Starting phenix.real_space_refine
on Tue Feb 13 05:28:32 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a00_15043/02_2024/8a00_15043.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a00_15043/02_2024/8a00_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a00_15043/02_2024/8a00_15043.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a00_15043/02_2024/8a00_15043.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a00_15043/02_2024/8a00_15043.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a00_15043/02_2024/8a00_15043.pdb"
  }
  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
    Residue "A GLU  145": "OE1" <-> "OE2"
    Residue "A TYR  161": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  161": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  166": "OD1" <-> "OD2"
    Residue "B ASP  146": "OD1" <-> "OD2"
    Residue "B ASP  177": "OD1" <-> "OD2"
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 2.38, per 1000 atoms: 0.72
  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  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.27
  Conformation dependent library (CDL) restraints added in 617.8 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: 0.41
  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: 0.76

  Time building geometry restraints manager: 1.35 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:
       99.66 -   106.53: 98
      106.53 -   113.41: 1760
      113.41 -   120.29: 1170
      120.29 -   127.16: 1524
      127.16 -   134.04: 41
  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 2.440
  nonbonded pdb=" NH2 ARG A 135 "
            pdb=" OE1 GLU B 151 "
     model   vdw
     2.341 2.520
  nonbonded pdb=" OG  SER A 134 "
            pdb=" O   ALA C 112 "
     model   vdw
     2.356 2.440
  nonbonded pdb=" O   TRP A  98 "
            pdb=" ND2 ASN A 142 "
     model   vdw
     2.413 2.520
  nonbonded pdb=" O   TRP C  98 "
            pdb=" ND2 ASN C 142 "
     model   vdw
     2.485 2.520
  ... (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
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:             5.770
  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:             0.010
  Extract box with map and model:          21.190
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     13.960
  Find NCS groups from input model:        0.190
  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:12.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   53.820
-------------------------------------------------------------------------------
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 fitting.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.403 
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: 1.7558
  time to fit residues: 141.4008
Evaluate side-chains
  74 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 15 optimal weight:    1.9990
   chunk 30 optimal weight:    0.1980
   chunk 11 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8643
moved from start:          0.1276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.048   3396  Z= 0.476
  Angle     :  0.759   5.857   4593  Z= 0.426
  Chirality :  0.051   0.164    465
  Planarity :  0.004   0.034    606
  Dihedral  :  5.585  15.210    462
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.21 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  :  5.93 %
    Favored  : 92.37 %
  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   0.014   0.004   TRP A  98 
 HIS   0.005   0.001   HIS B 139 
 PHE   0.015   0.003   PHE A 197 
 TYR   0.023   0.002   TYR A 156 
 ARG   0.003   0.001   ARG A 135 

*********************** 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 fitting.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.414 
Fit side-chains
REVERT: A  147 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7690 (mtp180)
REVERT: A  155 ARG cc_start: 0.7063 (mtt180) cc_final: 0.5889 (mtp180)
REVERT: C  100 LYS cc_start: 0.8379 (mtmm) cc_final: 0.7951 (tttt)
REVERT: C  133 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8136 (tpp)
REVERT: C  155 ARG cc_start: 0.7261 (mtt-85) cc_final: 0.6771 (mtp180)
REVERT: B  109 LYS cc_start: 0.8073 (mttt) cc_final: 0.7096 (tttm)
REVERT: B  153 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.6973 (mpp)
REVERT: B  155 ARG cc_start: 0.7007 (mtt180) cc_final: 0.5504 (mtp-110)
REVERT: B  184 LYS cc_start: 0.8257 (pttp) cc_final: 0.7919 (ptmt)
REVERT: B  196 ASN cc_start: 0.8188 (t0) cc_final: 0.7962 (t0)
  outliers start: 6
  outliers final: 1
  residues processed: 77
  average time/residue: 1.7696
  time to fit residues: 138.9387
Evaluate side-chains
  77 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
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 19 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 38 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 28 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.1334

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= 0.278
  Angle     :  0.659   6.710   4593  Z= 0.371
  Chirality :  0.048   0.158    465
  Planarity :  0.003   0.023    606
  Dihedral  :  5.387  14.779    462
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  6.97 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  :  8.47 %
    Favored  : 89.27 %
  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: -3.82 (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   0.013   0.003   TRP A  98 
 HIS   0.004   0.001   HIS B 139 
 PHE   0.012   0.002   PHE A 197 
 TYR   0.018   0.002   TYR A 148 
 ARG   0.005   0.001   ARG A 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
  86 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 0.396 
Fit side-chains
REVERT: A  155 ARG cc_start: 0.7003 (mtt180) cc_final: 0.5841 (mtp180)
REVERT: C  100 LYS cc_start: 0.8331 (mtmm) cc_final: 0.7888 (tttt)
REVERT: C  155 ARG cc_start: 0.7247 (mtt-85) cc_final: 0.6748 (mtp180)
REVERT: C  196 ASN cc_start: 0.7405 (m-40) cc_final: 0.6967 (t0)
REVERT: C  228 ARG cc_start: 0.8060 (mtm180) cc_final: 0.6046 (mmt-90)
REVERT: B  109 LYS cc_start: 0.8193 (mttt) cc_final: 0.7130 (tttm)
REVERT: B  135 ARG cc_start: 0.8321 (ttm-80) cc_final: 0.8074 (ptm160)
REVERT: B  155 ARG cc_start: 0.6940 (mtt180) cc_final: 0.5467 (mtp-110)
REVERT: B  184 LYS cc_start: 0.8167 (pttp) cc_final: 0.7893 (ptmt)
  outliers start: 8
  outliers final: 1
  residues processed: 79
  average time/residue: 1.7307
  time to fit residues: 139.4582
Evaluate side-chains
  78 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
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 18 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.8382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.1455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   3396  Z= 0.310
  Angle     :  0.667   5.664   4593  Z= 0.375
  Chirality :  0.049   0.161    465
  Planarity :  0.003   0.023    606
  Dihedral  :  5.367  15.323    462
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.75 %
    Allowed  :  6.72 %
    Favored  : 92.54 %
  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: -3.81 (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   0.012   0.003   TRP A  98 
 HIS   0.004   0.001   HIS B 139 
 PHE   0.013   0.003   PHE A 197 
 TYR   0.019   0.002   TYR B 148 
 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
  84 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.363 
Fit side-chains
REVERT: A  155 ARG cc_start: 0.6995 (mtt180) cc_final: 0.5795 (mtp180)
REVERT: C  100 LYS cc_start: 0.8320 (mtmm) cc_final: 0.7851 (tttt)
REVERT: C  155 ARG cc_start: 0.7264 (mtt-85) cc_final: 0.6766 (mtp180)
REVERT: C  196 ASN cc_start: 0.7413 (m-40) cc_final: 0.6970 (t0)
REVERT: B  109 LYS cc_start: 0.8208 (mttt) cc_final: 0.7118 (tttm)
REVERT: B  135 ARG cc_start: 0.8364 (ttm-80) cc_final: 0.8007 (ptm-80)
REVERT: B  155 ARG cc_start: 0.6980 (mtt180) cc_final: 0.5426 (mtp-110)
REVERT: B  184 LYS cc_start: 0.8224 (pttp) cc_final: 0.7943 (ptmt)
  outliers start: 7
  outliers final: 2
  residues processed: 77
  average time/residue: 1.7653
  time to fit residues: 138.5218
Evaluate side-chains
  78 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
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 28 optimal weight:    0.5980
   chunk 15 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 9 optimal weight:    4.9990
   chunk 12 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.1488

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= 0.261
  Angle     :  0.632   5.236   4593  Z= 0.357
  Chirality :  0.048   0.156    465
  Planarity :  0.003   0.022    606
  Dihedral  :  5.258  15.045    462
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.75 %
    Allowed  :  6.72 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 10.73 %
    Favored  : 87.57 %
  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   0.012   0.003   TRP A  98 
 HIS   0.004   0.001   HIS B 139 
 PHE   0.012   0.003   PHE A 140 
 TYR   0.018   0.002   TYR B 148 
 ARG   0.006   0.000   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 fitting.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.411 
Fit side-chains
REVERT: A  155 ARG cc_start: 0.6923 (mtt180) cc_final: 0.5731 (mtp180)
REVERT: C  100 LYS cc_start: 0.8297 (mtmm) cc_final: 0.7830 (tttt)
REVERT: C  155 ARG cc_start: 0.7258 (mtt-85) cc_final: 0.6752 (mtp180)
REVERT: C  177 ASP cc_start: 0.7178 (p0) cc_final: 0.6971 (p0)
REVERT: C  196 ASN cc_start: 0.7436 (m-40) cc_final: 0.6980 (t0)
REVERT: B  109 LYS cc_start: 0.8231 (mttt) cc_final: 0.7079 (tttm)
REVERT: B  135 ARG cc_start: 0.8257 (ttm-80) cc_final: 0.7947 (ptm-80)
REVERT: B  153 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7104 (mpp)
REVERT: B  155 ARG cc_start: 0.6995 (mtt180) cc_final: 0.5452 (mtp-110)
REVERT: B  184 LYS cc_start: 0.8250 (pttp) cc_final: 0.7975 (ptmt)
  outliers start: 6
  outliers final: 2
  residues processed: 77
  average time/residue: 1.7488
  time to fit residues: 137.2823
Evaluate side-chains
  79 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 MET
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 9 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 17 optimal weight:    0.3980
   chunk 3 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.7982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8619
moved from start:          0.1579

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= 0.294
  Angle     :  0.653   5.223   4593  Z= 0.368
  Chirality :  0.048   0.159    465
  Planarity :  0.003   0.024    606
  Dihedral  :  5.288  15.460    462
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 4.65
  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: -3.82 (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   0.012   0.003   TRP A  98 
 HIS   0.004   0.001   HIS B 139 
 PHE   0.014   0.003   PHE A 140 
 TYR   0.018   0.002   TYR B 148 
 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 fitting.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.398 
Fit side-chains
REVERT: A  155 ARG cc_start: 0.6927 (mtt180) cc_final: 0.5726 (mtp180)
REVERT: C  100 LYS cc_start: 0.8273 (mtmm) cc_final: 0.7808 (tttt)
REVERT: C  155 ARG cc_start: 0.7270 (mtt-85) cc_final: 0.6757 (mtp180)
REVERT: C  163 ARG cc_start: 0.7701 (ttm170) cc_final: 0.7445 (ttp-170)
REVERT: C  177 ASP cc_start: 0.6901 (p0) cc_final: 0.6674 (p0)
REVERT: C  196 ASN cc_start: 0.7478 (m-40) cc_final: 0.7022 (t0)
REVERT: B  109 LYS cc_start: 0.8220 (mttt) cc_final: 0.7079 (tttm)
REVERT: B  135 ARG cc_start: 0.8260 (ttm-80) cc_final: 0.7943 (ptm-80)
REVERT: B  153 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7114 (mpp)
REVERT: B  155 ARG cc_start: 0.6991 (mtt180) cc_final: 0.5434 (mtp-110)
REVERT: B  184 LYS cc_start: 0.8246 (pttp) cc_final: 0.7919 (ptmm)
REVERT: B  196 ASN cc_start: 0.8262 (t0) cc_final: 0.8038 (t0)
  outliers start: 5
  outliers final: 3
  residues processed: 77
  average time/residue: 1.7562
  time to fit residues: 137.8657
Evaluate side-chains
  80 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
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 21 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 22 optimal weight:    0.3980
   chunk 17 optimal weight:    0.5980
   chunk 15 optimal weight:    3.9990
   chunk 11 optimal weight:    0.5980
   chunk 7 optimal weight:    0.8980
   chunk 25 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.6180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8601
moved from start:          0.1601

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= 0.235
  Angle     :  0.617   4.960   4593  Z= 0.348
  Chirality :  0.047   0.156    465
  Planarity :  0.003   0.032    606
  Dihedral  :  5.191  15.174    462
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.75 %
    Allowed  :  6.72 %
    Favored  : 92.54 %
  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: -3.80 (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   0.012   0.003   TRP A  98 
 HIS   0.004   0.001   HIS A 139 
 PHE   0.012   0.003   PHE A 197 
 TYR   0.017   0.002   TYR A 148 
 ARG   0.006   0.001   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
  79 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.417 
Fit side-chains
REVERT: A  155 ARG cc_start: 0.6937 (mtt180) cc_final: 0.5696 (mtp180)
REVERT: C  100 LYS cc_start: 0.8250 (mtmm) cc_final: 0.7799 (tttt)
REVERT: C  155 ARG cc_start: 0.7250 (mtt-85) cc_final: 0.6747 (mtp180)
REVERT: C  177 ASP cc_start: 0.6766 (p0) cc_final: 0.6504 (p0)
REVERT: C  196 ASN cc_start: 0.7433 (m-40) cc_final: 0.6988 (t0)
REVERT: B  109 LYS cc_start: 0.8229 (mttt) cc_final: 0.7072 (tttm)
REVERT: B  135 ARG cc_start: 0.8137 (ttm-80) cc_final: 0.7822 (ptm-80)
REVERT: B  153 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7095 (mpp)
REVERT: B  155 ARG cc_start: 0.7016 (mtt180) cc_final: 0.5459 (mtp-110)
REVERT: B  184 LYS cc_start: 0.8236 (pttp) cc_final: 0.7916 (ptmm)
  outliers start: 5
  outliers final: 2
  residues processed: 75
  average time/residue: 1.8114
  time to fit residues: 138.4557
Evaluate side-chains
  77 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 74
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain B residue  153 MET
Chi-restraints excluded: chain B residue  182 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 29 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   chunk 35 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.6780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.1665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3396  Z= 0.257
  Angle     :  0.639   6.166   4593  Z= 0.360
  Chirality :  0.048   0.158    465
  Planarity :  0.004   0.036    606
  Dihedral  :  5.213  15.304    462
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.75 %
    Allowed  :  7.21 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 11.58 %
    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: -3.82 (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   0.012   0.003   TRP A  98 
 HIS   0.004   0.001   HIS B 139 
 PHE   0.012   0.003   PHE A 197 
 TYR   0.018   0.002   TYR A 148 
 ARG   0.007   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
  81 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.406 
Fit side-chains
REVERT: A  155 ARG cc_start: 0.6878 (mtt180) cc_final: 0.5672 (mtp180)
REVERT: C  100 LYS cc_start: 0.8248 (mtmm) cc_final: 0.7800 (tttt)
REVERT: C  155 ARG cc_start: 0.7244 (mtt-85) cc_final: 0.6742 (mtp180)
REVERT: C  163 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7263 (tpp-160)
REVERT: C  177 ASP cc_start: 0.6756 (p0) cc_final: 0.6475 (p0)
REVERT: C  196 ASN cc_start: 0.7455 (m-40) cc_final: 0.7011 (t0)
REVERT: B  109 LYS cc_start: 0.8229 (mttt) cc_final: 0.7075 (tttm)
REVERT: B  135 ARG cc_start: 0.8134 (ttm-80) cc_final: 0.7819 (ptm-80)
REVERT: B  153 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.7115 (mpp)
REVERT: B  155 ARG cc_start: 0.7017 (mtt180) cc_final: 0.5442 (mtp-110)
REVERT: B  184 LYS cc_start: 0.8222 (pttp) cc_final: 0.7892 (ptmm)
REVERT: B  196 ASN cc_start: 0.8227 (t0) cc_final: 0.7994 (t0)
  outliers start: 6
  outliers final: 3
  residues processed: 76
  average time/residue: 1.7669
  time to fit residues: 136.8357
Evaluate side-chains
  79 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
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  163 ARG
Chi-restraints excluded: chain B residue  153 MET
Chi-restraints excluded: chain B residue  182 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    0.4980
   chunk 22 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 30 optimal weight:    0.3980
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3396  Z= 0.260
  Angle     :  0.639   6.230   4593  Z= 0.361
  Chirality :  0.048   0.157    465
  Planarity :  0.004   0.038    606
  Dihedral  :  5.233  15.873    462
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.75 %
    Allowed  :  7.46 %
    Favored  : 91.79 %
  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: -3.83 (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   0.012   0.003   TRP A  98 
 HIS   0.004   0.001   HIS A 139 
 PHE   0.012   0.003   PHE A 197 
 TYR   0.019   0.002   TYR A 148 
 ARG   0.007   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
  79 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.419 
Fit side-chains
REVERT: A  155 ARG cc_start: 0.6879 (mtt180) cc_final: 0.5668 (mtp180)
REVERT: C  100 LYS cc_start: 0.8246 (mtmm) cc_final: 0.7799 (tttt)
REVERT: C  155 ARG cc_start: 0.7242 (mtt-85) cc_final: 0.6739 (mtp180)
REVERT: C  163 ARG cc_start: 0.7531 (ptm160) cc_final: 0.7116 (tpp-160)
REVERT: C  177 ASP cc_start: 0.6567 (p0) cc_final: 0.6306 (p0)
REVERT: C  196 ASN cc_start: 0.7461 (m-40) cc_final: 0.7029 (t0)
REVERT: B  109 LYS cc_start: 0.8243 (mttt) cc_final: 0.7078 (tttm)
REVERT: B  135 ARG cc_start: 0.8092 (ttm-80) cc_final: 0.7799 (ptm-80)
REVERT: B  153 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.7102 (mpp)
REVERT: B  155 ARG cc_start: 0.7039 (mtt180) cc_final: 0.5460 (mtp-110)
REVERT: B  184 LYS cc_start: 0.8235 (pttp) cc_final: 0.7898 (ptmm)
REVERT: B  196 ASN cc_start: 0.8232 (t0) cc_final: 0.8008 (t0)
  outliers start: 5
  outliers final: 3
  residues processed: 75
  average time/residue: 1.8500
  time to fit residues: 141.4243
Evaluate side-chains
  78 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.1745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3396  Z= 0.272
  Angle     :  0.647   6.355   4593  Z= 0.365
  Chirality :  0.048   0.159    465
  Planarity :  0.004   0.039    606
  Dihedral  :  5.247  16.078    462
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.75 %
    Allowed  :  7.46 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 12.43 %
    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: -3.83 (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   0.012   0.003   TRP A  98 
 HIS   0.004   0.001   HIS A 139 
 PHE   0.013   0.003   PHE C 140 
 TYR   0.018   0.002   TYR B 148 
 ARG   0.007   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
  80 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.418 
Fit side-chains
REVERT: A  155 ARG cc_start: 0.6893 (mtt180) cc_final: 0.5672 (mtp180)
REVERT: C  100 LYS cc_start: 0.8259 (mtmm) cc_final: 0.7807 (tttt)
REVERT: C  155 ARG cc_start: 0.7248 (mtt-85) cc_final: 0.6742 (mtp180)
REVERT: C  163 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7105 (tpp-160)
REVERT: C  177 ASP cc_start: 0.6528 (p0) cc_final: 0.6260 (p0)
REVERT: C  196 ASN cc_start: 0.7463 (m-40) cc_final: 0.7063 (t0)
REVERT: B  109 LYS cc_start: 0.8235 (mttt) cc_final: 0.7081 (tttm)
REVERT: B  135 ARG cc_start: 0.8106 (ttm-80) cc_final: 0.7819 (ptm-80)
REVERT: B  153 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.7105 (mpp)
REVERT: B  155 ARG cc_start: 0.7029 (mtt180) cc_final: 0.5447 (mtp-110)
REVERT: B  184 LYS cc_start: 0.8225 (pttp) cc_final: 0.7892 (ptmm)
  outliers start: 5
  outliers final: 3
  residues processed: 76
  average time/residue: 1.8129
  time to fit residues: 140.4523
Evaluate side-chains
  81 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
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  163 ARG
Chi-restraints excluded: chain B residue  153 MET
Chi-restraints excluded: chain B residue  182 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 27 optimal weight:    0.4980
   chunk 1 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0970
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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 = 0.3845 r_free = 0.3845 target = 0.128710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.112851 restraints weight = 3641.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 1.49
r_work: 0.3534 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.3434 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8830
moved from start:          0.1739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3396  Z= 0.226
  Angle     :  0.622   6.288   4593  Z= 0.351
  Chirality :  0.047   0.156    465
  Planarity :  0.003   0.041    606
  Dihedral  :  5.194  16.075    462
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.75 %
    Allowed  :  6.97 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 12.71 %
    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: -3.83 (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   0.011   0.002   TRP A  98 
 HIS   0.004   0.001   HIS A 139 
 PHE   0.011   0.002   PHE C 140 
 TYR   0.017   0.002   TYR B 148 
 ARG   0.007   0.000   ARG A 135 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2763.92 seconds
wall clock time: 49 minutes 27.93 seconds (2967.93 seconds total)