Starting phenix.real_space_refine
on Fri Aug 22 19:31:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t03_40933/08_2025/8t03_40933.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t03_40933/08_2025/8t03_40933.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t03_40933/08_2025/8t03_40933.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t03_40933/08_2025/8t03_40933.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t03_40933/08_2025/8t03_40933.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t03_40933/08_2025/8t03_40933.cif"
  }
  resolution = 2.72
  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=   0.002 sd=   0.094
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: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P       2      5.49       5
     S      44      5.16       5
     C    4492      2.51       5
     N    1092      2.21       5
     O    1246      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6878
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 199, 1593
          Classifications: {'peptide': 199}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 190}
    Chain: "C"
      Number of atoms: 936
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 936
          Classifications: {'peptide': 120}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 115}
    Chain: "D"
      Number of atoms: 832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 832
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 100}
    Chain: "A"
      Number of atoms: 76
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 76
          Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 5
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B, E, F
  Time building chain proxies: 1.68, per 1000 atoms: 0.24
  Number of scatterers: 6878
  At special positions: 0
  Unit cell: (92.13, 103.75, 103.75, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      44     16.00
     P       2     15.00
     O    1246      8.00
     N    1092      7.00
     C    4492      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  50 " - pdb=" SG  CYS A  59 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  50 " - pdb=" SG  CYS B  59 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 472.4 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 301 "
        pdb="ZN    ZN A 301 " - pdb=" NE2 HIS A 184 "
        pdb="ZN    ZN A 301 " - pdb=" NE2 HIS A 180 "
        pdb="ZN    ZN A 301 " - pdb=" NE2 HIS A  48 "
      pdb="  ZN B 301 "
        pdb="ZN    ZN B 301 " - pdb=" NE2 HIS B 184 "
        pdb="ZN    ZN B 301 " - pdb=" NE2 HIS B 180 "
        pdb="ZN    ZN B 301 " - pdb=" NE2 HIS B  48 "


  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1572

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 12 sheets defined
      41.0% alpha, 26.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 15
      removed outlier: 3.975A  pdb=" N   LEU A   9 " --> pdb=" O   VAL A   5 " (cutoff:3.500A)
      Proline residue:  A  11  - end of helix
    Processing helix  chain 'A' and resid 18 through 28
    Processing helix  chain 'A' and resid 30 through 52
    Processing helix  chain 'A' and resid 62 through 87
    Processing helix  chain 'A' and resid 91 through 111
    Processing helix  chain 'A' and resid 118 through 141
    Processing helix  chain 'A' and resid 146 through 153
    Processing helix  chain 'A' and resid 153 through 170
    Processing helix  chain 'A' and resid 171 through 174
    Processing helix  chain 'A' and resid 176 through 195
      removed outlier: 3.704A  pdb=" N   SER A 181 " --> pdb=" O   THR A 177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 15
      Proline residue:  B  11  - end of helix
    Processing helix  chain 'B' and resid 18 through 28
    Processing helix  chain 'B' and resid 30 through 52
    Processing helix  chain 'B' and resid 62 through 87
    Processing helix  chain 'B' and resid 91 through 111
    Processing helix  chain 'B' and resid 118 through 141
    Processing helix  chain 'B' and resid 146 through 153
    Processing helix  chain 'B' and resid 153 through 170
    Processing helix  chain 'B' and resid 171 through 174
    Processing helix  chain 'B' and resid 176 through 195
      removed outlier: 3.704A  pdb=" N   SER B 181 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 88 through 91
    Processing helix  chain 'D' and resid 79 through 83
      removed outlier: 3.516A  pdb=" N   ILE D  83 " --> pdb=" O   PRO D  80 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 88 through 91
    Processing helix  chain 'F' and resid 79 through 83
      removed outlier: 3.515A  pdb=" N   ILE F  83 " --> pdb=" O   PRO F  80 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'C' and resid 11 through 12
      removed outlier: 3.597A  pdb=" N   LEU C  12 " --> pdb=" O   THR C 117 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   VAL C  36 " --> pdb=" O   HIS C  52 " (cutoff:3.500A)
      removed outlier: 4.793A  pdb=" N   HIS C  52 " --> pdb=" O   VAL C  36 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   TRP C  38 " --> pdb=" O   LEU C  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 11 through 12
      removed outlier: 3.597A  pdb=" N   LEU C  12 " --> pdb=" O   THR C 117 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   TYR C 109 " --> pdb=" O   ARG C  99 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 4 through 6
    Processing sheet with id=AA5, first strand: chain 'D' and resid 10 through 13
      removed outlier: 6.419A  pdb=" N   LEU D  11 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ILE D  33 " --> pdb=" O   HIS D  49 " (cutoff:3.500A)
      removed outlier: 4.702A  pdb=" N   HIS D  49 " --> pdb=" O   ILE D  33 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   TRP D  35 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 10 through 13
      removed outlier: 6.419A  pdb=" N   LEU D  11 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 11 through 12
      removed outlier: 3.598A  pdb=" N   LEU E  12 " --> pdb=" O   THR E 117 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   VAL E  36 " --> pdb=" O   HIS E  52 " (cutoff:3.500A)
      removed outlier: 4.793A  pdb=" N   HIS E  52 " --> pdb=" O   VAL E  36 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   TRP E  38 " --> pdb=" O   LEU E  50 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12
      removed outlier: 3.598A  pdb=" N   LEU E  12 " --> pdb=" O   THR E 117 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   TYR E 109 " --> pdb=" O   ARG E  99 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 4 through 6
    Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 13
      removed outlier: 6.418A  pdb=" N   LEU F  11 " --> pdb=" O   GLU F 105 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   ILE F  33 " --> pdb=" O   HIS F  49 " (cutoff:3.500A)
      removed outlier: 4.702A  pdb=" N   HIS F  49 " --> pdb=" O   ILE F  33 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   TRP F  35 " --> pdb=" O   LEU F  47 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 13
      removed outlier: 6.418A  pdb=" N   LEU F  11 " --> pdb=" O   GLU F 105 " (cutoff:3.500A)

    386 hydrogen bonds defined for protein.
    1038 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.79

  Time building geometry restraints manager: 0.77 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1145
        1.33 -     1.45: 1929
        1.45 -     1.57: 3908
        1.57 -     1.69: 4
        1.69 -     1.82: 72
  Bond restraints: 7058
  Sorted by residual:
  bond pdb=" N   LEU A  55 "
       pdb=" CA  LEU A  55 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.00e-02 1.00e+04 1.37e+01
  bond pdb=" N   LEU B  55 "
       pdb=" CA  LEU B  55 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.037 1.00e-02 1.00e+04 1.33e+01
  bond pdb=" N   LEU B  10 "
       pdb=" CA  LEU B  10 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 9.20e-03 1.18e+04 1.33e+01
  bond pdb=" N   LEU A  10 "
       pdb=" CA  LEU A  10 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 9.20e-03 1.18e+04 1.28e+01
  bond pdb=" N   ARG E  68 "
       pdb=" CA  ARG E  68 "
    ideal  model  delta    sigma   weight residual
    1.454  1.504 -0.050 1.42e-02 4.96e+03 1.24e+01
  ... (remaining 7053 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.25: 7570
        2.25 -     4.50: 1874
        4.50 -     6.75: 114
        6.75 -     9.00: 4
        9.00 -    11.25: 2
  Bond angle restraints: 9564
  Sorted by residual:
  angle pdb=" C   PHE E  54 "
        pdb=" N   TRP E  55 "
        pdb=" CA  TRP E  55 "
      ideal   model   delta    sigma   weight residual
     120.38  127.50   -7.12 1.37e+00 5.33e-01 2.70e+01
  angle pdb=" C   PHE C  54 "
        pdb=" N   TRP C  55 "
        pdb=" CA  TRP C  55 "
      ideal   model   delta    sigma   weight residual
     120.38  127.48   -7.10 1.37e+00 5.33e-01 2.68e+01
  angle pdb=" CA  GLY C 113 "
        pdb=" C   GLY C 113 "
        pdb=" O   GLY C 113 "
      ideal   model   delta    sigma   weight residual
     122.24  117.94    4.30 8.70e-01 1.32e+00 2.44e+01
  angle pdb=" CA  GLY E 113 "
        pdb=" C   GLY E 113 "
        pdb=" O   GLY E 113 "
      ideal   model   delta    sigma   weight residual
     122.24  117.97    4.27 8.70e-01 1.32e+00 2.41e+01
  angle pdb=" CA  GLY D 101 "
        pdb=" C   GLY D 101 "
        pdb=" O   GLY D 101 "
      ideal   model   delta    sigma   weight residual
     122.29  118.46    3.83 8.10e-01 1.52e+00 2.24e+01
  ... (remaining 9559 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.87: 4118
       35.87 -    71.74: 116
       71.74 -   107.61: 4
      107.61 -   143.48: 2
      143.48 -   179.35: 4
  Dihedral angle restraints: 4244
    sinusoidal: 1782
      harmonic: 2462
  Sorted by residual:
  dihedral pdb=" CA  GLU A  90 "
           pdb=" C   GLU A  90 "
           pdb=" N   PRO A  91 "
           pdb=" CA  PRO A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   38.51  -38.51     0      5.00e+00 4.00e-02 5.93e+01
  dihedral pdb=" CA  GLU B  90 "
           pdb=" C   GLU B  90 "
           pdb=" N   PRO B  91 "
           pdb=" CA  PRO B  91 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   38.43  -38.43     0      5.00e+00 4.00e-02 5.91e+01
  dihedral pdb=" C1  LBN B 303 "
           pdb=" O1  LBN B 303 "
           pdb=" P1  LBN B 303 "
           pdb=" O3  LBN B 303 "
      ideal   model   delta sinusoidal    sigma   weight residual
     275.40   96.05  179.35     1      3.00e+01 1.11e-03 2.13e+01
  ... (remaining 4241 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.970: 1052
       0.970 -    1.939: 0
       1.939 -    2.909: 0
       2.909 -    3.879: 0
       3.879 -    4.848: 2
  Chirality restraints: 1054
  Sorted by residual:
  chirality pdb=" C2  LBN B 303 "
            pdb=" C1  LBN B 303 "
            pdb=" C3  LBN B 303 "
            pdb=" O7  LBN B 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36    2.48   -4.85 2.00e-01 2.50e+01 5.88e+02
  chirality pdb=" C2  LBN A 303 "
            pdb=" C1  LBN A 303 "
            pdb=" C3  LBN A 303 "
            pdb=" O7  LBN A 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36    2.48   -4.85 2.00e-01 2.50e+01 5.87e+02
  chirality pdb=" CA  ILE D  75 "
            pdb=" N   ILE D  75 "
            pdb=" C   ILE D  75 "
            pdb=" CB  ILE D  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.69   -0.26 2.00e-01 2.50e+01 1.68e+00
  ... (remaining 1051 not shown)

  Planarity restraints: 1156
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C41 LBN B 303 "   -0.038 2.00e-02 2.50e+03   3.86e-02 1.49e+01
        pdb=" C42 LBN B 303 "    0.038 2.00e-02 2.50e+03
        pdb=" C5  LBN B 303 "    0.039 2.00e-02 2.50e+03
        pdb=" C8  LBN B 303 "   -0.039 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C41 LBN A 303 "    0.038 2.00e-02 2.50e+03   3.86e-02 1.49e+01
        pdb=" C42 LBN A 303 "   -0.038 2.00e-02 2.50e+03
        pdb=" C5  LBN A 303 "   -0.039 2.00e-02 2.50e+03
        pdb=" C8  LBN A 303 "    0.039 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A  90 "    0.034 5.00e-02 4.00e+02   5.15e-02 4.24e+00
        pdb=" N   PRO A  91 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO A  91 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A  91 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1153 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 33
        2.60 -     3.18: 5347
        3.18 -     3.75: 10509
        3.75 -     4.33: 15424
        4.33 -     4.90: 26178
  Nonbonded interactions: 57491
  Sorted by model distance:
  nonbonded pdb=" SG  CYS C  22 "
            pdb=" SG  CYS C  97 "
     model   vdw
     2.028 3.760
  nonbonded pdb=" SG  CYS E  22 "
            pdb=" SG  CYS E  97 "
     model   vdw
     2.029 3.760
  nonbonded pdb=" OD1 ASP D  28 "
            pdb=" O   GLY D  68 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" OD1 ASP F  28 "
            pdb=" O   GLY F  68 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" CE1 TYR D  86 "
            pdb=" CD1 LEU D 104 "
     model   vdw
     2.395 3.760
  ... (remaining 57486 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.550
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6984
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      :  0.015   0.208   7066  Z= 1.050
  Angle     :  1.758  11.254   9568  Z= 1.287
  Chirality :  0.227   4.848   1054
  Planarity :  0.004   0.051   1156
  Dihedral  : 17.024 179.354   2666
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  4.90 %
    Favored  : 93.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.46 (0.29), residues: 840
  helix: -0.62 (0.26), residues: 294
  sheet:  0.45 (0.39), residues: 196
  loop : -0.27 (0.36), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 168 
 TYR   0.027   0.003   TYR F  71 
 PHE   0.022   0.003   PHE A  46 
 TRP   0.029   0.003   TRP E 110 
 HIS   0.008   0.002   HIS B 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.01374 ( 7058)
  covalent geometry    : angle       1.75848 ( 9564)
  SS BOND              : bond        0.00908 (    2)
  SS BOND              : angle       0.89766 (    4)
  hydrogen bonds       : bond        0.17264 (  374)
  hydrogen bonds       : angle       8.60404 ( 1038)
  metal coordination   : bond        0.17156 (    6)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 126
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A   29 ARG cc_start: 0.7286 (mmm160) cc_final: 0.7076 (mtp180)
REVERT: A   61 MET cc_start: 0.7701 (mtm) cc_final: 0.7328 (mtp)
REVERT: A  134 LEU cc_start: 0.7325 (mt) cc_final: 0.7024 (mm)
REVERT: A  138 LYS cc_start: 0.6890 (mptt) cc_final: 0.6518 (mptt)
REVERT: A  139 GLU cc_start: 0.6813 (tt0) cc_final: 0.6456 (tt0)
REVERT: B   29 ARG cc_start: 0.7294 (mmm160) cc_final: 0.7089 (mtp180)
REVERT: B   61 MET cc_start: 0.7670 (mtm) cc_final: 0.7319 (mtp)
REVERT: B  134 LEU cc_start: 0.7320 (mt) cc_final: 0.7023 (mm)
REVERT: B  138 LYS cc_start: 0.6891 (mptt) cc_final: 0.6506 (mptt)
REVERT: B  139 GLU cc_start: 0.6827 (tt0) cc_final: 0.6470 (tt0)
REVERT: C   41 LYS cc_start: 0.7093 (tttt) cc_final: 0.6753 (ttpp)
REVERT: C   61 TYR cc_start: 0.8446 (m-80) cc_final: 0.8099 (m-80)
REVERT: C  112 GLN cc_start: 0.7583 (tt0) cc_final: 0.7178 (tt0)
REVERT: D   31 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6359 (mp0)
REVERT: D   42 LYS cc_start: 0.7527 (mtpp) cc_final: 0.6803 (mtmt)
REVERT: E   41 LYS cc_start: 0.7062 (tttt) cc_final: 0.6705 (ttpp)
REVERT: E   61 TYR cc_start: 0.8424 (m-80) cc_final: 0.8081 (m-80)
REVERT: E   83 MET cc_start: 0.6350 (mmm) cc_final: 0.6123 (mpt)
REVERT: F   31 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6297 (mp0)
REVERT: F   42 LYS cc_start: 0.7644 (mtpp) cc_final: 0.6966 (mtmt)
  outliers start: 12
  outliers final: 2
  residues processed: 134
  average time/residue: 0.5453
  time to fit residues: 76.7826
Evaluate side-chains
  100 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 98
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   61 ARG
Chi-restraints excluded: chain F residue   61 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0670
   chunk 33 optimal weight:    0.4980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    9.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
D  30 ASN
F  30 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.162827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.116275 restraints weight = 7016.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 2.41
r_work: 0.3099 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2942 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.2028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7066  Z= 0.126
  Angle     :  0.580   6.343   9568  Z= 0.302
  Chirality :  0.043   0.146   1054
  Planarity :  0.004   0.033   1156
  Dihedral  : 13.732 163.209   1144
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  :  8.72 %
    Favored  : 88.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.04 (0.30), residues: 840
  helix:  1.63 (0.28), residues: 304
  sheet:  0.67 (0.35), residues: 230
  loop : -0.15 (0.39), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  68 
 TYR   0.012   0.001   TYR F  91 
 PHE   0.017   0.002   PHE A  39 
 TRP   0.014   0.001   TRP C 110 
 HIS   0.003   0.001   HIS E  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 7058)
  covalent geometry    : angle       0.58054 ( 9564)
  SS BOND              : bond        0.00065 (    2)
  SS BOND              : angle       0.46613 (    4)
  hydrogen bonds       : bond        0.04235 (  374)
  hydrogen bonds       : angle       5.13318 ( 1038)
  metal coordination   : bond        0.00129 (    6)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 0.179 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.8272 (ttmt) cc_final: 0.7767 (mttt)
REVERT: A  139 GLU cc_start: 0.7818 (tt0) cc_final: 0.7561 (tt0)
REVERT: B   27 LYS cc_start: 0.8288 (ttmt) cc_final: 0.7740 (mttt)
REVERT: B  139 GLU cc_start: 0.7812 (tt0) cc_final: 0.7557 (tt0)
REVERT: D   31 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8023 (mp0)
REVERT: D   42 LYS cc_start: 0.8238 (mtpp) cc_final: 0.7893 (mtmm)
REVERT: D   45 ARG cc_start: 0.8213 (mtm180) cc_final: 0.7975 (mtp180)
REVERT: D   67 SER cc_start: 0.7236 (OUTLIER) cc_final: 0.6748 (p)
REVERT: E   41 LYS cc_start: 0.7836 (tttt) cc_final: 0.7245 (tptp)
REVERT: F   31 GLU cc_start: 0.8543 (mt-10) cc_final: 0.7991 (mp0)
REVERT: F   42 LYS cc_start: 0.8221 (mtpp) cc_final: 0.7770 (mtmm)
REVERT: F   67 SER cc_start: 0.7420 (OUTLIER) cc_final: 0.6964 (p)
  outliers start: 20
  outliers final: 5
  residues processed: 126
  average time/residue: 0.5577
  time to fit residues: 73.6130
Evaluate side-chains
  114 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   68 ARG
Chi-restraints excluded: chain D residue   12 SER
Chi-restraints excluded: chain D residue   67 SER
Chi-restraints excluded: chain E residue   68 ARG
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue  112 GLN
Chi-restraints excluded: chain F residue   67 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 18 optimal weight:    0.6980
   chunk 56 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 69 optimal weight:    5.9990
   chunk 7 optimal weight:    0.6980
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C  16 GLN
D  30 ASN
F  30 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.161167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.112620 restraints weight = 6997.318|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 2.08
r_work: 0.3079 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2922 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.2526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7066  Z= 0.121
  Angle     :  0.542   6.272   9568  Z= 0.280
  Chirality :  0.042   0.141   1054
  Planarity :  0.004   0.033   1156
  Dihedral  : 12.809 163.396   1136
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 12.67 %
    Favored  : 84.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.39 (0.30), residues: 840
  helix:  1.97 (0.28), residues: 306
  sheet:  0.74 (0.34), residues: 240
  loop :  0.06 (0.40), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 168 
 TYR   0.012   0.001   TYR F  91 
 PHE   0.015   0.002   PHE B  46 
 TRP   0.013   0.001   TRP C 110 
 HIS   0.003   0.001   HIS E  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 7058)
  covalent geometry    : angle       0.54237 ( 9564)
  SS BOND              : bond        0.00038 (    2)
  SS BOND              : angle       0.24894 (    4)
  hydrogen bonds       : bond        0.04206 (  374)
  hydrogen bonds       : angle       4.82612 ( 1038)
  metal coordination   : bond        0.00202 (    6)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.8324 (ttmt) cc_final: 0.7847 (mttt)
REVERT: A  139 GLU cc_start: 0.7887 (tt0) cc_final: 0.7607 (tt0)
REVERT: B   27 LYS cc_start: 0.8394 (ttmt) cc_final: 0.7923 (mttt)
REVERT: B  139 GLU cc_start: 0.7887 (tt0) cc_final: 0.7605 (tt0)
REVERT: C   41 LYS cc_start: 0.8146 (tttp) cc_final: 0.7787 (tptm)
REVERT: D   31 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8104 (mp0)
REVERT: D   42 LYS cc_start: 0.8331 (mtpp) cc_final: 0.7861 (mtpt)
REVERT: D   45 ARG cc_start: 0.8217 (mtm180) cc_final: 0.8007 (mtp180)
REVERT: F    5 THR cc_start: 0.7726 (m) cc_final: 0.7442 (p)
REVERT: F   31 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8018 (mp0)
REVERT: F   42 LYS cc_start: 0.8308 (mtpp) cc_final: 0.7863 (mtmm)
  outliers start: 20
  outliers final: 6
  residues processed: 110
  average time/residue: 0.5715
  time to fit residues: 65.9124
Evaluate side-chains
  108 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 102
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  189 MET
Chi-restraints excluded: chain C residue   68 ARG
Chi-restraints excluded: chain E residue   68 ARG
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue  112 GLN
Chi-restraints excluded: chain F residue   45 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 64 optimal weight:    0.0970
   chunk 2 optimal weight:    0.8980
   chunk 10 optimal weight:    0.4980
   chunk 80 optimal weight:    0.9990
   chunk 71 optimal weight:    8.9990
   chunk 78 optimal weight:    0.8980
   chunk 68 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
C  16 GLN
D  30 ASN
F  30 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.162416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.113997 restraints weight = 7019.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 2.09
r_work: 0.3100 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2942 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.2727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7066  Z= 0.109
  Angle     :  0.515   6.152   9568  Z= 0.266
  Chirality :  0.041   0.134   1054
  Planarity :  0.004   0.038   1156
  Dihedral  : 12.255 157.456   1136
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 13.22 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.65 (0.30), residues: 840
  helix:  2.24 (0.28), residues: 306
  sheet:  1.00 (0.35), residues: 240
  loop : -0.01 (0.39), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  29 
 TYR   0.010   0.001   TYR C  96 
 PHE   0.015   0.001   PHE B  39 
 TRP   0.011   0.001   TRP E 110 
 HIS   0.003   0.001   HIS C  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 7058)
  covalent geometry    : angle       0.51558 ( 9564)
  SS BOND              : bond        0.00018 (    2)
  SS BOND              : angle       0.21931 (    4)
  hydrogen bonds       : bond        0.03949 (  374)
  hydrogen bonds       : angle       4.57311 ( 1038)
  metal coordination   : bond        0.00157 (    6)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.185 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.8398 (ttmt) cc_final: 0.7950 (mttt)
REVERT: A  139 GLU cc_start: 0.7894 (tt0) cc_final: 0.7584 (tt0)
REVERT: B   27 LYS cc_start: 0.8369 (ttmt) cc_final: 0.7913 (mttt)
REVERT: B  139 GLU cc_start: 0.7896 (tt0) cc_final: 0.7590 (tt0)
REVERT: C   41 LYS cc_start: 0.8167 (tttp) cc_final: 0.7682 (tptp)
REVERT: C   48 GLU cc_start: 0.8145 (tt0) cc_final: 0.7940 (tt0)
REVERT: D   31 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8069 (mp0)
REVERT: D   42 LYS cc_start: 0.8281 (mtpp) cc_final: 0.7814 (mtpt)
REVERT: D   45 ARG cc_start: 0.8165 (mtm180) cc_final: 0.7885 (mtp180)
REVERT: E   48 GLU cc_start: 0.8173 (tt0) cc_final: 0.7959 (tt0)
REVERT: F   31 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8071 (mp0)
REVERT: F   42 LYS cc_start: 0.8290 (mtpp) cc_final: 0.7842 (mtmm)
  outliers start: 18
  outliers final: 7
  residues processed: 119
  average time/residue: 0.6583
  time to fit residues: 81.9389
Evaluate side-chains
  111 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain B residue   41 MET
Chi-restraints excluded: chain B residue  189 MET
Chi-restraints excluded: chain C residue   68 ARG
Chi-restraints excluded: chain E residue   68 ARG
Chi-restraints excluded: chain E residue   70 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 60 optimal weight:    7.9990
   chunk 21 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
D  30 ASN
D  49 HIS
F  30 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.157874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.112976 restraints weight = 7100.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 2.00
r_work: 0.3015 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2858 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.2805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7066  Z= 0.179
  Angle     :  0.576   6.541   9568  Z= 0.298
  Chirality :  0.044   0.148   1054
  Planarity :  0.005   0.044   1156
  Dihedral  : 12.321 154.909   1136
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 14.17 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.54 (0.30), residues: 840
  helix:  2.06 (0.28), residues: 304
  sheet:  0.98 (0.35), residues: 240
  loop :  0.05 (0.39), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  29 
 TYR   0.013   0.002   TYR F  91 
 PHE   0.019   0.002   PHE B  69 
 TRP   0.016   0.001   TRP E 110 
 HIS   0.004   0.001   HIS D  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 7058)
  covalent geometry    : angle       0.57641 ( 9564)
  SS BOND              : bond        0.00068 (    2)
  SS BOND              : angle       0.21213 (    4)
  hydrogen bonds       : bond        0.04748 (  374)
  hydrogen bonds       : angle       4.83734 ( 1038)
  metal coordination   : bond        0.00326 (    6)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.8234 (ttmt) cc_final: 0.7781 (mttt)
REVERT: A  139 GLU cc_start: 0.7916 (tt0) cc_final: 0.7622 (tt0)
REVERT: A  166 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7740 (mmm)
REVERT: B   27 LYS cc_start: 0.8239 (ttmt) cc_final: 0.7787 (mttt)
REVERT: B  139 GLU cc_start: 0.7905 (tt0) cc_final: 0.7616 (tt0)
REVERT: C   41 LYS cc_start: 0.8186 (tttp) cc_final: 0.7828 (tptp)
REVERT: C   48 GLU cc_start: 0.8203 (tt0) cc_final: 0.7981 (tt0)
REVERT: D   31 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8147 (mp0)
REVERT: D   42 LYS cc_start: 0.8350 (mtpp) cc_final: 0.7907 (mtmm)
REVERT: D   45 ARG cc_start: 0.8350 (mtm180) cc_final: 0.8095 (mtp180)
REVERT: D   61 ARG cc_start: 0.7314 (ptp-170) cc_final: 0.6997 (ptp90)
REVERT: E   48 GLU cc_start: 0.8248 (tt0) cc_final: 0.8026 (tt0)
REVERT: F   31 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8087 (mp0)
REVERT: F   42 LYS cc_start: 0.8313 (mtpp) cc_final: 0.7881 (mtmm)
REVERT: F   61 ARG cc_start: 0.7269 (ptp-170) cc_final: 0.6966 (ptp90)
  outliers start: 19
  outliers final: 11
  residues processed: 116
  average time/residue: 0.6314
  time to fit residues: 76.6647
Evaluate side-chains
  117 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain B residue   10 LEU
Chi-restraints excluded: chain B residue   41 MET
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain C residue   68 ARG
Chi-restraints excluded: chain C residue  112 GLN
Chi-restraints excluded: chain E residue   68 ARG
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain F residue   45 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 39 optimal weight:    0.6980
   chunk 57 optimal weight:    6.9990
   chunk 56 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 78 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9980
   chunk 24 optimal weight:    6.9990
   chunk 63 optimal weight:    6.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
D  30 ASN
E 112 GLN
F  30 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.159478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.110488 restraints weight = 7014.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 2.11
r_work: 0.3054 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2896 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.2878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7066  Z= 0.137
  Angle     :  0.542   6.334   9568  Z= 0.279
  Chirality :  0.042   0.137   1054
  Planarity :  0.005   0.050   1156
  Dihedral  : 11.734 149.516   1136
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 14.17 %
    Favored  : 83.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.66 (0.30), residues: 840
  helix:  2.18 (0.28), residues: 304
  sheet:  1.11 (0.35), residues: 240
  loop :  0.02 (0.39), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 107 
 TYR   0.012   0.001   TYR D  86 
 PHE   0.016   0.002   PHE B  39 
 TRP   0.013   0.001   TRP E 110 
 HIS   0.003   0.001   HIS E  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 7058)
  covalent geometry    : angle       0.54240 ( 9564)
  SS BOND              : bond        0.00006 (    2)
  SS BOND              : angle       0.13841 (    4)
  hydrogen bonds       : bond        0.04283 (  374)
  hydrogen bonds       : angle       4.66276 ( 1038)
  metal coordination   : bond        0.00231 (    6)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.8222 (ttmt) cc_final: 0.7769 (mttt)
REVERT: A  139 GLU cc_start: 0.7895 (tt0) cc_final: 0.7620 (tt0)
REVERT: A  166 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7718 (mmm)
REVERT: B   27 LYS cc_start: 0.8231 (ttmt) cc_final: 0.7776 (mttt)
REVERT: B  139 GLU cc_start: 0.7886 (tt0) cc_final: 0.7615 (tt0)
REVERT: B  166 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7724 (mmm)
REVERT: C   41 LYS cc_start: 0.8201 (tttp) cc_final: 0.7814 (tptp)
REVERT: C   48 GLU cc_start: 0.8179 (tt0) cc_final: 0.7971 (tt0)
REVERT: D   31 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8079 (mp0)
REVERT: D   42 LYS cc_start: 0.8294 (mtpp) cc_final: 0.7851 (mtmm)
REVERT: D   61 ARG cc_start: 0.7271 (ptp-170) cc_final: 0.7068 (ptp90)
REVERT: E   48 GLU cc_start: 0.8212 (tt0) cc_final: 0.8002 (tt0)
REVERT: F   31 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8056 (mp0)
REVERT: F   42 LYS cc_start: 0.8296 (mtpp) cc_final: 0.7839 (mtmm)
  outliers start: 18
  outliers final: 6
  residues processed: 111
  average time/residue: 0.6306
  time to fit residues: 73.0285
Evaluate side-chains
  110 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 102
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain B residue   10 LEU
Chi-restraints excluded: chain B residue   41 MET
Chi-restraints excluded: chain B residue  166 MET
Chi-restraints excluded: chain C residue   68 ARG
Chi-restraints excluded: chain E residue   70 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 40 optimal weight:    5.9990
   chunk 20 optimal weight:    0.5980
   chunk 68 optimal weight:    5.9990
   chunk 21 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    5.9990
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
C 112 GLN
D  30 ASN
E 112 GLN
F  30 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.160392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.111714 restraints weight = 7001.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 2.11
r_work: 0.3073 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2916 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.3069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7066  Z= 0.116
  Angle     :  0.518   6.255   9568  Z= 0.267
  Chirality :  0.041   0.140   1054
  Planarity :  0.005   0.050   1156
  Dihedral  : 11.268 142.774   1136
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 14.31 %
    Favored  : 83.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.80 (0.30), residues: 840
  helix:  2.29 (0.28), residues: 304
  sheet:  1.21 (0.35), residues: 240
  loop :  0.06 (0.39), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 107 
 TYR   0.011   0.001   TYR D  86 
 PHE   0.016   0.001   PHE A  69 
 TRP   0.011   0.001   TRP E 110 
 HIS   0.003   0.001   HIS E  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 7058)
  covalent geometry    : angle       0.51816 ( 9564)
  SS BOND              : bond        0.00026 (    2)
  SS BOND              : angle       0.10209 (    4)
  hydrogen bonds       : bond        0.04045 (  374)
  hydrogen bonds       : angle       4.52731 ( 1038)
  metal coordination   : bond        0.00178 (    6)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.284 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.8260 (ttmt) cc_final: 0.7805 (mttt)
REVERT: A  138 LYS cc_start: 0.7902 (mptt) cc_final: 0.7630 (mptt)
REVERT: A  139 GLU cc_start: 0.7881 (tt0) cc_final: 0.7574 (tt0)
REVERT: A  166 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7732 (mmm)
REVERT: B   27 LYS cc_start: 0.8245 (ttmt) cc_final: 0.7804 (mttt)
REVERT: B  138 LYS cc_start: 0.7896 (mptt) cc_final: 0.7623 (mptt)
REVERT: B  139 GLU cc_start: 0.7896 (tt0) cc_final: 0.7629 (tt0)
REVERT: B  166 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7748 (mmm)
REVERT: C   17 THR cc_start: 0.6777 (p) cc_final: 0.6542 (m)
REVERT: C   41 LYS cc_start: 0.8188 (tttp) cc_final: 0.7805 (tptp)
REVERT: C   48 GLU cc_start: 0.8180 (tt0) cc_final: 0.7971 (tt0)
REVERT: D   31 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8066 (mp0)
REVERT: D   42 LYS cc_start: 0.8313 (mtpp) cc_final: 0.7876 (mtmm)
REVERT: D   61 ARG cc_start: 0.7272 (ptp-170) cc_final: 0.7068 (ptp90)
REVERT: E   48 GLU cc_start: 0.8202 (tt0) cc_final: 0.7986 (tt0)
REVERT: F   31 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8058 (mp0)
REVERT: F   42 LYS cc_start: 0.8307 (mtpp) cc_final: 0.7845 (mtmm)
REVERT: F   61 ARG cc_start: 0.7396 (ptp90) cc_final: 0.7174 (ptp90)
  outliers start: 15
  outliers final: 7
  residues processed: 113
  average time/residue: 0.6369
  time to fit residues: 75.3040
Evaluate side-chains
  110 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain B residue   41 MET
Chi-restraints excluded: chain B residue  166 MET
Chi-restraints excluded: chain B residue  189 MET
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain C residue   68 ARG
Chi-restraints excluded: chain E residue   70 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 55 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 75 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 78 optimal weight:    7.9990
   chunk 72 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
C 112 GLN
D  30 ASN
E 112 GLN
F  30 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.158377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.113838 restraints weight = 7090.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 1.92
r_work: 0.3017 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2862 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.3006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   7066  Z= 0.154
  Angle     :  0.557   6.387   9568  Z= 0.285
  Chirality :  0.043   0.142   1054
  Planarity :  0.005   0.049   1156
  Dihedral  : 11.487 142.682   1136
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.58 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.68 (0.30), residues: 840
  helix:  2.12 (0.28), residues: 304
  sheet:  1.18 (0.35), residues: 240
  loop :  0.04 (0.40), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 107 
 TYR   0.012   0.002   TYR D  86 
 PHE   0.018   0.002   PHE B  69 
 TRP   0.014   0.001   TRP C 110 
 HIS   0.003   0.001   HIS F  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 7058)
  covalent geometry    : angle       0.55683 ( 9564)
  SS BOND              : bond        0.00050 (    2)
  SS BOND              : angle       0.16223 (    4)
  hydrogen bonds       : bond        0.04468 (  374)
  hydrogen bonds       : angle       4.67136 ( 1038)
  metal coordination   : bond        0.00250 (    6)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.198 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.8263 (ttmt) cc_final: 0.7831 (mttt)
REVERT: A  139 GLU cc_start: 0.7947 (tt0) cc_final: 0.7635 (tt0)
REVERT: A  166 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7812 (mmm)
REVERT: B   27 LYS cc_start: 0.8262 (ttmt) cc_final: 0.7826 (mttt)
REVERT: B  139 GLU cc_start: 0.7958 (tt0) cc_final: 0.7691 (tt0)
REVERT: B  166 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7820 (mmm)
REVERT: B  168 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8481 (ttt-90)
REVERT: C   17 THR cc_start: 0.6876 (p) cc_final: 0.6647 (m)
REVERT: C   41 LYS cc_start: 0.8202 (tttp) cc_final: 0.7818 (tptp)
REVERT: C   48 GLU cc_start: 0.8211 (tt0) cc_final: 0.8000 (tt0)
REVERT: D   31 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8121 (mp0)
REVERT: D   42 LYS cc_start: 0.8324 (mtpp) cc_final: 0.7898 (mtmm)
REVERT: D   61 ARG cc_start: 0.7298 (ptp-170) cc_final: 0.7051 (ptp90)
REVERT: E   48 GLU cc_start: 0.8239 (tt0) cc_final: 0.8023 (tt0)
REVERT: F   31 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8120 (mp0)
REVERT: F   42 LYS cc_start: 0.8369 (mtpp) cc_final: 0.7853 (mtmm)
  outliers start: 16
  outliers final: 8
  residues processed: 115
  average time/residue: 0.6182
  time to fit residues: 74.3006
Evaluate side-chains
  119 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 SER
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain B residue   41 MET
Chi-restraints excluded: chain B residue  166 MET
Chi-restraints excluded: chain B residue  168 ARG
Chi-restraints excluded: chain B residue  189 MET
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain C residue   68 ARG
Chi-restraints excluded: chain E residue   70 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 50 optimal weight:    0.0870
   chunk 48 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 80 optimal weight:    3.9990
   chunk 26 optimal weight:    0.5980
   chunk 68 optimal weight:    6.9990
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
D  30 ASN
E 112 GLN
F  30 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.161185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.112801 restraints weight = 7046.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 2.11
r_work: 0.3089 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2932 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.3207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7066  Z= 0.105
  Angle     :  0.505   6.181   9568  Z= 0.261
  Chirality :  0.040   0.147   1054
  Planarity :  0.005   0.050   1156
  Dihedral  : 10.997 139.655   1136
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 15.40 %
    Favored  : 82.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.92 (0.30), residues: 840
  helix:  2.36 (0.28), residues: 304
  sheet:  1.30 (0.35), residues: 240
  loop :  0.16 (0.40), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  68 
 TYR   0.010   0.001   TYR D  86 
 PHE   0.015   0.001   PHE A  39 
 TRP   0.011   0.001   TRP E 110 
 HIS   0.003   0.001   HIS E  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 7058)
  covalent geometry    : angle       0.50538 ( 9564)
  SS BOND              : bond        0.00054 (    2)
  SS BOND              : angle       0.11649 (    4)
  hydrogen bonds       : bond        0.03891 (  374)
  hydrogen bonds       : angle       4.47205 ( 1038)
  metal coordination   : bond        0.00146 (    6)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.8225 (ttmt) cc_final: 0.7798 (mttt)
REVERT: A  139 GLU cc_start: 0.7870 (tt0) cc_final: 0.7553 (tt0)
REVERT: B   27 LYS cc_start: 0.8226 (ttmt) cc_final: 0.7798 (mttt)
REVERT: B  139 GLU cc_start: 0.7875 (tt0) cc_final: 0.7607 (tt0)
REVERT: C   41 LYS cc_start: 0.8168 (tttp) cc_final: 0.7797 (tptp)
REVERT: C   48 GLU cc_start: 0.8130 (tt0) cc_final: 0.7916 (tt0)
REVERT: D   31 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8023 (mp0)
REVERT: D   42 LYS cc_start: 0.8274 (mtpp) cc_final: 0.7836 (mtmm)
REVERT: D   61 ARG cc_start: 0.7238 (ptp-170) cc_final: 0.6961 (ptp90)
REVERT: E   48 GLU cc_start: 0.8149 (tt0) cc_final: 0.7911 (tt0)
REVERT: F   31 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8039 (mp0)
REVERT: F   42 LYS cc_start: 0.8260 (mtpp) cc_final: 0.7807 (mtmm)
  outliers start: 14
  outliers final: 6
  residues processed: 116
  average time/residue: 0.5977
  time to fit residues: 72.6100
Evaluate side-chains
  112 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 106
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain B residue   41 MET
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain C residue   68 ARG
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue   94 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 50 optimal weight:    8.9990
   chunk 6 optimal weight:    0.5980
   chunk 23 optimal weight:    5.9990
   chunk 3 optimal weight:    0.5980
   chunk 55 optimal weight:    3.9990
   chunk 46 optimal weight:    8.9990
   chunk 18 optimal weight:    0.2980
   chunk 28 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
D  30 ASN
E 112 GLN
F  30 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.159388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.110567 restraints weight = 6964.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.3234 rms_B_bonded: 2.09
r_work: 0.3057 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2899 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.3155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7066  Z= 0.135
  Angle     :  0.541   6.281   9568  Z= 0.278
  Chirality :  0.042   0.142   1054
  Planarity :  0.005   0.050   1156
  Dihedral  : 11.177 139.421   1136
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 15.53 %
    Favored  : 82.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.82 (0.30), residues: 840
  helix:  2.20 (0.28), residues: 304
  sheet:  1.27 (0.35), residues: 240
  loop :  0.16 (0.40), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 168 
 TYR   0.012   0.001   TYR F  86 
 PHE   0.016   0.002   PHE B  69 
 TRP   0.012   0.001   TRP E 110 
 HIS   0.003   0.001   HIS E  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 7058)
  covalent geometry    : angle       0.54133 ( 9564)
  SS BOND              : bond        0.00004 (    2)
  SS BOND              : angle       0.08546 (    4)
  hydrogen bonds       : bond        0.04285 (  374)
  hydrogen bonds       : angle       4.56955 ( 1038)
  metal coordination   : bond        0.00190 (    6)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.283 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.8211 (ttmt) cc_final: 0.7784 (mttt)
REVERT: A  139 GLU cc_start: 0.7854 (tt0) cc_final: 0.7566 (tt0)
REVERT: B   27 LYS cc_start: 0.8207 (ttmt) cc_final: 0.7777 (mttt)
REVERT: B  139 GLU cc_start: 0.7863 (tt0) cc_final: 0.7574 (tt0)
REVERT: B  166 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7722 (mmm)
REVERT: C   48 GLU cc_start: 0.8147 (tt0) cc_final: 0.7926 (tt0)
REVERT: D   31 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8043 (mp0)
REVERT: D   42 LYS cc_start: 0.8273 (mtpp) cc_final: 0.7845 (mtmm)
REVERT: D   61 ARG cc_start: 0.7285 (ptp-170) cc_final: 0.6976 (ptp90)
REVERT: E   48 GLU cc_start: 0.8168 (tt0) cc_final: 0.7932 (tt0)
REVERT: F   31 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8044 (mp0)
REVERT: F   42 LYS cc_start: 0.8271 (mtpp) cc_final: 0.7736 (mtmm)
  outliers start: 11
  outliers final: 7
  residues processed: 114
  average time/residue: 0.6076
  time to fit residues: 72.4492
Evaluate side-chains
  114 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain B residue   41 MET
Chi-restraints excluded: chain B residue  166 MET
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain C residue   68 ARG
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue   94 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 72 optimal weight:    6.9990
   chunk 30 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 68 optimal weight:    8.9990
   chunk 2 optimal weight:    0.6980
   chunk 29 optimal weight:    0.5980
   chunk 69 optimal weight:    3.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
D  30 ASN
F  30 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.159349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.110594 restraints weight = 6981.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 2.08
r_work: 0.3056 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2899 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.3205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7066  Z= 0.140
  Angle     :  0.545   6.344   9568  Z= 0.281
  Chirality :  0.042   0.148   1054
  Planarity :  0.005   0.050   1156
  Dihedral  : 11.240 140.615   1136
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 16.08 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.81 (0.30), residues: 840
  helix:  2.16 (0.28), residues: 304
  sheet:  1.29 (0.35), residues: 240
  loop :  0.16 (0.40), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  61 
 TYR   0.012   0.001   TYR D  86 
 PHE   0.016   0.002   PHE B  69 
 TRP   0.013   0.001   TRP E 110 
 HIS   0.003   0.001   HIS F  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 7058)
  covalent geometry    : angle       0.54554 ( 9564)
  SS BOND              : bond        0.00008 (    2)
  SS BOND              : angle       0.11314 (    4)
  hydrogen bonds       : bond        0.04303 (  374)
  hydrogen bonds       : angle       4.59373 ( 1038)
  metal coordination   : bond        0.00243 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2979.84 seconds
wall clock time: 51 minutes 25.43 seconds (3085.43 seconds total)