Starting phenix.real_space_refine
on Wed Mar  4 09:20:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xzy_33534/03_2026/7xzy_33534.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xzy_33534/03_2026/7xzy_33534.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xzy_33534/03_2026/7xzy_33534.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xzy_33534/03_2026/7xzy_33534.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xzy_33534/03_2026/7xzy_33534.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xzy_33534/03_2026/7xzy_33534.map"
  }
  resolution = 3.97
  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=   0.003
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: 5
    Type Number    sf(0)   Gaussians
     P     330      5.49       5
     S      14      5.16       5
     C    7015      2.51       5
     N    2417      2.21       5
     O    3045      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12821
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 801
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "C"
      Number of atoms: 844
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 844
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 810
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
    Chain: "H"
      Number of atoms: 746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 746
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 3372
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 3372
          Classifications: {'DNA': 165}
          Link IDs: {'rna3p': 164}
    Chain: "J"
      Number of atoms: 3393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 3393
          Classifications: {'DNA': 165}
          Link IDs: {'rna3p': 164}
  Time building chain proxies: 3.07, per 1000 atoms: 0.24
  Number of scatterers: 12821
  At special positions: 0
  Unit cell: (127.6, 151.8, 105.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     P     330     15.00
     O    3045      8.00
     N    2417      7.00
     C    7015      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: 1.10
  Conformation dependent library (CDL) restraints added in 403.6 milliseconds
  

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1420

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 9 sheets defined
      73.5% alpha, 2.4% beta
      163 base pairs and 262 stacking pairs defined.
    Time for finding SS restraints: 2.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.654A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.345A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.175A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
      removed outlier: 4.127A  pdb=" N   ILE D  91 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 121
      removed outlier: 3.536A  pdb=" N   ALA D 121 " --> pdb=" O   LYS D 117 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.519A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 23 through 29
      removed outlier: 4.152A  pdb=" N   ILE F  26 " --> pdb=" O   ARG F  23 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.723A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.306A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 122
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.699A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.602A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78
      removed outlier: 4.222A  pdb=" N   ILE C  78 " --> pdb=" O   GLY D  50 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 101
      removed outlier: 3.639A  pdb=" N   THR C 101 " --> pdb=" O   THR F  96 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.771A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.555A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78
      removed outlier: 3.735A  pdb=" N   ILE G  78 " --> pdb=" O   GLY H  50 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    410 hydrogen bonds defined for protein.
    1206 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      423 hydrogen bonds
      842 hydrogen bond angles
      0 basepair planarities
      163 basepair parallelities
      262 stacking parallelities
  Total time for adding SS restraints: 2.32

  Time building geometry restraints manager: 1.52 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2094
        1.33 -     1.45: 4796
        1.45 -     1.57: 6152
        1.57 -     1.69: 658
        1.69 -     1.81: 24
  Bond restraints: 13724
  Sorted by residual:
  bond pdb=" N   ILE H  66 "
       pdb=" CA  ILE H  66 "
    ideal  model  delta    sigma   weight residual
    1.461  1.499 -0.038 1.17e-02 7.31e+03 1.04e+01
  bond pdb=" N   ASN H  81 "
       pdb=" CA  ASN H  81 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.036 1.26e-02 6.30e+03 8.21e+00
  bond pdb=" N   ILE G  87 "
       pdb=" CA  ILE G  87 "
    ideal  model  delta    sigma   weight residual
    1.460  1.491 -0.031 1.21e-02 6.83e+03 6.56e+00
  bond pdb=" N   ILE D  66 "
       pdb=" CA  ILE D  66 "
    ideal  model  delta    sigma   weight residual
    1.461  1.490 -0.029 1.17e-02 7.31e+03 6.21e+00
  bond pdb=" N   LYS C 118 "
       pdb=" CA  LYS C 118 "
    ideal  model  delta    sigma   weight residual
    1.454  1.480 -0.026 1.23e-02 6.61e+03 4.51e+00
  ... (remaining 13719 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 19164
        1.62 -     3.24: 711
        3.24 -     4.87: 51
        4.87 -     6.49: 15
        6.49 -     8.11: 7
  Bond angle restraints: 19948
  Sorted by residual:
  angle pdb=" CA  ILE D  66 "
        pdb=" C   ILE D  66 "
        pdb=" O   ILE D  66 "
      ideal   model   delta    sigma   weight residual
     121.17  117.11    4.06 1.06e+00 8.90e-01 1.47e+01
  angle pdb=" N   ILE D  66 "
        pdb=" CA  ILE D  66 "
        pdb=" C   ILE D  66 "
      ideal   model   delta    sigma   weight residual
     110.42  107.00    3.42 9.60e-01 1.09e+00 1.27e+01
  angle pdb=" C   THR A  80 "
        pdb=" N   ASP A  81 "
        pdb=" CA  ASP A  81 "
      ideal   model   delta    sigma   weight residual
     121.54  128.31   -6.77 1.91e+00 2.74e-01 1.26e+01
  angle pdb=" CA  GLU A  73 "
        pdb=" CB  GLU A  73 "
        pdb=" CG  GLU A  73 "
      ideal   model   delta    sigma   weight residual
     114.10  121.03   -6.93 2.00e+00 2.50e-01 1.20e+01
  angle pdb=" C   ALA C  86 "
        pdb=" N   ILE C  87 "
        pdb=" CA  ILE C  87 "
      ideal   model   delta    sigma   weight residual
     120.56  116.25    4.31 1.28e+00 6.10e-01 1.14e+01
  ... (remaining 19943 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 4731
       17.96 -    35.91: 1186
       35.91 -    53.87: 1116
       53.87 -    71.82: 317
       71.82 -    89.78: 23
  Dihedral angle restraints: 7373
    sinusoidal: 5169
      harmonic: 2204
  Sorted by residual:
  dihedral pdb=" CA  ILE B  29 "
           pdb=" C   ILE B  29 "
           pdb=" N   THR B  30 "
           pdb=" CA  THR B  30 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.93  -16.07     0      5.00e+00 4.00e-02 1.03e+01
  dihedral pdb=" CA  ILE G  87 "
           pdb=" CB  ILE G  87 "
           pdb=" CG1 ILE G  87 "
           pdb=" CD1 ILE G  87 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  124.96   55.04     3      1.50e+01 4.44e-03 9.32e+00
  dihedral pdb=" CG  ARG E 128 "
           pdb=" CD  ARG E 128 "
           pdb=" NE  ARG E 128 "
           pdb=" CZ  ARG E 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -138.82  -41.18     2      1.50e+01 4.44e-03 9.25e+00
  ... (remaining 7370 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 2042
       0.061 -    0.123: 209
       0.123 -    0.184: 10
       0.184 -    0.245: 1
       0.245 -    0.306: 2
  Chirality restraints: 2264
  Sorted by residual:
  chirality pdb=" CB  ILE B  29 "
            pdb=" CA  ILE B  29 "
            pdb=" CG1 ILE B  29 "
            pdb=" CG2 ILE B  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.31 2.00e-01 2.50e+01 2.35e+00
  chirality pdb=" CB  ILE F  29 "
            pdb=" CA  ILE F  29 "
            pdb=" CG1 ILE F  29 "
            pdb=" CG2 ILE F  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" CA  ILE C  87 "
            pdb=" N   ILE C  87 "
            pdb=" C   ILE C  87 "
            pdb=" CB  ILE C  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.16e+00
  ... (remaining 2261 not shown)

  Planarity restraints: 1381
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B  64 "    0.016 2.00e-02 2.50e+03   3.15e-02 9.90e+00
        pdb=" C   ASN B  64 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   ASN B  64 "    0.020 2.00e-02 2.50e+03
        pdb=" N   VAL B  65 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B  62 "   -0.014 2.00e-02 2.50e+03   2.79e-02 7.76e+00
        pdb=" C   LEU B  62 "    0.048 2.00e-02 2.50e+03
        pdb=" O   LEU B  62 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   GLU B  63 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B  69 "   -0.012 2.00e-02 2.50e+03   2.38e-02 5.67e+00
        pdb=" C   ALA B  69 "    0.041 2.00e-02 2.50e+03
        pdb=" O   ALA B  69 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   VAL B  70 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1378 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 199
        2.63 -     3.20: 10916
        3.20 -     3.76: 24685
        3.76 -     4.33: 30688
        4.33 -     4.90: 43141
  Nonbonded interactions: 109629
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C  39 "
            pdb=" OE1 GLU D  68 "
     model   vdw
     2.062 3.040
  nonbonded pdb=" O   ARG C  20 "
            pdb=" NZ  LYS D 117 "
     model   vdw
     2.080 3.120
  nonbonded pdb=" OG  SER B  47 "
            pdb=" OP1  DC J 105 "
     model   vdw
     2.136 3.040
  nonbonded pdb=" O2   DC I  73 "
            pdb=" N2   DG J 121 "
     model   vdw
     2.162 2.496
  nonbonded pdb=" NH2 ARG H  30 "
            pdb=" OP2  DA I 146 "
     model   vdw
     2.222 3.120
  ... (remaining 109624 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 'E' and resid 38 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 23 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 13 through 118)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 28 through 121)
  selection = (chain 'H' and resid 28 through 121)
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.430
  Find NCS groups from input model:        0.130
  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:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6874
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      :  0.004   0.041  13724  Z= 0.200
  Angle     :  0.688   8.112  19948  Z= 0.424
  Chirality :  0.039   0.306   2264
  Planarity :  0.005   0.039   1381
  Dihedral  : 27.844  89.778   5953
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 14.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.79 %
    Favored  : 99.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.28), residues: 746
  helix:  1.20 (0.20), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.54 (0.41), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F  92 
 TYR   0.023   0.002   TYR C  50 
 PHE   0.018   0.002   PHE G  25 
 HIS   0.006   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 (13724)
  covalent geometry    : angle       0.68759 (19948)
  hydrogen bonds       : bond        0.10071 (  833)
  hydrogen bonds       : angle       3.78212 ( 2048)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 182
  time to evaluate  : 0.316 
Fit side-chains
REVERT: B   59 LYS cc_start: 0.8792 (tttm) cc_final: 0.8221 (tttm)
REVERT: B   63 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7949 (mp0)
REVERT: C   64 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8299 (mm-30)
REVERT: C   92 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7633 (mt-10)
REVERT: F   85 ASP cc_start: 0.8274 (m-30) cc_final: 0.8031 (m-30)
REVERT: G   39 TYR cc_start: 0.7474 (m-10) cc_final: 0.7231 (m-80)
REVERT: G   92 GLU cc_start: 0.8786 (mp0) cc_final: 0.8585 (mp0)
REVERT: H   31 LYS cc_start: 0.8302 (mmmm) cc_final: 0.7981 (mmmt)
REVERT: H   73 GLU cc_start: 0.8204 (tp30) cc_final: 0.7912 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 182
  average time/residue: 0.0946
  time to fit residues: 25.2606
Evaluate side-chains
  143 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    8.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 ASN
H  81 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.097177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.075948 restraints weight = 85725.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.077159 restraints weight = 47256.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.077943 restraints weight = 33123.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.078324 restraints weight = 27163.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 63)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.078706 restraints weight = 24567.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.3459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13724  Z= 0.189
  Angle     :  0.635   9.965  19948  Z= 0.372
  Chirality :  0.036   0.176   2264
  Planarity :  0.005   0.048   1381
  Dihedral  : 31.514  88.795   4432
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  :  9.92 %
    Favored  : 86.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.09 (0.29), residues: 746
  helix:  2.08 (0.21), residues: 545
  sheet:  None (None), residues: 0
  loop : -0.53 (0.39), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  40 
 TYR   0.035   0.003   TYR B  88 
 PHE   0.023   0.002   PHE E  67 
 HIS   0.010   0.002   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (13724)
  covalent geometry    : angle       0.63471 (19948)
  hydrogen bonds       : bond        0.05438 (  833)
  hydrogen bonds       : angle       3.03331 ( 2048)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 169
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8739 (mt-10)
REVERT: A   77 ASP cc_start: 0.8048 (t0) cc_final: 0.7837 (t0)
REVERT: B   73 THR cc_start: 0.9457 (m) cc_final: 0.9229 (t)
REVERT: C   36 LYS cc_start: 0.8533 (mmmt) cc_final: 0.8284 (mmtp)
REVERT: C   64 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8400 (tp30)
REVERT: E   50 GLU cc_start: 0.8908 (pt0) cc_final: 0.8474 (pt0)
REVERT: E  123 ASP cc_start: 0.9107 (m-30) cc_final: 0.8871 (m-30)
REVERT: F   53 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8488 (mp0)
REVERT: F   79 LYS cc_start: 0.7814 (mtpt) cc_final: 0.7564 (mtmt)
REVERT: F   93 GLN cc_start: 0.8809 (tp40) cc_final: 0.8533 (tp40)
REVERT: G   92 GLU cc_start: 0.8910 (mp0) cc_final: 0.8654 (mp0)
REVERT: H   42 LEU cc_start: 0.9633 (tp) cc_final: 0.9348 (tp)
REVERT: H   65 ASP cc_start: 0.8790 (t70) cc_final: 0.8413 (t0)
  outliers start: 23
  outliers final: 8
  residues processed: 181
  average time/residue: 0.1049
  time to fit residues: 27.9132
Evaluate side-chains
  137 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 129
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain F residue   59 LYS
Chi-restraints excluded: chain G residue   79 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 26 optimal weight:    6.9990
   chunk 71 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 78 optimal weight:    9.9990
   chunk 82 optimal weight:   10.0000
   chunk 16 optimal weight:    3.9990
   chunk 91 optimal weight:   10.0000
   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  93 GLN
B  75 HIS
E  93 GLN
G 110 ASN
H  81 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.093704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.072301 restraints weight = 86489.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.073496 restraints weight = 47176.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.074273 restraints weight = 32658.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.074653 restraints weight = 26573.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.074774 restraints weight = 23976.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.4395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13724  Z= 0.154
  Angle     :  0.561   7.903  19948  Z= 0.331
  Chirality :  0.033   0.140   2264
  Planarity :  0.004   0.053   1381
  Dihedral  : 31.297  89.340   4432
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 14.49 %
    Favored  : 83.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.38 (0.30), residues: 746
  helix:  2.38 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.79 (0.38), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  67 
 TYR   0.017   0.002   TYR B  88 
 PHE   0.014   0.001   PHE E  67 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (13724)
  covalent geometry    : angle       0.56108 (19948)
  hydrogen bonds       : bond        0.04270 (  833)
  hydrogen bonds       : angle       2.81577 ( 2048)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 148
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   73 THR cc_start: 0.9443 (m) cc_final: 0.9178 (t)
REVERT: C   64 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8322 (tp30)
REVERT: C   91 GLU cc_start: 0.8663 (pm20) cc_final: 0.8455 (pm20)
REVERT: D   44 GLN cc_start: 0.8863 (tm-30) cc_final: 0.8537 (tm-30)
REVERT: D   90 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7900 (pm20)
REVERT: F   53 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8347 (mp0)
REVERT: F   79 LYS cc_start: 0.7625 (mtpt) cc_final: 0.7349 (mtmt)
REVERT: F   93 GLN cc_start: 0.8931 (tp40) cc_final: 0.8715 (tp40)
REVERT: G   50 TYR cc_start: 0.8768 (OUTLIER) cc_final: 0.8071 (m-80)
REVERT: G   56 GLU cc_start: 0.8540 (tt0) cc_final: 0.8289 (mt-10)
REVERT: G   92 GLU cc_start: 0.8759 (mp0) cc_final: 0.8415 (mp0)
REVERT: H   65 ASP cc_start: 0.8844 (t70) cc_final: 0.8480 (t0)
REVERT: H   73 GLU cc_start: 0.8582 (tp30) cc_final: 0.8214 (tp30)
  outliers start: 15
  outliers final: 8
  residues processed: 156
  average time/residue: 0.0982
  time to fit residues: 22.6512
Evaluate side-chains
  139 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 129
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain G residue   50 TYR
Chi-restraints excluded: chain G residue   79 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 29 optimal weight:    6.9990
   chunk 35 optimal weight:    3.9990
   chunk 85 optimal weight:    8.9990
   chunk 5 optimal weight:    2.9990
   chunk 80 optimal weight:    8.9990
   chunk 30 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 55 optimal weight:    0.3980
   chunk 0 optimal weight:   10.0000
   overall best weight:    2.0788

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

Flipped N/Q/H residues before XYZ refinement:
B  75 HIS
D  46 HIS
D  60 ASN
E  93 GLN
H  81 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.074488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.051803 restraints weight = 85048.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.052759 restraints weight = 47395.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.053375 restraints weight = 33710.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.053667 restraints weight = 27867.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.053796 restraints weight = 25425.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.8346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13724  Z= 0.205
  Angle     :  0.695  12.144  19948  Z= 0.401
  Chirality :  0.038   0.250   2264
  Planarity :  0.005   0.065   1381
  Dihedral  : 31.338  88.466   4432
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.41 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 17.17 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.88 (0.30), residues: 746
  helix:  2.10 (0.21), residues: 546
  sheet:  None (None), residues: 0
  loop : -1.21 (0.39), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG G  77 
 TYR   0.027   0.002   TYR D  37 
 PHE   0.012   0.002   PHE C  25 
 HIS   0.007   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 (13724)
  covalent geometry    : angle       0.69483 (19948)
  hydrogen bonds       : bond        0.06933 (  833)
  hydrogen bonds       : angle       3.28901 ( 2048)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 144
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.8030 (tptp) cc_final: 0.7776 (tptm)
REVERT: B   88 TYR cc_start: 0.8758 (m-10) cc_final: 0.8490 (m-80)
REVERT: C   50 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.8682 (m-80)
REVERT: C   64 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8555 (tm-30)
REVERT: C   92 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7898 (mt-10)
REVERT: D   81 ASN cc_start: 0.9070 (m-40) cc_final: 0.8856 (m-40)
REVERT: D   90 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8045 (pm20)
REVERT: F   53 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8526 (mp0)
REVERT: G   36 LYS cc_start: 0.9148 (tppt) cc_final: 0.8901 (tppp)
REVERT: H   32 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8521 (mm-30)
REVERT: H   65 ASP cc_start: 0.9044 (t70) cc_final: 0.8681 (t0)
REVERT: H   73 GLU cc_start: 0.8811 (tp30) cc_final: 0.8505 (tp30)
REVERT: H   81 ASN cc_start: 0.8868 (OUTLIER) cc_final: 0.8588 (t0)
  outliers start: 28
  outliers final: 8
  residues processed: 161
  average time/residue: 0.1130
  time to fit residues: 25.8692
Evaluate side-chains
  132 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 121
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   50 TYR
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain G residue   50 TYR
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain H residue   49 THR
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   81 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 26 optimal weight:    5.9990
   chunk 58 optimal weight:    8.9990
   chunk 3 optimal weight:    1.9990
   chunk 19 optimal weight:   10.0000
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
B  75 HIS
G  38 ASN
H  81 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.073590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.051403 restraints weight = 85835.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.052342 restraints weight = 46081.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.052968 restraints weight = 31967.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.053459 restraints weight = 26107.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.053639 restraints weight = 23213.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.8923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  13724  Z= 0.165
  Angle     :  0.584   7.878  19948  Z= 0.345
  Chirality :  0.033   0.150   2264
  Planarity :  0.004   0.051   1381
  Dihedral  : 31.170  89.861   4432
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 20.79 %
    Favored  : 77.01 %
  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 are not related in a simple way.
  whole:  2.42 (0.31), residues: 746
  helix:  2.52 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -1.12 (0.40), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  30 
 TYR   0.010   0.001   TYR D  37 
 PHE   0.007   0.001   PHE C  25 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (13724)
  covalent geometry    : angle       0.58407 (19948)
  hydrogen bonds       : bond        0.04401 (  833)
  hydrogen bonds       : angle       2.74753 ( 2048)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 131
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8802 (m-10) cc_final: 0.8460 (m-10)
REVERT: C   50 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.8307 (m-80)
REVERT: C   56 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8582 (mm-30)
REVERT: C   64 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8630 (tm-30)
REVERT: D   32 GLU cc_start: 0.7784 (mp0) cc_final: 0.7565 (mp0)
REVERT: D   83 ARG cc_start: 0.8031 (tpp80) cc_final: 0.7640 (tpp80)
REVERT: D   90 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8102 (pm20)
REVERT: F   53 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8305 (mp0)
REVERT: F   93 GLN cc_start: 0.9095 (tp40) cc_final: 0.8869 (tp40)
REVERT: G   50 TYR cc_start: 0.8939 (OUTLIER) cc_final: 0.8038 (m-80)
REVERT: H   31 LYS cc_start: 0.8517 (mmmm) cc_final: 0.8038 (mmmt)
REVERT: H   65 ASP cc_start: 0.9038 (t70) cc_final: 0.8719 (t0)
REVERT: H   73 GLU cc_start: 0.8889 (tp30) cc_final: 0.8572 (tp30)
REVERT: H   81 ASN cc_start: 0.7706 (OUTLIER) cc_final: 0.7406 (t0)
  outliers start: 14
  outliers final: 4
  residues processed: 138
  average time/residue: 0.1173
  time to fit residues: 22.8577
Evaluate side-chains
  124 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 116
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain C residue   50 TYR
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain G residue   50 TYR
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   81 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 54 optimal weight:    0.6980
   chunk 99 optimal weight:   10.0000
   chunk 96 optimal weight:   10.0000
   chunk 83 optimal weight:   10.0000
   chunk 65 optimal weight:    9.9990
   chunk 95 optimal weight:    8.9990
   chunk 6 optimal weight:    7.9990
   chunk 68 optimal weight:    7.9990
   overall best weight:    2.5186

-------------------------------------------------------------------------------
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 = 0.3478 r_free = 0.3478 target = 0.067110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.044153 restraints weight = 83662.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 71)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.045109 restraints weight = 45782.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 69)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.045749 restraints weight = 32157.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.045960 restraints weight = 26291.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.046241 restraints weight = 24034.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          1.0336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  13724  Z= 0.202
  Angle     :  0.651  13.758  19948  Z= 0.377
  Chirality :  0.035   0.172   2264
  Planarity :  0.004   0.048   1381
  Dihedral  : 31.159  89.324   4432
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 23.15 %
    Favored  : 74.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.24 (0.31), residues: 746
  helix:  2.38 (0.22), residues: 547
  sheet:  None (None), residues: 0
  loop : -1.15 (0.41), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG H  83 
 TYR   0.026   0.002   TYR H  80 
 PHE   0.010   0.001   PHE E  67 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 (13724)
  covalent geometry    : angle       0.65114 (19948)
  hydrogen bonds       : bond        0.06193 (  833)
  hydrogen bonds       : angle       3.16254 ( 2048)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 134
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8866 (m-10) cc_final: 0.7845 (m-10)
REVERT: C   50 TYR cc_start: 0.8945 (OUTLIER) cc_final: 0.8713 (m-80)
REVERT: C   64 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8700 (tm-30)
REVERT: C   75 LYS cc_start: 0.8286 (mmmt) cc_final: 0.8020 (mmmm)
REVERT: D   32 GLU cc_start: 0.8130 (mp0) cc_final: 0.7917 (mp0)
REVERT: D   44 GLN cc_start: 0.9203 (tm-30) cc_final: 0.8927 (tm-30)
REVERT: D   80 TYR cc_start: 0.7722 (m-10) cc_final: 0.7120 (m-10)
REVERT: D   90 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8012 (pm20)
REVERT: F   53 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8552 (mp0)
REVERT: H   65 ASP cc_start: 0.9043 (t70) cc_final: 0.8723 (t0)
REVERT: H   81 ASN cc_start: 0.8911 (m-40) cc_final: 0.8591 (t0)
  outliers start: 12
  outliers final: 5
  residues processed: 137
  average time/residue: 0.1160
  time to fit residues: 22.6198
Evaluate side-chains
  121 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 114
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue   50 TYR
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain H residue   49 THR
Chi-restraints excluded: chain H residue   51 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 95 optimal weight:   10.0000
   chunk 93 optimal weight:   10.0000
   chunk 64 optimal weight:    0.9990
   chunk 73 optimal weight:   20.0000
   chunk 44 optimal weight:    7.9990
   chunk 66 optimal weight:    0.9990
   chunk 69 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0070
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.7602

-------------------------------------------------------------------------------
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 = 0.3527 r_free = 0.3527 target = 0.069271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 93)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.047008 restraints weight = 84414.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.048017 restraints weight = 45606.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.048696 restraints weight = 31386.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.048912 restraints weight = 25308.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.049163 restraints weight = 23003.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          1.0522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13724  Z= 0.155
  Angle     :  0.594  12.223  19948  Z= 0.347
  Chirality :  0.033   0.167   2264
  Planarity :  0.004   0.051   1381
  Dihedral  : 30.978  89.997   4432
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 23.94 %
    Favored  : 74.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.47 (0.31), residues: 746
  helix:  2.58 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -1.16 (0.40), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  40 
 TYR   0.009   0.001   TYR F  88 
 PHE   0.006   0.001   PHE E  67 
 HIS   0.004   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (13724)
  covalent geometry    : angle       0.59351 (19948)
  hydrogen bonds       : bond        0.04051 (  833)
  hydrogen bonds       : angle       2.67029 ( 2048)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 125
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8863 (m-10) cc_final: 0.8060 (m-10)
REVERT: C   50 TYR cc_start: 0.8580 (m-80) cc_final: 0.8332 (m-80)
REVERT: D   32 GLU cc_start: 0.8073 (mp0) cc_final: 0.7827 (mp0)
REVERT: D   44 GLN cc_start: 0.9220 (tm-30) cc_final: 0.8969 (tm-30)
REVERT: D   80 TYR cc_start: 0.7290 (m-10) cc_final: 0.6979 (m-10)
REVERT: D   90 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8142 (pm20)
REVERT: E   81 ASP cc_start: 0.8987 (p0) cc_final: 0.8753 (p0)
REVERT: F   53 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8320 (mp0)
REVERT: G   50 TYR cc_start: 0.8902 (OUTLIER) cc_final: 0.7995 (m-80)
REVERT: H   51 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7789 (tp)
REVERT: H   65 ASP cc_start: 0.9040 (t70) cc_final: 0.8719 (t0)
REVERT: H   90 GLU cc_start: 0.8766 (pm20) cc_final: 0.8359 (pm20)
  outliers start: 9
  outliers final: 3
  residues processed: 128
  average time/residue: 0.1008
  time to fit residues: 19.1321
Evaluate side-chains
  122 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 116
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain G residue   50 TYR
Chi-restraints excluded: chain G residue   56 GLU
Chi-restraints excluded: chain H residue   49 THR
Chi-restraints excluded: chain H residue   51 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 93 optimal weight:   10.0000
   chunk 35 optimal weight:    1.9990
   chunk 101 optimal weight:   10.0000
   chunk 52 optimal weight:    4.9990
   chunk 77 optimal weight:   10.0000
   chunk 65 optimal weight:    0.7980
   chunk 75 optimal weight:   10.0000
   chunk 36 optimal weight:    7.9990
   chunk 83 optimal weight:   10.0000
   chunk 95 optimal weight:   10.0000
   overall best weight:    4.3588

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

Flipped N/Q/H residues before XYZ refinement:
E 113 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.061815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.2643 r_free = 0.2643 target = 0.038804 restraints weight = 83446.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.039702 restraints weight = 45478.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2701 r_free = 0.2701 target = 0.040226 restraints weight = 31758.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 69)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.040648 restraints weight = 25997.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.040767 restraints weight = 23173.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.2631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8759
moved from start:          1.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060  13724  Z= 0.268
  Angle     :  0.746  12.764  19948  Z= 0.428
  Chirality :  0.038   0.196   2264
  Planarity :  0.005   0.047   1381
  Dihedral  : 31.204  86.123   4432
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 24.41 %
    Favored  : 73.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.82 (0.31), residues: 746
  helix:  2.14 (0.22), residues: 547
  sheet:  None (None), residues: 0
  loop : -1.54 (0.41), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  30 
 TYR   0.023   0.002   TYR H  80 
 PHE   0.012   0.002   PHE E 104 
 HIS   0.008   0.002   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00597 (13724)
  covalent geometry    : angle       0.74563 (19948)
  hydrogen bonds       : bond        0.07250 (  833)
  hydrogen bonds       : angle       3.57867 ( 2048)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8935 (m-10) cc_final: 0.8638 (m-80)
REVERT: C   56 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8530 (mm-30)
REVERT: D   32 GLU cc_start: 0.8551 (mp0) cc_final: 0.8274 (mp0)
REVERT: D   44 GLN cc_start: 0.9243 (tm-30) cc_final: 0.8921 (tm-30)
REVERT: E   79 LYS cc_start: 0.8389 (tptp) cc_final: 0.8083 (tptm)
REVERT: E   81 ASP cc_start: 0.9016 (p0) cc_final: 0.8744 (p0)
  outliers start: 11
  outliers final: 7
  residues processed: 116
  average time/residue: 0.1141
  time to fit residues: 19.0318
Evaluate side-chains
  111 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 ARG
Chi-restraints excluded: chain C residue   50 TYR
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain G residue   56 GLU
Chi-restraints excluded: chain H residue   49 THR
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   80 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 98 optimal weight:   10.0000
   chunk 88 optimal weight:   20.0000
   chunk 101 optimal weight:   10.0000
   chunk 19 optimal weight:    5.9990
   chunk 87 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 78 optimal weight:    8.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    1.3788

-------------------------------------------------------------------------------
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 = 0.3399 r_free = 0.3399 target = 0.061962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2720 r_free = 0.2720 target = 0.038618 restraints weight = 79650.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.039413 restraints weight = 41165.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.040008 restraints weight = 27853.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 61)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.040366 restraints weight = 22369.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.040521 restraints weight = 19798.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8651
moved from start:          1.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13724  Z= 0.168
  Angle     :  0.634  16.218  19948  Z= 0.366
  Chirality :  0.033   0.173   2264
  Planarity :  0.004   0.050   1381
  Dihedral  : 30.898  89.527   4432
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 25.83 %
    Favored  : 73.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.26 (0.31), residues: 746
  helix:  2.52 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -1.54 (0.41), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  89 
 TYR   0.017   0.001   TYR H  80 
 PHE   0.005   0.001   PHE E  67 
 HIS   0.009   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (13724)
  covalent geometry    : angle       0.63354 (19948)
  hydrogen bonds       : bond        0.04463 (  833)
  hydrogen bonds       : angle       2.83120 ( 2048)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 122
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8923 (m-10) cc_final: 0.8145 (m-80)
REVERT: C   56 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8490 (mm-30)
REVERT: C   64 GLU cc_start: 0.9121 (tt0) cc_final: 0.8787 (tm-30)
REVERT: D   32 GLU cc_start: 0.8333 (mp0) cc_final: 0.8034 (mp0)
REVERT: D   44 GLN cc_start: 0.9211 (tm-30) cc_final: 0.8938 (tm-30)
REVERT: D   80 TYR cc_start: 0.7595 (m-10) cc_final: 0.6976 (m-10)
REVERT: D   90 GLU cc_start: 0.8690 (mp0) cc_final: 0.8319 (pm20)
REVERT: E   81 ASP cc_start: 0.8942 (p0) cc_final: 0.8710 (p0)
REVERT: F   53 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8311 (mp0)
REVERT: G   15 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.9224 (ptmm)
REVERT: H   90 GLU cc_start: 0.8771 (pm20) cc_final: 0.8421 (pm20)
  outliers start: 7
  outliers final: 5
  residues processed: 124
  average time/residue: 0.1057
  time to fit residues: 19.3572
Evaluate side-chains
  118 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 112
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 ARG
Chi-restraints excluded: chain G residue   15 LYS
Chi-restraints excluded: chain G residue   56 GLU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   80 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 28 optimal weight:    2.9990
   chunk 75 optimal weight:   10.0000
   chunk 91 optimal weight:   10.0000
   chunk 73 optimal weight:   20.0000
   chunk 55 optimal weight:    7.9990
   chunk 44 optimal weight:   10.0000
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
H  81 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.063051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.040509 restraints weight = 83647.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.041327 restraints weight = 44794.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.041945 restraints weight = 31020.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.042215 restraints weight = 25074.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.042439 restraints weight = 22516.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.2689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8705
moved from start:          1.2652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13724  Z= 0.190
  Angle     :  0.663  16.410  19948  Z= 0.380
  Chirality :  0.034   0.182   2264
  Planarity :  0.004   0.049   1381
  Dihedral  : 30.858  87.922   4432
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 26.46 %
    Favored  : 72.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.16 (0.32), residues: 746
  helix:  2.45 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.57 (0.42), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  83 
 TYR   0.023   0.001   TYR F  88 
 PHE   0.008   0.001   PHE E  67 
 HIS   0.009   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 (13724)
  covalent geometry    : angle       0.66317 (19948)
  hydrogen bonds       : bond        0.05296 (  833)
  hydrogen bonds       : angle       3.00967 ( 2048)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 0.307 
Fit side-chains
REVERT: B   88 TYR cc_start: 0.8921 (m-10) cc_final: 0.8004 (m-10)
REVERT: C   56 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8499 (mm-30)
REVERT: C   64 GLU cc_start: 0.9107 (tt0) cc_final: 0.8800 (tm-30)
REVERT: D   32 GLU cc_start: 0.8398 (mp0) cc_final: 0.8082 (mp0)
REVERT: D   44 GLN cc_start: 0.9189 (tm-30) cc_final: 0.8914 (tm-30)
REVERT: D   80 TYR cc_start: 0.7584 (m-10) cc_final: 0.6936 (m-10)
REVERT: F   53 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8433 (mp0)
REVERT: H   90 GLU cc_start: 0.8788 (pm20) cc_final: 0.8379 (pm20)
  outliers start: 9
  outliers final: 6
  residues processed: 114
  average time/residue: 0.1077
  time to fit residues: 17.9781
Evaluate side-chains
  114 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 108
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain G residue   56 GLU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   49 THR
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   81 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 89 optimal weight:   10.0000
   chunk 98 optimal weight:   10.0000
   chunk 14 optimal weight:    0.8980
   chunk 74 optimal weight:   10.0000
   chunk 73 optimal weight:   20.0000
   chunk 76 optimal weight:   10.0000
   chunk 79 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 95 optimal weight:   10.0000
   chunk 82 optimal weight:   10.0000
   overall best weight:    5.1590

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

Flipped N/Q/H residues before XYZ refinement:
B  75 HIS
D  60 ASN
H  81 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.057554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2596 r_free = 0.2596 target = 0.034932 restraints weight = 77917.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2633 r_free = 0.2633 target = 0.035802 restraints weight = 38500.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.036353 restraints weight = 25481.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 63)----------------|
| r_work = 0.2667 r_free = 0.2667 target = 0.036670 restraints weight = 19981.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2673 r_free = 0.2673 target = 0.036820 restraints weight = 17520.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.2589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8778
moved from start:          1.3434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  13724  Z= 0.289
  Angle     :  0.766  16.264  19948  Z= 0.439
  Chirality :  0.039   0.187   2264
  Planarity :  0.005   0.044   1381
  Dihedral  : 30.945  89.766   4432
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 26.46 %
    Favored  : 71.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.51 (0.31), residues: 746
  helix:  2.00 (0.22), residues: 547
  sheet:  None (None), residues: 0
  loop : -1.95 (0.42), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG H  83 
 TYR   0.025   0.002   TYR F  88 
 PHE   0.012   0.001   PHE E  67 
 HIS   0.014   0.002   HIS H  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00648 (13724)
  covalent geometry    : angle       0.76625 (19948)
  hydrogen bonds       : bond        0.07933 (  833)
  hydrogen bonds       : angle       3.63502 ( 2048)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2179.99 seconds
wall clock time: 38 minutes 6.05 seconds (2286.05 seconds total)