Starting phenix.real_space_refine
on Mon Apr 28 09:08:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t03_40933/04_2025/8t03_40933.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t03_40933/04_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_40933/04_2025/8t03_40933.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t03_40933/04_2025/8t03_40933.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t03_40933/04_2025/8t03_40933.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t03_40933/04_2025/8t03_40933.cif"
  }
  resolution = 2.72
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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:
    E, F, B
  Time building chain proxies: 6.08, per 1000 atoms: 0.88
  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: 1.67
  Conformation dependent library (CDL) restraints added in 943.1 milliseconds
  
  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: 1.00
  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: 1.97

  Time building geometry restraints manager: 1.99 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             3.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     23.300
  Find NCS groups from input model:        0.120
  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:13.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.200
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.029   0.003   TRP E 110 
 HIS   0.008   0.002   HIS B 110 
 PHE   0.022   0.003   PHE A  46 
 TYR   0.027   0.003   TYR F  71 
 ARG   0.003   0.001   ARG B 168 

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

*********************** 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  : 0.717 
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: 1.2868
  time to fit residues: 181.7250
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  : 0.739 
-------------------------------------------------------------------------------
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 69 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0870
   chunk 64 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9980
   chunk 74 optimal weight:    6.9990
   overall best weight:    0.7158

-------------------------------------------------------------------------------
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 = 0.3846 r_free = 0.3846 target = 0.162287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.117157 restraints weight = 6893.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 2.41
r_work: 0.3100 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.1964

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= 0.130
  Angle     :  0.587   6.356   9568  Z= 0.305
  Chirality :  0.043   0.147   1054
  Planarity :  0.004   0.034   1156
  Dihedral  : 13.858 162.556   1144
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  :  8.86 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.30), residues: 840
  helix:  1.60 (0.28), residues: 304
  sheet:  0.64 (0.35), residues: 230
  loop : -0.17 (0.39), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 110 
 HIS   0.003   0.001   HIS A 110 
 PHE   0.018   0.002   PHE A  39 
 TYR   0.012   0.001   TYR F  91 
 ARG   0.002   0.000   ARG C  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04372 (  374)
  hydrogen bonds       : angle       5.18280 ( 1038)
  metal coordination   : bond        0.00102 (    6)
  SS BOND              : bond        0.00017 (    2)
  SS BOND              : angle       0.51612 (    4)
  covalent geometry    : bond        0.00288 ( 7058)
  covalent geometry    : angle       0.58719 ( 9564)

*********************** 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
  139 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 1.102 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.8185 (ttmt) cc_final: 0.7700 (mttt)
REVERT: A  139 GLU cc_start: 0.7852 (tt0) cc_final: 0.7604 (tt0)
REVERT: B   27 LYS cc_start: 0.8298 (ttmt) cc_final: 0.7761 (mttt)
REVERT: B  139 GLU cc_start: 0.7839 (tt0) cc_final: 0.7592 (tt0)
REVERT: D   31 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8040 (mp0)
REVERT: D   45 ARG cc_start: 0.8263 (mtm180) cc_final: 0.8012 (mtp180)
REVERT: E   41 LYS cc_start: 0.7883 (tttt) cc_final: 0.7641 (ttpp)
REVERT: F   31 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8012 (mp0)
REVERT: F   42 LYS cc_start: 0.8269 (mtpp) cc_final: 0.7832 (mtmm)
REVERT: F   67 SER cc_start: 0.7448 (OUTLIER) cc_final: 0.6993 (p)
  outliers start: 19
  outliers final: 5
  residues processed: 125
  average time/residue: 1.9683
  time to fit residues: 258.6030
Evaluate side-chains
  115 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 109
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   68 ARG
Chi-restraints excluded: chain D residue   12 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 61 optimal weight:    8.9990
   chunk 42 optimal weight:    3.9990
   chunk 67 optimal weight:    0.0370
   chunk 13 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 72 optimal weight:    3.9990
   chunk 3 optimal weight:    0.5980
   overall best weight:    0.5658

-------------------------------------------------------------------------------
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 = 0.162244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.113903 restraints weight = 7029.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 2.08
r_work: 0.3099 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.2549

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     :  0.530   6.215   9568  Z= 0.273
  Chirality :  0.041   0.144   1054
  Planarity :  0.004   0.033   1156
  Dihedral  : 12.712 162.830   1136
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 12.94 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.30), residues: 840
  helix:  2.05 (0.28), residues: 306
  sheet:  0.75 (0.34), residues: 240
  loop :  0.08 (0.39), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 110 
 HIS   0.003   0.001   HIS E  52 
 PHE   0.015   0.001   PHE A  46 
 TYR   0.011   0.001   TYR D  91 
 ARG   0.001   0.000   ARG A 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04029 (  374)
  hydrogen bonds       : angle       4.77508 ( 1038)
  metal coordination   : bond        0.00180 (    6)
  SS BOND              : bond        0.00072 (    2)
  SS BOND              : angle       0.32645 (    4)
  covalent geometry    : bond        0.00234 ( 7058)
  covalent geometry    : angle       0.52983 ( 9564)

*********************** 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
  130 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.867 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.8402 (ttmt) cc_final: 0.7941 (mttt)
REVERT: A  139 GLU cc_start: 0.7890 (tt0) cc_final: 0.7614 (tt0)
REVERT: B   27 LYS cc_start: 0.8408 (ttmt) cc_final: 0.7944 (mttt)
REVERT: B  139 GLU cc_start: 0.7885 (tt0) cc_final: 0.7606 (tt0)
REVERT: C   41 LYS cc_start: 0.8174 (tttp) cc_final: 0.7794 (tptm)
REVERT: D   31 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8061 (mp0)
REVERT: F    5 THR cc_start: 0.7730 (m) cc_final: 0.7463 (p)
REVERT: F   31 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8012 (mp0)
REVERT: F   42 LYS cc_start: 0.8306 (mtpp) cc_final: 0.7859 (mtmm)
  outliers start: 20
  outliers final: 7
  residues processed: 114
  average time/residue: 1.4693
  time to fit residues: 176.9095
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  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 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
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 43 optimal weight:    0.8980
   chunk 79 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 38 optimal weight:    8.9990
   chunk 48 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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 = 0.3795 r_free = 0.3795 target = 0.157834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.112774 restraints weight = 7050.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 1.96
r_work: 0.3005 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.2850 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.2600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7066  Z= 0.185
  Angle     :  0.594   6.564   9568  Z= 0.305
  Chirality :  0.044   0.151   1054
  Planarity :  0.005   0.038   1156
  Dihedral  : 12.915 160.478   1136
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 12.81 %
    Favored  : 83.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.30), residues: 840
  helix:  1.96 (0.28), residues: 304
  sheet:  0.91 (0.35), residues: 240
  loop : -0.00 (0.39), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP E 110 
 HIS   0.004   0.001   HIS F  38 
 PHE   0.019   0.002   PHE B  69 
 TYR   0.014   0.002   TYR D  86 
 ARG   0.003   0.001   ARG B 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04771 (  374)
  hydrogen bonds       : angle       4.92172 ( 1038)
  metal coordination   : bond        0.00334 (    6)
  SS BOND              : bond        0.00075 (    2)
  SS BOND              : angle       0.16686 (    4)
  covalent geometry    : bond        0.00432 ( 7058)
  covalent geometry    : angle       0.59406 ( 9564)

*********************** 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
  135 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.820 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.8314 (ttmt) cc_final: 0.7869 (mttt)
REVERT: A  139 GLU cc_start: 0.8005 (tt0) cc_final: 0.7721 (tt0)
REVERT: A  166 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7920 (mmm)
REVERT: A  168 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.7548 (ttt180)
REVERT: B   27 LYS cc_start: 0.8320 (ttmt) cc_final: 0.7870 (mttt)
REVERT: B  139 GLU cc_start: 0.7995 (tt0) cc_final: 0.7713 (tt0)
REVERT: B  166 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7927 (mmm)
REVERT: C   41 LYS cc_start: 0.8240 (tttp) cc_final: 0.7896 (tptp)
REVERT: D   31 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8265 (mp0)
REVERT: D   42 LYS cc_start: 0.8522 (mtpp) cc_final: 0.7972 (mtpt)
REVERT: D   61 ARG cc_start: 0.7136 (ptt90) cc_final: 0.6825 (ptp90)
REVERT: F    5 THR cc_start: 0.7761 (m) cc_final: 0.7508 (p)
REVERT: F   31 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8193 (mp0)
REVERT: F   42 LYS cc_start: 0.8411 (mtpp) cc_final: 0.7989 (mtmm)
  outliers start: 25
  outliers final: 8
  residues processed: 114
  average time/residue: 1.3009
  time to fit residues: 155.6444
Evaluate side-chains
  112 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain B residue   10 LEU
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  166 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 63 optimal weight:    6.9990
   chunk 19 optimal weight:    6.9990
   chunk 56 optimal weight:    8.9990
   chunk 79 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 44 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 47 optimal weight:    5.9990
   overall best weight:    1.3588

-------------------------------------------------------------------------------
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
D  49 HIS
F  30 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.157280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.112186 restraints weight = 6999.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.01
r_work: 0.3009 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2853 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.2751

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= 0.180
  Angle     :  0.580   6.548   9568  Z= 0.299
  Chirality :  0.044   0.146   1054
  Planarity :  0.005   0.043   1156
  Dihedral  : 12.428 157.110   1136
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 13.62 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.30), residues: 840
  helix:  1.91 (0.28), residues: 304
  sheet:  0.95 (0.35), residues: 240
  loop : -0.04 (0.39), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 110 
 HIS   0.004   0.001   HIS F  38 
 PHE   0.018   0.002   PHE B  69 
 TYR   0.014   0.002   TYR D  86 
 ARG   0.003   0.000   ARG B 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04672 (  374)
  hydrogen bonds       : angle       4.86769 ( 1038)
  metal coordination   : bond        0.00299 (    6)
  SS BOND              : bond        0.00057 (    2)
  SS BOND              : angle       0.18750 (    4)
  covalent geometry    : bond        0.00419 ( 7058)
  covalent geometry    : angle       0.57996 ( 9564)

*********************** 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
  129 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 0.803 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.8298 (ttmt) cc_final: 0.7864 (mttt)
REVERT: A   63 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7657 (mtp85)
REVERT: A  139 GLU cc_start: 0.7971 (tt0) cc_final: 0.7701 (tt0)
REVERT: A  166 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7900 (mmm)
REVERT: A  168 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7525 (ttt180)
REVERT: B   27 LYS cc_start: 0.8309 (ttmt) cc_final: 0.7871 (mttt)
REVERT: B  139 GLU cc_start: 0.7965 (tt0) cc_final: 0.7684 (tt0)
REVERT: C   41 LYS cc_start: 0.8308 (tttp) cc_final: 0.7936 (tptp)
REVERT: D   31 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8253 (mp0)
REVERT: D   42 LYS cc_start: 0.8487 (mtpp) cc_final: 0.7957 (mtmm)
REVERT: F   31 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8193 (mp0)
REVERT: F   42 LYS cc_start: 0.8428 (mtpp) cc_final: 0.7970 (mtmm)
  outliers start: 21
  outliers final: 8
  residues processed: 115
  average time/residue: 1.6524
  time to fit residues: 198.9575
Evaluate side-chains
  116 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 ARG
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain B residue   10 LEU
Chi-restraints excluded: chain B residue  134 LEU
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   94 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 70 optimal weight:    0.1980
   chunk 34 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 60 optimal weight:    4.9990
   chunk 46 optimal weight:    7.9990
   chunk 52 optimal weight:    5.9990
   chunk 61 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9990
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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
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 = 0.3815 r_free = 0.3815 target = 0.159515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.110968 restraints weight = 7037.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 2.10
r_work: 0.3063 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2906 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.2956

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     :  0.528   6.279   9568  Z= 0.273
  Chirality :  0.041   0.140   1054
  Planarity :  0.005   0.047   1156
  Dihedral  : 11.692 150.144   1136
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 13.76 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.30), residues: 840
  helix:  2.14 (0.28), residues: 306
  sheet:  1.11 (0.35), residues: 240
  loop :  0.00 (0.40), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 110 
 HIS   0.004   0.001   HIS E  52 
 PHE   0.016   0.001   PHE A  39 
 TYR   0.011   0.001   TYR F  86 
 ARG   0.002   0.000   ARG B  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04106 (  374)
  hydrogen bonds       : angle       4.60565 ( 1038)
  metal coordination   : bond        0.00200 (    6)
  SS BOND              : bond        0.00010 (    2)
  SS BOND              : angle       0.06527 (    4)
  covalent geometry    : bond        0.00266 ( 7058)
  covalent geometry    : angle       0.52823 ( 9564)

*********************** 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
  134 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 111
  time to evaluate  : 0.807 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.8228 (ttmt) cc_final: 0.7780 (mttt)
REVERT: A  139 GLU cc_start: 0.7881 (tt0) cc_final: 0.7560 (tt0)
REVERT: A  166 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7728 (mmm)
REVERT: B   27 LYS cc_start: 0.8235 (ttmt) cc_final: 0.7782 (mttt)
REVERT: B  139 GLU cc_start: 0.7871 (tt0) cc_final: 0.7551 (tt0)
REVERT: B  166 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7727 (mmm)
REVERT: C   41 LYS cc_start: 0.8189 (tttp) cc_final: 0.7797 (tptp)
REVERT: D   31 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8088 (mp0)
REVERT: D   42 LYS cc_start: 0.8377 (mtpp) cc_final: 0.7840 (mtmm)
REVERT: F   31 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8078 (mp0)
REVERT: F   42 LYS cc_start: 0.8299 (mtpp) cc_final: 0.7849 (mtmm)
  outliers start: 23
  outliers final: 9
  residues processed: 118
  average time/residue: 2.0332
  time to fit residues: 251.2743
Evaluate side-chains
  114 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 1.217 
-------------------------------------------------------------------------------
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  189 MET
Chi-restraints excluded: chain C residue   68 ARG
Chi-restraints excluded: chain C residue  112 GLN
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue   94 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 79 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 23 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 70 optimal weight:    0.0170
   chunk 76 optimal weight:    0.1980
   chunk 27 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:
D  30 ASN
E  16 GLN
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 = 0.3828 r_free = 0.3828 target = 0.160526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.112281 restraints weight = 6957.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 2.09
r_work: 0.3081 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2924 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.3083

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= 0.110
  Angle     :  0.513   6.241   9568  Z= 0.265
  Chirality :  0.041   0.141   1054
  Planarity :  0.005   0.050   1156
  Dihedral  : 11.274 143.609   1136
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 14.71 %
    Favored  : 82.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.30), residues: 840
  helix:  2.31 (0.28), residues: 304
  sheet:  1.21 (0.35), residues: 240
  loop :  0.05 (0.39), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 110 
 HIS   0.003   0.001   HIS E  52 
 PHE   0.016   0.001   PHE B  39 
 TYR   0.010   0.001   TYR F  86 
 ARG   0.001   0.000   ARG B  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03968 (  374)
  hydrogen bonds       : angle       4.49872 ( 1038)
  metal coordination   : bond        0.00157 (    6)
  SS BOND              : bond        0.00014 (    2)
  SS BOND              : angle       0.09817 (    4)
  covalent geometry    : bond        0.00239 ( 7058)
  covalent geometry    : angle       0.51304 ( 9564)

*********************** 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
  124 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 2.753 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.8380 (ttmt) cc_final: 0.7973 (mttt)
REVERT: A  139 GLU cc_start: 0.7892 (tt0) cc_final: 0.7580 (tt0)
REVERT: B   27 LYS cc_start: 0.8389 (ttmt) cc_final: 0.7978 (mttt)
REVERT: B  139 GLU cc_start: 0.7875 (tt0) cc_final: 0.7563 (tt0)
REVERT: B  166 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7782 (mmm)
REVERT: C   17 THR cc_start: 0.6641 (p) cc_final: 0.6407 (m)
REVERT: C   41 LYS cc_start: 0.8172 (tttp) cc_final: 0.7767 (tptp)
REVERT: D   31 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8068 (mp0)
REVERT: D   42 LYS cc_start: 0.8391 (mtpp) cc_final: 0.7827 (mtpt)
REVERT: F   31 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8046 (mp0)
REVERT: F   42 LYS cc_start: 0.8301 (mtpp) cc_final: 0.7843 (mtmm)
  outliers start: 22
  outliers final: 9
  residues processed: 111
  average time/residue: 2.0102
  time to fit residues: 233.9836
Evaluate side-chains
  110 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
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  189 MET
Chi-restraints excluded: chain B residue   13 LEU
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   68 ARG
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue   94 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0980
   chunk 41 optimal weight:    4.9990
   chunk 30 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   chunk 58 optimal weight:    5.9990
   chunk 74 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3831 r_free = 0.3831 target = 0.160828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.112318 restraints weight = 7038.420|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 2.10
r_work: 0.3083 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2927 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.3200

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= 0.110
  Angle     :  0.513   6.216   9568  Z= 0.264
  Chirality :  0.041   0.140   1054
  Planarity :  0.005   0.051   1156
  Dihedral  : 11.089 140.221   1136
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 15.53 %
    Favored  : 82.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.30), residues: 840
  helix:  2.35 (0.28), residues: 304
  sheet:  1.33 (0.36), residues: 240
  loop :  0.12 (0.40), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 110 
 HIS   0.004   0.001   HIS E  52 
 PHE   0.015   0.001   PHE B  39 
 TYR   0.010   0.001   TYR F  86 
 ARG   0.001   0.000   ARG C  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03943 (  374)
  hydrogen bonds       : angle       4.44329 ( 1038)
  metal coordination   : bond        0.00162 (    6)
  SS BOND              : bond        0.00007 (    2)
  SS BOND              : angle       0.05476 (    4)
  covalent geometry    : bond        0.00237 ( 7058)
  covalent geometry    : angle       0.51297 ( 9564)

*********************** 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
  122 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.778 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.8339 (ttmt) cc_final: 0.7828 (mttt)
REVERT: A  138 LYS cc_start: 0.7977 (mptt) cc_final: 0.7732 (mptt)
REVERT: A  139 GLU cc_start: 0.7888 (tt0) cc_final: 0.7578 (tt0)
REVERT: B   27 LYS cc_start: 0.8346 (ttmt) cc_final: 0.7829 (mttt)
REVERT: B  138 LYS cc_start: 0.7969 (mptt) cc_final: 0.7725 (mptt)
REVERT: B  139 GLU cc_start: 0.7886 (tt0) cc_final: 0.7577 (tt0)
REVERT: B  152 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8173 (mt0)
REVERT: B  166 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7728 (mmm)
REVERT: C   41 LYS cc_start: 0.8163 (tttp) cc_final: 0.7752 (tptp)
REVERT: D   31 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8058 (mp0)
REVERT: D   42 LYS cc_start: 0.8312 (mtpp) cc_final: 0.7779 (mtmm)
REVERT: D   61 ARG cc_start: 0.7432 (ptp90) cc_final: 0.7134 (ptp90)
REVERT: F   31 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8070 (mp0)
REVERT: F   42 LYS cc_start: 0.8299 (mtpp) cc_final: 0.7849 (mtmm)
REVERT: F   61 ARG cc_start: 0.7297 (ptp-170) cc_final: 0.7046 (ptp90)
  outliers start: 15
  outliers final: 10
  residues processed: 113
  average time/residue: 1.2899
  time to fit residues: 153.1692
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  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   14 SER
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   14 SER
Chi-restraints excluded: chain B residue   41 MET
Chi-restraints excluded: chain B residue  152 GLN
Chi-restraints excluded: chain B residue  166 MET
Chi-restraints excluded: chain B residue  189 MET
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 81 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 14 optimal weight:    0.5980
   chunk 63 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.3791 r_free = 0.3791 target = 0.157370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.110967 restraints weight = 7022.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3234 rms_B_bonded: 2.41
r_work: 0.3041 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2884 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.3083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7066  Z= 0.175
  Angle     :  0.576   6.504   9568  Z= 0.295
  Chirality :  0.043   0.143   1054
  Planarity :  0.005   0.051   1156
  Dihedral  : 11.609 142.629   1136
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 14.85 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.30), residues: 840
  helix:  2.05 (0.28), residues: 304
  sheet:  1.27 (0.35), residues: 240
  loop :  0.11 (0.40), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 110 
 HIS   0.004   0.001   HIS D  38 
 PHE   0.018   0.002   PHE A  69 
 TYR   0.013   0.002   TYR F  86 
 ARG   0.003   0.000   ARG A 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04619 (  374)
  hydrogen bonds       : angle       4.71304 ( 1038)
  metal coordination   : bond        0.00317 (    6)
  SS BOND              : bond        0.00085 (    2)
  SS BOND              : angle       0.23390 (    4)
  covalent geometry    : bond        0.00405 ( 7058)
  covalent geometry    : angle       0.57617 ( 9564)

*********************** 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
  128 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.715 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.8121 (ttmt) cc_final: 0.7675 (mttt)
REVERT: A  139 GLU cc_start: 0.7814 (tt0) cc_final: 0.7531 (tt0)
REVERT: A  166 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7611 (mmm)
REVERT: B   27 LYS cc_start: 0.8121 (ttmt) cc_final: 0.7671 (mttt)
REVERT: B  139 GLU cc_start: 0.7811 (tt0) cc_final: 0.7529 (tt0)
REVERT: B  166 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7569 (mmm)
REVERT: C   41 LYS cc_start: 0.8098 (tttp) cc_final: 0.7850 (ttpp)
REVERT: D   31 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8006 (mp0)
REVERT: D   42 LYS cc_start: 0.8306 (mtpp) cc_final: 0.7801 (mtmm)
REVERT: D   61 ARG cc_start: 0.7457 (ptp90) cc_final: 0.7194 (ptp90)
REVERT: F   31 GLU cc_start: 0.8577 (mt-10) cc_final: 0.7977 (mp0)
REVERT: F   42 LYS cc_start: 0.8233 (mtpp) cc_final: 0.7699 (mtmm)
  outliers start: 19
  outliers final: 9
  residues processed: 118
  average time/residue: 1.3198
  time to fit residues: 163.2821
Evaluate side-chains
  120 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
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 B residue   14 SER
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   68 ARG
Chi-restraints excluded: chain E residue   22 CYS
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 49 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 54 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 81 optimal weight:    0.5980
   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 = 0.3822 r_free = 0.3822 target = 0.160032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.111505 restraints weight = 7045.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 2.10
r_work: 0.3068 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2912 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.3216

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= 0.117
  Angle     :  0.527   6.267   9568  Z= 0.270
  Chirality :  0.041   0.148   1054
  Planarity :  0.005   0.050   1156
  Dihedral  : 11.195 141.181   1136
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 15.67 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.30), residues: 840
  helix:  2.23 (0.28), residues: 304
  sheet:  1.34 (0.35), residues: 240
  loop :  0.18 (0.40), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 110 
 HIS   0.003   0.001   HIS E  52 
 PHE   0.015   0.002   PHE B  39 
 TYR   0.011   0.001   TYR F  86 
 ARG   0.002   0.000   ARG D  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04038 (  374)
  hydrogen bonds       : angle       4.52439 ( 1038)
  metal coordination   : bond        0.00177 (    6)
  SS BOND              : bond        0.00024 (    2)
  SS BOND              : angle       0.05093 (    4)
  covalent geometry    : bond        0.00256 ( 7058)
  covalent geometry    : angle       0.52666 ( 9564)

********************** 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
  117 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.725 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.8225 (ttmt) cc_final: 0.7808 (mttt)
REVERT: A  139 GLU cc_start: 0.7865 (tt0) cc_final: 0.7601 (tt0)
REVERT: B   27 LYS cc_start: 0.8228 (ttmt) cc_final: 0.7807 (mttt)
REVERT: B  139 GLU cc_start: 0.7862 (tt0) cc_final: 0.7599 (tt0)
REVERT: B  166 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7730 (mmm)
REVERT: C   41 LYS cc_start: 0.8183 (tttp) cc_final: 0.7952 (ttpp)
REVERT: D   31 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8088 (mp0)
REVERT: D   42 LYS cc_start: 0.8338 (mtpp) cc_final: 0.7832 (mtmm)
REVERT: D   61 ARG cc_start: 0.7503 (ptp90) cc_final: 0.7201 (ptp90)
REVERT: F   31 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8058 (mp0)
REVERT: F   42 LYS cc_start: 0.8297 (mtpp) cc_final: 0.7770 (mtmm)
  outliers start: 10
  outliers final: 9
  residues processed: 111
  average time/residue: 1.3756
  time to fit residues: 160.1808
Evaluate side-chains
  116 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 SER
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   14 SER
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   68 ARG
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E residue   70 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 63 optimal weight:    4.9990
   chunk 75 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   chunk 62 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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
F  30 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.158984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.110315 restraints weight = 7000.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 2.10
r_work: 0.3043 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2885 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.3219

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= 0.133
  Angle     :  0.538   6.304   9568  Z= 0.278
  Chirality :  0.042   0.146   1054
  Planarity :  0.005   0.051   1156
  Dihedral  : 11.255 140.217   1136
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 15.80 %
    Favored  : 82.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.30), residues: 840
  helix:  2.16 (0.28), residues: 304
  sheet:  1.32 (0.35), residues: 240
  loop :  0.18 (0.40), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 110 
 HIS   0.003   0.001   HIS E  52 
 PHE   0.016   0.002   PHE B  46 
 TYR   0.013   0.001   TYR F  91 
 ARG   0.002   0.000   ARG B 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04233 (  374)
  hydrogen bonds       : angle       4.57273 ( 1038)
  metal coordination   : bond        0.00213 (    6)
  SS BOND              : bond        0.00001 (    2)
  SS BOND              : angle       0.07270 (    4)
  covalent geometry    : bond        0.00299 ( 7058)
  covalent geometry    : angle       0.53842 ( 9564)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7519.81 seconds
wall clock time: 133 minutes 58.81 seconds (8038.81 seconds total)