Starting phenix.real_space_refine
on Wed Apr 30 20:20:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gmd_51448/04_2025/9gmd_51448.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gmd_51448/04_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_51448/04_2025/9gmd_51448.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gmd_51448/04_2025/9gmd_51448.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gmd_51448/04_2025/9gmd_51448.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gmd_51448/04_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-5669/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: 5.54, per 1000 atoms: 0.56
  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: 3.05
  Conformation dependent library (CDL) restraints added in 751.9 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: 1.35
  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: 4.39

  Time building geometry restraints manager: 3.81 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:             0.530
  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:             0.180
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     28.240
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.050
  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:             0.010
  Load rotamer database and sin/cos tables:3.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.360
-------------------------------------------------------------------------------
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  : 0.721 
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: 0.5432
  time to fit residues: 97.7518
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  : 0.860 
-------------------------------------------------------------------------------
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 = 40)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.064728 restraints weight = 42950.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.068364 restraints weight = 19235.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.070630 restraints weight = 11732.896|
|-----------------------------------------------------------------------------|
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  : 0.837 
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: 0.8875 (mtp180)
REVERT: C  311 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8402 (tm-30)
REVERT: E   93 MET cc_start: 0.9049 (mmm) cc_final: 0.8829 (mmm)
REVERT: F   10 MET cc_start: 0.8173 (ppp) cc_final: 0.7924 (ppp)
REVERT: I   14 ASN cc_start: 0.9032 (m-40) cc_final: 0.8640 (m110)
REVERT: I   24 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8396 (tm-30)
REVERT: I   28 ASP cc_start: 0.9046 (m-30) cc_final: 0.8786 (m-30)
REVERT: J   19 TYR cc_start: 0.8383 (t80) cc_final: 0.8037 (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: 0.4654
  time to fit residues: 76.4689
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  : 0.870 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0170
   chunk 33 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.6018

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.089117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.064760 restraints weight = 43115.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.068429 restraints weight = 19296.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.070724 restraints weight = 11803.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.2742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   5077  Z= 0.122
  Angle     :  0.523   5.774   6843  Z= 0.278
  Chirality :  0.034   0.155    744
  Planarity :  0.004   0.051    901
  Dihedral  :  3.693  16.194    681
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 21.75 %
    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:  2.02 (0.36), residues: 593
  helix:  2.15 (0.27), residues: 389
  sheet:  0.99 (1.07), residues: 22
  loop : -0.39 (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   0.013   0.001   TYR E 101 
 ARG   0.004   0.000   ARG C 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04019 (  288)
  hydrogen bonds       : angle       4.29433 (  819)
  covalent geometry    : bond        0.00263 ( 5077)
  covalent geometry    : angle       0.52305 ( 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
  141 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 0.760 
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  268 GLN cc_start: 0.8978 (mp10) cc_final: 0.8766 (mp10)
REVERT: C  282 HIS cc_start: 0.8796 (m-70) cc_final: 0.8157 (m-70)
REVERT: C  295 ARG cc_start: 0.9126 (ttt180) cc_final: 0.8857 (mtp180)
REVERT: C  311 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8334 (tm-30)
REVERT: I   14 ASN cc_start: 0.9038 (m-40) cc_final: 0.8632 (m110)
REVERT: I   24 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8520 (tm-30)
REVERT: I   28 ASP cc_start: 0.9200 (m-30) cc_final: 0.8852 (m-30)
REVERT: J   19 TYR cc_start: 0.8376 (t80) cc_final: 0.7891 (t80)
REVERT: J   23 LEU cc_start: 0.9114 (mp) cc_final: 0.8819 (mp)
  outliers start: 10
  outliers final: 7
  residues processed: 136
  average time/residue: 0.5008
  time to fit residues: 81.8578
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  : 0.756 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 5 optimal weight:    0.2980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.3451 r_free = 0.3451 target = 0.087255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.063413 restraints weight = 42599.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.066915 restraints weight = 19050.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.069112 restraints weight = 11635.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.3030

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= 0.155
  Angle     :  0.524   6.167   6843  Z= 0.280
  Chirality :  0.034   0.136    744
  Planarity :  0.004   0.049    901
  Dihedral  :  3.791  16.253    681
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 22.49 %
    Favored  : 75.09 %
  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:  2.14 (0.27), residues: 390
  sheet:  0.74 (1.05), residues: 22
  loop : -0.50 (0.48), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 266 
 HIS   0.003   0.001   HIS E  44 
 PHE   0.018   0.001   PHE E 115 
 TYR   0.012   0.002   TYR C 277 
 ARG   0.003   0.000   ARG C 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03790 (  288)
  hydrogen bonds       : angle       4.31497 (  819)
  covalent geometry    : bond        0.00327 ( 5077)
  covalent geometry    : angle       0.52436 ( 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
  136 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.832 
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  268 GLN cc_start: 0.8970 (mp10) cc_final: 0.8743 (mp10)
REVERT: C  282 HIS cc_start: 0.8787 (m-70) cc_final: 0.8150 (m-70)
REVERT: C  295 ARG cc_start: 0.9132 (ttt180) cc_final: 0.8869 (mtp180)
REVERT: C  311 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8254 (tm-30)
REVERT: E  182 GLU cc_start: 0.8885 (pm20) cc_final: 0.8666 (pm20)
REVERT: I   14 ASN cc_start: 0.9061 (m-40) cc_final: 0.8636 (m110)
REVERT: I   24 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8513 (tm-30)
REVERT: I   28 ASP cc_start: 0.9273 (m-30) cc_final: 0.8875 (m-30)
REVERT: I   30 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9139 (tt)
REVERT: J   19 TYR cc_start: 0.8395 (t80) cc_final: 0.8076 (t80)
  outliers start: 13
  outliers final: 10
  residues processed: 130
  average time/residue: 0.4711
  time to fit residues: 74.6176
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  : 1.136 
-------------------------------------------------------------------------------
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   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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3447 r_free = 0.3447 target = 0.086907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.063167 restraints weight = 42529.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.066658 restraints weight = 18989.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.068861 restraints weight = 11585.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.3284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5077  Z= 0.160
  Angle     :  0.530   6.740   6843  Z= 0.282
  Chirality :  0.034   0.151    744
  Planarity :  0.004   0.049    901
  Dihedral  :  3.734  15.709    681
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 23.42 %
    Favored  : 74.16 %
  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:  1.95 (0.35), residues: 593
  helix:  2.17 (0.27), residues: 389
  sheet:  0.62 (1.05), residues: 22
  loop : -0.56 (0.47), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 266 
 HIS   0.004   0.001   HIS E  44 
 PHE   0.009   0.001   PHE E 115 
 TYR   0.011   0.001   TYR C 277 
 ARG   0.003   0.000   ARG E 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03663 (  288)
  hydrogen bonds       : angle       4.27487 (  819)
  covalent geometry    : bond        0.00337 ( 5077)
  covalent geometry    : angle       0.52965 ( 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
  132 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 119
  time to evaluate  : 1.080 
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  268 GLN cc_start: 0.8984 (mp10) cc_final: 0.8726 (mp10)
REVERT: C  282 HIS cc_start: 0.8844 (m-70) cc_final: 0.8271 (m-70)
REVERT: C  295 ARG cc_start: 0.9134 (ttt180) cc_final: 0.8867 (mtp180)
REVERT: I   14 ASN cc_start: 0.9072 (m-40) cc_final: 0.8627 (m110)
REVERT: I   24 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8497 (tm-30)
REVERT: I   25 ARG cc_start: 0.9125 (tpp80) cc_final: 0.8923 (tpp80)
REVERT: I   28 ASP cc_start: 0.9302 (m-30) cc_final: 0.8885 (m-30)
REVERT: J   19 TYR cc_start: 0.8391 (t80) cc_final: 0.8118 (t80)
  outliers start: 13
  outliers final: 13
  residues processed: 126
  average time/residue: 0.4853
  time to fit residues: 74.0372
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  : 0.756 
-------------------------------------------------------------------------------
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 303 GLN
** F   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.087077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.063188 restraints weight = 42968.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.066688 restraints weight = 19105.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.068806 restraints weight = 11690.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.3543

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     :  0.515   7.165   6843  Z= 0.270
  Chirality :  0.034   0.143    744
  Planarity :  0.004   0.049    901
  Dihedral  :  3.662  15.378    681
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 23.23 %
    Favored  : 73.98 %
  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:  2.07 (0.36), residues: 593
  helix:  2.26 (0.27), residues: 390
  sheet:  0.46 (1.05), residues: 22
  loop : -0.51 (0.48), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 266 
 HIS   0.003   0.001   HIS C 280 
 PHE   0.009   0.001   PHE E 115 
 TYR   0.014   0.001   TYR E 101 
 ARG   0.002   0.000   ARG E 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03478 (  288)
  hydrogen bonds       : angle       4.17019 (  819)
  covalent geometry    : bond        0.00296 ( 5077)
  covalent geometry    : angle       0.51495 ( 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
  136 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 0.881 
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  268 GLN cc_start: 0.8953 (mp10) cc_final: 0.8676 (mp10)
REVERT: C  282 HIS cc_start: 0.8831 (m-70) cc_final: 0.8259 (m-70)
REVERT: C  295 ARG cc_start: 0.9107 (ttt180) cc_final: 0.8791 (mtp180)
REVERT: E   39 ASP cc_start: 0.8048 (t0) cc_final: 0.7648 (t0)
REVERT: F  150 LYS cc_start: 0.9534 (mttt) cc_final: 0.9309 (ptpp)
REVERT: I   14 ASN cc_start: 0.9044 (m-40) cc_final: 0.8574 (m110)
REVERT: I   24 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8455 (tm-30)
REVERT: I   28 ASP cc_start: 0.9310 (m-30) cc_final: 0.8882 (m-30)
REVERT: I   30 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9017 (tt)
REVERT: J   19 TYR cc_start: 0.8387 (t80) cc_final: 0.8132 (t80)
  outliers start: 15
  outliers final: 12
  residues processed: 130
  average time/residue: 0.5067
  time to fit residues: 81.4929
Evaluate side-chains
  129 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
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   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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 27 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.3426 r_free = 0.3426 target = 0.085715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.062204 restraints weight = 43507.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.065639 restraints weight = 19222.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.067773 restraints weight = 11737.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.3690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5077  Z= 0.194
  Angle     :  0.547   7.414   6843  Z= 0.293
  Chirality :  0.034   0.138    744
  Planarity :  0.004   0.054    901
  Dihedral  :  3.757  15.396    681
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 23.42 %
    Favored  : 73.79 %
  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:  1.82 (0.36), residues: 593
  helix:  2.11 (0.27), residues: 390
  sheet:  0.27 (1.04), residues: 22
  loop : -0.68 (0.48), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C 266 
 HIS   0.005   0.001   HIS C 280 
 PHE   0.009   0.001   PHE F  57 
 TYR   0.019   0.002   TYR E 101 
 ARG   0.006   0.000   ARG I  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03665 (  288)
  hydrogen bonds       : angle       4.40528 (  819)
  covalent geometry    : bond        0.00403 ( 5077)
  covalent geometry    : angle       0.54710 ( 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
  131 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.761 
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: 0.8849 (m-70) cc_final: 0.8305 (m-70)
REVERT: C  295 ARG cc_start: 0.9139 (ttt180) cc_final: 0.8823 (mtp180)
REVERT: F  150 LYS cc_start: 0.9559 (mttt) cc_final: 0.9239 (ptpp)
REVERT: I   15 ASP cc_start: 0.8577 (t70) cc_final: 0.8371 (t0)
REVERT: I   24 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8621 (tm-30)
REVERT: I   28 ASP cc_start: 0.9339 (m-30) cc_final: 0.9038 (m-30)
REVERT: J   19 TYR cc_start: 0.8292 (t80) cc_final: 0.8049 (t80)
  outliers start: 15
  outliers final: 15
  residues processed: 125
  average time/residue: 0.4431
  time to fit residues: 67.6230
Evaluate side-chains
  130 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
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   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 F residue  151 LEU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 41 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   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:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 = 0.3442 r_free = 0.3442 target = 0.086455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.063116 restraints weight = 43194.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.066496 restraints weight = 19623.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.068619 restraints weight = 12181.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.3824

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= 0.153
  Angle     :  0.536   7.799   6843  Z= 0.283
  Chirality :  0.034   0.140    744
  Planarity :  0.004   0.048    901
  Dihedral  :  3.716  15.203    681
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 23.42 %
    Favored  : 73.61 %
  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:  1.98 (0.36), residues: 593
  helix:  2.23 (0.27), residues: 390
  sheet:  0.19 (1.04), residues: 22
  loop : -0.62 (0.48), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C 266 
 HIS   0.004   0.001   HIS C 280 
 PHE   0.008   0.001   PHE E 115 
 TYR   0.017   0.001   TYR E 101 
 ARG   0.007   0.000   ARG I  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03469 (  288)
  hydrogen bonds       : angle       4.28445 (  819)
  covalent geometry    : bond        0.00327 ( 5077)
  covalent geometry    : angle       0.53566 ( 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
  136 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.868 
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: 0.8709 (m-70) cc_final: 0.8162 (m-70)
REVERT: C  295 ARG cc_start: 0.9017 (ttt180) cc_final: 0.8812 (mtp180)
REVERT: E   39 ASP cc_start: 0.7956 (t0) cc_final: 0.7576 (t0)
REVERT: I   14 ASN cc_start: 0.9127 (m-40) cc_final: 0.8659 (m110)
REVERT: I   24 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8581 (tm-30)
REVERT: I   28 ASP cc_start: 0.9239 (m-30) cc_final: 0.8936 (m-30)
REVERT: I   30 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9126 (tt)
REVERT: J   19 TYR cc_start: 0.8202 (t80) cc_final: 0.8000 (t80)
  outliers start: 16
  outliers final: 15
  residues processed: 130
  average time/residue: 0.4691
  time to fit residues: 74.3505
Evaluate side-chains
  134 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
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 F residue  151 LEU
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:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0970
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** C 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 = 0.3481 r_free = 0.3481 target = 0.087702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.064240 restraints weight = 43537.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.067760 restraints weight = 19782.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.069943 restraints weight = 12288.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.3952

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= 0.139
  Angle     :  0.538   8.020   6843  Z= 0.282
  Chirality :  0.034   0.140    744
  Planarity :  0.004   0.050    901
  Dihedral  :  3.662  14.712    681
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 23.61 %
    Favored  : 73.61 %
  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:  2.09 (0.36), residues: 593
  helix:  2.35 (0.27), residues: 390
  sheet:  0.18 (1.05), residues: 22
  loop : -0.62 (0.48), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP C 266 
 HIS   0.004   0.001   HIS C 280 
 PHE   0.007   0.001   PHE F 170 
 TYR   0.014   0.001   TYR E 101 
 ARG   0.007   0.000   ARG I  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03343 (  288)
  hydrogen bonds       : angle       4.18656 (  819)
  covalent geometry    : bond        0.00304 ( 5077)
  covalent geometry    : angle       0.53846 ( 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
  138 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.775 
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: 0.8714 (m-70) cc_final: 0.8165 (m-70)
REVERT: C  295 ARG cc_start: 0.9066 (ttt180) cc_final: 0.8810 (mtp180)
REVERT: E   39 ASP cc_start: 0.7945 (t0) cc_final: 0.7564 (t0)
REVERT: I   14 ASN cc_start: 0.9082 (m-40) cc_final: 0.8633 (m110)
REVERT: I   24 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8570 (tm-30)
REVERT: I   28 ASP cc_start: 0.9236 (m-30) cc_final: 0.8930 (m-30)
REVERT: I   30 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9113 (tt)
  outliers start: 15
  outliers final: 14
  residues processed: 133
  average time/residue: 0.4512
  time to fit residues: 73.4717
Evaluate side-chains
  134 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
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   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 F residue  151 LEU
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:    0.9980
   chunk 22 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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 = 0.3479 r_free = 0.3479 target = 0.087576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.064143 restraints weight = 43745.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.067683 restraints weight = 19806.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.069877 restraints weight = 12252.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.4031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5077  Z= 0.143
  Angle     :  0.545   8.174   6843  Z= 0.285
  Chirality :  0.034   0.139    744
  Planarity :  0.004   0.049    901
  Dihedral  :  3.665  14.584    681
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 6.66
  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:  2.17 (0.36), residues: 593
  helix:  2.45 (0.27), residues: 384
  sheet:  0.08 (1.03), residues: 22
  loop : -0.56 (0.47), residues: 187

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   0.007   0.001   PHE E 115 
 TYR   0.014   0.001   TYR E 101 
 ARG   0.007   0.000   ARG I  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03308 (  288)
  hydrogen bonds       : angle       4.18294 (  819)
  covalent geometry    : bond        0.00311 ( 5077)
  covalent geometry    : angle       0.54478 ( 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
  132 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.832 
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: 0.8710 (m-70) cc_final: 0.8163 (m-70)
REVERT: C  295 ARG cc_start: 0.9064 (ttt180) cc_final: 0.8807 (mtp180)
REVERT: E   39 ASP cc_start: 0.7947 (t0) cc_final: 0.7565 (t0)
REVERT: F  177 LYS cc_start: 0.8722 (mmtt) cc_final: 0.8391 (mmmt)
REVERT: I   14 ASN cc_start: 0.9083 (m-40) cc_final: 0.8643 (m110)
REVERT: I   24 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8571 (tm-30)
REVERT: I   28 ASP cc_start: 0.9233 (m-30) cc_final: 0.8927 (m-30)
REVERT: I   30 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9121 (tt)
  outliers start: 14
  outliers final: 13
  residues processed: 128
  average time/residue: 0.4698
  time to fit residues: 74.3622
Evaluate side-chains
  131 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
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   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 F residue  151 LEU
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 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:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0030
   chunk 15 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 52 optimal weight:    0.0670
   overall best weight:    0.5728

-------------------------------------------------------------------------------
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 = 0.3485 r_free = 0.3485 target = 0.087937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.064511 restraints weight = 43745.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.068105 restraints weight = 19457.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.070345 restraints weight = 11879.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.4098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5077  Z= 0.118
  Angle     :  0.540   8.118   6843  Z= 0.279
  Chirality :  0.034   0.141    744
  Planarity :  0.004   0.050    901
  Dihedral  :  3.582  14.491    681
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 24.72 %
    Favored  : 72.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.39 (0.36), residues: 593
  helix:  2.63 (0.27), residues: 384
  sheet:  0.06 (1.01), residues: 22
  loop : -0.49 (0.47), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP C 266 
 HIS   0.003   0.001   HIS C 280 
 PHE   0.007   0.001   PHE E 115 
 TYR   0.013   0.001   TYR E 101 
 ARG   0.006   0.000   ARG I  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03133 (  288)
  hydrogen bonds       : angle       4.02202 (  819)
  covalent geometry    : bond        0.00270 ( 5077)
  covalent geometry    : angle       0.53963 ( 6843)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3975.52 seconds
wall clock time: 69 minutes 28.74 seconds (4168.74 seconds total)