Starting phenix.real_space_refine
on Wed Sep 17 17:13:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ct3_45897/09_2025/9ct3_45897.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ct3_45897/09_2025/9ct3_45897.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.09
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ct3_45897/09_2025/9ct3_45897.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ct3_45897/09_2025/9ct3_45897.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ct3_45897/09_2025/9ct3_45897.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ct3_45897/09_2025/9ct3_45897.cif"
  }
  resolution = 3.09
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.001 sd=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     Cl      2      4.86       5
     C    6508      2.51       5
     N    1772      2.21       5
     O    1788      1.98       5
     F      16      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10138
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2508
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 319, 2508
          Classifications: {'peptide': 319}
          Link IDs: {'PTRANS': 18, 'TRANS': 300}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2477
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 314, 2477
          Classifications: {'peptide': 314}
          Link IDs: {'PTRANS': 17, 'TRANS': 296}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 2508
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 319, 2508
          Classifications: {'peptide': 319}
          Link IDs: {'PTRANS': 18, 'TRANS': 300}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 2477
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 314, 2477
          Classifications: {'peptide': 314}
          Link IDs: {'PTRANS': 17, 'TRANS': 296}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 59
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 59
          Unusual residues: {'9IM': 1, 'V67': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'V67': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 59
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 59
          Unusual residues: {'9IM': 1, 'V67': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'V67': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.42, per 1000 atoms: 0.24
  Number of scatterers: 10138
  At special positions: 0
  Unit cell: (104.11, 91.186, 104.11, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      2     17.00
     S      52     16.00
     F      16      9.00
     O    1788      8.00
     N    1772      7.00
     C    6508      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.85
  Conformation dependent library (CDL) restraints added in 291.7 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2352

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 8 sheets defined
      64.8% alpha, 11.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 37
    Processing helix  chain 'A' and resid 39 through 70
      removed outlier: 3.786A  pdb=" N   GLU A  68 " --> pdb=" O   CYS A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 77
    Processing helix  chain 'A' and resid 80 through 90
      removed outlier: 3.677A  pdb=" N   THR A  84 " --> pdb=" O   SER A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 108
    Processing helix  chain 'A' and resid 116 through 134
    Processing helix  chain 'A' and resid 140 through 152
    Processing helix  chain 'A' and resid 154 through 167
      removed outlier: 3.696A  pdb=" N   GLY A 158 " --> pdb=" O   ASN A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 185
      Proline residue:  A 173  - end of helix
      removed outlier: 4.358A  pdb=" N   GLN A 176 " --> pdb=" O   LEU A 172 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   ALA A 177 " --> pdb=" O   PRO A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 216
    Processing helix  chain 'A' and resid 262 through 274
      removed outlier: 3.678A  pdb=" N   GLN A 266 " --> pdb=" O   ALA A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 302
    Processing helix  chain 'A' and resid 324 through 333
      removed outlier: 3.610A  pdb=" N   GLU A 328 " --> pdb=" O   SER A 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 16 through 37
      removed outlier: 3.757A  pdb=" N   GLY B  37 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 39 through 70
      removed outlier: 3.749A  pdb=" N   THR B  43 " --> pdb=" O   PRO B  39 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 73
      No H-bonds generated for 'chain 'B' and resid 71 through 73'
    Processing helix  chain 'B' and resid 80 through 90
    Processing helix  chain 'B' and resid 91 through 109
    Processing helix  chain 'B' and resid 117 through 135
    Processing helix  chain 'B' and resid 140 through 152
    Processing helix  chain 'B' and resid 154 through 167
      removed outlier: 3.566A  pdb=" N   GLY B 158 " --> pdb=" O   ASN B 154 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 186
      Proline residue:  B 173  - end of helix
      removed outlier: 4.465A  pdb=" N   GLN B 176 " --> pdb=" O   LEU B 172 " (cutoff:3.500A)
      removed outlier: 4.975A  pdb=" N   ALA B 177 " --> pdb=" O   PRO B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 216
    Processing helix  chain 'B' and resid 262 through 274
      removed outlier: 3.501A  pdb=" N   GLN B 266 " --> pdb=" O   ALA B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 302
      removed outlier: 3.775A  pdb=" N   ASP B 301 " --> pdb=" O   ASP B 297 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 333
    Processing helix  chain 'C' and resid 16 through 37
      removed outlier: 3.663A  pdb=" N   GLY C  37 " --> pdb=" O   LEU C  33 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 39 through 70
      removed outlier: 3.782A  pdb=" N   GLU C  68 " --> pdb=" O   CYS C  64 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 77
    Processing helix  chain 'C' and resid 80 through 90
      removed outlier: 3.539A  pdb=" N   THR C  84 " --> pdb=" O   SER C  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 108
    Processing helix  chain 'C' and resid 116 through 134
    Processing helix  chain 'C' and resid 140 through 152
    Processing helix  chain 'C' and resid 154 through 167
      removed outlier: 3.670A  pdb=" N   GLY C 158 " --> pdb=" O   ASN C 154 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 167 through 186
      Proline residue:  C 173  - end of helix
      removed outlier: 4.341A  pdb=" N   GLN C 176 " --> pdb=" O   LEU C 172 " (cutoff:3.500A)
      removed outlier: 4.882A  pdb=" N   ALA C 177 " --> pdb=" O   PRO C 173 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 211 through 216
    Processing helix  chain 'C' and resid 262 through 274
      removed outlier: 3.604A  pdb=" N   GLN C 266 " --> pdb=" O   ALA C 262 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 280 through 302
    Processing helix  chain 'C' and resid 324 through 333
      removed outlier: 3.601A  pdb=" N   GLU C 328 " --> pdb=" O   SER C 324 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 16 through 36
    Processing helix  chain 'D' and resid 39 through 70
      removed outlier: 3.787A  pdb=" N   THR D  43 " --> pdb=" O   PRO D  39 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 71 through 73
      No H-bonds generated for 'chain 'D' and resid 71 through 73'
    Processing helix  chain 'D' and resid 80 through 90
      removed outlier: 3.566A  pdb=" N   THR D  84 " --> pdb=" O   SER D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 91 through 109
    Processing helix  chain 'D' and resid 117 through 135
    Processing helix  chain 'D' and resid 140 through 152
    Processing helix  chain 'D' and resid 154 through 167
      removed outlier: 3.526A  pdb=" N   GLY D 158 " --> pdb=" O   ASN D 154 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 167 through 186
      Proline residue:  D 173  - end of helix
    Processing helix  chain 'D' and resid 211 through 216
    Processing helix  chain 'D' and resid 262 through 274
      removed outlier: 3.579A  pdb=" N   GLN D 266 " --> pdb=" O   ALA D 262 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 280 through 301
      removed outlier: 3.647A  pdb=" N   ASP D 301 " --> pdb=" O   ASP D 297 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 324 through 333
    Processing sheet with id=AA1, first strand: chain 'A' and resid 219 through 224
      removed outlier: 6.236A  pdb=" N   ILE A 219 " --> pdb=" O   LEU A 248 " (cutoff:3.500A)
      removed outlier: 7.239A  pdb=" N   LEU A 248 " --> pdb=" O   ILE A 219 " (cutoff:3.500A)
      removed outlier: 5.547A  pdb=" N   PHE A 221 " --> pdb=" O   GLU A 246 " (cutoff:3.500A)
      removed outlier: 5.810A  pdb=" N   GLU A 246 " --> pdb=" O   PHE A 221 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ASP A 223 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 5.876A  pdb=" N   SER A 243 " --> pdb=" O   LEU A 259 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   LEU A 259 " --> pdb=" O   SER A 243 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   GLU A 249 " --> pdb=" O   ARG A 253 " (cutoff:3.500A)
      removed outlier: 5.426A  pdb=" N   ARG A 253 " --> pdb=" O   GLU A 249 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 232
      removed outlier: 6.821A  pdb=" N   HIS A 232 " --> pdb=" O   LYS A 236 " (cutoff:3.500A)
      removed outlier: 5.389A  pdb=" N   LYS A 236 " --> pdb=" O   HIS A 232 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 219 through 224
      removed outlier: 6.810A  pdb=" N   ILE B 244 " --> pdb=" O   LEU B 222 " (cutoff:3.500A)
      removed outlier: 7.284A  pdb=" N   SER B 243 " --> pdb=" O   VAL B 258 " (cutoff:3.500A)
      removed outlier: 4.879A  pdb=" N   VAL B 258 " --> pdb=" O   SER B 243 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   TYR B 245 " --> pdb=" O   THR B 256 " (cutoff:3.500A)
      removed outlier: 4.847A  pdb=" N   THR B 256 " --> pdb=" O   TYR B 245 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   LEU B 247 " --> pdb=" O   ALA B 254 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 228 through 230
    Processing sheet with id=AA5, first strand: chain 'C' and resid 219 through 224
      removed outlier: 6.227A  pdb=" N   ILE C 219 " --> pdb=" O   LEU C 248 " (cutoff:3.500A)
      removed outlier: 7.553A  pdb=" N   LEU C 248 " --> pdb=" O   ILE C 219 " (cutoff:3.500A)
      removed outlier: 5.921A  pdb=" N   PHE C 221 " --> pdb=" O   GLU C 246 " (cutoff:3.500A)
      removed outlier: 6.079A  pdb=" N   GLU C 246 " --> pdb=" O   PHE C 221 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   SER C 243 " --> pdb=" O   LEU C 259 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   LEU C 259 " --> pdb=" O   SER C 243 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   GLY C 255 " --> pdb=" O   LEU C 247 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   GLU C 249 " --> pdb=" O   ARG C 253 " (cutoff:3.500A)
      removed outlier: 5.266A  pdb=" N   ARG C 253 " --> pdb=" O   GLU C 249 " (cutoff:3.500A)
      removed outlier: 9.526A  pdb=" N   SER C 195 " --> pdb=" O   ALA C 254 " (cutoff:3.500A)
      removed outlier: 8.190A  pdb=" N   THR C 256 " --> pdb=" O   SER C 195 " (cutoff:3.500A)
      removed outlier: 7.729A  pdb=" N   ARG C 197 " --> pdb=" O   THR C 256 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   VAL C 258 " --> pdb=" O   ARG C 197 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLU C 260 " --> pdb=" O   TYR C 199 " (cutoff:3.500A)
      removed outlier: 7.804A  pdb=" N   ARG C 310 " --> pdb=" O   GLN C 196 " (cutoff:3.500A)
      removed outlier: 5.789A  pdb=" N   LEU C 198 " --> pdb=" O   ARG C 310 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   ILE C 312 " --> pdb=" O   LEU C 198 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   ILE C 200 " --> pdb=" O   ILE C 312 " (cutoff:3.500A)
      removed outlier: 7.707A  pdb=" N   TYR C 314 " --> pdb=" O   ILE C 200 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   LEU C 202 " --> pdb=" O   TYR C 314 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 228 through 232
      removed outlier: 6.794A  pdb=" N   HIS C 232 " --> pdb=" O   LYS C 236 " (cutoff:3.500A)
      removed outlier: 5.596A  pdb=" N   LYS C 236 " --> pdb=" O   HIS C 232 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 219 through 224
      removed outlier: 6.882A  pdb=" N   ILE D 244 " --> pdb=" O   LEU D 222 " (cutoff:3.500A)
      removed outlier: 5.267A  pdb=" N   SER D 243 " --> pdb=" O   LEU D 259 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   LEU D 259 " --> pdb=" O   SER D 243 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   GLU D 249 " --> pdb=" O   ARG D 253 " (cutoff:3.500A)
      removed outlier: 5.465A  pdb=" N   ARG D 253 " --> pdb=" O   GLU D 249 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 228 through 230

    643 hydrogen bonds defined for protein.
    1890 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.63

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1592
        1.31 -     1.43: 2884
        1.43 -     1.56: 5838
        1.56 -     1.68: 0
        1.68 -     1.81: 66
  Bond restraints: 10380
  Sorted by residual:
  bond pdb=" C16 9IM A 402 "
       pdb=" N06 9IM A 402 "
    ideal  model  delta    sigma   weight residual
    1.393  1.528 -0.135 2.00e-02 2.50e+03 4.54e+01
  bond pdb=" C16 9IM C 402 "
       pdb=" N06 9IM C 402 "
    ideal  model  delta    sigma   weight residual
    1.393  1.525 -0.132 2.00e-02 2.50e+03 4.34e+01
  bond pdb=" C8  V67 B 401 "
       pdb=" N10 V67 B 401 "
    ideal  model  delta    sigma   weight residual
    1.343  1.455 -0.112 2.00e-02 2.50e+03 3.15e+01
  bond pdb=" C8  V67 D 401 "
       pdb=" N10 V67 D 401 "
    ideal  model  delta    sigma   weight residual
    1.343  1.455 -0.112 2.00e-02 2.50e+03 3.13e+01
  bond pdb=" C8  V67 A 401 "
       pdb=" N10 V67 A 401 "
    ideal  model  delta    sigma   weight residual
    1.343  1.454 -0.111 2.00e-02 2.50e+03 3.08e+01
  ... (remaining 10375 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.66: 14039
        3.66 -     7.31: 63
        7.31 -    10.97: 4
       10.97 -    14.62: 8
       14.62 -    18.28: 4
  Bond angle restraints: 14118
  Sorted by residual:
  angle pdb=" C23 9IM A 402 "
        pdb=" C30 9IM A 402 "
        pdb=" F31 9IM A 402 "
      ideal   model   delta    sigma   weight residual
     118.60  136.88  -18.28 3.00e+00 1.11e-01 3.71e+01
  angle pdb=" C23 9IM C 402 "
        pdb=" C30 9IM C 402 "
        pdb=" F31 9IM C 402 "
      ideal   model   delta    sigma   weight residual
     118.60  136.83  -18.23 3.00e+00 1.11e-01 3.69e+01
  angle pdb=" C08 9IM C 402 "
        pdb=" C09 9IM C 402 "
        pdb=" F10 9IM C 402 "
      ideal   model   delta    sigma   weight residual
     118.31  133.27  -14.96 3.00e+00 1.11e-01 2.49e+01
  angle pdb=" C08 9IM A 402 "
        pdb=" C09 9IM A 402 "
        pdb=" F10 9IM A 402 "
      ideal   model   delta    sigma   weight residual
     118.31  133.03  -14.72 3.00e+00 1.11e-01 2.41e+01
  angle pdb=" C08 9IM A 402 "
        pdb=" C14 9IM A 402 "
        pdb="CL1  9IM A 402 "
      ideal   model   delta    sigma   weight residual
     119.61  134.07  -14.46 3.00e+00 1.11e-01 2.32e+01
  ... (remaining 14113 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.20: 5406
       17.20 -    34.39: 611
       34.39 -    51.58: 99
       51.58 -    68.78: 14
       68.78 -    85.97: 12
  Dihedral angle restraints: 6142
    sinusoidal: 2470
      harmonic: 3672
  Sorted by residual:
  dihedral pdb=" CA  ILE D 171 "
           pdb=" C   ILE D 171 "
           pdb=" N   LEU D 172 "
           pdb=" CA  LEU D 172 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.69  -19.31     0      5.00e+00 4.00e-02 1.49e+01
  dihedral pdb=" CA  GLU B  38 "
           pdb=" C   GLU B  38 "
           pdb=" N   PRO B  39 "
           pdb=" CA  PRO B  39 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.06  -17.94     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  GLU D  38 "
           pdb=" C   GLU D  38 "
           pdb=" N   PRO D  39 "
           pdb=" CA  PRO D  39 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.12  -16.88     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 6139 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1039
       0.030 -    0.061: 350
       0.061 -    0.091: 93
       0.091 -    0.122: 67
       0.122 -    0.152: 9
  Chirality restraints: 1558
  Sorted by residual:
  chirality pdb=" CA  ILE A 219 "
            pdb=" N   ILE A 219 "
            pdb=" C   ILE A 219 "
            pdb=" CB  ILE A 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.80e-01
  chirality pdb=" CA  ILE A 312 "
            pdb=" N   ILE A 312 "
            pdb=" C   ILE A 312 "
            pdb=" CB  ILE A 312 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.53e-01
  chirality pdb=" CA  ILE D 219 "
            pdb=" N   ILE D 219 "
            pdb=" C   ILE D 219 "
            pdb=" CB  ILE D 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.77e-01
  ... (remaining 1555 not shown)

  Planarity restraints: 1798
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 106 "    0.016 2.00e-02 2.50e+03   1.11e-02 2.46e+00
        pdb=" CG  TYR D 106 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 106 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 106 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 106 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 106 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 106 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR D 106 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 263 "    0.025 5.00e-02 4.00e+02   3.81e-02 2.32e+00
        pdb=" N   PRO B 264 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO B 264 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 264 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 140 "   -0.024 5.00e-02 4.00e+02   3.67e-02 2.15e+00
        pdb=" N   PRO C 141 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO C 141 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C 141 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 1795 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1019
        2.75 -     3.29: 9855
        3.29 -     3.82: 17367
        3.82 -     4.36: 20350
        4.36 -     4.90: 35664
  Nonbonded interactions: 84255
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 234 "
            pdb=" OH  TYR B 245 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" NH2 ARG B  45 "
            pdb=" O   PRO B 110 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" NH2 ARG D  45 "
            pdb=" O   PRO D 110 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" NH1 ARG A  45 "
            pdb=" OE2 GLU C  41 "
     model   vdw
     2.304 3.120
  nonbonded pdb=" OH  TYR A 167 "
            pdb=" OE1 GLU A 260 "
     model   vdw
     2.307 3.040
  ... (remaining 84250 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' and (resid 5 through 110 or resid 116 through 401))
  selection = chain 'B'
  selection = (chain 'C' and (resid 5 through 110 or resid 116 through 401))
  selection = chain 'D'
}

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:             3.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.280
  Find NCS groups from input model:        0.210
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
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      :  0.006   0.135  10380  Z= 0.284
  Angle     :  0.758  18.277  14118  Z= 0.324
  Chirality :  0.039   0.152   1558
  Planarity :  0.004   0.038   1798
  Dihedral  : 14.488  85.974   3790
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.20 (0.25), residues: 1238
  helix:  2.47 (0.18), residues: 746
  sheet: -1.01 (0.39), residues: 154
  loop :  0.49 (0.39), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  45 
 TYR   0.027   0.001   TYR D 106 
 PHE   0.012   0.001   PHE B 279 
 TRP   0.009   0.001   TRP A 119 
 HIS   0.003   0.001   HIS A 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00582 (10380)
  covalent geometry    : angle       0.75811 (14118)
  hydrogen bonds       : bond        0.10921 (  643)
  hydrogen bonds       : angle       6.18947 ( 1890)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 ARG cc_start: 0.7057 (ttm110) cc_final: 0.6201 (mtt90)
REVERT: A  106 TYR cc_start: 0.7523 (t80) cc_final: 0.7130 (t80)
REVERT: A  197 ARG cc_start: 0.7551 (mtp85) cc_final: 0.7303 (mtp85)
REVERT: A  218 ASN cc_start: 0.8049 (m-40) cc_final: 0.7758 (m-40)
REVERT: B  120 MET cc_start: 0.7430 (mmt) cc_final: 0.6804 (mmt)
REVERT: B  180 ARG cc_start: 0.6448 (ttp-110) cc_final: 0.6187 (mtp-110)
REVERT: B  326 SER cc_start: 0.7507 (p) cc_final: 0.7293 (p)
REVERT: C  218 ASN cc_start: 0.8047 (m-40) cc_final: 0.7739 (m-40)
REVERT: D  120 MET cc_start: 0.7630 (mmt) cc_final: 0.7131 (mmt)
REVERT: D  220 ARG cc_start: 0.6674 (mtm110) cc_final: 0.6226 (mtp-110)
REVERT: D  310 ARG cc_start: 0.7979 (tpt170) cc_final: 0.7702 (tpt90)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.1529
  time to fit residues: 23.5725
Evaluate side-chains
  115 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9980
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.5980
   chunk 123 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B 232 HIS
B 332 HIS
D 232 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.152515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.125780 restraints weight = 11068.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 1.85
r_work: 0.3195 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3035 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.0725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10380  Z= 0.132
  Angle     :  0.516   6.045  14118  Z= 0.259
  Chirality :  0.038   0.147   1558
  Planarity :  0.004   0.036   1798
  Dihedral  :  4.453  35.391   1450
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  5.25 %
    Favored  : 94.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.35 (0.25), residues: 1238
  helix:  2.64 (0.18), residues: 744
  sheet: -0.74 (0.40), residues: 142
  loop :  0.23 (0.38), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 281 
 TYR   0.016   0.001   TYR D 106 
 PHE   0.011   0.002   PHE B 279 
 TRP   0.007   0.001   TRP A  34 
 HIS   0.004   0.001   HIS B 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (10380)
  covalent geometry    : angle       0.51560 (14118)
  hydrogen bonds       : bond        0.04034 (  643)
  hydrogen bonds       : angle       4.77665 ( 1890)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 129
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: A  176 GLN cc_start: 0.7459 (mm-40) cc_final: 0.7189 (mm-40)
REVERT: A  218 ASN cc_start: 0.8024 (m-40) cc_final: 0.7367 (t0)
REVERT: B  120 MET cc_start: 0.7363 (mmt) cc_final: 0.6769 (mmt)
REVERT: B  180 ARG cc_start: 0.6539 (ttp-110) cc_final: 0.6200 (mtp-110)
REVERT: B  214 MET cc_start: 0.7797 (mmt) cc_final: 0.7108 (ttt)
REVERT: B  324 SER cc_start: 0.7990 (p) cc_final: 0.7780 (p)
REVERT: C  218 ASN cc_start: 0.8017 (m-40) cc_final: 0.7739 (m-40)
REVERT: D  120 MET cc_start: 0.7638 (mmt) cc_final: 0.7145 (mmt)
REVERT: D  220 ARG cc_start: 0.6651 (mtm110) cc_final: 0.6193 (mtp-110)
REVERT: D  310 ARG cc_start: 0.8012 (tpt170) cc_final: 0.7751 (tpt90)
  outliers start: 6
  outliers final: 5
  residues processed: 131
  average time/residue: 0.1301
  time to fit residues: 21.9763
Evaluate side-chains
  123 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 118
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain C residue  326 SER
Chi-restraints excluded: chain D residue  184 GLN
Chi-restraints excluded: chain D residue  237 ASP
Chi-restraints excluded: chain D residue  256 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 113 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
D 332 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.145467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.118187 restraints weight = 11170.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 1.70
r_work: 0.3117 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2955 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
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      :  0.005   0.065  10380  Z= 0.218
  Angle     :  0.584   5.779  14118  Z= 0.293
  Chirality :  0.042   0.144   1558
  Planarity :  0.005   0.039   1798
  Dihedral  :  4.471  28.711   1450
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  7.79 %
    Favored  : 90.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.24), residues: 1238
  helix:  2.22 (0.18), residues: 748
  sheet: -0.72 (0.40), residues: 142
  loop : -0.02 (0.38), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  95 
 TYR   0.021   0.002   TYR C 106 
 PHE   0.013   0.002   PHE A 291 
 TRP   0.010   0.002   TRP C 161 
 HIS   0.003   0.001   HIS A 185 

Details of bonding type rmsd
  covalent geometry    : bond        0.00528 (10380)
  covalent geometry    : angle       0.58430 (14118)
  hydrogen bonds       : bond        0.04733 (  643)
  hydrogen bonds       : angle       4.91785 ( 1890)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 127
  time to evaluate  : 0.380 
Fit side-chains
REVERT: A  176 GLN cc_start: 0.7498 (mm-40) cc_final: 0.7245 (mm-40)
REVERT: A  218 ASN cc_start: 0.8068 (m-40) cc_final: 0.7766 (m-40)
REVERT: A  220 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7647 (ptm160)
REVERT: A  252 GLN cc_start: 0.7205 (mm-40) cc_final: 0.7002 (mm-40)
REVERT: B  180 ARG cc_start: 0.6662 (ttp-110) cc_final: 0.6048 (mtm-85)
REVERT: B  214 MET cc_start: 0.7843 (mmt) cc_final: 0.7199 (ttt)
REVERT: B  324 SER cc_start: 0.8043 (p) cc_final: 0.7831 (p)
REVERT: C  120 MET cc_start: 0.8316 (ttp) cc_final: 0.8063 (ttp)
REVERT: C  218 ASN cc_start: 0.8004 (m-40) cc_final: 0.7693 (m-40)
REVERT: D  120 MET cc_start: 0.7635 (mmt) cc_final: 0.7332 (mmm)
REVERT: D  220 ARG cc_start: 0.6706 (mtm110) cc_final: 0.6212 (mtp-110)
REVERT: D  310 ARG cc_start: 0.8094 (tpt170) cc_final: 0.7825 (tpt90)
  outliers start: 13
  outliers final: 8
  residues processed: 134
  average time/residue: 0.1471
  time to fit residues: 25.3812
Evaluate side-chains
  127 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 118
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 ARG
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  326 SER
Chi-restraints excluded: chain C residue   80 SER
Chi-restraints excluded: chain C residue  326 SER
Chi-restraints excluded: chain D residue  184 GLN
Chi-restraints excluded: chain D residue  237 ASP
Chi-restraints excluded: chain D residue  324 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 99 optimal weight:    0.9990
   chunk 92 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 98 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 89 optimal weight:    3.9990
   chunk 85 optimal weight:    0.0570
   chunk 8 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    1.2106

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

Flipped N/Q/H residues before XYZ refinement:
A 232 HIS
D 332 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.148643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.121282 restraints weight = 11232.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 1.73
r_work: 0.3189 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3030 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.1291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10380  Z= 0.153
  Angle     :  0.512   5.320  14118  Z= 0.260
  Chirality :  0.039   0.142   1558
  Planarity :  0.004   0.040   1798
  Dihedral  :  4.285  27.110   1450
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 10.04 %
    Favored  : 88.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.02 (0.25), residues: 1238
  helix:  2.38 (0.18), residues: 748
  sheet: -0.69 (0.41), residues: 142
  loop : -0.02 (0.38), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  95 
 TYR   0.022   0.001   TYR C 106 
 PHE   0.009   0.002   PHE B 279 
 TRP   0.008   0.001   TRP A 161 
 HIS   0.003   0.001   HIS D 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (10380)
  covalent geometry    : angle       0.51221 (14118)
  hydrogen bonds       : bond        0.04124 (  643)
  hydrogen bonds       : angle       4.64439 ( 1890)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A  120 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.8030 (ttt)
REVERT: A  218 ASN cc_start: 0.8053 (m-40) cc_final: 0.7759 (m-40)
REVERT: A  220 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.6831 (ptm160)
REVERT: A  252 GLN cc_start: 0.7188 (mm-40) cc_final: 0.6975 (mm-40)
REVERT: B  120 MET cc_start: 0.7417 (mmt) cc_final: 0.6792 (mmt)
REVERT: B  180 ARG cc_start: 0.6579 (ttp-110) cc_final: 0.5980 (mtm-85)
REVERT: B  214 MET cc_start: 0.7770 (mmt) cc_final: 0.7045 (ttt)
REVERT: B  245 TYR cc_start: 0.8687 (m-80) cc_final: 0.8469 (m-80)
REVERT: B  324 SER cc_start: 0.7948 (p) cc_final: 0.7742 (p)
REVERT: C  218 ASN cc_start: 0.8002 (m-40) cc_final: 0.7675 (m-40)
REVERT: C  252 GLN cc_start: 0.7203 (mm110) cc_final: 0.6919 (mm-40)
REVERT: D  120 MET cc_start: 0.7615 (mmt) cc_final: 0.6921 (mmm)
REVERT: D  214 MET cc_start: 0.7855 (mmt) cc_final: 0.7248 (ttt)
REVERT: D  220 ARG cc_start: 0.6624 (mtm110) cc_final: 0.6137 (mtp-110)
REVERT: D  310 ARG cc_start: 0.8060 (tpt170) cc_final: 0.7779 (tpt90)
  outliers start: 13
  outliers final: 6
  residues processed: 133
  average time/residue: 0.1385
  time to fit residues: 23.8713
Evaluate side-chains
  129 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 121
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain A residue  220 ARG
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain C residue   80 SER
Chi-restraints excluded: chain C residue  326 SER
Chi-restraints excluded: chain D residue  237 ASP
Chi-restraints excluded: chain D residue  324 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 90 optimal weight:    0.6980
   chunk 88 optimal weight:    5.9990
   chunk 53 optimal weight:    6.9990
   chunk 61 optimal weight:    0.0970
   chunk 21 optimal weight:    3.9990
   chunk 74 optimal weight:    0.6980
   chunk 26 optimal weight:    4.9990
   chunk 1 optimal weight:    4.9990
   chunk 33 optimal weight:    0.6980
   chunk 75 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 232 HIS
D 332 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.150892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.123641 restraints weight = 11114.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 1.73
r_work: 0.3171 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3009 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10380  Z= 0.125
  Angle     :  0.483   5.156  14118  Z= 0.246
  Chirality :  0.038   0.140   1558
  Planarity :  0.004   0.040   1798
  Dihedral  :  4.139  26.166   1450
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 11.54 %
    Favored  : 86.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.24 (0.25), residues: 1238
  helix:  2.59 (0.18), residues: 748
  sheet: -0.66 (0.41), residues: 142
  loop :  0.02 (0.38), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  95 
 TYR   0.020   0.001   TYR C 106 
 PHE   0.008   0.001   PHE B 279 
 TRP   0.007   0.001   TRP A 161 
 HIS   0.003   0.001   HIS A 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (10380)
  covalent geometry    : angle       0.48318 (14118)
  hydrogen bonds       : bond        0.03827 (  643)
  hydrogen bonds       : angle       4.45263 ( 1890)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 123
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A  120 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.8043 (ttt)
REVERT: A  218 ASN cc_start: 0.8040 (m-40) cc_final: 0.7780 (m-40)
REVERT: A  220 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7338 (ptm160)
REVERT: A  252 GLN cc_start: 0.7184 (mm-40) cc_final: 0.6954 (mm-40)
REVERT: B  120 MET cc_start: 0.7511 (mmt) cc_final: 0.6851 (mmt)
REVERT: B  180 ARG cc_start: 0.6630 (ttp-110) cc_final: 0.6029 (mtm-85)
REVERT: B  214 MET cc_start: 0.7729 (mmt) cc_final: 0.7125 (ttt)
REVERT: B  246 GLU cc_start: 0.7322 (tp30) cc_final: 0.6973 (mm-30)
REVERT: B  324 SER cc_start: 0.7873 (p) cc_final: 0.7672 (p)
REVERT: C  106 TYR cc_start: 0.7764 (t80) cc_final: 0.7538 (t80)
REVERT: C  218 ASN cc_start: 0.8031 (m-40) cc_final: 0.7718 (m-40)
REVERT: C  252 GLN cc_start: 0.7191 (mm110) cc_final: 0.6905 (mm-40)
REVERT: D  120 MET cc_start: 0.7579 (mmt) cc_final: 0.7121 (mmt)
REVERT: D  214 MET cc_start: 0.7862 (mmt) cc_final: 0.7322 (ttt)
REVERT: D  220 ARG cc_start: 0.6718 (mtm110) cc_final: 0.6214 (mtp-110)
REVERT: D  310 ARG cc_start: 0.8091 (tpt170) cc_final: 0.7813 (tpt90)
  outliers start: 16
  outliers final: 9
  residues processed: 133
  average time/residue: 0.1391
  time to fit residues: 24.0398
Evaluate side-chains
  130 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain A residue  220 ARG
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  332 HIS
Chi-restraints excluded: chain C residue   80 SER
Chi-restraints excluded: chain C residue  326 SER
Chi-restraints excluded: chain D residue  184 GLN
Chi-restraints excluded: chain D residue  237 ASP
Chi-restraints excluded: chain D residue  324 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 47 optimal weight:    0.0970
   chunk 114 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 32 optimal weight:    5.9990
   chunk 78 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   chunk 97 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 232 HIS
D 332 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.151441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.124191 restraints weight = 11200.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 1.74
r_work: 0.3199 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3040 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.1343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10380  Z= 0.117
  Angle     :  0.475   5.084  14118  Z= 0.242
  Chirality :  0.037   0.141   1558
  Planarity :  0.004   0.044   1798
  Dihedral  :  4.050  25.864   1450
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 12.48 %
    Favored  : 86.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.42 (0.25), residues: 1238
  helix:  2.72 (0.18), residues: 750
  sheet: -0.58 (0.42), residues: 138
  loop :  0.08 (0.38), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 293 
 TYR   0.018   0.001   TYR C 106 
 PHE   0.008   0.001   PHE B 279 
 TRP   0.006   0.001   TRP A 161 
 HIS   0.003   0.001   HIS A 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (10380)
  covalent geometry    : angle       0.47510 (14118)
  hydrogen bonds       : bond        0.03677 (  643)
  hydrogen bonds       : angle       4.34340 ( 1890)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A  218 ASN cc_start: 0.8032 (m-40) cc_final: 0.7766 (m-40)
REVERT: A  252 GLN cc_start: 0.7222 (mm-40) cc_final: 0.6990 (mm-40)
REVERT: B  120 MET cc_start: 0.7429 (mmt) cc_final: 0.6655 (mmt)
REVERT: B  180 ARG cc_start: 0.6618 (ttp-110) cc_final: 0.6167 (mtm-85)
REVERT: B  214 MET cc_start: 0.7700 (mmt) cc_final: 0.7118 (ttt)
REVERT: B  246 GLU cc_start: 0.7373 (tp30) cc_final: 0.6966 (mm-30)
REVERT: B  324 SER cc_start: 0.7851 (p) cc_final: 0.7639 (p)
REVERT: C  218 ASN cc_start: 0.7980 (m-40) cc_final: 0.7689 (m-40)
REVERT: C  252 GLN cc_start: 0.7194 (mm110) cc_final: 0.6915 (mm-40)
REVERT: D  120 MET cc_start: 0.7527 (mmt) cc_final: 0.6990 (mmt)
REVERT: D  214 MET cc_start: 0.7825 (mmt) cc_final: 0.7250 (ttt)
REVERT: D  220 ARG cc_start: 0.6694 (mtm110) cc_final: 0.6183 (mtp-110)
REVERT: D  310 ARG cc_start: 0.8050 (tpt170) cc_final: 0.7700 (tpt90)
  outliers start: 14
  outliers final: 10
  residues processed: 130
  average time/residue: 0.1404
  time to fit residues: 23.5853
Evaluate side-chains
  127 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 117
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  332 HIS
Chi-restraints excluded: chain C residue   80 SER
Chi-restraints excluded: chain C residue  326 SER
Chi-restraints excluded: chain D residue  184 GLN
Chi-restraints excluded: chain D residue  237 ASP
Chi-restraints excluded: chain D residue  256 THR
Chi-restraints excluded: chain D residue  324 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 86 optimal weight:    0.2980
   chunk 61 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   chunk 39 optimal weight:    6.9990
   chunk 10 optimal weight:    0.0980
   chunk 85 optimal weight:    0.0040
   chunk 93 optimal weight:    3.9990
   chunk 113 optimal weight:    4.9990
   overall best weight:    0.8594

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

Flipped N/Q/H residues before XYZ refinement:
D 332 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.149673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.122829 restraints weight = 11128.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 1.70
r_work: 0.3237 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.1392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10380  Z= 0.126
  Angle     :  0.488   8.311  14118  Z= 0.246
  Chirality :  0.038   0.143   1558
  Planarity :  0.004   0.047   1798
  Dihedral  :  4.097  26.374   1450
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 12.76 %
    Favored  : 85.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.44 (0.25), residues: 1238
  helix:  2.76 (0.18), residues: 748
  sheet: -0.56 (0.42), residues: 138
  loop :  0.05 (0.38), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 281 
 TYR   0.017   0.001   TYR A 106 
 PHE   0.008   0.001   PHE A 291 
 TRP   0.006   0.001   TRP A 161 
 HIS   0.003   0.001   HIS A 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (10380)
  covalent geometry    : angle       0.48798 (14118)
  hydrogen bonds       : bond        0.03751 (  643)
  hydrogen bonds       : angle       4.33173 ( 1890)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 0.370 
Fit side-chains
REVERT: A  218 ASN cc_start: 0.8046 (m-40) cc_final: 0.7793 (m-40)
REVERT: A  220 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7441 (ptm160)
REVERT: A  252 GLN cc_start: 0.7228 (mm-40) cc_final: 0.6992 (mm-40)
REVERT: B   33 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7010 (mp)
REVERT: B  120 MET cc_start: 0.7441 (mmt) cc_final: 0.6735 (mmt)
REVERT: B  180 ARG cc_start: 0.6645 (ttp-110) cc_final: 0.6198 (mtm-85)
REVERT: B  214 MET cc_start: 0.7714 (mmt) cc_final: 0.7161 (ttt)
REVERT: B  246 GLU cc_start: 0.7380 (tp30) cc_final: 0.6914 (mm-30)
REVERT: B  324 SER cc_start: 0.7857 (p) cc_final: 0.7644 (p)
REVERT: C  218 ASN cc_start: 0.7988 (m-40) cc_final: 0.7690 (m-40)
REVERT: C  252 GLN cc_start: 0.7181 (mm110) cc_final: 0.6902 (mm-40)
REVERT: D  120 MET cc_start: 0.7477 (mmt) cc_final: 0.6707 (mmt)
REVERT: D  214 MET cc_start: 0.7835 (mmt) cc_final: 0.7419 (ttt)
REVERT: D  220 ARG cc_start: 0.6679 (mtm110) cc_final: 0.6158 (mtp-110)
REVERT: D  310 ARG cc_start: 0.8005 (tpt170) cc_final: 0.7695 (tpt90)
  outliers start: 15
  outliers final: 11
  residues processed: 130
  average time/residue: 0.1480
  time to fit residues: 24.9068
Evaluate side-chains
  133 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  220 ARG
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  332 HIS
Chi-restraints excluded: chain C residue   80 SER
Chi-restraints excluded: chain C residue  326 SER
Chi-restraints excluded: chain D residue  184 GLN
Chi-restraints excluded: chain D residue  237 ASP
Chi-restraints excluded: chain D residue  256 THR
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain D residue  332 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 55 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 114 optimal weight:    8.9990
   chunk 88 optimal weight:    0.0970
   chunk 109 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 117 optimal weight:    0.7980
   overall best weight:    0.7778

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

Flipped N/Q/H residues before XYZ refinement:
D 332 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.150750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.123577 restraints weight = 11120.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 1.73
r_work: 0.3258 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3100 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.1425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10380  Z= 0.121
  Angle     :  0.482   7.438  14118  Z= 0.243
  Chirality :  0.037   0.143   1558
  Planarity :  0.004   0.050   1798
  Dihedral  :  4.062  25.917   1450
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 13.32 %
    Favored  : 85.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.49 (0.25), residues: 1238
  helix:  2.79 (0.18), residues: 748
  sheet: -0.51 (0.42), residues: 138
  loop :  0.08 (0.38), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 281 
 TYR   0.014   0.001   TYR C 106 
 PHE   0.008   0.001   PHE A 291 
 TRP   0.006   0.001   TRP A 161 
 HIS   0.004   0.001   HIS D 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (10380)
  covalent geometry    : angle       0.48215 (14118)
  hydrogen bonds       : bond        0.03680 (  643)
  hydrogen bonds       : angle       4.29841 ( 1890)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.359 
Fit side-chains
REVERT: A  218 ASN cc_start: 0.8045 (m-40) cc_final: 0.7799 (m-40)
REVERT: A  220 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7452 (ptm160)
REVERT: A  252 GLN cc_start: 0.7229 (mm-40) cc_final: 0.6996 (mm-40)
REVERT: B   33 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.6988 (mp)
REVERT: B  120 MET cc_start: 0.7427 (mmt) cc_final: 0.6649 (mmt)
REVERT: B  180 ARG cc_start: 0.6639 (ttp-110) cc_final: 0.6191 (mtm-85)
REVERT: B  214 MET cc_start: 0.7732 (mmt) cc_final: 0.7239 (ttt)
REVERT: B  246 GLU cc_start: 0.7406 (tp30) cc_final: 0.6911 (mm-30)
REVERT: B  324 SER cc_start: 0.7832 (p) cc_final: 0.7621 (p)
REVERT: C  218 ASN cc_start: 0.7980 (m-40) cc_final: 0.7685 (m-40)
REVERT: C  252 GLN cc_start: 0.7158 (mm110) cc_final: 0.6875 (mm-40)
REVERT: D  120 MET cc_start: 0.7511 (mmt) cc_final: 0.6781 (mmt)
REVERT: D  214 MET cc_start: 0.7834 (mmt) cc_final: 0.7455 (ttt)
REVERT: D  220 ARG cc_start: 0.6673 (mtm110) cc_final: 0.6157 (mtp-110)
REVERT: D  310 ARG cc_start: 0.8023 (tpt170) cc_final: 0.7711 (tpt90)
  outliers start: 16
  outliers final: 13
  residues processed: 129
  average time/residue: 0.1409
  time to fit residues: 23.4912
Evaluate side-chains
  133 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  220 ARG
Chi-restraints excluded: chain A residue  301 ASP
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  332 HIS
Chi-restraints excluded: chain C residue   80 SER
Chi-restraints excluded: chain C residue  326 SER
Chi-restraints excluded: chain D residue  106 TYR
Chi-restraints excluded: chain D residue  184 GLN
Chi-restraints excluded: chain D residue  237 ASP
Chi-restraints excluded: chain D residue  256 THR
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain D residue  332 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 115 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 93 optimal weight:    5.9990
   chunk 103 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 54 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0030
   chunk 99 optimal weight:    0.5980
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
D 332 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.152248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.125131 restraints weight = 11205.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 1.74
r_work: 0.3248 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3090 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.1448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10380  Z= 0.114
  Angle     :  0.475   7.065  14118  Z= 0.240
  Chirality :  0.037   0.142   1558
  Planarity :  0.004   0.051   1798
  Dihedral  :  4.010  25.333   1450
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 13.23 %
    Favored  : 85.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.56 (0.25), residues: 1238
  helix:  2.86 (0.18), residues: 748
  sheet: -0.59 (0.44), residues: 126
  loop :  0.07 (0.37), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 281 
 TYR   0.014   0.001   TYR A 106 
 PHE   0.007   0.001   PHE A 291 
 TRP   0.006   0.001   TRP A 119 
 HIS   0.007   0.001   HIS D 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (10380)
  covalent geometry    : angle       0.47490 (14118)
  hydrogen bonds       : bond        0.03613 (  643)
  hydrogen bonds       : angle       4.24806 ( 1890)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A  218 ASN cc_start: 0.8040 (m-40) cc_final: 0.7799 (m-40)
REVERT: A  220 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7445 (ptm160)
REVERT: B   33 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.6937 (mp)
REVERT: B  120 MET cc_start: 0.7430 (mmt) cc_final: 0.6607 (mmt)
REVERT: B  180 ARG cc_start: 0.6641 (ttp-110) cc_final: 0.6194 (mtm-85)
REVERT: B  214 MET cc_start: 0.7716 (mmt) cc_final: 0.7237 (ttt)
REVERT: B  246 GLU cc_start: 0.7391 (tp30) cc_final: 0.6902 (mm-30)
REVERT: B  324 SER cc_start: 0.7817 (p) cc_final: 0.7604 (p)
REVERT: C  120 MET cc_start: 0.8246 (ttp) cc_final: 0.7969 (ttp)
REVERT: C  218 ASN cc_start: 0.7978 (m-40) cc_final: 0.7685 (m-40)
REVERT: C  252 GLN cc_start: 0.7164 (mm110) cc_final: 0.6884 (mm-40)
REVERT: D  120 MET cc_start: 0.7532 (mmt) cc_final: 0.6830 (mmm)
REVERT: D  214 MET cc_start: 0.7818 (mmt) cc_final: 0.7456 (ttt)
REVERT: D  220 ARG cc_start: 0.6667 (mtm110) cc_final: 0.6153 (mtp-110)
REVERT: D  310 ARG cc_start: 0.8022 (tpt170) cc_final: 0.7713 (tpt90)
  outliers start: 18
  outliers final: 13
  residues processed: 132
  average time/residue: 0.1374
  time to fit residues: 23.4912
Evaluate side-chains
  134 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  220 ARG
Chi-restraints excluded: chain A residue  301 ASP
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  332 HIS
Chi-restraints excluded: chain C residue   80 SER
Chi-restraints excluded: chain C residue  326 SER
Chi-restraints excluded: chain D residue  106 TYR
Chi-restraints excluded: chain D residue  184 GLN
Chi-restraints excluded: chain D residue  237 ASP
Chi-restraints excluded: chain D residue  256 THR
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain D residue  332 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 84 optimal weight:    0.2980
   chunk 27 optimal weight:    3.9990
   chunk 48 optimal weight:    7.9990
   chunk 99 optimal weight:    0.8980
   chunk 60 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 3 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
D 332 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.144543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.117392 restraints weight = 11161.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 1.71
r_work: 0.3160 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3003 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.1651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065  10380  Z= 0.222
  Angle     :  0.594   9.476  14118  Z= 0.295
  Chirality :  0.042   0.152   1558
  Planarity :  0.005   0.057   1798
  Dihedral  :  4.473  29.608   1450
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 14.17 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.90 (0.25), residues: 1238
  helix:  2.28 (0.18), residues: 750
  sheet: -0.56 (0.42), residues: 142
  loop : -0.16 (0.38), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  95 
 TYR   0.022   0.002   TYR A 106 
 PHE   0.014   0.002   PHE A 291 
 TRP   0.013   0.002   TRP D 119 
 HIS   0.006   0.001   HIS D 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 (10380)
  covalent geometry    : angle       0.59415 (14118)
  hydrogen bonds       : bond        0.04668 (  643)
  hydrogen bonds       : angle       4.70875 ( 1890)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.365 
Fit side-chains
REVERT: A  106 TYR cc_start: 0.7695 (t80) cc_final: 0.7475 (t80)
REVERT: A  218 ASN cc_start: 0.8023 (m-40) cc_final: 0.7735 (m-40)
REVERT: A  220 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.6983 (ptm160)
REVERT: A  252 GLN cc_start: 0.7218 (mm-40) cc_final: 0.6975 (mm-40)
REVERT: B   33 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7339 (mp)
REVERT: B  120 MET cc_start: 0.7441 (mmt) cc_final: 0.6597 (mmt)
REVERT: B  180 ARG cc_start: 0.6681 (ttp-110) cc_final: 0.6216 (mtm-85)
REVERT: B  214 MET cc_start: 0.7766 (mmt) cc_final: 0.7274 (ttt)
REVERT: B  246 GLU cc_start: 0.7527 (tp30) cc_final: 0.7006 (mm-30)
REVERT: B  324 SER cc_start: 0.7952 (p) cc_final: 0.7717 (p)
REVERT: C  218 ASN cc_start: 0.8038 (m-40) cc_final: 0.7697 (m-40)
REVERT: C  252 GLN cc_start: 0.7170 (mm110) cc_final: 0.6893 (mm-40)
REVERT: D  120 MET cc_start: 0.7572 (mmt) cc_final: 0.6770 (mmm)
REVERT: D  214 MET cc_start: 0.7841 (mmt) cc_final: 0.7449 (ttt)
REVERT: D  220 ARG cc_start: 0.6668 (mtm110) cc_final: 0.6134 (mtp-110)
REVERT: D  310 ARG cc_start: 0.8076 (tpt170) cc_final: 0.7765 (tpt90)
  outliers start: 13
  outliers final: 8
  residues processed: 130
  average time/residue: 0.1459
  time to fit residues: 24.4868
Evaluate side-chains
  129 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 ARG
Chi-restraints excluded: chain A residue  301 ASP
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain C residue   80 SER
Chi-restraints excluded: chain C residue  326 SER
Chi-restraints excluded: chain D residue  184 GLN
Chi-restraints excluded: chain D residue  237 ASP
Chi-restraints excluded: chain D residue  332 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 58 optimal weight:    0.8980
   chunk 74 optimal weight:    0.8980
   chunk 75 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 21 optimal weight:    5.9990
   chunk 52 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   chunk 34 optimal weight:    0.7980
   chunk 54 optimal weight:    0.6980
   chunk 79 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
D 332 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.154572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.127981 restraints weight = 11014.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 1.69
r_work: 0.3264 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3109 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.1536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10380  Z= 0.126
  Angle     :  0.498   7.804  14118  Z= 0.252
  Chirality :  0.038   0.146   1558
  Planarity :  0.004   0.055   1798
  Dihedral  :  4.156  26.227   1450
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 14.54 %
    Favored  : 84.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.25 (0.25), residues: 1238
  helix:  2.62 (0.18), residues: 750
  sheet: -0.61 (0.42), residues: 142
  loop : -0.07 (0.38), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 281 
 TYR   0.014   0.001   TYR A 106 
 PHE   0.008   0.001   PHE A 291 
 TRP   0.005   0.001   TRP A 161 
 HIS   0.009   0.001   HIS D 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (10380)
  covalent geometry    : angle       0.49790 (14118)
  hydrogen bonds       : bond        0.03806 (  643)
  hydrogen bonds       : angle       4.38618 ( 1890)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2645.66 seconds
wall clock time: 46 minutes 1.93 seconds (2761.93 seconds total)