrogen bonds       : bond        0.04200 (  297)
  hydrogen bonds       : angle       4.36261 (  843)

*********************** 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
  91 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 87
  time to evaluate  : 0.136 
Fit side-chains
REVERT: A    3 ASN cc_start: 0.7342 (m-40) cc_final: 0.6517 (t0)
REVERT: A   75 GLN cc_start: 0.9255 (OUTLIER) cc_final: 0.8999 (mt0)
REVERT: A  148 ARG cc_start: 0.8484 (mtp180) cc_final: 0.7991 (mmt90)
REVERT: B    3 ASN cc_start: 0.7342 (m-40) cc_final: 0.6420 (t0)
REVERT: B  148 ARG cc_start: 0.8443 (mtp180) cc_final: 0.8002 (mmt90)
REVERT: C    3 ASN cc_start: 0.7368 (m-40) cc_final: 0.6468 (t0)
REVERT: C  148 ARG cc_start: 0.8465 (mtp180) cc_final: 0.8008 (mmt90)
REVERT: D    3 ASN cc_start: 0.7343 (m-40) cc_final: 0.6440 (t0)
REVERT: D   75 GLN cc_start: 0.9268 (OUTLIER) cc_final: 0.9026 (mt0)
REVERT: D  148 ARG cc_start: 0.8454 (mtp180) cc_final: 0.7979 (mmt90)
  outliers start: 4
  outliers final: 1
  residues processed: 91
  average time/residue: 0.7207
  time to fit residues: 67.3941
Evaluate side-chains
  85 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 82
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 GLN
Chi-restraints excluded: chain B 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 31 optimal weight:    4.9990
   chunk 49 optimal weight:   10.0000
   chunk 33 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 43 optimal weight:    9.9990
   chunk 59 optimal weight:   10.0000
   chunk 44 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    1.2986

-------------------------------------------------------------------------------
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 = 0.3641 r_free = 0.3641 target = 0.145361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.108948 restraints weight = 4342.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.3099 rms_B_bonded: 1.65
r_work: 0.2877 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2739 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9018
moved from start:          0.2814

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= 0.140
  Angle     :  0.455   5.285   6756  Z= 0.256
  Chirality :  0.040   0.139    704
  Planarity :  0.004   0.037    896
  Dihedral  :  4.240  18.772    656
  Min Nonbonded Distance : 2.673

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  6.35 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.02 (0.34), residues: 592
  helix:  1.68 (0.29), residues: 344
  sheet:  2.32 (0.48), residues: 72
  loop :  0.35 (0.48), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  19 
 TYR   0.009   0.001   TYR B 118 
 PHE   0.007   0.001   PHE B  88 
 TRP   0.019   0.002   TRP D  18 
 HIS   0.002   0.001   HIS B  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 4960)
  covalent geometry    : angle       0.45490 ( 6756)
  hydrogen bonds       : bond        0.04629 (  297)
  hydrogen bonds       : angle       4.46528 (  843)

*********************** 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
  93 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 87
  time to evaluate  : 0.188 
Fit side-chains
REVERT: A    3 ASN cc_start: 0.7351 (m-40) cc_final: 0.6509 (t0)
REVERT: A   75 GLN cc_start: 0.9268 (OUTLIER) cc_final: 0.9011 (mt0)
REVERT: A  148 ARG cc_start: 0.8483 (mtp180) cc_final: 0.7985 (mmt90)
REVERT: B    3 ASN cc_start: 0.7307 (m-40) cc_final: 0.6354 (t0)
REVERT: B  148 ARG cc_start: 0.8453 (mtp180) cc_final: 0.8015 (mmt90)
REVERT: C    3 ASN cc_start: 0.7374 (m-40) cc_final: 0.6459 (t0)
REVERT: C  148 ARG cc_start: 0.8476 (mtp180) cc_final: 0.8022 (mmt90)
REVERT: D    3 ASN cc_start: 0.7340 (m-40) cc_final: 0.6407 (t0)
REVERT: D   75 GLN cc_start: 0.9283 (OUTLIER) cc_final: 0.9042 (mt0)
REVERT: D  148 ARG cc_start: 0.8489 (mtp180) cc_final: 0.8007 (mmt90)
  outliers start: 6
  outliers final: 3
  residues processed: 92
  average time/residue: 0.7563
  time to fit residues: 71.5320
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  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 GLN
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 35 optimal weight:    0.3980
   chunk 17 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0570
   chunk 50 optimal weight:    0.9980
   chunk 3 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.6098

-------------------------------------------------------------------------------
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 = 0.3662 r_free = 0.3662 target = 0.147190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.110643 restraints weight = 4333.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 1.67
r_work: 0.2923 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2787 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8980
moved from start:          0.2723

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= 0.099
  Angle     :  0.406   5.223   6756  Z= 0.226
  Chirality :  0.037   0.124    704
  Planarity :  0.003   0.037    896
  Dihedral  :  3.971  15.789    656
  Min Nonbonded Distance : 2.666

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  7.17 %
    Favored  : 92.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.01 (0.34), residues: 592
  helix:  1.73 (0.28), residues: 348
  sheet:  2.32 (0.50), residues: 72
  loop :  0.17 (0.48), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 123 
 TYR   0.009   0.001   TYR B 118 
 PHE   0.006   0.001   PHE D  88 
 TRP   0.016   0.002   TRP D  18 
 HIS   0.002   0.000   HIS D  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00192 ( 4960)
  covalent geometry    : angle       0.40628 ( 6756)
  hydrogen bonds       : bond        0.03896 (  297)
  hydrogen bonds       : angle       4.19036 (  843)

*********************** 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
  92 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 88
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A    3 ASN cc_start: 0.7350 (m-40) cc_final: 0.6531 (t0)
REVERT: A   75 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.8984 (mt0)
REVERT: A  148 ARG cc_start: 0.8463 (mtp180) cc_final: 0.7992 (mmt90)
REVERT: B    3 ASN cc_start: 0.7300 (m-40) cc_final: 0.6868 (t0)
REVERT: B  148 ARG cc_start: 0.8419 (mtp180) cc_final: 0.7958 (mmt90)
REVERT: C    3 ASN cc_start: 0.7339 (m-40) cc_final: 0.6442 (t0)
REVERT: C  148 ARG cc_start: 0.8446 (mtp180) cc_final: 0.7976 (mmt90)
REVERT: D    3 ASN cc_start: 0.7318 (m-40) cc_final: 0.6432 (t0)
REVERT: D   75 GLN cc_start: 0.9252 (OUTLIER) cc_final: 0.9009 (mt0)
REVERT: D  148 ARG cc_start: 0.8444 (mtp180) cc_final: 0.7970 (mmt90)
  outliers start: 4
  outliers final: 2
  residues processed: 92
  average time/residue: 0.7880
  time to fit residues: 74.4956
Evaluate side-chains
  85 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 GLN
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain D residue   16 LEU
Chi-restraints excluded: chain D residue   75 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 34 optimal weight:    9.9990
   chunk 13 optimal weight:    8.9990
   chunk 6 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 32 optimal weight:    0.1980
   chunk 17 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 45 optimal weight:    5.9990
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.3623 r_free = 0.3623 target = 0.144357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.107089 restraints weight = 4363.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 1.68
r_work: 0.2899 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2761 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.2761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9002
moved from start:          0.2813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   4960  Z= 0.121
  Angle     :  0.432   5.260   6756  Z= 0.242
  Chirality :  0.039   0.132    704
  Planarity :  0.004   0.037    896
  Dihedral  :  4.097  17.602    656
  Min Nonbonded Distance : 2.666

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  8.20 %
    Favored  : 90.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.99 (0.34), residues: 592
  helix:  1.72 (0.28), residues: 348
  sheet:  2.31 (0.49), residues: 72
  loop :  0.16 (0.48), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 123 
 TYR   0.009   0.001   TYR C 118 
 PHE   0.007   0.001   PHE D  88 
 TRP   0.016   0.002   TRP D  18 
 HIS   0.002   0.001   HIS C  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 4960)
  covalent geometry    : angle       0.43176 ( 6756)
  hydrogen bonds       : bond        0.04295 (  297)
  hydrogen bonds       : angle       4.30285 (  843)

*********************** 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
  89 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 0.222 
Fit side-chains
REVERT: A    3 ASN cc_start: 0.7353 (m-40) cc_final: 0.6509 (t0)
REVERT: A   75 GLN cc_start: 0.9250 (OUTLIER) cc_final: 0.8990 (mt0)
REVERT: A  148 ARG cc_start: 0.8468 (mtp180) cc_final: 0.7967 (mmt90)
REVERT: B    3 ASN cc_start: 0.7300 (m-40) cc_final: 0.6868 (t0)
REVERT: B  148 ARG cc_start: 0.8430 (mtp180) cc_final: 0.7980 (mmt90)
REVERT: C    3 ASN cc_start: 0.7343 (m-40) cc_final: 0.6424 (t0)
REVERT: C  148 ARG cc_start: 0.8449 (mtp180) cc_final: 0.7998 (mmt90)
REVERT: D    3 ASN cc_start: 0.7316 (m-40) cc_final: 0.6396 (t0)
REVERT: D   75 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.9031 (mt0)
REVERT: D  148 ARG cc_start: 0.8452 (mtp180) cc_final: 0.7971 (mmt90)
  outliers start: 4
  outliers final: 2
  residues processed: 89
  average time/residue: 0.7941
  time to fit residues: 72.7002
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  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 GLN
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain D residue   16 LEU
Chi-restraints excluded: chain D residue   75 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 13 optimal weight:    0.2980
   chunk 23 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 15 optimal weight:    7.9990
   chunk 59 optimal weight:    4.9990
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3647 r_free = 0.3647 target = 0.146134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.109233 restraints weight = 4304.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 1.67
r_work: 0.2941 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2805 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8979
moved from start:          0.2762

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= 0.102
  Angle     :  0.409   5.235   6756  Z= 0.228
  Chirality :  0.038   0.126    704
  Planarity :  0.003   0.037    896
  Dihedral  :  3.963  16.141    656
  Min Nonbonded Distance : 2.665

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  7.99 %
    Favored  : 90.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.06 (0.34), residues: 592
  helix:  1.78 (0.28), residues: 348
  sheet:  2.32 (0.50), residues: 72
  loop :  0.16 (0.48), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 123 
 TYR   0.009   0.001   TYR C 118 
 PHE   0.006   0.001   PHE B  88 
 TRP   0.015   0.002   TRP D  18 
 HIS   0.002   0.000   HIS C  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00197 ( 4960)
  covalent geometry    : angle       0.40877 ( 6756)
  hydrogen bonds       : bond        0.03925 (  297)
  hydrogen bonds       : angle       4.15809 (  843)

*********************** 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  : 0.128 
Fit side-chains
REVERT: A    3 ASN cc_start: 0.7355 (m-40) cc_final: 0.6537 (t0)
REVERT: A   75 GLN cc_start: 0.9239 (OUTLIER) cc_final: 0.8980 (mt0)
REVERT: A  148 ARG cc_start: 0.8457 (mtp180) cc_final: 0.7979 (mmt90)
REVERT: B    3 ASN cc_start: 0.7313 (m-40) cc_final: 0.6901 (t0)
REVERT: B  148 ARG cc_start: 0.8414 (mtp180) cc_final: 0.7947 (mmt90)
REVERT: C    3 ASN cc_start: 0.7325 (m-40) cc_final: 0.6442 (t0)
REVERT: C  148 ARG cc_start: 0.8426 (mtp180) cc_final: 0.7948 (mmt90)
REVERT: D    3 ASN cc_start: 0.7302 (m-40) cc_final: 0.6422 (t0)
REVERT: D   75 GLN cc_start: 0.9256 (OUTLIER) cc_final: 0.9013 (mt0)
REVERT: D  148 ARG cc_start: 0.8439 (mtp180) cc_final: 0.7966 (mmt90)
  outliers start: 5
  outliers final: 3
  residues processed: 89
  average time/residue: 0.7608
  time to fit residues: 69.4538
Evaluate side-chains
  88 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 GLN
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 34 optimal weight:    8.9990
   chunk 17 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0870
   chunk 45 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 29 optimal weight:    7.9990
   chunk 53 optimal weight:    0.6980
   chunk 57 optimal weight:    3.9990
   overall best weight:    0.9360

-------------------------------------------------------------------------------
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 = 0.3641 r_free = 0.3641 target = 0.145542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.108432 restraints weight = 4296.888|
|-----------------------------------------------------------------------------|
r_work (start): 0.3120 rms_B_bonded: 1.67
r_work: 0.2901 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2764 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8998
moved from start:          0.2833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   4960  Z= 0.116
  Angle     :  0.426   5.264   6756  Z= 0.238
  Chirality :  0.038   0.130    704
  Planarity :  0.004   0.037    896
  Dihedral  :  4.086  17.915    656
  Min Nonbonded Distance : 2.664

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  8.20 %
    Favored  : 90.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.03 (0.35), residues: 592
  helix:  1.74 (0.28), residues: 348
  sheet:  2.33 (0.50), residues: 72
  loop :  0.17 (0.48), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 123 
 TYR   0.009   0.001   TYR C 118 
 PHE   0.006   0.001   PHE D  88 
 TRP   0.016   0.002   TRP D  18 
 HIS   0.002   0.001   HIS D  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 4960)
  covalent geometry    : angle       0.42630 ( 6756)
  hydrogen bonds       : bond        0.04230 (  297)
  hydrogen bonds       : angle       4.23876 (  843)

********************** 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
  88 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A    3 ASN cc_start: 0.7344 (m-40) cc_final: 0.6526 (t0)
REVERT: A   75 GLN cc_start: 0.9248 (OUTLIER) cc_final: 0.8987 (mt0)
REVERT: A  148 ARG cc_start: 0.8472 (mtp180) cc_final: 0.7967 (mmt90)
REVERT: B    3 ASN cc_start: 0.7312 (m-40) cc_final: 0.6880 (t0)
REVERT: B  148 ARG cc_start: 0.8427 (mtp180) cc_final: 0.7976 (mmt90)
REVERT: C    3 ASN cc_start: 0.7335 (m-40) cc_final: 0.6423 (t0)
REVERT: C  148 ARG cc_start: 0.8437 (mtp180) cc_final: 0.7990 (mmt90)
REVERT: D    3 ASN cc_start: 0.7290 (m-40) cc_final: 0.6388 (t0)
REVERT: D   75 GLN cc_start: 0.9269 (OUTLIER) cc_final: 0.9026 (mt0)
REVERT: D  148 ARG cc_start: 0.8458 (mtp180) cc_final: 0.7971 (mmt90)
  outliers start: 5
  outliers final: 3
  residues processed: 87
  average time/residue: 0.7325
  time to fit residues: 65.4433
Evaluate side-chains
  84 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 GLN
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 49 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 15 optimal weight:    7.9990
   chunk 56 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3655 r_free = 0.3655 target = 0.146533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.109623 restraints weight = 4348.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 1.67
r_work: 0.2906 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2768 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8986
moved from start:          0.2819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   4960  Z= 0.107
  Angle     :  0.414   5.250   6756  Z= 0.231
  Chirality :  0.038   0.128    704
  Planarity :  0.003   0.037    896
  Dihedral  :  4.000  17.197    656
  Min Nonbonded Distance : 2.664

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  8.20 %
    Favored  : 90.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.08 (0.35), residues: 592
  helix:  1.79 (0.28), residues: 348
  sheet:  2.36 (0.50), residues: 72
  loop :  0.16 (0.48), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 123 
 TYR   0.008   0.001   TYR C 118 
 PHE   0.006   0.001   PHE D  88 
 TRP   0.015   0.002   TRP D  18 
 HIS   0.002   0.000   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 4960)
  covalent geometry    : angle       0.41387 ( 6756)
  hydrogen bonds       : bond        0.04019 (  297)
  hydrogen bonds       : angle       4.16924 (  843)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2180.38 seconds
wall clock time: 37 minutes 42.86 seconds (2262.86 seconds total)