Starting phenix.real_space_refine
on Thu Jul 24 00:20:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pkd_17735/07_2025/8pkd_17735.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pkd_17735/07_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_17735/07_2025/8pkd_17735.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pkd_17735/07_2025/8pkd_17735.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pkd_17735/07_2025/8pkd_17735.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pkd_17735/07_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-5711/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: 3.79, per 1000 atoms: 0.78
  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 599.9 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: 0.55
  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: 1.28

  Time building geometry restraints manager: 1.48 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: 0.03
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:             1.650
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.550
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  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:14.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.130
-------------------------------------------------------------------------------
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 (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 

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

*********************** 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: 1.6812
  time to fit residues: 200.4838
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  : 0.587 
-------------------------------------------------------------------------------
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 = 0.106168 restraints weight = 4294.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3081 rms_B_bonded: 1.71
r_work: 0.2850 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2709 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9000
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= 0.152
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04649 (  297)
  hydrogen bonds       : angle       4.74792 (  843)
  covalent geometry    : bond        0.00313 ( 4960)
  covalent geometry    : angle       0.46972 ( 6756)

*********************** 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  : 0.551 
Fit side-chains
REVERT: A    3 ASN cc_start: 0.7405 (m-40) cc_final: 0.6591 (t0)
REVERT: A   75 GLN cc_start: 0.9230 (OUTLIER) cc_final: 0.8974 (mt0)
REVERT: A  148 ARG cc_start: 0.8512 (mtp180) cc_final: 0.7927 (mmt90)
REVERT: B    3 ASN cc_start: 0.7465 (m-40) cc_final: 0.6575 (t0)
REVERT: B  148 ARG cc_start: 0.8491 (mtp180) cc_final: 0.7946 (mmt90)
REVERT: C    3 ASN cc_start: 0.7371 (m-40) cc_final: 0.6521 (t0)
REVERT: C  148 ARG cc_start: 0.8510 (mtp180) cc_final: 0.7959 (mmt90)
REVERT: D    3 ASN cc_start: 0.7353 (m-40) cc_final: 0.6531 (t0)
REVERT: D  148 ARG cc_start: 0.8509 (mtp180) cc_final: 0.7968 (mmt90)
  outliers start: 2
  outliers final: 0
  residues processed: 89
  average time/residue: 1.6837
  time to fit residues: 154.2038
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  : 0.548 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    1.5786

-------------------------------------------------------------------------------
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 = 0.3571 r_free = 0.3571 target = 0.141344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.103023 restraints weight = 4297.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3058 rms_B_bonded: 1.73
r_work: 0.2837 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2700 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9015
moved from start:          0.2614

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= 0.160
  Angle     :  0.476   5.322   6756  Z= 0.268
  Chirality :  0.041   0.142    704
  Planarity :  0.004   0.037    896
  Dihedral  :  4.216  16.531    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  :  6.15 %
    Favored  : 93.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.89 (0.34), residues: 592
  helix:  1.56 (0.28), residues: 344
  sheet:  2.37 (0.49), residues: 72
  loop :  0.28 (0.47), residues: 176

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04888 (  297)
  hydrogen bonds       : angle       4.63818 (  843)
  covalent geometry    : bond        0.00336 ( 4960)
  covalent geometry    : angle       0.47602 ( 6756)

*********************** 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  : 0.491 
Fit side-chains
REVERT: A    3 ASN cc_start: 0.7333 (m-40) cc_final: 0.6492 (t0)
REVERT: A  148 ARG cc_start: 0.8523 (mtp180) cc_final: 0.7939 (mmt90)
REVERT: B    3 ASN cc_start: 0.7370 (m-40) cc_final: 0.6433 (t0)
REVERT: B  148 ARG cc_start: 0.8496 (mtp180) cc_final: 0.7967 (mmt90)
REVERT: C    3 ASN cc_start: 0.7326 (m-40) cc_final: 0.6420 (t0)
REVERT: C  148 ARG cc_start: 0.8506 (mtp180) cc_final: 0.7958 (mmt90)
REVERT: D    3 ASN cc_start: 0.7285 (m-40) cc_final: 0.6405 (t0)
REVERT: D   75 GLN cc_start: 0.9282 (OUTLIER) cc_final: 0.9039 (mt0)
REVERT: D  148 ARG cc_start: 0.8528 (mtp180) cc_final: 0.7981 (mmt90)
  outliers start: 3
  outliers final: 0
  residues processed: 89
  average time/residue: 1.6230
  time to fit residues: 148.7849
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  : 0.579 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   chunk 47 optimal weight:    7.9990
   chunk 42 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 1 optimal weight:    0.6980
   chunk 50 optimal weight:    3.9990
   chunk 13 optimal weight:    0.3980
   chunk 37 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3595 r_free = 0.3595 target = 0.143460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.105944 restraints weight = 4368.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3099 rms_B_bonded: 1.73
r_work: 0.2888 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2754 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8982
moved from start:          0.2596

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= 0.109
  Angle     :  0.419   5.274   6756  Z= 0.233
  Chirality :  0.038   0.131    704
  Planarity :  0.003   0.036    896
  Dihedral  :  4.005  14.925    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:  1.93 (0.34), residues: 592
  helix:  1.65 (0.28), residues: 348
  sheet:  2.33 (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 B  18 
 HIS   0.001   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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04097 (  297)
  hydrogen bonds       : angle       4.35829 (  843)
  covalent geometry    : bond        0.00215 ( 4960)
  covalent geometry    : angle       0.41866 ( 6756)

*********************** 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  : 0.517 
Fit side-chains
REVERT: A    3 ASN cc_start: 0.7313 (m-40) cc_final: 0.6480 (t0)
REVERT: A  148 ARG cc_start: 0.8489 (mtp180) cc_final: 0.7931 (mmt90)
REVERT: B    3 ASN cc_start: 0.7377 (m-40) cc_final: 0.6442 (t0)
REVERT: B  148 ARG cc_start: 0.8468 (mtp180) cc_final: 0.7955 (mmt90)
REVERT: C    3 ASN cc_start: 0.7348 (m-40) cc_final: 0.6455 (t0)
REVERT: C  148 ARG cc_start: 0.8466 (mtp180) cc_final: 0.7945 (mmt90)
REVERT: D    3 ASN cc_start: 0.7321 (m-40) cc_final: 0.6435 (t0)
REVERT: D   75 GLN cc_start: 0.9267 (OUTLIER) cc_final: 0.9024 (mt0)
REVERT: D  148 ARG cc_start: 0.8486 (mtp180) cc_final: 0.7956 (mmt90)
  outliers start: 3
  outliers final: 0
  residues processed: 90
  average time/residue: 1.5792
  time to fit residues: 146.4457
Evaluate side-chains
  81 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 48 optimal weight:    1.9990
   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:    0.0870
   chunk 53 optimal weight:    0.8980
   chunk 55 optimal weight:    0.5980
   chunk 28 optimal weight:    9.9990
   overall best weight:    0.8960

-------------------------------------------------------------------------------
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 = 0.3583 r_free = 0.3583 target = 0.142785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.105443 restraints weight = 4319.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 1.69
r_work: 0.2897 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2763 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8993
moved from start:          0.2676

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= 0.115
  Angle     :  0.425   5.273   6756  Z= 0.237
  Chirality :  0.038   0.132    704
  Planarity :  0.003   0.036    896
  Dihedral  :  4.038  15.399    656
  Min Nonbonded Distance : 2.668

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  7.17 %
    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:  1.97 (0.35), residues: 592
  helix:  1.69 (0.29), residues: 348
  sheet:  2.31 (0.49), residues: 72
  loop :  0.16 (0.48), 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 B  88 
 TYR   0.009   0.001   TYR C 118 
 ARG   0.002   0.000   ARG B 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04201 (  297)
  hydrogen bonds       : angle       4.33577 (  843)
  covalent geometry    : bond        0.00230 ( 4960)
  covalent geometry    : angle       0.42475 ( 6756)

*********************** 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
  89 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 86
  time to evaluate  : 0.624 
Fit side-chains
REVERT: A    3 ASN cc_start: 0.7333 (m-40) cc_final: 0.6484 (t0)
REVERT: A  148 ARG cc_start: 0.8504 (mtp180) cc_final: 0.7955 (mmt90)
REVERT: B    3 ASN cc_start: 0.7321 (m-40) cc_final: 0.6398 (t0)
REVERT: B  148 ARG cc_start: 0.8487 (mtp180) cc_final: 0.7988 (mmt90)
REVERT: C    3 ASN cc_start: 0.7351 (m-40) cc_final: 0.6442 (t0)
REVERT: C  148 ARG cc_start: 0.8488 (mtp180) cc_final: 0.7968 (mmt90)
REVERT: D    3 ASN cc_start: 0.7329 (m-40) cc_final: 0.6422 (t0)
REVERT: D   75 GLN cc_start: 0.9261 (OUTLIER) cc_final: 0.9021 (mt0)
REVERT: D  148 ARG cc_start: 0.8490 (mtp180) cc_final: 0.7981 (mmt90)
  outliers start: 3
  outliers final: 2
  residues processed: 89
  average time/residue: 1.7137
  time to fit residues: 156.9420
Evaluate side-chains
  84 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 81
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    0.2980
   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:   10.0000
   chunk 17 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    1.2186

-------------------------------------------------------------------------------
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 = 0.3571 r_free = 0.3571 target = 0.141704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.104339 restraints weight = 4281.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.3075 rms_B_bonded: 1.67
r_work: 0.2857 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2720 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9006
moved from start:          0.2759

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= 0.135
  Angle     :  0.448   5.281   6756  Z= 0.252
  Chirality :  0.039   0.136    704
  Planarity :  0.004   0.036    896
  Dihedral  :  4.208  18.249    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  :  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 (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 (0.35), residues: 592
  helix:  1.74 (0.29), residues: 344
  sheet:  2.28 (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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04529 (  297)
  hydrogen bonds       : angle       4.42189 (  843)
  covalent geometry    : bond        0.00276 ( 4960)
  covalent geometry    : angle       0.44833 ( 6756)

*********************** 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: 4
    poor density    : 86
  time to evaluate  : 0.430 
Fit side-chains
REVERT: A    3 ASN cc_start: 0.7318 (m-40) cc_final: 0.6468 (t0)
REVERT: A  148 ARG cc_start: 0.8504 (mtp180) cc_final: 0.7941 (mmt90)
REVERT: B    3 ASN cc_start: 0.7291 (m-40) cc_final: 0.6342 (t0)
REVERT: B  148 ARG cc_start: 0.8470 (mtp180) cc_final: 0.7981 (mmt90)
REVERT: C    3 ASN cc_start: 0.7357 (m-40) cc_final: 0.6434 (t0)
REVERT: C  148 ARG cc_start: 0.8495 (mtp180) cc_final: 0.7961 (mmt90)
REVERT: D    3 ASN cc_start: 0.7330 (m-40) cc_final: 0.6405 (t0)
REVERT: D   75 GLN cc_start: 0.9275 (OUTLIER) cc_final: 0.9032 (mt0)
REVERT: D  148 ARG cc_start: 0.8501 (mtp180) cc_final: 0.7984 (mmt90)
  outliers start: 4
  outliers final: 3
  residues processed: 90
  average time/residue: 1.7578
  time to fit residues: 162.5864
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  : 0.569 
-------------------------------------------------------------------------------
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
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:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 56 optimal weight:    0.6980
   chunk 20 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 57 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    1.2782

-------------------------------------------------------------------------------
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 = 0.3610 r_free = 0.3610 target = 0.143349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.105969 restraints weight = 4243.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 1.67
r_work: 0.2874 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2736 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9012
moved from start:          0.2841

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= 0.138
  Angle     :  0.451   5.267   6756  Z= 0.254
  Chirality :  0.040   0.136    704
  Planarity :  0.004   0.036    896
  Dihedral  :  4.249  20.058    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:  2.06 (0.35), residues: 592
  helix:  1.71 (0.29), residues: 344
  sheet:  2.28 (0.48), residues: 72
  loop :  0.39 (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   0.007   0.001   PHE D  88 
 TYR   0.009   0.001   TYR C 118 
 ARG   0.002   0.000   ARG B 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04542 (  297)
  hydrogen bonds       : angle       4.41940 (  843)
  covalent geometry    : bond        0.00284 ( 4960)
  covalent geometry    : angle       0.45090 ( 6756)

*********************** 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
  91 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 86
  time to evaluate  : 1.217 
Fit side-chains
REVERT: A    3 ASN cc_start: 0.7331 (m-40) cc_final: 0.6479 (t0)
REVERT: A  148 ARG cc_start: 0.8471 (mtp180) cc_final: 0.7969 (mmt90)
REVERT: B    3 ASN cc_start: 0.7298 (m-40) cc_final: 0.6862 (t0)
REVERT: B  148 ARG cc_start: 0.8449 (mtp180) cc_final: 0.8013 (mmt90)
REVERT: C    3 ASN cc_start: 0.7339 (m-40) cc_final: 0.6404 (t0)
REVERT: C  148 ARG cc_start: 0.8457 (mtp180) cc_final: 0.8008 (mmt90)
REVERT: D    3 ASN cc_start: 0.7313 (m-40) cc_final: 0.6375 (t0)
REVERT: D   75 GLN cc_start: 0.9284 (OUTLIER) cc_final: 0.9041 (mt0)
REVERT: D  148 ARG cc_start: 0.8477 (mtp180) cc_final: 0.8002 (mmt90)
  outliers start: 5
  outliers final: 4
  residues processed: 91
  average time/residue: 2.6083
  time to fit residues: 243.2861
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  : 0.582 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 54 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 28 optimal weight:    8.9990
   chunk 17 optimal weight:    4.9990
   chunk 31 optimal weight:    0.1980
   chunk 21 optimal weight:    2.9990
   chunk 5 optimal weight:    8.9990
   chunk 8 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   overall best weight:    1.6386

-------------------------------------------------------------------------------
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
D  32 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.143868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.106492 restraints weight = 4280.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3081 rms_B_bonded: 1.67
r_work: 0.2858 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2720 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9028
moved from start:          0.2920

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= 0.161
  Angle     :  0.480   5.305   6756  Z= 0.271
  Chirality :  0.041   0.142    704
  Planarity :  0.004   0.037    896
  Dihedral  :  4.435  22.539    656
  Min Nonbonded Distance : 2.669

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  7.17 %
    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:  2.03 (0.35), residues: 592
  helix:  1.67 (0.29), residues: 344
  sheet:  2.28 (0.48), residues: 72
  loop :  0.43 (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   0.008   0.001   PHE B  88 
 TYR   0.009   0.001   TYR C 118 
 ARG   0.002   0.000   ARG B 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04884 (  297)
  hydrogen bonds       : angle       4.52455 (  843)
  covalent geometry    : bond        0.00339 ( 4960)
  covalent geometry    : angle       0.48040 ( 6756)

*********************** 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: 6
    poor density    : 84
  time to evaluate  : 0.459 
Fit side-chains
REVERT: A    3 ASN cc_start: 0.7361 (m-40) cc_final: 0.6516 (t0)
REVERT: A  148 ARG cc_start: 0.8502 (mtp180) cc_final: 0.8011 (mmt90)
REVERT: B    3 ASN cc_start: 0.7359 (m-40) cc_final: 0.6938 (t0)
REVERT: B  148 ARG cc_start: 0.8472 (mtp180) cc_final: 0.8031 (mmt90)
REVERT: C    3 ASN cc_start: 0.7331 (m-40) cc_final: 0.6427 (t0)
REVERT: C  148 ARG cc_start: 0.8467 (mtp180) cc_final: 0.8014 (mmt90)
REVERT: D    3 ASN cc_start: 0.7320 (m-40) cc_final: 0.6388 (t0)
REVERT: D   75 GLN cc_start: 0.9290 (OUTLIER) cc_final: 0.9048 (mt0)
REVERT: D  148 ARG cc_start: 0.8477 (mtp180) cc_final: 0.7994 (mmt90)
  outliers start: 6
  outliers final: 5
  residues processed: 90
  average time/residue: 4.6646
  time to fit residues: 426.4154
Evaluate side-chains
  86 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain C residue   77 TRP
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:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 49 optimal weight:    8.9990
   chunk 12 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0980
   chunk 50 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.3619 r_free = 0.3619 target = 0.143940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.106775 restraints weight = 4229.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3106 rms_B_bonded: 1.66
r_work: 0.2888 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2751 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9000
moved from start:          0.2881

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= 0.120
  Angle     :  0.432   5.237   6756  Z= 0.243
  Chirality :  0.039   0.133    704
  Planarity :  0.004   0.036    896
  Dihedral  :  4.206  19.801    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  :  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:  1.98 (0.34), residues: 592
  helix:  1.67 (0.28), residues: 348
  sheet:  2.31 (0.49), residues: 72
  loop :  0.23 (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 A  32 
 PHE   0.007   0.001   PHE B  88 
 TYR   0.009   0.001   TYR C 118 
 ARG   0.002   0.000   ARG B 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04295 (  297)
  hydrogen bonds       : angle       4.33917 (  843)
  covalent geometry    : bond        0.00241 ( 4960)
  covalent geometry    : angle       0.43247 ( 6756)

*********************** 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  : 1.032 
Fit side-chains
REVERT: A    3 ASN cc_start: 0.7346 (m-40) cc_final: 0.6510 (t0)
REVERT: A  148 ARG cc_start: 0.8464 (mtp180) cc_final: 0.7969 (mmt90)
REVERT: B    3 ASN cc_start: 0.7301 (m-40) cc_final: 0.6865 (t0)
REVERT: B  148 ARG cc_start: 0.8416 (mtp180) cc_final: 0.7966 (mmt90)
REVERT: C    3 ASN cc_start: 0.7306 (m-40) cc_final: 0.6415 (t0)
REVERT: C  148 ARG cc_start: 0.8437 (mtp180) cc_final: 0.7969 (mmt90)
REVERT: D    3 ASN cc_start: 0.7320 (m-40) cc_final: 0.6398 (t0)
REVERT: D   75 GLN cc_start: 0.9269 (OUTLIER) cc_final: 0.9027 (mt0)
REVERT: D  148 ARG cc_start: 0.8443 (mtp180) cc_final: 0.7962 (mmt90)
  outliers start: 5
  outliers final: 4
  residues processed: 90
  average time/residue: 3.7354
  time to fit residues: 342.5970
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  : 0.517 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 5 optimal weight:   10.0000
   chunk 20 optimal weight:    0.8980
   chunk 2 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0070
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.7398

-------------------------------------------------------------------------------
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
D  32 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.145619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.108629 restraints weight = 4334.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 1.67
r_work: 0.2905 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2767 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8988
moved from start:          0.2840

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= 0.106
  Angle     :  0.416   5.228   6756  Z= 0.232
  Chirality :  0.038   0.128    704
  Planarity :  0.004   0.036    896
  Dihedral  :  4.054  17.466    656
  Min Nonbonded Distance : 2.667

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  7.58 %
    Favored  : 91.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.35), residues: 592
  helix:  1.76 (0.28), residues: 348
  sheet:  2.40 (0.51), residues: 72
  loop :  0.20 (0.48), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP D  18 
 HIS   0.002   0.001   HIS B  32 
 PHE   0.007   0.001   PHE D  88 
 TYR   0.009   0.001   TYR C 118 
 ARG   0.002   0.000   ARG D 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04027 (  297)
  hydrogen bonds       : angle       4.21570 (  843)
  covalent geometry    : bond        0.00208 ( 4960)
  covalent geometry    : angle       0.41608 ( 6756)

********************** 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  : 0.620 
Fit side-chains
REVERT: A    3 ASN cc_start: 0.7355 (m-40) cc_final: 0.6517 (t0)
REVERT: A  148 ARG cc_start: 0.8460 (mtp180) cc_final: 0.7976 (mmt90)
REVERT: B    3 ASN cc_start: 0.7300 (m-40) cc_final: 0.6888 (t0)
REVERT: B  148 ARG cc_start: 0.8421 (mtp180) cc_final: 0.7969 (mmt90)
REVERT: C    3 ASN cc_start: 0.7284 (m-40) cc_final: 0.6420 (t0)
REVERT: C  148 ARG cc_start: 0.8429 (mtp180) cc_final: 0.7966 (mmt90)
REVERT: D    3 ASN cc_start: 0.7296 (m-40) cc_final: 0.6390 (t0)
REVERT: D   75 GLN cc_start: 0.9262 (OUTLIER) cc_final: 0.9019 (mt0)
REVERT: D  148 ARG cc_start: 0.8449 (mtp180) cc_final: 0.7979 (mmt90)
  outliers start: 5
  outliers final: 2
  residues processed: 89
  average time/residue: 1.6242
  time to fit residues: 148.9699
Evaluate side-chains
  84 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 81
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 43 optimal weight:    0.0370
   chunk 42 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 10 optimal weight:    4.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.7058

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.147026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.110233 restraints weight = 4309.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 1.68
r_work: 0.2906 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2767 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8984
moved from start:          0.2862

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= 0.104
  Angle     :  0.414   5.229   6756  Z= 0.231
  Chirality :  0.038   0.128    704
  Planarity :  0.003   0.036    896
  Dihedral  :  4.006  16.954    656
  Min Nonbonded Distance : 2.664

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  8.20 %
    Favored  : 91.19 %
  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:  2.10 (0.35), residues: 592
  helix:  1.80 (0.29), residues: 348
  sheet:  2.40 (0.52), residues: 72
  loop :  0.18 (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 C  32 
 PHE   0.006   0.001   PHE B  88 
 TYR   0.009   0.001   TYR C 118 
 ARG   0.002   0.000   ARG D 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03976 (  297)
  hydrogen bonds       : angle       4.15925 (  843)
  covalent geometry    : bond        0.00203 ( 4960)
  covalent geometry    : angle       0.41371 ( 6756)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5632.37 seconds
wall clock time: 100 minutes 24.91 seconds (6024.91 seconds total)