Starting phenix.real_space_refine
on Sun May 11 02:08:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t03_40933/05_2025/8t03_40933.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t03_40933/05_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_40933/05_2025/8t03_40933.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t03_40933/05_2025/8t03_40933.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t03_40933/05_2025/8t03_40933.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t03_40933/05_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-5687/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: 4.52, per 1000 atoms: 0.66
  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: 1.57
  Conformation dependent library (CDL) restraints added in 889.3 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: 0.84
  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: 1.82

  Time building geometry restraints manager: 1.83 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:             1.200
  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:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.390
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.010
-------------------------------------------------------------------------------
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  : 0.696 
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: 1.1594
  time to fit residues: 163.8327
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  : 0.733 
-------------------------------------------------------------------------------
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: 0.3099 rms_B_bonded: 2.81 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  : 0.756 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.8185 (ttmt) cc_final: 0.7700 (mttt)
REVERT: A  139 GLU cc_start: 0.7851 (tt0) cc_final: 0.7603 (tt0)
REVERT: B   27 LYS cc_start: 0.8297 (ttmt) cc_final: 0.7760 (mttt)
REVERT: B  139 GLU cc_start: 0.7838 (tt0) cc_final: 0.7591 (tt0)
REVERT: D   31 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8040 (mp0)
REVERT: D   45 ARG cc_start: 0.8262 (mtm180) cc_final: 0.8011 (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: 0.7447 (OUTLIER) cc_final: 0.6992 (p)
  outliers start: 19
  outliers final: 5
  residues processed: 125
  average time/residue: 1.2617
  time to fit residues: 165.6818
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  : 0.728 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 67 optimal weight:    7.9990
   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:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3828 r_free = 0.3828 target = 0.160722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.112171 restraints weight = 7023.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 2.07
r_work: 0.3072 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2914 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.2510

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= 0.127
  Angle     :  0.547   6.352   9568  Z= 0.282
  Chirality :  0.042   0.140   1054
  Planarity :  0.004   0.033   1156
  Dihedral  : 12.885 163.740   1136
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 12.81 %
    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:  1.38 (0.30), residues: 840
  helix:  1.95 (0.28), residues: 306
  sheet:  0.73 (0.34), residues: 240
  loop :  0.07 (0.40), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 110 
 HIS   0.003   0.001   HIS B 110 
 PHE   0.016   0.002   PHE A  46 
 TYR   0.012   0.001   TYR F  91 
 ARG   0.002   0.000   ARG B 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04248 (  374)
  hydrogen bonds       : angle       4.85314 ( 1038)
  metal coordination   : bond        0.00209 (    6)
  SS BOND              : bond        0.00035 (    2)
  SS BOND              : angle       0.21877 (    4)
  covalent geometry    : bond        0.00283 ( 7058)
  covalent geometry    : angle       0.54673 ( 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
  126 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.753 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.8257 (ttmt) cc_final: 0.7767 (mttt)
REVERT: A  139 GLU cc_start: 0.7890 (tt0) cc_final: 0.7609 (tt0)
REVERT: B   27 LYS cc_start: 0.8399 (ttmt) cc_final: 0.7924 (mttt)
REVERT: B  139 GLU cc_start: 0.7890 (tt0) cc_final: 0.7606 (tt0)
REVERT: C   41 LYS cc_start: 0.8188 (tttp) cc_final: 0.7806 (tptm)
REVERT: D   31 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8081 (mp0)
REVERT: D   45 ARG cc_start: 0.8272 (mtm180) cc_final: 0.8057 (mtp180)
REVERT: E   48 GLU cc_start: 0.8234 (tt0) cc_final: 0.7985 (tt0)
REVERT: F   31 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8020 (mp0)
REVERT: F   42 LYS cc_start: 0.8321 (mtpp) cc_final: 0.7880 (mtmm)
  outliers start: 21
  outliers final: 5
  residues processed: 109
  average time/residue: 1.3107
  time to fit residues: 150.0582
Evaluate side-chains
  105 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 100
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    4.9990
   chunk 79 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 = 0.3809 r_free = 0.3809 target = 0.159092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.114342 restraints weight = 7078.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 2.02
r_work: 0.3036 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2879 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.2653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7066  Z= 0.151
  Angle     :  0.560   6.439   9568  Z= 0.289
  Chirality :  0.043   0.144   1054
  Planarity :  0.005   0.039   1156
  Dihedral  : 12.585 159.426   1136
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 13.49 %
    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:  1.48 (0.30), residues: 840
  helix:  2.07 (0.28), residues: 304
  sheet:  0.89 (0.34), residues: 240
  loop : -0.00 (0.39), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 110 
 HIS   0.003   0.001   HIS F  38 
 PHE   0.017   0.002   PHE B  69 
 TYR   0.012   0.002   TYR D  91 
 ARG   0.003   0.000   ARG B  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04474 (  374)
  hydrogen bonds       : angle       4.79583 ( 1038)
  metal coordination   : bond        0.00249 (    6)
  SS BOND              : bond        0.00031 (    2)
  SS BOND              : angle       0.09681 (    4)
  covalent geometry    : bond        0.00344 ( 7058)
  covalent geometry    : angle       0.56031 ( 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
  125 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.783 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.8381 (ttmt) cc_final: 0.7942 (mttt)
REVERT: A  139 GLU cc_start: 0.7971 (tt0) cc_final: 0.7699 (tt0)
REVERT: B   27 LYS cc_start: 0.8321 (ttmt) cc_final: 0.7872 (mttt)
REVERT: B  139 GLU cc_start: 0.7979 (tt0) cc_final: 0.7709 (tt0)
REVERT: B  166 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7871 (mmm)
REVERT: C   41 LYS cc_start: 0.8238 (tttp) cc_final: 0.7729 (tptp)
REVERT: D    5 THR cc_start: 0.7788 (m) cc_final: 0.7544 (p)
REVERT: D   31 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8247 (mp0)
REVERT: D   42 LYS cc_start: 0.8513 (mtpp) cc_final: 0.7971 (mtpt)
REVERT: D   45 ARG cc_start: 0.8387 (mtm180) cc_final: 0.8163 (mtp180)
REVERT: E   48 GLU cc_start: 0.8244 (tt0) cc_final: 0.8030 (tt0)
REVERT: F    5 THR cc_start: 0.7774 (m) cc_final: 0.7567 (p)
REVERT: F   31 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8154 (mp0)
REVERT: F   42 LYS cc_start: 0.8395 (mtpp) cc_final: 0.7971 (mtmm)
  outliers start: 20
  outliers final: 10
  residues processed: 111
  average time/residue: 1.2973
  time to fit residues: 151.1533
Evaluate side-chains
  110 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 LEU
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 C residue  112 GLN
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 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:    5.9990
   chunk 79 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   overall best weight:    1.7988

-------------------------------------------------------------------------------
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 = 0.3775 r_free = 0.3775 target = 0.156039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.111551 restraints weight = 6993.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 1.89
r_work: 0.2973 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2817 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.2770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   7066  Z= 0.226
  Angle     :  0.622   6.776   9568  Z= 0.320
  Chirality :  0.046   0.153   1054
  Planarity :  0.005   0.045   1156
  Dihedral  : 12.706 156.306   1136
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 13.62 %
    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 (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:  1.87 (0.28), residues: 302
  sheet:  0.94 (0.35), residues: 240
  loop :  0.03 (0.39), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 110 
 HIS   0.005   0.001   HIS D  38 
 PHE   0.021   0.002   PHE B  69 
 TYR   0.014   0.002   TYR F  91 
 ARG   0.004   0.001   ARG A 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05082 (  374)
  hydrogen bonds       : angle       5.01273 ( 1038)
  metal coordination   : bond        0.00376 (    6)
  SS BOND              : bond        0.00117 (    2)
  SS BOND              : angle       0.33323 (    4)
  covalent geometry    : bond        0.00531 ( 7058)
  covalent geometry    : angle       0.62242 ( 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
  136 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.835 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.8290 (ttmt) cc_final: 0.7863 (mttt)
REVERT: A   63 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7685 (mtp85)
REVERT: A  139 GLU cc_start: 0.7998 (tt0) cc_final: 0.7717 (tt0)
REVERT: A  166 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7895 (mmm)
REVERT: B   27 LYS cc_start: 0.8288 (ttmt) cc_final: 0.7861 (mttt)
REVERT: B   63 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7690 (mtp85)
REVERT: B  139 GLU cc_start: 0.7986 (tt0) cc_final: 0.7708 (tt0)
REVERT: B  166 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7889 (mmm)
REVERT: D   31 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8264 (mp0)
REVERT: D   42 LYS cc_start: 0.8514 (mtpp) cc_final: 0.7983 (mtmm)
REVERT: D   61 ARG cc_start: 0.7398 (ptp90) cc_final: 0.7179 (ptp90)
REVERT: E   48 GLU cc_start: 0.8320 (tt0) cc_final: 0.8101 (tt0)
REVERT: F   31 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8244 (mp0)
REVERT: F   42 LYS cc_start: 0.8447 (mtpp) cc_final: 0.7989 (mtmm)
  outliers start: 23
  outliers final: 7
  residues processed: 120
  average time/residue: 1.5067
  time to fit residues: 189.2653
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  : 0.744 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 SER
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 B residue   10 LEU
Chi-restraints excluded: chain B residue   63 ARG
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   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 70 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 60 optimal weight:    3.9990
   chunk 46 optimal weight:    7.9990
   chunk 52 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0010
   chunk 9 optimal weight:    0.9990
   chunk 73 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.7586

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

Flipped N/Q/H residues before XYZ refinement:
C  16 GLN
C 112 GLN
D  30 ASN
E 112 GLN
F  30 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.159223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.110611 restraints weight = 7035.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 2.10
r_work: 0.3053 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2896 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.2930

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= 0.125
  Angle     :  0.537   6.278   9568  Z= 0.277
  Chirality :  0.042   0.142   1054
  Planarity :  0.005   0.047   1156
  Dihedral  : 11.822 151.389   1136
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 14.03 %
    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:  1.61 (0.30), residues: 840
  helix:  2.14 (0.28), residues: 304
  sheet:  1.11 (0.35), residues: 240
  loop : -0.04 (0.39), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 110 
 HIS   0.004   0.001   HIS E  52 
 PHE   0.016   0.002   PHE A  39 
 TYR   0.011   0.001   TYR D  86 
 ARG   0.002   0.000   ARG A  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04173 (  374)
  hydrogen bonds       : angle       4.67304 ( 1038)
  metal coordination   : bond        0.00200 (    6)
  SS BOND              : bond        0.00013 (    2)
  SS BOND              : angle       0.05101 (    4)
  covalent geometry    : bond        0.00277 ( 7058)
  covalent geometry    : angle       0.53673 ( 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
  127 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.708 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.8204 (ttmt) cc_final: 0.7772 (mttt)
REVERT: A  139 GLU cc_start: 0.7880 (tt0) cc_final: 0.7606 (tt0)
REVERT: A  166 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7715 (mmm)
REVERT: B   27 LYS cc_start: 0.8186 (ttmt) cc_final: 0.7762 (mttt)
REVERT: B  139 GLU cc_start: 0.7865 (tt0) cc_final: 0.7595 (tt0)
REVERT: C   41 LYS cc_start: 0.8209 (ttpp) cc_final: 0.7557 (tptp)
REVERT: D   31 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8089 (mp0)
REVERT: D   42 LYS cc_start: 0.8389 (mtpp) cc_final: 0.7863 (mtmm)
REVERT: D   61 ARG cc_start: 0.7434 (ptp90) cc_final: 0.7110 (ptp90)
REVERT: E   48 GLU cc_start: 0.8245 (tt0) cc_final: 0.8004 (tt0)
REVERT: E   65 LEU cc_start: 0.7506 (mp) cc_final: 0.7273 (mp)
REVERT: F   31 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8084 (mp0)
REVERT: F   42 LYS cc_start: 0.8331 (mtpp) cc_final: 0.7875 (mtmm)
  outliers start: 18
  outliers final: 7
  residues processed: 114
  average time/residue: 1.3316
  time to fit residues: 159.0625
Evaluate side-chains
  112 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   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:    0.5980
   chunk 76 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3799 r_free = 0.3799 target = 0.158207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.109540 restraints weight = 6935.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 2.09
r_work: 0.3039 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2880 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.3025

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= 0.150
  Angle     :  0.552   6.441   9568  Z= 0.285
  Chirality :  0.042   0.141   1054
  Planarity :  0.005   0.050   1156
  Dihedral  : 11.751 148.058   1136
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 13.90 %
    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:  1.64 (0.30), residues: 840
  helix:  2.09 (0.28), residues: 304
  sheet:  1.17 (0.35), residues: 240
  loop :  0.02 (0.40), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 110 
 HIS   0.003   0.001   HIS E  52 
 PHE   0.017   0.002   PHE A  69 
 TYR   0.012   0.002   TYR F  86 
 ARG   0.002   0.000   ARG B 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04425 (  374)
  hydrogen bonds       : angle       4.70090 ( 1038)
  metal coordination   : bond        0.00265 (    6)
  SS BOND              : bond        0.00034 (    2)
  SS BOND              : angle       0.12094 (    4)
  covalent geometry    : bond        0.00342 ( 7058)
  covalent geometry    : angle       0.55165 ( 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
  129 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.766 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.8178 (ttmt) cc_final: 0.7765 (mttt)
REVERT: A  139 GLU cc_start: 0.7893 (tt0) cc_final: 0.7619 (tt0)
REVERT: A  166 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7723 (mmm)
REVERT: B   27 LYS cc_start: 0.8171 (ttmt) cc_final: 0.7754 (mttt)
REVERT: B  139 GLU cc_start: 0.7888 (tt0) cc_final: 0.7567 (tt0)
REVERT: B  166 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7711 (mmm)
REVERT: C   41 LYS cc_start: 0.8264 (ttpp) cc_final: 0.8011 (tptp)
REVERT: D   31 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8091 (mp0)
REVERT: D   42 LYS cc_start: 0.8409 (mtpp) cc_final: 0.7890 (mtmm)
REVERT: D   61 ARG cc_start: 0.7448 (ptp90) cc_final: 0.7164 (ptp90)
REVERT: E   34 MET cc_start: 0.8129 (tpp) cc_final: 0.7618 (mtt)
REVERT: E   48 GLU cc_start: 0.8223 (tt0) cc_final: 0.7980 (tt0)
REVERT: F   31 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8074 (mp0)
REVERT: F   42 LYS cc_start: 0.8345 (mtpp) cc_final: 0.7815 (mtmm)
  outliers start: 23
  outliers final: 13
  residues processed: 116
  average time/residue: 1.3932
  time to fit residues: 169.2384
Evaluate side-chains
  117 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
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   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   22 CYS
Chi-restraints excluded: chain C residue   68 ARG
Chi-restraints excluded: chain C residue  112 GLN
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E 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:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 10 optimal weight:    0.3980
   chunk 41 optimal weight:    3.9990
   chunk 30 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   chunk 74 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 40 optimal weight:    5.9990
   chunk 50 optimal weight:    4.9990
   overall best weight:    0.7180

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.159660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.111031 restraints weight = 7023.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 2.11
r_work: 0.3064 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2906 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.3087

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= 0.120
  Angle     :  0.529   6.304   9568  Z= 0.272
  Chirality :  0.041   0.144   1054
  Planarity :  0.005   0.051   1156
  Dihedral  : 11.403 145.715   1136
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 15.12 %
    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:  1.77 (0.30), residues: 840
  helix:  2.22 (0.28), residues: 304
  sheet:  1.26 (0.35), residues: 240
  loop :  0.05 (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   0.016   0.002   PHE A  39 
 TYR   0.011   0.001   TYR D  86 
 ARG   0.001   0.000   ARG A 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04090 (  374)
  hydrogen bonds       : angle       4.56470 ( 1038)
  metal coordination   : bond        0.00175 (    6)
  SS BOND              : bond        0.00015 (    2)
  SS BOND              : angle       0.01883 (    4)
  covalent geometry    : bond        0.00265 ( 7058)
  covalent geometry    : angle       0.52888 ( 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: 17
    poor density    : 105
  time to evaluate  : 0.773 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.8230 (ttmt) cc_final: 0.7799 (mttt)
REVERT: A  139 GLU cc_start: 0.7878 (tt0) cc_final: 0.7559 (tt0)
REVERT: A  166 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7713 (mmm)
REVERT: B   27 LYS cc_start: 0.8224 (ttmt) cc_final: 0.7790 (mttt)
REVERT: B  139 GLU cc_start: 0.7875 (tt0) cc_final: 0.7554 (tt0)
REVERT: C   17 THR cc_start: 0.6827 (p) cc_final: 0.6597 (m)
REVERT: C   41 LYS cc_start: 0.8229 (ttpp) cc_final: 0.7944 (tptp)
REVERT: D   31 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8099 (mp0)
REVERT: D   42 LYS cc_start: 0.8389 (mtpp) cc_final: 0.7867 (mtmm)
REVERT: D   61 ARG cc_start: 0.7445 (ptp90) cc_final: 0.7126 (ptp90)
REVERT: E   34 MET cc_start: 0.8134 (tpp) cc_final: 0.7646 (mtt)
REVERT: E   48 GLU cc_start: 0.8191 (tt0) cc_final: 0.7958 (tt0)
REVERT: F   31 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8061 (mp0)
REVERT: F   42 LYS cc_start: 0.8300 (mtpp) cc_final: 0.7781 (mtmm)
  outliers start: 17
  outliers final: 10
  residues processed: 112
  average time/residue: 1.2371
  time to fit residues: 145.8088
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  : 0.695 
-------------------------------------------------------------------------------
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   14 SER
Chi-restraints excluded: chain B residue   41 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   22 CYS
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue   94 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 81 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 63 optimal weight:    0.3980
   chunk 69 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
C 112 GLN
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 = 0.3801 r_free = 0.3801 target = 0.158318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.112081 restraints weight = 7017.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 2.34
r_work: 0.3052 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2893 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.3125

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= 0.153
  Angle     :  0.561   6.423   9568  Z= 0.288
  Chirality :  0.043   0.144   1054
  Planarity :  0.005   0.051   1156
  Dihedral  : 11.557 144.548   1136
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 15.40 %
    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:  1.72 (0.30), residues: 840
  helix:  2.08 (0.28), residues: 304
  sheet:  1.29 (0.35), residues: 240
  loop :  0.09 (0.40), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 110 
 HIS   0.003   0.001   HIS D  38 
 PHE   0.018   0.002   PHE B  69 
 TYR   0.013   0.002   TYR D  91 
 ARG   0.002   0.000   ARG B 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04444 (  374)
  hydrogen bonds       : angle       4.67432 ( 1038)
  metal coordination   : bond        0.00272 (    6)
  SS BOND              : bond        0.00054 (    2)
  SS BOND              : angle       0.16059 (    4)
  covalent geometry    : bond        0.00351 ( 7058)
  covalent geometry    : angle       0.56136 ( 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
  124 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 0.691 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.8129 (ttmt) cc_final: 0.7694 (mttt)
REVERT: A  139 GLU cc_start: 0.7787 (tt0) cc_final: 0.7506 (tt0)
REVERT: A  166 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7605 (mmm)
REVERT: B   27 LYS cc_start: 0.8097 (ttmt) cc_final: 0.7681 (mttt)
REVERT: B  139 GLU cc_start: 0.7805 (tt0) cc_final: 0.7519 (tt0)
REVERT: B  166 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7595 (mmm)
REVERT: C   17 THR cc_start: 0.6874 (p) cc_final: 0.6649 (m)
REVERT: C   41 LYS cc_start: 0.8167 (ttpp) cc_final: 0.7863 (tptp)
REVERT: D   31 GLU cc_start: 0.8553 (mt-10) cc_final: 0.7983 (mp0)
REVERT: D   42 LYS cc_start: 0.8290 (mtpp) cc_final: 0.7733 (mtpt)
REVERT: D   61 ARG cc_start: 0.7407 (ptp90) cc_final: 0.7128 (ptp90)
REVERT: E   34 MET cc_start: 0.8097 (tpp) cc_final: 0.7588 (mtt)
REVERT: E   48 GLU cc_start: 0.8148 (tt0) cc_final: 0.7879 (tt0)
REVERT: F   31 GLU cc_start: 0.8556 (mt-10) cc_final: 0.7983 (mp0)
REVERT: F   42 LYS cc_start: 0.8240 (mtpp) cc_final: 0.7701 (mtmm)
REVERT: F   61 ARG cc_start: 0.7221 (ptp-170) cc_final: 0.7002 (ptp90)
  outliers start: 15
  outliers final: 12
  residues processed: 117
  average time/residue: 1.2225
  time to fit residues: 150.2785
Evaluate side-chains
  121 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
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   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   22 CYS
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:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 54 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   overall best weight:    0.8182

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.159291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.110589 restraints weight = 7043.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 2.11
r_work: 0.3055 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2899 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.3183

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= 0.129
  Angle     :  0.540   6.337   9568  Z= 0.277
  Chirality :  0.041   0.147   1054
  Planarity :  0.005   0.052   1156
  Dihedral  : 11.347 143.806   1136
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 15.53 %
    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 (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:  1.82 (0.30), residues: 840
  helix:  2.16 (0.28), residues: 304
  sheet:  1.33 (0.35), residues: 240
  loop :  0.16 (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 A  39 
 TYR   0.011   0.001   TYR D  86 
 ARG   0.002   0.000   ARG A 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04186 (  374)
  hydrogen bonds       : angle       4.58214 ( 1038)
  metal coordination   : bond        0.00214 (    6)
  SS BOND              : bond        0.00001 (    2)
  SS BOND              : angle       0.05060 (    4)
  covalent geometry    : bond        0.00288 ( 7058)
  covalent geometry    : angle       0.54000 ( 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
  124 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 111
  time to evaluate  : 0.767 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.8240 (ttmt) cc_final: 0.7815 (mttt)
REVERT: A  139 GLU cc_start: 0.7844 (tt0) cc_final: 0.7561 (tt0)
REVERT: A  166 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7735 (mmm)
REVERT: B   27 LYS cc_start: 0.8211 (ttmt) cc_final: 0.7792 (mttt)
REVERT: B  139 GLU cc_start: 0.7850 (tt0) cc_final: 0.7572 (tt0)
REVERT: C   17 THR cc_start: 0.6908 (p) cc_final: 0.6707 (m)
REVERT: C   41 LYS cc_start: 0.8252 (ttpp) cc_final: 0.7973 (tptp)
REVERT: D   31 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8091 (mp0)
REVERT: D   42 LYS cc_start: 0.8389 (mtpp) cc_final: 0.7874 (mtmm)
REVERT: D   61 ARG cc_start: 0.7466 (ptp90) cc_final: 0.7146 (ptp90)
REVERT: E   34 MET cc_start: 0.8151 (tpp) cc_final: 0.7628 (mtt)
REVERT: E   48 GLU cc_start: 0.8189 (tt0) cc_final: 0.7945 (tt0)
REVERT: F   31 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8079 (mp0)
REVERT: F   42 LYS cc_start: 0.8298 (mtpp) cc_final: 0.7769 (mtmm)
  outliers start: 13
  outliers final: 10
  residues processed: 116
  average time/residue: 1.2513
  time to fit residues: 152.7862
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  : 0.755 
-------------------------------------------------------------------------------
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   14 SER
Chi-restraints excluded: chain B residue   41 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   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 9 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9990
   chunk 78 optimal weight:    9.9990
   chunk 63 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9990
   chunk 67 optimal weight:   10.0000
   chunk 62 optimal weight:    0.5980
   chunk 76 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
C 112 GLN
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 = 0.3809 r_free = 0.3809 target = 0.158934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.110324 restraints weight = 6993.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 2.10
r_work: 0.3056 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2897 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.3238

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     :  0.540   6.334   9568  Z= 0.279
  Chirality :  0.042   0.148   1054
  Planarity :  0.005   0.051   1156
  Dihedral  : 11.327 142.495   1136
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 16.35 %
    Favored  : 81.61 %
  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:  1.79 (0.30), residues: 840
  helix:  2.13 (0.28), residues: 304
  sheet:  1.31 (0.35), residues: 240
  loop :  0.16 (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 A  39 
 TYR   0.012   0.001   TYR D  86 
 ARG   0.002   0.000   ARG B 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04248 (  374)
  hydrogen bonds       : angle       4.58853 ( 1038)
  metal coordination   : bond        0.00222 (    6)
  SS BOND              : bond        0.00008 (    2)
  SS BOND              : angle       0.08119 (    4)
  covalent geometry    : bond        0.00299 ( 7058)
  covalent geometry    : angle       0.54042 ( 9564)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6044.67 seconds
wall clock time: 104 minutes 41.58 seconds (6281.58 seconds total)