Starting phenix.real_space_refine
on Tue May 13 07:54:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gmd_51448/05_2025/9gmd_51448.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gmd_51448/05_2025/9gmd_51448.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gmd_51448/05_2025/9gmd_51448.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gmd_51448/05_2025/9gmd_51448.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gmd_51448/05_2025/9gmd_51448.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gmd_51448/05_2025/9gmd_51448.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    3144      2.51       5
     N     882      2.21       5
     O     948      1.98       5
     H    4925      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 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: 9919
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C"
      Number of atoms: 1224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 1224
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 1, 'TRANS': 70}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 557
          Classifications: {'peptide': 38}
          Link IDs: {'TRANS': 37}
          Chain breaks: 2
    Chain: "E"
      Number of atoms: 3333
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 205, 3333
          Classifications: {'peptide': 205}
          Link IDs: {'PTRANS': 9, 'TRANS': 195}
    Chain: "F"
      Number of atoms: 3305
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 203, 3305
          Classifications: {'peptide': 203}
          Link IDs: {'PTRANS': 8, 'TRANS': 194}
    Chain: "I"
      Number of atoms: 738
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 738
          Classifications: {'peptide': 46}
          Link IDs: {'PTRANS': 1, 'TRANS': 44}
    Chain: "J"
      Number of atoms: 762
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 762
          Classifications: {'peptide': 47}
          Link IDs: {'PTRANS': 1, 'TRANS': 45}
  Time building chain proxies: 4.47, per 1000 atoms: 0.45
  Number of scatterers: 9919
  At special positions: 0
  Unit cell: (83.953, 91.0677, 92.4906, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      20     16.00
     O     948      8.00
     N     882      7.00
     C    3144      6.00
     H    4925      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.33
  Conformation dependent library (CDL) restraints added in 574.5 milliseconds
  

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1162

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 8 sheets defined
      68.1% alpha, 7.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'C' and resid 191 through 196
      removed outlier: 3.620A  pdb=" N   ASP C 196 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 264 through 289
      removed outlier: 3.657A  pdb=" N   GLN C 268 " --> pdb=" O   ILE C 264 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 295 through 307
      removed outlier: 3.669A  pdb=" N   GLN C 299 " --> pdb=" O   ARG C 295 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 308 through 311
    Processing helix  chain 'D' and resid 48 through 55
    Processing helix  chain 'D' and resid 70 through 79
    Processing helix  chain 'D' and resid 95 through 99
      removed outlier: 4.298A  pdb=" N   ALA D  99 " --> pdb=" O   GLU D  96 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 11 through 19
    Processing helix  chain 'E' and resid 22 through 31
      removed outlier: 3.825A  pdb=" N   LEU E  26 " --> pdb=" O   LEU E  22 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ARG E  31 " --> pdb=" O   ASP E  27 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 40 through 50
    Processing helix  chain 'E' and resid 50 through 59
    Processing helix  chain 'E' and resid 89 through 105
      removed outlier: 3.739A  pdb=" N   LEU E 104 " --> pdb=" O   CYS E 100 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 106 through 112
      removed outlier: 3.649A  pdb=" N   LEU E 109 " --> pdb=" O   PRO E 106 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ALA E 110 " --> pdb=" O   GLU E 107 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 117 through 125
    Processing helix  chain 'E' and resid 129 through 138
      removed outlier: 4.170A  pdb=" N   LEU E 136 " --> pdb=" O   LYS E 132 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 144 through 165
      removed outlier: 3.597A  pdb=" N   ARG E 156 " --> pdb=" O   GLN E 152 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU E 165 " --> pdb=" O   ARG E 161 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 182 through 187
    Processing helix  chain 'E' and resid 188 through 193
      removed outlier: 4.620A  pdb=" N   ALA E 193 " --> pdb=" O   ALA E 189 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 196 through 208
    Processing helix  chain 'F' and resid 11 through 19
    Processing helix  chain 'F' and resid 22 through 32
      removed outlier: 3.677A  pdb=" N   LEU F  26 " --> pdb=" O   LEU F  22 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 40 through 50
    Processing helix  chain 'F' and resid 50 through 59
      removed outlier: 3.597A  pdb=" N   LEU F  54 " --> pdb=" O   PHE F  50 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 89 through 104
      removed outlier: 3.819A  pdb=" N   LEU F 104 " --> pdb=" O   CYS F 100 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 106 through 112
      removed outlier: 4.267A  pdb=" N   ALA F 110 " --> pdb=" O   PRO F 106 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 116 through 128
      removed outlier: 3.586A  pdb=" N   LEU F 120 " --> pdb=" O   THR F 116 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 129 through 138
    Processing helix  chain 'F' and resid 144 through 166
      removed outlier: 3.576A  pdb=" N   ARG F 148 " --> pdb=" O   SER F 144 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 182 through 192
      removed outlier: 3.580A  pdb=" N   PHE F 185 " --> pdb=" O   GLU F 182 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   ALA F 189 " --> pdb=" O   ARG F 186 " (cutoff:3.500A)
      removed outlier: 4.908A  pdb=" N   ASP F 190 " --> pdb=" O   PHE F 187 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 196 through 208
    Processing helix  chain 'I' and resid 10 through 49
      removed outlier: 3.538A  pdb=" N   ASN I  32 " --> pdb=" O   ASP I  28 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 10 through 49
      removed outlier: 4.285A  pdb=" N   ASP J  15 " --> pdb=" O   ASP J  11 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   ILE J  16 " --> pdb=" O   VAL J  12 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLN J  17 " --> pdb=" O   TRP J  13 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ASP J  21 " --> pdb=" O   GLN J  17 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 313 through 315
      removed outlier: 3.747A  pdb=" N   ALA C 314 " --> pdb=" O   MET E 211 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 317 through 318
    Processing sheet with id=AA3, first strand: chain 'C' and resid 323 through 325
      removed outlier: 5.828A  pdb=" N   LEU C 323 " --> pdb=" O   SER F  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'E' and resid 63 through 66
    Processing sheet with id=AA5, first strand: chain 'E' and resid 114 through 116
      removed outlier: 3.743A  pdb=" N   PHE E 178 " --> pdb=" O   PHE E 115 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 63 through 67
    Processing sheet with id=AA7, first strand: chain 'F' and resid 114 through 115
    Processing sheet with id=AA8, first strand: chain 'I' and resid 5 through 9

    288 hydrogen bonds defined for protein.
    819 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: 2.88

  Time building geometry restraints manager: 2.84 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 4923
        1.03 -     1.23: 4
        1.23 -     1.42: 2155
        1.42 -     1.61: 2882
        1.61 -     1.81: 38
  Bond restraints: 10002
  Sorted by residual:
  bond pdb=" CB  PRO E 197 "
       pdb=" CG  PRO E 197 "
    ideal  model  delta    sigma   weight residual
    1.492  1.612 -0.120 5.00e-02 4.00e+02 5.79e+00
  bond pdb=" CG  LEU E 127 "
       pdb=" CD2 LEU E 127 "
    ideal  model  delta    sigma   weight residual
    1.521  1.481  0.040 3.30e-02 9.18e+02 1.44e+00
  bond pdb=" CB  LYS C 283 "
       pdb=" CG  LYS C 283 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.08e+00
  bond pdb=" CB  GLU I  24 "
       pdb=" CG  GLU I  24 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.05e+00
  bond pdb=" CG  LYS E 132 "
       pdb=" CD  LYS E 132 "
    ideal  model  delta    sigma   weight residual
    1.520  1.546 -0.026 3.00e-02 1.11e+03 7.44e-01
  ... (remaining 9997 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 17805
        1.79 -     3.58: 180
        3.58 -     5.37: 24
        5.37 -     7.16: 1
        7.16 -     8.94: 1
  Bond angle restraints: 18011
  Sorted by residual:
  angle pdb=" CA  PRO E 197 "
        pdb=" N   PRO E 197 "
        pdb=" CD  PRO E 197 "
      ideal   model   delta    sigma   weight residual
     112.00  103.06    8.94 1.40e+00 5.10e-01 4.08e+01
  angle pdb=" N   ASP C 292 "
        pdb=" CA  ASP C 292 "
        pdb=" C   ASP C 292 "
      ideal   model   delta    sigma   weight residual
     110.44  107.15    3.29 1.20e+00 6.94e-01 7.51e+00
  angle pdb=" N   PRO E 197 "
        pdb=" CA  PRO E 197 "
        pdb=" CB  PRO E 197 "
      ideal   model   delta    sigma   weight residual
     103.25  100.44    2.81 1.05e+00 9.07e-01 7.18e+00
  angle pdb=" CA  LYS C 283 "
        pdb=" CB  LYS C 283 "
        pdb=" CG  LYS C 283 "
      ideal   model   delta    sigma   weight residual
     114.10  119.10   -5.00 2.00e+00 2.50e-01 6.25e+00
  angle pdb=" CA  GLU I  24 "
        pdb=" CB  GLU I  24 "
        pdb=" CG  GLU I  24 "
      ideal   model   delta    sigma   weight residual
     114.10  119.00   -4.90 2.00e+00 2.50e-01 6.01e+00
  ... (remaining 18006 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.88: 4065
       16.88 -    33.76: 402
       33.76 -    50.63: 135
       50.63 -    67.51: 44
       67.51 -    84.39: 7
  Dihedral angle restraints: 4653
    sinusoidal: 2577
      harmonic: 2076
  Sorted by residual:
  dihedral pdb=" CG  ARG F 108 "
           pdb=" CD  ARG F 108 "
           pdb=" NE  ARG F 108 "
           pdb=" CZ  ARG F 108 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -133.67   43.67     2      1.50e+01 4.44e-03 1.02e+01
  dihedral pdb=" CG  ARG E  60 "
           pdb=" CD  ARG E  60 "
           pdb=" NE  ARG E  60 "
           pdb=" CZ  ARG E  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -136.91  -43.09     2      1.50e+01 4.44e-03 9.96e+00
  dihedral pdb=" CB  GLU E 119 "
           pdb=" CG  GLU E 119 "
           pdb=" CD  GLU E 119 "
           pdb=" OE1 GLU E 119 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -84.39   84.39     1      3.00e+01 1.11e-03 9.62e+00
  ... (remaining 4650 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 495
       0.027 -    0.053: 161
       0.053 -    0.080: 51
       0.080 -    0.106: 27
       0.106 -    0.133: 10
  Chirality restraints: 744
  Sorted by residual:
  chirality pdb=" CA  ILE J   8 "
            pdb=" N   ILE J   8 "
            pdb=" C   ILE J   8 "
            pdb=" CB  ILE J   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.40e-01
  chirality pdb=" CA  PRO E 197 "
            pdb=" N   PRO E 197 "
            pdb=" C   PRO E 197 "
            pdb=" CB  PRO E 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.11e-01
  chirality pdb=" CA  ILE F  83 "
            pdb=" N   ILE F  83 "
            pdb=" C   ILE F  83 "
            pdb=" CB  ILE F  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.70e-01
  ... (remaining 741 not shown)

  Planarity restraints: 1483
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP E 196 "   -0.077 5.00e-02 4.00e+02   1.11e-01 1.99e+01
        pdb=" N   PRO E 197 "    0.193 5.00e-02 4.00e+02
        pdb=" CA  PRO E 197 "   -0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO E 197 "   -0.060 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 302 "   -0.358 9.50e-02 1.11e+02   1.20e-01 1.58e+01
        pdb=" NE  ARG C 302 "    0.024 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 302 "    0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 302 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 302 "   -0.006 2.00e-02 2.50e+03
        pdb="HH11 ARG C 302 "   -0.002 2.00e-02 2.50e+03
        pdb="HH12 ARG C 302 "    0.003 2.00e-02 2.50e+03
        pdb="HH21 ARG C 302 "   -0.004 2.00e-02 2.50e+03
        pdb="HH22 ARG C 302 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 286 "   -0.151 9.50e-02 1.11e+02   5.05e-02 3.10e+00
        pdb=" NE  ARG C 286 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 286 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 286 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 286 "    0.000 2.00e-02 2.50e+03
        pdb="HH11 ARG C 286 "    0.003 2.00e-02 2.50e+03
        pdb="HH12 ARG C 286 "    0.001 2.00e-02 2.50e+03
        pdb="HH21 ARG C 286 "   -0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG C 286 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1480 not shown)

  Histogram of nonbonded interaction distances:
        1.54 -     2.15: 386
        2.15 -     2.77: 18806
        2.77 -     3.38: 27108
        3.38 -     3.99: 31872
        3.99 -     4.60: 50047
  Nonbonded interactions: 128219
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU F 119 "
            pdb=" H   GLU F 119 "
     model   vdw
     1.542 2.450
  nonbonded pdb="HH12 ARG C 300 "
            pdb=" O   ALA E 193 "
     model   vdw
     1.545 2.450
  nonbonded pdb=" OE1 GLU E  52 "
            pdb=" H   GLU E  52 "
     model   vdw
     1.586 2.450
  nonbonded pdb=" OE1 GLU F  40 "
            pdb=" H   GLU F  40 "
     model   vdw
     1.624 2.450
  nonbonded pdb=" HG  SER E 175 "
            pdb=" OG  SER I  22 "
     model   vdw
     1.645 2.450
  ... (remaining 128214 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'E' and resid 9 through 209)
  selection = (chain 'F' and resid 9 through 209)
}
ncs_group {
  reference = chain 'I'
  selection = (chain 'J' and resid 4 through 49)
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.500
  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:             0.150
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     21.430
  Find NCS groups from input model:        0.210
  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:2.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.120   5077  Z= 0.175
  Angle     :  0.615   8.944   6843  Z= 0.336
  Chirality :  0.035   0.133    744
  Planarity :  0.008   0.159    901
  Dihedral  : 16.616  84.391   1941
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  : 22.30 %
    Favored  : 77.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.35), residues: 593
  helix:  1.89 (0.27), residues: 371
  sheet:  0.92 (1.07), residues: 22
  loop : -0.32 (0.45), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP I  13 
 HIS   0.005   0.001   HIS E  44 
 PHE   0.008   0.001   PHE F  73 
 TYR   0.015   0.002   TYR E 101 
 ARG   0.009   0.001   ARG C 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16852 (  288)
  hydrogen bonds       : angle       5.83350 (  819)
  covalent geometry    : bond        0.00410 ( 5077)
  covalent geometry    : angle       0.61464 ( 6843)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 152
  time to evaluate  : 0.736 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  282 HIS cc_start: 0.8214 (m-70) cc_final: 0.7795 (m-70)
REVERT: I   27 ASN cc_start: 0.8791 (t0) cc_final: 0.8291 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 153
  average time/residue: 0.5471
  time to fit residues: 98.1733
Evaluate side-chains
  127 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 29 optimal weight:    0.3980
   chunk 23 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
I  27 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.088832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.064734 restraints weight = 42950.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.068364 restraints weight = 19222.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.070636 restraints weight = 11731.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.2220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5077  Z= 0.138
  Angle     :  0.565   5.760   6843  Z= 0.302
  Chirality :  0.035   0.148    744
  Planarity :  0.005   0.060    901
  Dihedral  :  3.797  16.099    681
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 21.56 %
    Favored  : 76.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.36), residues: 593
  helix:  1.94 (0.27), residues: 390
  sheet:  1.20 (1.07), residues: 22
  loop : -0.44 (0.48), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP I  13 
 HIS   0.004   0.001   HIS E  44 
 PHE   0.008   0.001   PHE C 297 
 TYR   0.013   0.001   TYR E 101 
 ARG   0.004   0.001   ARG C 302 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04609 (  288)
  hydrogen bonds       : angle       4.63801 (  819)
  covalent geometry    : bond        0.00296 ( 5077)
  covalent geometry    : angle       0.56490 ( 6843)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 130
  time to evaluate  : 0.777 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  282 HIS cc_start: 0.8834 (m-70) cc_final: 0.8199 (m-70)
REVERT: C  295 ARG cc_start: 0.9142 (ttt180) cc_final: 0.8874 (mtp180)
REVERT: C  311 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8403 (tm-30)
REVERT: E   93 MET cc_start: 0.9048 (mmm) cc_final: 0.8828 (mmm)
REVERT: F   10 MET cc_start: 0.8172 (ppp) cc_final: 0.7924 (ppp)
REVERT: I   14 ASN cc_start: 0.9032 (m-40) cc_final: 0.8639 (m110)
REVERT: I   24 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8397 (tm-30)
REVERT: I   28 ASP cc_start: 0.9046 (m-30) cc_final: 0.8786 (m-30)
REVERT: J   19 TYR cc_start: 0.8382 (t80) cc_final: 0.8036 (t80)
REVERT: J   24 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7216 (mt-10)
  outliers start: 11
  outliers final: 5
  residues processed: 135
  average time/residue: 0.4724
  time to fit residues: 77.3829
Evaluate side-chains
  128 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 123
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain E residue   32 SER
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain I residue   41 VAL
Chi-restraints excluded: chain J residue   31 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 40 optimal weight:    0.4980
   chunk 56 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 54 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
C 191 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.088555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.064369 restraints weight = 42971.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.067972 restraints weight = 19238.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.070260 restraints weight = 11768.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.2669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5077  Z= 0.140
  Angle     :  0.535   6.017   6843  Z= 0.286
  Chirality :  0.034   0.152    744
  Planarity :  0.004   0.051    901
  Dihedral  :  3.734  16.038    681
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 22.30 %
    Favored  : 75.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.36), residues: 593
  helix:  2.08 (0.27), residues: 389
  sheet:  1.02 (1.07), residues: 22
  loop : -0.45 (0.47), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 266 
 HIS   0.003   0.001   HIS E  44 
 PHE   0.012   0.001   PHE F 115 
 TYR   0.011   0.001   TYR E 101 
 ARG   0.003   0.000   ARG C 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04148 (  288)
  hydrogen bonds       : angle       4.41374 (  819)
  covalent geometry    : bond        0.00299 ( 5077)
  covalent geometry    : angle       0.53487 ( 6843)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 128
  time to evaluate  : 0.858 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  282 HIS cc_start: 0.8842 (m-70) cc_final: 0.8208 (m-70)
REVERT: C  295 ARG cc_start: 0.9161 (ttt180) cc_final: 0.8865 (mtp180)
REVERT: C  311 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8346 (tm-30)
REVERT: I   14 ASN cc_start: 0.9011 (m-40) cc_final: 0.8646 (m110)
REVERT: I   24 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8515 (tm-30)
REVERT: I   28 ASP cc_start: 0.9247 (m-30) cc_final: 0.8905 (m-30)
REVERT: J   19 TYR cc_start: 0.8408 (t80) cc_final: 0.7916 (t80)
REVERT: J   23 LEU cc_start: 0.9108 (mp) cc_final: 0.8819 (mp)
  outliers start: 10
  outliers final: 7
  residues processed: 133
  average time/residue: 0.4923
  time to fit residues: 78.5881
Evaluate side-chains
  129 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 122
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  283 LYS
Chi-restraints excluded: chain E residue   32 SER
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  181 THR
Chi-restraints excluded: chain I residue   27 ASN
Chi-restraints excluded: chain I residue   41 VAL
Chi-restraints excluded: chain J residue   31 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 31 optimal weight:    0.2980
   chunk 9 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 3 optimal weight:    0.3980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
C 191 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.088204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.064428 restraints weight = 42350.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.067968 restraints weight = 18769.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.070220 restraints weight = 11408.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.2974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5077  Z= 0.116
  Angle     :  0.510   6.372   6843  Z= 0.268
  Chirality :  0.034   0.141    744
  Planarity :  0.004   0.049    901
  Dihedral  :  3.703  16.288    681
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 23.05 %
    Favored  : 74.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.28 (0.36), residues: 593
  helix:  2.40 (0.27), residues: 380
  sheet:  0.74 (1.06), residues: 22
  loop : -0.23 (0.48), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 266 
 HIS   0.003   0.001   HIS E  44 
 PHE   0.011   0.001   PHE F 115 
 TYR   0.018   0.002   TYR E 101 
 ARG   0.004   0.000   ARG C 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03710 (  288)
  hydrogen bonds       : angle       4.16105 (  819)
  covalent geometry    : bond        0.00252 ( 5077)
  covalent geometry    : angle       0.50999 ( 6843)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 129
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  282 HIS cc_start: 0.8769 (m-70) cc_final: 0.8129 (m-70)
REVERT: C  295 ARG cc_start: 0.9104 (ttt180) cc_final: 0.8845 (mtp180)
REVERT: C  311 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8288 (tm-30)
REVERT: E   39 ASP cc_start: 0.7917 (t0) cc_final: 0.7527 (t0)
REVERT: E  182 GLU cc_start: 0.8878 (pm20) cc_final: 0.8655 (pm20)
REVERT: I   14 ASN cc_start: 0.8982 (m-40) cc_final: 0.8576 (m110)
REVERT: I   24 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8505 (tm-30)
REVERT: I   28 ASP cc_start: 0.9215 (m-30) cc_final: 0.8823 (m-30)
REVERT: J   19 TYR cc_start: 0.8367 (t80) cc_final: 0.7919 (t80)
REVERT: J   23 LEU cc_start: 0.9135 (mp) cc_final: 0.8845 (mp)
  outliers start: 12
  outliers final: 9
  residues processed: 135
  average time/residue: 0.4577
  time to fit residues: 74.8735
Evaluate side-chains
  130 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain E residue   32 SER
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain E residue  181 THR
Chi-restraints excluded: chain I residue    7 THR
Chi-restraints excluded: chain I residue   27 ASN
Chi-restraints excluded: chain I residue   41 VAL
Chi-restraints excluded: chain J residue   31 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0470
   chunk 20 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.7880

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

Flipped N/Q/H residues before XYZ refinement:
C 191 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.087719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.064189 restraints weight = 42261.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.067693 restraints weight = 18655.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.069893 restraints weight = 11291.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.3307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5077  Z= 0.134
  Angle     :  0.514   6.774   6843  Z= 0.270
  Chirality :  0.034   0.150    744
  Planarity :  0.004   0.050    901
  Dihedral  :  3.675  15.874    681
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 23.05 %
    Favored  : 74.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.17 (0.36), residues: 593
  helix:  2.32 (0.27), residues: 389
  sheet:  0.70 (1.06), residues: 22
  loop : -0.42 (0.47), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 266 
 HIS   0.003   0.001   HIS C 280 
 PHE   0.020   0.001   PHE E 115 
 TYR   0.015   0.001   TYR E 101 
 ARG   0.005   0.000   ARG C 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03525 (  288)
  hydrogen bonds       : angle       4.10921 (  819)
  covalent geometry    : bond        0.00290 ( 5077)
  covalent geometry    : angle       0.51382 ( 6843)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 123
  time to evaluate  : 0.878 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  282 HIS cc_start: 0.8841 (m-70) cc_final: 0.8262 (m-70)
REVERT: C  295 ARG cc_start: 0.9109 (ttt180) cc_final: 0.8852 (mtp180)
REVERT: I   14 ASN cc_start: 0.9000 (m-40) cc_final: 0.8456 (m110)
REVERT: I   15 ASP cc_start: 0.8468 (t70) cc_final: 0.8258 (t0)
REVERT: I   24 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8463 (tm-30)
REVERT: I   25 ARG cc_start: 0.9127 (tpp80) cc_final: 0.8920 (tpp80)
REVERT: I   28 ASP cc_start: 0.9260 (m-30) cc_final: 0.8846 (m-30)
REVERT: J   19 TYR cc_start: 0.8368 (t80) cc_final: 0.7928 (t80)
REVERT: J   23 LEU cc_start: 0.9164 (mp) cc_final: 0.8893 (mp)
  outliers start: 12
  outliers final: 11
  residues processed: 127
  average time/residue: 0.4742
  time to fit residues: 72.6690
Evaluate side-chains
  129 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  283 LYS
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain E residue   32 SER
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  181 THR
Chi-restraints excluded: chain I residue    7 THR
Chi-restraints excluded: chain I residue   27 ASN
Chi-restraints excluded: chain I residue   41 VAL
Chi-restraints excluded: chain J residue   31 LYS
Chi-restraints excluded: chain J residue   39 GLU
Chi-restraints excluded: chain J residue   45 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 55 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 303 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.086373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.062750 restraints weight = 43062.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.066201 restraints weight = 19137.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.068365 restraints weight = 11697.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.3540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   5077  Z= 0.187
  Angle     :  0.551   7.170   6843  Z= 0.296
  Chirality :  0.034   0.139    744
  Planarity :  0.004   0.049    901
  Dihedral  :  3.755  15.450    681
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 23.98 %
    Favored  : 73.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.96 (0.35), residues: 593
  helix:  2.20 (0.27), residues: 390
  sheet:  0.52 (1.05), residues: 22
  loop : -0.61 (0.47), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C 266 
 HIS   0.004   0.001   HIS C 280 
 PHE   0.009   0.001   PHE F  57 
 TYR   0.011   0.001   TYR C 277 
 ARG   0.004   0.000   ARG E 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03684 (  288)
  hydrogen bonds       : angle       4.32271 (  819)
  covalent geometry    : bond        0.00391 ( 5077)
  covalent geometry    : angle       0.55080 ( 6843)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 0.874 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  282 HIS cc_start: 0.8872 (m-70) cc_final: 0.8326 (m-70)
REVERT: C  295 ARG cc_start: 0.9140 (ttt180) cc_final: 0.8806 (mtp180)
REVERT: F  154 LYS cc_start: 0.9245 (mtpt) cc_final: 0.9030 (mtmt)
REVERT: F  177 LYS cc_start: 0.8659 (mmtt) cc_final: 0.8434 (mmmt)
REVERT: I   24 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8422 (tm-30)
REVERT: I   28 ASP cc_start: 0.9273 (m-30) cc_final: 0.8860 (m-30)
REVERT: J   19 TYR cc_start: 0.8249 (t80) cc_final: 0.7975 (t80)
  outliers start: 14
  outliers final: 13
  residues processed: 128
  average time/residue: 0.4885
  time to fit residues: 76.1546
Evaluate side-chains
  130 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain E residue   32 SER
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  181 THR
Chi-restraints excluded: chain F residue   44 HIS
Chi-restraints excluded: chain F residue  100 CYS
Chi-restraints excluded: chain I residue    7 THR
Chi-restraints excluded: chain I residue   27 ASN
Chi-restraints excluded: chain I residue   41 VAL
Chi-restraints excluded: chain J residue   31 LYS
Chi-restraints excluded: chain J residue   39 GLU
Chi-restraints excluded: chain J residue   44 LEU
Chi-restraints excluded: chain J residue   45 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.086895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.063009 restraints weight = 43335.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.066512 restraints weight = 19299.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.068704 restraints weight = 11835.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.3677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5077  Z= 0.149
  Angle     :  0.535   7.603   6843  Z= 0.283
  Chirality :  0.034   0.141    744
  Planarity :  0.004   0.049    901
  Dihedral  :  3.705  15.288    681
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 23.98 %
    Favored  : 73.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.36), residues: 593
  helix:  2.27 (0.27), residues: 390
  sheet:  0.46 (1.06), residues: 22
  loop : -0.63 (0.47), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C 266 
 HIS   0.004   0.001   HIS C 280 
 PHE   0.011   0.001   PHE E 115 
 TYR   0.011   0.001   TYR E 101 
 ARG   0.007   0.000   ARG I  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03498 (  288)
  hydrogen bonds       : angle       4.19491 (  819)
  covalent geometry    : bond        0.00321 ( 5077)
  covalent geometry    : angle       0.53522 ( 6843)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  282 HIS cc_start: 0.8858 (m-70) cc_final: 0.8306 (m-70)
REVERT: C  295 ARG cc_start: 0.9124 (ttt180) cc_final: 0.8797 (mtp180)
REVERT: E   39 ASP cc_start: 0.8032 (t0) cc_final: 0.7623 (t0)
REVERT: I   14 ASN cc_start: 0.9057 (m-40) cc_final: 0.8579 (m110)
REVERT: I   24 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8461 (tm-30)
REVERT: I   28 ASP cc_start: 0.9272 (m-30) cc_final: 0.8857 (m-30)
REVERT: I   30 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9016 (tt)
REVERT: J   19 TYR cc_start: 0.8264 (t80) cc_final: 0.8013 (t80)
  outliers start: 14
  outliers final: 13
  residues processed: 129
  average time/residue: 0.4753
  time to fit residues: 74.4212
Evaluate side-chains
  136 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain E residue   32 SER
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  181 THR
Chi-restraints excluded: chain F residue   44 HIS
Chi-restraints excluded: chain F residue  100 CYS
Chi-restraints excluded: chain I residue    7 THR
Chi-restraints excluded: chain I residue   27 ASN
Chi-restraints excluded: chain I residue   30 LEU
Chi-restraints excluded: chain I residue   41 VAL
Chi-restraints excluded: chain J residue   31 LYS
Chi-restraints excluded: chain J residue   39 GLU
Chi-restraints excluded: chain J residue   44 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.085700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.062256 restraints weight = 43552.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.065663 restraints weight = 19293.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.067781 restraints weight = 11839.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.3805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   5077  Z= 0.190
  Angle     :  0.553   7.692   6843  Z= 0.297
  Chirality :  0.035   0.136    744
  Planarity :  0.004   0.047    901
  Dihedral  :  3.783  15.566    681
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 23.79 %
    Favored  : 73.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.36), residues: 593
  helix:  2.13 (0.27), residues: 390
  sheet:  0.26 (1.06), residues: 22
  loop : -0.70 (0.48), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP C 266 
 HIS   0.004   0.001   HIS C 280 
 PHE   0.010   0.001   PHE E 115 
 TYR   0.011   0.001   TYR C 277 
 ARG   0.007   0.000   ARG I  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03638 (  288)
  hydrogen bonds       : angle       4.37278 (  819)
  covalent geometry    : bond        0.00399 ( 5077)
  covalent geometry    : angle       0.55332 ( 6843)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 0.759 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  282 HIS cc_start: 0.8859 (m-70) cc_final: 0.8303 (m-70)
REVERT: C  295 ARG cc_start: 0.9163 (ttt180) cc_final: 0.8815 (mtp180)
REVERT: E   39 ASP cc_start: 0.8128 (t0) cc_final: 0.7675 (t0)
REVERT: I   24 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8620 (tm-30)
REVERT: I   28 ASP cc_start: 0.9303 (m-30) cc_final: 0.9010 (m-30)
REVERT: I   30 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9047 (tt)
REVERT: J   19 TYR cc_start: 0.8279 (t80) cc_final: 0.8036 (t80)
  outliers start: 15
  outliers final: 14
  residues processed: 129
  average time/residue: 0.4534
  time to fit residues: 71.1094
Evaluate side-chains
  133 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain E residue   32 SER
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain E residue  181 THR
Chi-restraints excluded: chain F residue   44 HIS
Chi-restraints excluded: chain F residue  100 CYS
Chi-restraints excluded: chain I residue    7 THR
Chi-restraints excluded: chain I residue   27 ASN
Chi-restraints excluded: chain I residue   30 LEU
Chi-restraints excluded: chain I residue   41 VAL
Chi-restraints excluded: chain J residue   31 LYS
Chi-restraints excluded: chain J residue   39 GLU
Chi-restraints excluded: chain J residue   44 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 9 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   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 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.088002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.064507 restraints weight = 43693.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.068039 restraints weight = 19965.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.070226 restraints weight = 12420.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.3890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5077  Z= 0.145
  Angle     :  0.549   7.858   6843  Z= 0.290
  Chirality :  0.034   0.140    744
  Planarity :  0.004   0.050    901
  Dihedral  :  3.726  15.145    681
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 24.54 %
    Favored  : 72.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.05 (0.36), residues: 593
  helix:  2.29 (0.27), residues: 390
  sheet:  0.25 (1.06), residues: 22
  loop : -0.61 (0.49), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP C 266 
 HIS   0.004   0.001   HIS C 280 
 PHE   0.010   0.001   PHE E 115 
 TYR   0.016   0.001   TYR E 101 
 ARG   0.007   0.000   ARG I  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03447 (  288)
  hydrogen bonds       : angle       4.22198 (  819)
  covalent geometry    : bond        0.00316 ( 5077)
  covalent geometry    : angle       0.54949 ( 6843)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 125
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  282 HIS cc_start: 0.8735 (m-70) cc_final: 0.8183 (m-70)
REVERT: C  295 ARG cc_start: 0.9062 (ttt180) cc_final: 0.8807 (mtp180)
REVERT: E   39 ASP cc_start: 0.7914 (t0) cc_final: 0.7536 (t0)
REVERT: I   14 ASN cc_start: 0.9069 (m-40) cc_final: 0.8599 (m110)
REVERT: I   24 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8421 (tm-30)
REVERT: I   28 ASP cc_start: 0.9228 (m-30) cc_final: 0.8756 (m-30)
REVERT: I   30 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9110 (tt)
  outliers start: 15
  outliers final: 14
  residues processed: 134
  average time/residue: 0.4747
  time to fit residues: 76.8139
Evaluate side-chains
  136 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain E residue   32 SER
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain E residue  181 THR
Chi-restraints excluded: chain F residue   44 HIS
Chi-restraints excluded: chain F residue  100 CYS
Chi-restraints excluded: chain I residue    7 THR
Chi-restraints excluded: chain I residue   27 ASN
Chi-restraints excluded: chain I residue   30 LEU
Chi-restraints excluded: chain I residue   41 VAL
Chi-restraints excluded: chain J residue   31 LYS
Chi-restraints excluded: chain J residue   39 GLU
Chi-restraints excluded: chain J residue   44 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 13 optimal weight:    0.4980
   chunk 22 optimal weight:    1.9990
   chunk 20 optimal weight:    0.4980
   chunk 0 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
C 191 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.088188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.064570 restraints weight = 43508.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.068179 restraints weight = 19410.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.070351 restraints weight = 11878.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.4075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5077  Z= 0.123
  Angle     :  0.553   8.088   6843  Z= 0.287
  Chirality :  0.034   0.141    744
  Planarity :  0.004   0.050    901
  Dihedral  :  3.657  14.735    681
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 24.91 %
    Favored  : 72.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.19 (0.36), residues: 593
  helix:  2.43 (0.27), residues: 390
  sheet:  0.23 (1.06), residues: 22
  loop : -0.61 (0.49), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP C 266 
 HIS   0.003   0.001   HIS C 280 
 PHE   0.009   0.001   PHE E 115 
 TYR   0.013   0.001   TYR E 101 
 ARG   0.007   0.000   ARG I  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03273 (  288)
  hydrogen bonds       : angle       4.06720 (  819)
  covalent geometry    : bond        0.00277 ( 5077)
  covalent geometry    : angle       0.55336 ( 6843)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  282 HIS cc_start: 0.8785 (m-70) cc_final: 0.8228 (m-70)
REVERT: C  295 ARG cc_start: 0.9104 (ttt180) cc_final: 0.8793 (mtp180)
REVERT: E   39 ASP cc_start: 0.7949 (t0) cc_final: 0.7561 (t0)
REVERT: E   94 MET cc_start: 0.9162 (mtp) cc_final: 0.8891 (mtt)
REVERT: I   14 ASN cc_start: 0.9007 (m-40) cc_final: 0.8537 (m110)
REVERT: I   24 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8429 (tm-30)
REVERT: I   28 ASP cc_start: 0.9260 (m-30) cc_final: 0.8784 (m-30)
REVERT: I   30 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9083 (tt)
  outliers start: 15
  outliers final: 13
  residues processed: 130
  average time/residue: 0.4823
  time to fit residues: 75.5242
Evaluate side-chains
  135 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain E residue   32 SER
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain E residue  181 THR
Chi-restraints excluded: chain F residue   44 HIS
Chi-restraints excluded: chain F residue  100 CYS
Chi-restraints excluded: chain I residue    7 THR
Chi-restraints excluded: chain I residue   27 ASN
Chi-restraints excluded: chain I residue   30 LEU
Chi-restraints excluded: chain I residue   41 VAL
Chi-restraints excluded: chain J residue   31 LYS
Chi-restraints excluded: chain J residue   39 GLU
Chi-restraints excluded: chain J residue   44 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 44 optimal weight:    0.4980
   chunk 34 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
C 191 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.088156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.064520 restraints weight = 43748.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.068150 restraints weight = 19565.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.070387 restraints weight = 11987.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.4105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5077  Z= 0.129
  Angle     :  0.547   8.061   6843  Z= 0.285
  Chirality :  0.034   0.139    744
  Planarity :  0.004   0.049    901
  Dihedral  :  3.631  14.618    681
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 24.91 %
    Favored  : 72.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.33 (0.36), residues: 593
  helix:  2.58 (0.27), residues: 384
  sheet:  0.24 (1.05), residues: 22
  loop : -0.54 (0.48), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP C 266 
 HIS   0.004   0.001   HIS C 280 
 PHE   0.009   0.001   PHE E 115 
 TYR   0.014   0.001   TYR E 101 
 ARG   0.006   0.000   ARG I  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03206 (  288)
  hydrogen bonds       : angle       4.04022 (  819)
  covalent geometry    : bond        0.00290 ( 5077)
  covalent geometry    : angle       0.54696 ( 6843)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3687.80 seconds
wall clock time: 64 minutes 3.74 seconds (3843.74 seconds total)