Starting phenix.real_space_refine
on Wed Mar  5 19:04:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8a00_15043/03_2025/8a00_15043.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8a00_15043/03_2025/8a00_15043.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8a00_15043/03_2025/8a00_15043.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8a00_15043/03_2025/8a00_15043.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8a00_15043/03_2025/8a00_15043.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8a00_15043/03_2025/8a00_15043.cif"
  }
  resolution = 2.6
  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: 4
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    2061      2.51       5
     N     600      2.21       5
     O     627      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 3315
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 136, 1105
          Classifications: {'peptide': 136}
          Link IDs: {'PTRANS': 5, 'TRANS': 130}
    Chain: "C"
      Number of atoms: 1105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 136, 1105
          Classifications: {'peptide': 136}
          Link IDs: {'PTRANS': 5, 'TRANS': 130}
    Chain: "B"
      Number of atoms: 1105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 136, 1105
          Classifications: {'peptide': 136}
          Link IDs: {'PTRANS': 5, 'TRANS': 130}
  Time building chain proxies: 4.65, per 1000 atoms: 1.40
  Number of scatterers: 3315
  At special positions: 0
  Unit cell: (108.468, 113.436, 35.604, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      27     16.00
     O     627      8.00
     N     600      7.00
     C    2061      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 178 " - pdb=" SG  CYS A 213 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 178 " - pdb=" SG  CYS C 213 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 178 " - pdb=" SG  CYS B 213 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 362.8 milliseconds
  

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  756

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 13 sheets defined
      0.0% alpha, 64.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 95 through 99
      removed outlier: 6.403A  pdb=" N   HIS A  95 " --> pdb=" O   ASN B  96 " (cutoff:3.500A)
      removed outlier: 8.057A  pdb=" N   TRP B  98 " --> pdb=" O   HIS A  95 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   GLN A  97 " --> pdb=" O   TRP B  98 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 106 through 111
      removed outlier: 6.745A  pdb=" N   VAL A 111 " --> pdb=" O   HIS C 110 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   THR A 106 " --> pdb=" O   ASN B 107 " (cutoff:3.500A)
      removed outlier: 8.062A  pdb=" N   LYS B 109 " --> pdb=" O   THR A 106 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   LEU A 108 " --> pdb=" O   LYS B 109 " (cutoff:3.500A)
      removed outlier: 5.799A  pdb=" N   VAL B 111 " --> pdb=" O   LEU A 108 " (cutoff:3.500A)
      removed outlier: 7.625A  pdb=" N   HIS A 110 " --> pdb=" O   VAL B 111 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 114 through 116
      removed outlier: 6.557A  pdb=" N   ALA A 115 " --> pdb=" O   ALA C 116 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 119 through 121
      removed outlier: 6.369A  pdb=" N   VAL A 120 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 132 through 134
      removed outlier: 6.413A  pdb=" N   ALA A 132 " --> pdb=" O   MET B 133 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 137 through 144
    Processing sheet with id=AA7, first strand: chain 'C' and resid 149 through 150
      removed outlier: 6.332A  pdb=" N   TYR A 149 " --> pdb=" O   ARG B 150 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 154 through 155
      removed outlier: 6.717A  pdb=" N   TYR A 154 " --> pdb=" O   ARG C 155 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 158 through 162
      removed outlier: 6.364A  pdb=" N   ASN A 158 " --> pdb=" O   GLN C 159 " (cutoff:3.500A)
      removed outlier: 7.691A  pdb=" N   TYR C 161 " --> pdb=" O   ASN A 158 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   VAL A 160 " --> pdb=" O   TYR C 161 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 166 through 179
      removed outlier: 6.058A  pdb=" N   GLN A 167 " --> pdb=" O   TYR C 168 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   ASN C 170 " --> pdb=" O   GLN A 167 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   SER A 169 " --> pdb=" O   ASN C 170 " (cutoff:3.500A)
      removed outlier: 8.438A  pdb=" N   ASN C 172 " --> pdb=" O   SER A 169 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   GLN A 171 " --> pdb=" O   ASN C 172 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   PHE C 174 " --> pdb=" O   GLN A 171 " (cutoff:3.500A)
      removed outlier: 7.896A  pdb=" N   ASN A 173 " --> pdb=" O   PHE C 174 " (cutoff:3.500A)
      removed outlier: 9.936A  pdb=" N   HIS C 176 " --> pdb=" O   ASN A 173 " (cutoff:3.500A)
      removed outlier: 5.706A  pdb=" N   VAL A 175 " --> pdb=" O   HIS C 176 " (cutoff:3.500A)
      removed outlier: 8.651A  pdb=" N   CYS C 178 " --> pdb=" O   VAL A 175 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   ASP A 177 " --> pdb=" O   CYS C 178 " (cutoff:3.500A)
      removed outlier: 7.709A  pdb=" N   GLY C 194 " --> pdb=" O   THR A 191 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   LYS A 193 " --> pdb=" O   GLY C 194 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'C' and resid 182 through 191
      removed outlier: 7.622A  pdb=" N   ILE C 183 " --> pdb=" O   ASN A 180 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   THR A 182 " --> pdb=" O   ILE C 183 " (cutoff:3.500A)
      removed outlier: 8.360A  pdb=" N   GLN C 185 " --> pdb=" O   THR A 182 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   LYS A 184 " --> pdb=" O   GLN C 185 " (cutoff:3.500A)
      removed outlier: 8.097A  pdb=" N   THR C 187 " --> pdb=" O   LYS A 184 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   HIS A 186 " --> pdb=" O   THR C 187 " (cutoff:3.500A)
      removed outlier: 8.040A  pdb=" N   THR C 189 " --> pdb=" O   HIS A 186 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   VAL A 188 " --> pdb=" O   THR C 189 " (cutoff:3.500A)
      removed outlier: 7.945A  pdb=" N   THR C 191 " --> pdb=" O   VAL A 188 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   THR A 190 " --> pdb=" O   THR C 191 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   PHE A 174 " --> pdb=" O   ASN B 173 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   VAL B 175 " --> pdb=" O   PHE A 174 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   HIS A 176 " --> pdb=" O   VAL B 175 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   ILE B 181 " --> pdb=" O   ASN A 180 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   THR A 182 " --> pdb=" O   ILE B 181 " (cutoff:3.500A)
      removed outlier: 6.982A  pdb=" N   ILE B 183 " --> pdb=" O   THR A 182 " (cutoff:3.500A)
      removed outlier: 6.982A  pdb=" N   LYS A 184 " --> pdb=" O   ILE B 183 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   GLN B 185 " --> pdb=" O   LYS A 184 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   HIS A 186 " --> pdb=" O   GLN B 185 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   THR B 187 " --> pdb=" O   HIS A 186 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   VAL A 188 " --> pdb=" O   THR B 187 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   THR B 189 " --> pdb=" O   VAL A 188 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   THR A 190 " --> pdb=" O   THR B 189 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   THR B 191 " --> pdb=" O   THR A 190 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   THR A 192 " --> pdb=" O   THR B 191 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 198 through 206
      removed outlier: 6.144A  pdb=" N   THR A 198 " --> pdb=" O   GLU C 199 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   ASP C 201 " --> pdb=" O   THR A 198 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   THR A 200 " --> pdb=" O   ASP C 201 " (cutoff:3.500A)
      removed outlier: 7.937A  pdb=" N   LYS C 203 " --> pdb=" O   THR A 200 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   VAL A 202 " --> pdb=" O   LYS C 203 " (cutoff:3.500A)
      removed outlier: 8.137A  pdb=" N   MET C 205 " --> pdb=" O   VAL A 202 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   MET A 204 " --> pdb=" O   MET C 205 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 211 through 226
      removed outlier: 9.569A  pdb=" N   GLN A 211 " --> pdb=" O   MET C 212 " (cutoff:3.500A)
      removed outlier: 7.712A  pdb=" N   VAL C 214 " --> pdb=" O   GLN A 211 " (cutoff:3.500A)
      removed outlier: 5.847A  pdb=" N   CYS A 213 " --> pdb=" O   VAL C 214 " (cutoff:3.500A)
      removed outlier: 8.766A  pdb=" N   GLN C 216 " --> pdb=" O   CYS A 213 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   THR A 215 " --> pdb=" O   GLN C 216 " (cutoff:3.500A)
      removed outlier: 8.107A  pdb=" N   GLN C 218 " --> pdb=" O   THR A 215 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   TYR A 217 " --> pdb=" O   GLN C 218 " (cutoff:3.500A)
      removed outlier: 8.171A  pdb=" N   GLU C 220 " --> pdb=" O   TYR A 217 " (cutoff:3.500A)
      removed outlier: 8.369A  pdb=" N   LYS A 219 " --> pdb=" O   GLU C 220 " (cutoff:3.500A)
      removed outlier: 10.343A  pdb=" N   GLN C 222 " --> pdb=" O   LYS A 219 " (cutoff:3.500A)
      removed outlier: 9.175A  pdb=" N   SER A 221 " --> pdb=" O   GLN C 222 " (cutoff:3.500A)
      removed outlier: 9.673A  pdb=" N   TYR C 224 " --> pdb=" O   SER A 221 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   ALA A 223 " --> pdb=" O   TYR C 224 " (cutoff:3.500A)
      removed outlier: 8.258A  pdb=" N   ASP C 226 " --> pdb=" O   ALA A 223 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   TYR A 225 " --> pdb=" O   ASP C 226 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   CYS B 213 " --> pdb=" O   MET A 212 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   VAL A 214 " --> pdb=" O   CYS B 213 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   GLU A 220 " --> pdb=" O   LYS B 219 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   SER B 221 " --> pdb=" O   GLU A 220 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   GLN A 222 " --> pdb=" O   SER B 221 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   ALA B 223 " --> pdb=" O   GLN A 222 " (cutoff:3.500A)

    65 hydrogen bonds defined for protein.
    195 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.85

  Time building geometry restraints manager: 0.81 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1113
        1.34 -     1.46: 741
        1.46 -     1.57: 1494
        1.57 -     1.69: 0
        1.69 -     1.80: 48
  Bond restraints: 3396
  Sorted by residual:
  bond pdb=" N   THR B  94 "
       pdb=" CA  THR B  94 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.11e+00
  bond pdb=" N   THR A  94 "
       pdb=" CA  THR A  94 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.09e+00
  bond pdb=" N   THR C  94 "
       pdb=" CA  THR C  94 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.98e+00
  bond pdb=" CA  ASN A 173 "
       pdb=" C   ASN A 173 "
    ideal  model  delta    sigma   weight residual
    1.532  1.523  0.009 9.60e-03 1.09e+04 8.99e-01
  bond pdb=" N   GLU A 210 "
       pdb=" CA  GLU A 210 "
    ideal  model  delta    sigma   weight residual
    1.459  1.469 -0.010 1.28e-02 6.10e+03 6.33e-01
  ... (remaining 3391 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.08: 4292
        1.08 -     2.17: 250
        2.17 -     3.25: 42
        3.25 -     4.34: 8
        4.34 -     5.42: 1
  Bond angle restraints: 4593
  Sorted by residual:
  angle pdb=" CA  ASN A 173 "
        pdb=" C   ASN A 173 "
        pdb=" N   PHE A 174 "
      ideal   model   delta    sigma   weight residual
     114.17  117.40   -3.23 1.45e+00 4.76e-01 4.96e+00
  angle pdb=" CA  PRO A 104 "
        pdb=" C   PRO A 104 "
        pdb=" O   PRO A 104 "
      ideal   model   delta    sigma   weight residual
     123.16  120.17    2.99 1.49e+00 4.50e-01 4.03e+00
  angle pdb=" N   ALA C 117 "
        pdb=" CA  ALA C 117 "
        pdb=" C   ALA C 117 "
      ideal   model   delta    sigma   weight residual
     108.19  110.71   -2.52 1.29e+00 6.01e-01 3.81e+00
  angle pdb=" N   ALA A 117 "
        pdb=" CA  ALA A 117 "
        pdb=" C   ALA A 117 "
      ideal   model   delta    sigma   weight residual
     108.19  110.60   -2.41 1.29e+00 6.01e-01 3.48e+00
  angle pdb=" C   PRO C 164 "
        pdb=" N   VAL C 165 "
        pdb=" CA  VAL C 165 "
      ideal   model   delta    sigma   weight residual
     122.97  121.15    1.82 9.80e-01 1.04e+00 3.43e+00
  ... (remaining 4588 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 1843
       17.94 -    35.88: 138
       35.88 -    53.82: 33
       53.82 -    71.75: 3
       71.75 -    89.69: 8
  Dihedral angle restraints: 2025
    sinusoidal: 831
      harmonic: 1194
  Sorted by residual:
  dihedral pdb=" CB  CYS B 178 "
           pdb=" SG  CYS B 178 "
           pdb=" SG  CYS B 213 "
           pdb=" CB  CYS B 213 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -131.14   45.14     1      1.00e+01 1.00e-02 2.83e+01
  dihedral pdb=" CB  CYS A 178 "
           pdb=" SG  CYS A 178 "
           pdb=" SG  CYS A 213 "
           pdb=" CB  CYS A 213 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -129.93   43.93     1      1.00e+01 1.00e-02 2.69e+01
  dihedral pdb=" CB  CYS C 178 "
           pdb=" SG  CYS C 178 "
           pdb=" SG  CYS C 213 "
           pdb=" CB  CYS C 213 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -118.68   32.68     1      1.00e+01 1.00e-02 1.52e+01
  ... (remaining 2022 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 253
       0.032 -    0.064: 148
       0.064 -    0.096: 34
       0.096 -    0.128: 25
       0.128 -    0.160: 5
  Chirality restraints: 465
  Sorted by residual:
  chirality pdb=" CA  ILE C 183 "
            pdb=" N   ILE C 183 "
            pdb=" C   ILE C 183 "
            pdb=" CB  ILE C 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.37e-01
  chirality pdb=" CA  ILE A 183 "
            pdb=" N   ILE A 183 "
            pdb=" C   ILE A 183 "
            pdb=" CB  ILE A 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.40e-01
  chirality pdb=" CA  ILE B 183 "
            pdb=" N   ILE B 183 "
            pdb=" C   ILE B 183 "
            pdb=" CB  ILE B 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.09e-01
  ... (remaining 462 not shown)

  Planarity restraints: 606
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 103 "   -0.019 5.00e-02 4.00e+02   2.91e-02 1.36e+00
        pdb=" N   PRO C 104 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO C 104 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C 104 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 103 "   -0.018 5.00e-02 4.00e+02   2.80e-02 1.25e+00
        pdb=" N   PRO A 104 "    0.048 5.00e-02 4.00e+02
        pdb=" CA  PRO A 104 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 104 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A 176 "   -0.005 2.00e-02 2.50e+03   9.93e-03 9.86e-01
        pdb=" C   HIS A 176 "    0.017 2.00e-02 2.50e+03
        pdb=" O   HIS A 176 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   ASP A 177 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 603 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 930
        2.84 -     3.35: 2665
        3.35 -     3.87: 5785
        3.87 -     4.38: 6446
        4.38 -     4.90: 11760
  Nonbonded interactions: 27586
  Sorted by model distance:
  nonbonded pdb=" O   ALA A 112 "
            pdb=" OG  SER B 134 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" NH2 ARG A 135 "
            pdb=" OE1 GLU B 151 "
     model   vdw
     2.341 3.120
  nonbonded pdb=" OG  SER A 134 "
            pdb=" O   ALA C 112 "
     model   vdw
     2.356 3.040
  nonbonded pdb=" O   TRP A  98 "
            pdb=" ND2 ASN A 142 "
     model   vdw
     2.413 3.120
  nonbonded pdb=" O   TRP C  98 "
            pdb=" ND2 ASN C 142 "
     model   vdw
     2.485 3.120
  ... (remaining 27581 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             13.530
  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:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     14.650
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:14.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
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      :  0.002   0.033   3396  Z= 0.157
  Angle     :  0.581   5.421   4593  Z= 0.343
  Chirality :  0.047   0.160    465
  Planarity :  0.003   0.037    606
  Dihedral  : 14.424  89.691   1260
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 2.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -3.74 (0.29), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.84 (0.22), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A  98 
 HIS   0.003   0.001   HIS C 139 
 PHE   0.006   0.001   PHE A 174 
 TYR   0.014   0.001   TYR A 149 
 ARG   0.006   0.000   ARG A 135 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.379 
Fit side-chains
REVERT: A  155 ARG cc_start: 0.6769 (mtt180) cc_final: 0.5795 (mtp180)
REVERT: C  100 LYS cc_start: 0.8302 (mtmm) cc_final: 0.7976 (tttt)
REVERT: C  155 ARG cc_start: 0.7203 (mtt-85) cc_final: 0.6790 (mtp180)
REVERT: B  109 LYS cc_start: 0.7988 (mttt) cc_final: 0.7065 (tttm)
REVERT: B  155 ARG cc_start: 0.6937 (mtt180) cc_final: 0.5643 (mtp-110)
REVERT: B  184 LYS cc_start: 0.7916 (pttp) cc_final: 0.7691 (ptmt)
REVERT: B  193 LYS cc_start: 0.7783 (ttpt) cc_final: 0.7108 (tptp)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 1.7563
  time to fit residues: 141.4023
Evaluate side-chains
  74 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 107 ASN
A 218 GLN
C 196 ASN
B 107 ASN
B 218 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.126004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.109899 restraints weight = 3644.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3581 rms_B_bonded: 1.50
r_work: 0.3470 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3368 rms_B_bonded: 2.86 restraints_weight: 0.2500
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8882
moved from start:          0.1341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.051   3396  Z= 0.532
  Angle     :  0.792   6.256   4593  Z= 0.444
  Chirality :  0.053   0.166    465
  Planarity :  0.005   0.037    606
  Dihedral  :  5.632  15.320    462
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.46 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  :  6.21 %
    Favored  : 92.09 %
  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: -3.75 (0.29), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.85 (0.22), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.004   TRP A  98 
 HIS   0.005   0.001   HIS B 139 
 PHE   0.016   0.003   PHE A 197 
 TYR   0.025   0.003   TYR A 156 
 ARG   0.004   0.001   ARG B 150 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A  147 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8055 (mtp180)
REVERT: A  155 ARG cc_start: 0.7424 (mtt180) cc_final: 0.5969 (mtp180)
REVERT: C  100 LYS cc_start: 0.8640 (mtmm) cc_final: 0.8010 (tttt)
REVERT: C  133 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8569 (tpp)
REVERT: C  155 ARG cc_start: 0.7762 (mtt-85) cc_final: 0.6913 (mtp180)
REVERT: B  109 LYS cc_start: 0.8357 (mttt) cc_final: 0.7202 (tttm)
REVERT: B  153 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8136 (mpp)
REVERT: B  155 ARG cc_start: 0.7499 (mtt180) cc_final: 0.5711 (mtp-110)
REVERT: B  184 LYS cc_start: 0.8447 (pttp) cc_final: 0.8018 (ptmt)
REVERT: B  196 ASN cc_start: 0.8191 (t0) cc_final: 0.7980 (t0)
  outliers start: 6
  outliers final: 1
  residues processed: 77
  average time/residue: 1.7698
  time to fit residues: 138.8354
Evaluate side-chains
  77 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 ARG
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain B residue  153 MET
Chi-restraints excluded: chain B residue  182 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 12 optimal weight:    0.4980
   chunk 23 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C 196 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.129536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.113991 restraints weight = 3525.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3653 rms_B_bonded: 1.47
r_work: 0.3546 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3449 rms_B_bonded: 2.82 restraints_weight: 0.2500
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8837
moved from start:          0.1395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3396  Z= 0.276
  Angle     :  0.658   6.495   4593  Z= 0.369
  Chirality :  0.048   0.156    465
  Planarity :  0.003   0.022    606
  Dihedral  :  5.386  14.755    462
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  6.72 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  :  9.60 %
    Favored  : 88.42 %
  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: -3.84 (0.29), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.92 (0.22), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP C  98 
 HIS   0.005   0.001   HIS B 139 
 PHE   0.012   0.002   PHE A 197 
 TYR   0.017   0.002   TYR B 156 
 ARG   0.005   0.000   ARG B 135 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 78
  time to evaluate  : 0.348 
Fit side-chains
REVERT: A  155 ARG cc_start: 0.7364 (mtt180) cc_final: 0.5903 (mtp180)
REVERT: C  100 LYS cc_start: 0.8595 (mtmm) cc_final: 0.7924 (tttt)
REVERT: C  155 ARG cc_start: 0.7734 (mtt-85) cc_final: 0.6873 (mtp180)
REVERT: C  196 ASN cc_start: 0.7572 (m-40) cc_final: 0.6996 (t0)
REVERT: C  228 ARG cc_start: 0.8096 (mtm180) cc_final: 0.5702 (mmt-90)
REVERT: B  109 LYS cc_start: 0.8478 (mttt) cc_final: 0.7257 (tttm)
REVERT: B  135 ARG cc_start: 0.8554 (ttm-80) cc_final: 0.8319 (ptm160)
REVERT: B  155 ARG cc_start: 0.7393 (mtt180) cc_final: 0.5658 (mtp-110)
REVERT: B  184 LYS cc_start: 0.8409 (pttp) cc_final: 0.8023 (ptmt)
  outliers start: 7
  outliers final: 1
  residues processed: 80
  average time/residue: 1.8438
  time to fit residues: 150.2276
Evaluate side-chains
  78 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  182 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.9786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.127415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.111772 restraints weight = 3674.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.3619 rms_B_bonded: 1.50
r_work: 0.3507 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3406 rms_B_bonded: 2.87 restraints_weight: 0.2500
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8862
moved from start:          0.1587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   3396  Z= 0.362
  Angle     :  0.702   5.770   4593  Z= 0.395
  Chirality :  0.050   0.162    465
  Planarity :  0.004   0.024    606
  Dihedral  :  5.435  15.476    462
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.75 %
    Allowed  :  7.21 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  :  9.89 %
    Favored  : 88.14 %
  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: -3.88 (0.29), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.95 (0.22), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP C  98 
 HIS   0.005   0.001   HIS B 139 
 PHE   0.013   0.003   PHE A 197 
 TYR   0.020   0.002   TYR B 156 
 ARG   0.007   0.001   ARG A 135 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 79
  time to evaluate  : 0.385 
Fit side-chains
REVERT: A  155 ARG cc_start: 0.7455 (mtt180) cc_final: 0.5967 (mtp180)
REVERT: C  100 LYS cc_start: 0.8614 (mtmm) cc_final: 0.7908 (tttt)
REVERT: C  155 ARG cc_start: 0.7766 (mtt-85) cc_final: 0.6895 (mtp180)
REVERT: C  196 ASN cc_start: 0.7604 (m-40) cc_final: 0.7029 (t0)
REVERT: C  228 ARG cc_start: 0.8135 (mtm180) cc_final: 0.5832 (mmt-90)
REVERT: B  109 LYS cc_start: 0.8460 (mttt) cc_final: 0.7217 (tttm)
REVERT: B  155 ARG cc_start: 0.7452 (mtt180) cc_final: 0.5648 (mtp-110)
REVERT: B  184 LYS cc_start: 0.8448 (pttp) cc_final: 0.8054 (ptmt)
REVERT: B  196 ASN cc_start: 0.8239 (t0) cc_final: 0.8027 (t0)
  outliers start: 7
  outliers final: 2
  residues processed: 79
  average time/residue: 1.7751
  time to fit residues: 142.9508
Evaluate side-chains
  81 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  105 LYS
Chi-restraints excluded: chain B residue  182 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 37 optimal weight:    0.2980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.129756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.114165 restraints weight = 3635.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 1.49
r_work: 0.3545 rms_B_bonded: 1.69 restraints_weight: 0.5000
r_work: 0.3446 rms_B_bonded: 2.87 restraints_weight: 0.2500
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8842
moved from start:          0.1643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3396  Z= 0.278
  Angle     :  0.667   6.450   4593  Z= 0.374
  Chirality :  0.048   0.157    465
  Planarity :  0.003   0.021    606
  Dihedral  :  5.341  16.039    462
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.75 %
    Allowed  :  7.21 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 11.86 %
    Favored  : 86.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.85 (0.29), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.92 (0.22), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP C  98 
 HIS   0.004   0.001   HIS B 139 
 PHE   0.014   0.003   PHE A 140 
 TYR   0.017   0.002   TYR B 156 
 ARG   0.007   0.001   ARG A 135 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 0.356 
Fit side-chains
REVERT: A  155 ARG cc_start: 0.7323 (mtt180) cc_final: 0.5867 (mtp180)
REVERT: C  100 LYS cc_start: 0.8555 (mtmm) cc_final: 0.7890 (tttt)
REVERT: C  155 ARG cc_start: 0.7746 (mtt-85) cc_final: 0.6903 (mtp180)
REVERT: C  163 ARG cc_start: 0.8419 (ptm160) cc_final: 0.7340 (tpp-160)
REVERT: C  196 ASN cc_start: 0.7630 (m-40) cc_final: 0.7052 (t0)
REVERT: C  228 ARG cc_start: 0.8120 (mtm180) cc_final: 0.5832 (mmt-90)
REVERT: B  109 LYS cc_start: 0.8499 (mttt) cc_final: 0.7249 (tttm)
REVERT: B  153 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8114 (mpp)
REVERT: B  155 ARG cc_start: 0.7424 (mtt180) cc_final: 0.5661 (mtp-110)
REVERT: B  184 LYS cc_start: 0.8448 (pttp) cc_final: 0.8030 (ptmt)
  outliers start: 5
  outliers final: 1
  residues processed: 78
  average time/residue: 1.7263
  time to fit residues: 137.2288
Evaluate side-chains
  78 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  153 MET
Chi-restraints excluded: chain B residue  182 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.8984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.127665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.111998 restraints weight = 3759.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 1.53
r_work: 0.3505 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.3406 rms_B_bonded: 2.91 restraints_weight: 0.2500
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8862
moved from start:          0.1691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   3396  Z= 0.331
  Angle     :  0.694   5.913   4593  Z= 0.390
  Chirality :  0.050   0.160    465
  Planarity :  0.004   0.022    606
  Dihedral  :  5.363  15.974    462
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.75 %
    Allowed  :  7.21 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 11.30 %
    Favored  : 87.29 %
  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: -3.83 (0.29), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.91 (0.22), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.003   TRP C  98 
 HIS   0.005   0.001   HIS B 139 
 PHE   0.014   0.003   PHE A 140 
 TYR   0.019   0.002   TYR B 156 
 ARG   0.008   0.001   ARG A 135 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.358 
Fit side-chains
REVERT: A  155 ARG cc_start: 0.7378 (mtt180) cc_final: 0.5886 (mtp180)
REVERT: C  100 LYS cc_start: 0.8562 (mtmm) cc_final: 0.7880 (tttt)
REVERT: C  155 ARG cc_start: 0.7775 (mtt-85) cc_final: 0.6894 (mtp180)
REVERT: C  163 ARG cc_start: 0.8276 (ptm160) cc_final: 0.7135 (tpp-160)
REVERT: C  196 ASN cc_start: 0.7704 (m-40) cc_final: 0.7119 (t0)
REVERT: C  228 ARG cc_start: 0.8138 (mtm180) cc_final: 0.5860 (mmt-90)
REVERT: B  109 LYS cc_start: 0.8535 (mttt) cc_final: 0.7252 (tttm)
REVERT: B  153 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8177 (mpp)
REVERT: B  155 ARG cc_start: 0.7457 (mtt180) cc_final: 0.5654 (mtp-110)
REVERT: B  184 LYS cc_start: 0.8472 (pttp) cc_final: 0.8054 (ptmm)
REVERT: B  196 ASN cc_start: 0.8257 (t0) cc_final: 0.8031 (t0)
  outliers start: 5
  outliers final: 3
  residues processed: 76
  average time/residue: 1.7930
  time to fit residues: 138.8039
Evaluate side-chains
  79 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 75
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain C residue  105 LYS
Chi-restraints excluded: chain B residue  153 MET
Chi-restraints excluded: chain B residue  182 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 29 optimal weight:    0.4980
   chunk 11 optimal weight:    1.9990
   chunk 24 optimal weight:    0.3980
   chunk 30 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
C 139 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.129658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.114065 restraints weight = 3645.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 1.51
r_work: 0.3543 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3445 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8843
moved from start:          0.1706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3396  Z= 0.248
  Angle     :  0.639   6.394   4593  Z= 0.360
  Chirality :  0.048   0.156    465
  Planarity :  0.003   0.023    606
  Dihedral  :  5.250  16.242    462
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.75 %
    Allowed  :  6.72 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 11.58 %
    Favored  : 86.44 %
  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: -3.81 (0.29), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.89 (0.22), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP C  98 
 HIS   0.005   0.001   HIS B 139 
 PHE   0.012   0.003   PHE A 197 
 TYR   0.016   0.002   TYR A 148 
 ARG   0.007   0.000   ARG A 135 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.356 
Fit side-chains
REVERT: A  155 ARG cc_start: 0.7316 (mtt180) cc_final: 0.5844 (mtp180)
REVERT: C  100 LYS cc_start: 0.8520 (mtmm) cc_final: 0.7869 (tttt)
REVERT: C  155 ARG cc_start: 0.7747 (mtt-85) cc_final: 0.6898 (mtp180)
REVERT: C  196 ASN cc_start: 0.7662 (m-40) cc_final: 0.7096 (t0)
REVERT: C  228 ARG cc_start: 0.8114 (mtm180) cc_final: 0.5828 (mmt-90)
REVERT: B  109 LYS cc_start: 0.8506 (mttt) cc_final: 0.7241 (tttm)
REVERT: B  153 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8136 (mpp)
REVERT: B  155 ARG cc_start: 0.7454 (mtt180) cc_final: 0.5675 (mtp-110)
REVERT: B  184 LYS cc_start: 0.8441 (pttp) cc_final: 0.8042 (ptmm)
REVERT: B  204 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7930 (mpp)
  outliers start: 7
  outliers final: 3
  residues processed: 75
  average time/residue: 1.7586
  time to fit residues: 134.4115
Evaluate side-chains
  78 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain B residue  153 MET
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  204 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 4 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
C 139 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.127586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.111909 restraints weight = 3675.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3619 rms_B_bonded: 1.52
r_work: 0.3509 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3410 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8862
moved from start:          0.1767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   3396  Z= 0.323
  Angle     :  0.669   5.340   4593  Z= 0.378
  Chirality :  0.049   0.160    465
  Planarity :  0.003   0.025    606
  Dihedral  :  5.323  15.697    462
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.75 %
    Allowed  :  7.46 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 12.15 %
    Favored  : 85.88 %
  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: -3.79 (0.29), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.88 (0.22), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.003   TRP C  98 
 HIS   0.004   0.001   HIS A 139 
 PHE   0.013   0.003   PHE C 140 
 TYR   0.018   0.002   TYR A 156 
 ARG   0.006   0.001   ARG A 135 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.354 
Fit side-chains
REVERT: A  155 ARG cc_start: 0.7356 (mtt180) cc_final: 0.5867 (mtp180)
REVERT: C  100 LYS cc_start: 0.8552 (mtmm) cc_final: 0.7886 (tttt)
REVERT: C  155 ARG cc_start: 0.7765 (mtt-85) cc_final: 0.6898 (mtp180)
REVERT: C  196 ASN cc_start: 0.7661 (m-40) cc_final: 0.7118 (t0)
REVERT: C  228 ARG cc_start: 0.8103 (mtm180) cc_final: 0.5817 (mmt-90)
REVERT: B  109 LYS cc_start: 0.8546 (mttt) cc_final: 0.7252 (tttm)
REVERT: B  153 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8199 (mpp)
REVERT: B  155 ARG cc_start: 0.7431 (mtt180) cc_final: 0.5630 (mtp-110)
REVERT: B  184 LYS cc_start: 0.8457 (pttp) cc_final: 0.8048 (ptmm)
REVERT: B  204 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7941 (mpp)
REVERT: B  220 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7905 (mm-30)
  outliers start: 7
  outliers final: 4
  residues processed: 79
  average time/residue: 1.7410
  time to fit residues: 140.2099
Evaluate side-chains
  83 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain C residue  105 LYS
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain B residue  153 MET
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  204 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 38 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 28 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 107 ASN
A 196 ASN
C 139 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.128638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.112912 restraints weight = 3671.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 1.49
r_work: 0.3524 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3426 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8854
moved from start:          0.1789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3396  Z= 0.285
  Angle     :  0.646   5.136   4593  Z= 0.365
  Chirality :  0.049   0.158    465
  Planarity :  0.003   0.026    606
  Dihedral  :  5.294  15.885    462
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.75 %
    Allowed  :  7.46 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 11.58 %
    Favored  : 86.16 %
  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: -3.80 (0.29), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.89 (0.22), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP C  98 
 HIS   0.004   0.001   HIS B 139 
 PHE   0.013   0.003   PHE C 140 
 TYR   0.018   0.002   TYR B 156 
 ARG   0.004   0.000   ARG A 135 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.345 
Fit side-chains
REVERT: A  155 ARG cc_start: 0.7310 (mtt180) cc_final: 0.5856 (mtp180)
REVERT: C  100 LYS cc_start: 0.8554 (mtmm) cc_final: 0.7893 (tttt)
REVERT: C  155 ARG cc_start: 0.7765 (mtt-85) cc_final: 0.6923 (mtp180)
REVERT: C  196 ASN cc_start: 0.7649 (m-40) cc_final: 0.7098 (t0)
REVERT: C  228 ARG cc_start: 0.8122 (mtm180) cc_final: 0.5861 (mmt-90)
REVERT: B  109 LYS cc_start: 0.8510 (mttt) cc_final: 0.7180 (tttm)
REVERT: B  153 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8214 (mpp)
REVERT: B  155 ARG cc_start: 0.7486 (mtt180) cc_final: 0.5703 (mtp-110)
REVERT: B  184 LYS cc_start: 0.8440 (pttp) cc_final: 0.8046 (ptmm)
REVERT: B  204 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7941 (mpp)
REVERT: B  220 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7901 (mm-30)
  outliers start: 8
  outliers final: 4
  residues processed: 78
  average time/residue: 1.7618
  time to fit residues: 140.0220
Evaluate side-chains
  83 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain C residue  105 LYS
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain B residue  153 MET
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  204 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 26 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 196 ASN
C 139 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.128574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.112909 restraints weight = 3653.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 1.48
r_work: 0.3525 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3429 rms_B_bonded: 2.84 restraints_weight: 0.2500
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8852
moved from start:          0.1846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3396  Z= 0.280
  Angle     :  0.646   5.096   4593  Z= 0.365
  Chirality :  0.049   0.158    465
  Planarity :  0.003   0.025    606
  Dihedral  :  5.300  16.523    462
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.75 %
    Allowed  :  7.21 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 11.86 %
    Favored  : 86.44 %
  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: -3.81 (0.29), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.90 (0.22), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.003   TRP C  98 
 HIS   0.005   0.001   HIS B 139 
 PHE   0.014   0.003   PHE C 140 
 TYR   0.018   0.002   TYR B 156 
 ARG   0.003   0.000   ARG A 135 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.386 
Fit side-chains
REVERT: A  155 ARG cc_start: 0.7312 (mtt180) cc_final: 0.5866 (mtp180)
REVERT: C  100 LYS cc_start: 0.8551 (mtmm) cc_final: 0.7905 (tttt)
REVERT: C  155 ARG cc_start: 0.7770 (mtt-85) cc_final: 0.6938 (mtp180)
REVERT: C  196 ASN cc_start: 0.7653 (m-40) cc_final: 0.7113 (t0)
REVERT: C  228 ARG cc_start: 0.8138 (mtm180) cc_final: 0.5904 (mmt-90)
REVERT: B  109 LYS cc_start: 0.8493 (mttt) cc_final: 0.7169 (tttm)
REVERT: B  153 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8175 (mpp)
REVERT: B  155 ARG cc_start: 0.7469 (mtt180) cc_final: 0.5701 (mtp-110)
REVERT: B  184 LYS cc_start: 0.8442 (pttp) cc_final: 0.8046 (ptmm)
REVERT: B  204 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7931 (mpp)
REVERT: B  220 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7909 (mm-30)
  outliers start: 6
  outliers final: 4
  residues processed: 79
  average time/residue: 1.8077
  time to fit residues: 145.5857
Evaluate side-chains
  82 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain C residue  105 LYS
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain B residue  153 MET
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  204 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 20 optimal weight:    0.0670
   chunk 16 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 1 optimal weight:    0.0470
   chunk 37 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.5218

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

Flipped N/Q/H residues before XYZ refinement:
C 139 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.130545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.114930 restraints weight = 3634.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.3667 rms_B_bonded: 1.48
r_work: 0.3555 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3457 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8833
moved from start:          0.1822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3396  Z= 0.216
  Angle     :  0.611   4.833   4593  Z= 0.344
  Chirality :  0.048   0.154    465
  Planarity :  0.003   0.025    606
  Dihedral  :  5.201  16.698    462
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.75 %
    Allowed  :  7.21 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 12.15 %
    Favored  : 86.44 %
  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: -3.81 (0.29), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.89 (0.22), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP C  98 
 HIS   0.004   0.001   HIS B 139 
 PHE   0.011   0.002   PHE C 140 
 TYR   0.016   0.002   TYR A 148 
 ARG   0.004   0.000   ARG A 135 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3807.22 seconds
wall clock time: 65 minutes 52.21 seconds (3952.21 seconds total)