Starting phenix.real_space_refine
on Wed Mar  4 01:51:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ahe_11784/03_2026/7ahe_11784.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ahe_11784/03_2026/7ahe_11784.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ahe_11784/03_2026/7ahe_11784.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ahe_11784/03_2026/7ahe_11784.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ahe_11784/03_2026/7ahe_11784.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ahe_11784/03_2026/7ahe_11784.cif"
  }
  resolution = 4.1
  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=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      50      5.16       5
     C    6470      2.51       5
     N    1676      2.21       5
     O    1862      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10060
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2016
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 272, 2016
          Classifications: {'peptide': 272}
          Link IDs: {'PTRANS': 12, 'TRANS': 259}
    Chain: "B"
      Number of atoms: 2016
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 272, 2016
          Classifications: {'peptide': 272}
          Link IDs: {'PTRANS': 12, 'TRANS': 259}
    Chain: "C"
      Number of atoms: 2992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 382, 2992
          Classifications: {'peptide': 382}
          Link IDs: {'PTRANS': 14, 'TRANS': 367}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 382, 2992
          Classifications: {'peptide': 382}
          Link IDs: {'PTRANS': 14, 'TRANS': 367}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'2BA': 1}
          Classifications: {'RNA_mixed': 1}
  Time building chain proxies: 2.51, per 1000 atoms: 0.25
  Number of scatterers: 10060
  At special positions: 0
  Unit cell: (102.212, 86.02, 122.452, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      50     16.00
     P       2     15.00
     O    1862      8.00
     N    1676      7.00
     C    6470      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: 0.88
  Conformation dependent library (CDL) restraints added in 483.2 milliseconds
  

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2420

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 12 sheets defined
      65.5% alpha, 8.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 24
    Processing helix  chain 'A' and resid 26 through 49
    Processing helix  chain 'A' and resid 53 through 68
    Processing helix  chain 'A' and resid 72 through 89
    Processing helix  chain 'A' and resid 91 through 122
      Proline residue:  A 114  - end of helix
    Processing helix  chain 'A' and resid 122 through 139
      removed outlier: 3.636A  pdb=" N   ALA A 126 " --> pdb=" O   SER A 122 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LYS A 127 " --> pdb=" O   ASP A 123 " (cutoff:3.500A)
      Proline residue:  A 131  - end of helix
      removed outlier: 3.527A  pdb=" N   MET A 139 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 152
      removed outlier: 4.396A  pdb=" N   TYR A 144 " --> pdb=" O   PRO A 140 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   LEU A 145 " --> pdb=" O   GLY A 141 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   ILE A 146 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      Proline residue:  A 147  - end of helix
    Processing helix  chain 'A' and resid 155 through 181
      removed outlier: 4.016A  pdb=" N   GLY A 159 " --> pdb=" O   GLY A 155 " (cutoff:3.500A)
      Proline residue:  A 169  - end of helix
    Processing helix  chain 'A' and resid 183 through 193
      removed outlier: 3.555A  pdb=" N   VAL A 187 " --> pdb=" O   SER A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 204
    Processing helix  chain 'A' and resid 204 through 232
      removed outlier: 3.639A  pdb=" N   LEU A 208 " --> pdb=" O   LEU A 204 " (cutoff:3.500A)
      removed outlier: 5.810A  pdb=" N   GLY A 211 " --> pdb=" O   PRO A 207 " (cutoff:3.500A)
      removed outlier: 5.262A  pdb=" N   THR A 212 " --> pdb=" O   LEU A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 250
      removed outlier: 3.944A  pdb=" N   GLY A 242 " --> pdb=" O   GLY A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 275
      removed outlier: 3.877A  pdb=" N   LYS A 275 " --> pdb=" O   ARG A 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 51
      removed outlier: 7.668A  pdb=" N   SER B  28 " --> pdb=" O   SER B  24 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   GLY B  29 " --> pdb=" O   THR B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 68
    Processing helix  chain 'B' and resid 72 through 89
    Processing helix  chain 'B' and resid 91 through 122
      Proline residue:  B 114  - end of helix
    Processing helix  chain 'B' and resid 122 through 139
      removed outlier: 3.636A  pdb=" N   ALA B 126 " --> pdb=" O   SER B 122 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LYS B 127 " --> pdb=" O   ASP B 123 " (cutoff:3.500A)
      Proline residue:  B 131  - end of helix
      removed outlier: 3.528A  pdb=" N   MET B 139 " --> pdb=" O   PHE B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 152
      removed outlier: 4.396A  pdb=" N   TYR B 144 " --> pdb=" O   PRO B 140 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   LEU B 145 " --> pdb=" O   GLY B 141 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   ILE B 146 " --> pdb=" O   PHE B 142 " (cutoff:3.500A)
      Proline residue:  B 147  - end of helix
    Processing helix  chain 'B' and resid 155 through 181
      removed outlier: 4.017A  pdb=" N   GLY B 159 " --> pdb=" O   GLY B 155 " (cutoff:3.500A)
      Proline residue:  B 169  - end of helix
    Processing helix  chain 'B' and resid 183 through 193
      removed outlier: 3.556A  pdb=" N   VAL B 187 " --> pdb=" O   SER B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 204
    Processing helix  chain 'B' and resid 204 through 232
      removed outlier: 3.639A  pdb=" N   LEU B 208 " --> pdb=" O   LEU B 204 " (cutoff:3.500A)
      removed outlier: 5.809A  pdb=" N   GLY B 211 " --> pdb=" O   PRO B 207 " (cutoff:3.500A)
      removed outlier: 5.262A  pdb=" N   THR B 212 " --> pdb=" O   LEU B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 250
      removed outlier: 3.944A  pdb=" N   GLY B 242 " --> pdb=" O   GLY B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 275
      removed outlier: 3.876A  pdb=" N   LYS B 275 " --> pdb=" O   ARG B 271 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 26
      removed outlier: 3.963A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 30 through 39
    Processing helix  chain 'C' and resid 67 through 75
    Processing helix  chain 'C' and resid 96 through 107
    Processing helix  chain 'C' and resid 122 through 133
      removed outlier: 4.947A  pdb=" N   GLY C 130 " --> pdb=" O   ASN C 126 " (cutoff:3.500A)
      removed outlier: 5.423A  pdb=" N   LEU C 131 " --> pdb=" O   THR C 127 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 137 through 151
    Processing helix  chain 'C' and resid 152 through 153
      No H-bonds generated for 'chain 'C' and resid 152 through 153'
    Processing helix  chain 'C' and resid 154 through 158
    Processing helix  chain 'C' and resid 161 through 165
      removed outlier: 3.608A  pdb=" N   GLN C 164 " --> pdb=" O   TYR C 161 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 166 through 180
    Processing helix  chain 'C' and resid 190 through 195
      removed outlier: 3.802A  pdb=" N   ALA C 194 " --> pdb=" O   ALA C 191 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 196 through 214
    Processing helix  chain 'C' and resid 224 through 230
    Processing helix  chain 'C' and resid 250 through 255
    Processing helix  chain 'C' and resid 260 through 265
    Processing helix  chain 'C' and resid 292 through 304
    Processing helix  chain 'C' and resid 323 through 332
    Processing helix  chain 'C' and resid 356 through 361
      removed outlier: 4.357A  pdb=" N   TYR C 361 " --> pdb=" O   LEU C 357 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 382 through 390
      removed outlier: 3.998A  pdb=" N   LEU C 386 " --> pdb=" O   ARG C 382 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   GLU C 387 " --> pdb=" O   GLY C 383 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 17 through 26
      removed outlier: 3.964A  pdb=" N   ALA D  21 " --> pdb=" O   ARG D  17 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 30 through 39
    Processing helix  chain 'D' and resid 67 through 75
    Processing helix  chain 'D' and resid 96 through 107
    Processing helix  chain 'D' and resid 122 through 133
      removed outlier: 4.948A  pdb=" N   GLY D 130 " --> pdb=" O   ASN D 126 " (cutoff:3.500A)
      removed outlier: 5.423A  pdb=" N   LEU D 131 " --> pdb=" O   THR D 127 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 137 through 151
    Processing helix  chain 'D' and resid 152 through 153
      No H-bonds generated for 'chain 'D' and resid 152 through 153'
    Processing helix  chain 'D' and resid 154 through 158
    Processing helix  chain 'D' and resid 161 through 165
      removed outlier: 3.610A  pdb=" N   GLN D 164 " --> pdb=" O   TYR D 161 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 166 through 180
    Processing helix  chain 'D' and resid 190 through 195
      removed outlier: 3.802A  pdb=" N   ALA D 194 " --> pdb=" O   ALA D 191 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 196 through 214
    Processing helix  chain 'D' and resid 224 through 230
    Processing helix  chain 'D' and resid 250 through 255
    Processing helix  chain 'D' and resid 260 through 265
    Processing helix  chain 'D' and resid 292 through 304
    Processing helix  chain 'D' and resid 323 through 332
    Processing helix  chain 'D' and resid 358 through 363
      removed outlier: 3.930A  pdb=" N   ASP D 362 " --> pdb=" O   PRO D 358 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 382 through 390
      removed outlier: 3.998A  pdb=" N   LEU D 386 " --> pdb=" O   ARG D 382 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   GLU D 387 " --> pdb=" O   GLY D 383 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 42 through 47
      removed outlier: 5.457A  pdb=" N   TYR C  45 " --> pdb=" O   LYS C  12 " (cutoff:3.500A)
      removed outlier: 7.477A  pdb=" N   LYS C  12 " --> pdb=" O   TYR C  45 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 47
      removed outlier: 5.457A  pdb=" N   TYR C  45 " --> pdb=" O   LYS C  12 " (cutoff:3.500A)
      removed outlier: 7.477A  pdb=" N   LYS C  12 " --> pdb=" O   TYR C  45 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   LEU C  10 " --> pdb=" O   SER C  82 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   SER C  82 " --> pdb=" O   LEU C  10 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 57 through 59
    Processing sheet with id=AA4, first strand: chain 'C' and resid 237 through 238
      removed outlier: 3.940A  pdb=" N   MET C 244 " --> pdb=" O   ILE C 237 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 307 through 311
    Processing sheet with id=AA6, first strand: chain 'C' and resid 369 through 370
      removed outlier: 3.965A  pdb=" N   GLY C 378 " --> pdb=" O   VAL C 369 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 42 through 47
      removed outlier: 5.458A  pdb=" N   TYR D  45 " --> pdb=" O   LYS D  12 " (cutoff:3.500A)
      removed outlier: 7.478A  pdb=" N   LYS D  12 " --> pdb=" O   TYR D  45 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 42 through 47
      removed outlier: 5.458A  pdb=" N   TYR D  45 " --> pdb=" O   LYS D  12 " (cutoff:3.500A)
      removed outlier: 7.478A  pdb=" N   LYS D  12 " --> pdb=" O   TYR D  45 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   LEU D  10 " --> pdb=" O   SER D  82 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   SER D  82 " --> pdb=" O   LEU D  10 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 57 through 59
    Processing sheet with id=AB1, first strand: chain 'D' and resid 237 through 238
      removed outlier: 3.941A  pdb=" N   MET D 244 " --> pdb=" O   ILE D 237 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 307 through 311
    Processing sheet with id=AB3, first strand: chain 'D' and resid 369 through 370
      removed outlier: 3.966A  pdb=" N   GLY D 378 " --> pdb=" O   VAL D 369 " (cutoff:3.500A)

    591 hydrogen bonds defined for protein.
    1719 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: 1.17 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3207
        1.34 -     1.45: 1180
        1.45 -     1.57: 5721
        1.57 -     1.69: 4
        1.69 -     1.81: 100
  Bond restraints: 10212
  Sorted by residual:
  bond pdb=" C5' 2BA C 501 "
       pdb=" O5' 2BA C 501 "
    ideal  model  delta    sigma   weight residual
    1.433  1.357  0.076 2.00e-02 2.50e+03 1.44e+01
  bond pdb="C3'1 2BA C 501 "
       pdb="O3'1 2BA C 501 "
    ideal  model  delta    sigma   weight residual
    1.418  1.350  0.068 2.00e-02 2.50e+03 1.16e+01
  bond pdb="C5'1 2BA C 501 "
       pdb="O5'1 2BA C 501 "
    ideal  model  delta    sigma   weight residual
    1.427  1.363  0.064 2.00e-02 2.50e+03 1.03e+01
  bond pdb=" N   VAL D 353 "
       pdb=" CA  VAL D 353 "
    ideal  model  delta    sigma   weight residual
    1.462  1.497 -0.035 1.14e-02 7.69e+03 9.17e+00
  bond pdb=" N   LEU C 352 "
       pdb=" CA  LEU C 352 "
    ideal  model  delta    sigma   weight residual
    1.453  1.490 -0.037 1.22e-02 6.72e+03 9.11e+00
  ... (remaining 10207 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.45: 13443
        2.45 -     4.89: 292
        4.89 -     7.34: 51
        7.34 -     9.79: 25
        9.79 -    12.23: 17
  Bond angle restraints: 13828
  Sorted by residual:
  angle pdb=" C   SER A  16 "
        pdb=" N   SER A  17 "
        pdb=" CA  SER A  17 "
      ideal   model   delta    sigma   weight residual
     120.54  132.77  -12.23 1.35e+00 5.49e-01 8.21e+01
  angle pdb=" C   SER B  16 "
        pdb=" N   SER B  17 "
        pdb=" CA  SER B  17 "
      ideal   model   delta    sigma   weight residual
     120.54  132.76  -12.22 1.35e+00 5.49e-01 8.19e+01
  angle pdb=" C   LEU B  40 "
        pdb=" N   MET B  41 "
        pdb=" CA  MET B  41 "
      ideal   model   delta    sigma   weight residual
     120.44  131.09  -10.65 1.30e+00 5.92e-01 6.71e+01
  angle pdb=" C   GLY A  43 "
        pdb=" N   ILE A  44 "
        pdb=" CA  ILE A  44 "
      ideal   model   delta    sigma   weight residual
     120.60  131.11  -10.51 1.29e+00 6.01e-01 6.64e+01
  angle pdb=" C   LEU A  40 "
        pdb=" N   MET A  41 "
        pdb=" CA  MET A  41 "
      ideal   model   delta    sigma   weight residual
     120.44  131.03  -10.59 1.30e+00 5.92e-01 6.64e+01
  ... (remaining 13823 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.05: 5988
       23.05 -    46.10: 223
       46.10 -    69.16: 47
       69.16 -    92.21: 6
       92.21 -   115.26: 6
  Dihedral angle restraints: 6270
    sinusoidal: 2536
      harmonic: 3734
  Sorted by residual:
  dihedral pdb=" CA  ILE D 218 "
           pdb=" C   ILE D 218 "
           pdb=" N   ILE D 219 "
           pdb=" CA  ILE D 219 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.65   20.35     0      5.00e+00 4.00e-02 1.66e+01
  dihedral pdb=" CA  ILE C 218 "
           pdb=" C   ILE C 218 "
           pdb=" N   ILE C 219 "
           pdb=" CA  ILE C 219 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.66   20.34     0      5.00e+00 4.00e-02 1.65e+01
  dihedral pdb=" C5' 2BA C 501 "
           pdb=" O5' 2BA C 501 "
           pdb=" P   2BA C 501 "
           pdb=" O2P 2BA C 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -34.39   80.87 -115.26     1      3.00e+01 1.11e-03 1.52e+01
  ... (remaining 6267 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.172: 1647
       0.172 -    0.345: 22
       0.345 -    0.517: 11
       0.517 -    0.690: 2
       0.690 -    0.862: 6
  Chirality restraints: 1688
  Sorted by residual:
  chirality pdb=" CG  LEU A  66 "
            pdb=" CB  LEU A  66 "
            pdb=" CD1 LEU A  66 "
            pdb=" CD2 LEU A  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.73   -0.86 2.00e-01 2.50e+01 1.86e+01
  chirality pdb=" CG  LEU B  66 "
            pdb=" CB  LEU B  66 "
            pdb=" CD1 LEU B  66 "
            pdb=" CD2 LEU B  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.73   -0.86 2.00e-01 2.50e+01 1.85e+01
  chirality pdb=" CG  LEU B 208 "
            pdb=" CB  LEU B 208 "
            pdb=" CD1 LEU B 208 "
            pdb=" CD2 LEU B 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.86   -0.73 2.00e-01 2.50e+01 1.35e+01
  ... (remaining 1685 not shown)

  Planarity restraints: 1732
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A  34 "   -0.016 2.00e-02 2.50e+03   3.15e-02 9.95e+00
        pdb=" C   GLN A  34 "    0.055 2.00e-02 2.50e+03
        pdb=" O   GLN A  34 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   LYS A  35 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B  34 "   -0.016 2.00e-02 2.50e+03   3.15e-02 9.95e+00
        pdb=" C   GLN B  34 "    0.055 2.00e-02 2.50e+03
        pdb=" O   GLN B  34 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   LYS B  35 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A  61 "   -0.009 2.00e-02 2.50e+03   1.87e-02 3.49e+00
        pdb=" C   THR A  61 "    0.032 2.00e-02 2.50e+03
        pdb=" O   THR A  61 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ILE A  62 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1729 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1305
        2.74 -     3.28: 11475
        3.28 -     3.82: 16245
        3.82 -     4.36: 19894
        4.36 -     4.90: 33884
  Nonbonded interactions: 82803
  Sorted by model distance:
  nonbonded pdb=" O   ASP B  20 "
            pdb=" OG  SER B  24 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" O   ASP A  20 "
            pdb=" OG  SER A  24 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" O   LYS D 158 "
            pdb=" OD1 ASP D 159 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" O   LYS C 158 "
            pdb=" OD1 ASP C 159 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" N   ASP C 371 "
            pdb=" O   PHE C 375 "
     model   vdw
     2.228 3.120
  ... (remaining 82798 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = (chain 'C' and resid 3 through 391)
  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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.720
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
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      :  0.007   0.076  10212  Z= 0.324
  Angle     :  1.010  12.232  13828  Z= 0.616
  Chirality :  0.085   0.862   1688
  Planarity :  0.004   0.034   1732
  Dihedral  : 13.736 115.258   3850
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 16.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.65 %
    Favored  : 90.35 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  1.18 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.40 (0.17), residues: 1296
  helix: -2.87 (0.14), residues: 764
  sheet: -5.40 (0.25), residues: 98
  loop : -4.16 (0.23), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 104 
 TYR   0.005   0.001   TYR B 144 
 PHE   0.012   0.001   PHE D 115 
 TRP   0.010   0.001   TRP B  21 
 HIS   0.004   0.002   HIS C 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00655 (10212)
  covalent geometry    : angle       1.00965 (13828)
  hydrogen bonds       : bond        0.13685 (  587)
  hydrogen bonds       : angle       6.83015 ( 1719)

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  353 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 348
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 ASP cc_start: 0.7838 (m-30) cc_final: 0.7175 (m-30)
REVERT: C  284 LEU cc_start: 0.8771 (mt) cc_final: 0.8321 (mm)
REVERT: C  353 VAL cc_start: 0.7470 (OUTLIER) cc_final: 0.7191 (m)
REVERT: D   24 MET cc_start: 0.8969 (mtt) cc_final: 0.8225 (mmm)
REVERT: D  129 TYR cc_start: 0.8633 (t80) cc_final: 0.8377 (t80)
REVERT: D  160 GLN cc_start: 0.7918 (mt0) cc_final: 0.7654 (mt0)
REVERT: D  313 LYS cc_start: 0.8630 (ttpt) cc_final: 0.8388 (tptt)
  outliers start: 5
  outliers final: 0
  residues processed: 352
  average time/residue: 0.1107
  time to fit residues: 52.7889
Evaluate side-chains
  193 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 192
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 107 optimal weight:   20.0000
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9980
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    0.6980
   chunk 55 optimal weight:   10.0000
   chunk 129 optimal weight:    5.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
B 248 GLN
C  96 ASN
C 126 ASN
C 160 GLN
C 226 ASN
C 255 ASN
** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 325 GLN
D  90 GLN
D  96 ASN
D 114 ASN
D 126 ASN
D 211 GLN
D 226 ASN
D 255 ASN
D 325 GLN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.091270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.080087 restraints weight = 34069.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.082276 restraints weight = 19727.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.083741 restraints weight = 12840.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.084900 restraints weight = 9187.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.085636 restraints weight = 7016.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.3330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.119  10212  Z= 0.168
  Angle     :  0.675   7.599  13828  Z= 0.345
  Chirality :  0.046   0.296   1688
  Planarity :  0.005   0.057   1732
  Dihedral  :  6.820  60.769   1426
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  4.43 %
    Favored  : 95.48 %
  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 are not related in a simple way.
  whole: -2.17 (0.22), residues: 1296
  helix: -0.33 (0.18), residues: 786
  sheet: -4.41 (0.28), residues: 102
  loop : -2.69 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C  17 
 TYR   0.008   0.001   TYR D  45 
 PHE   0.019   0.002   PHE D  49 
 TRP   0.014   0.001   TRP B  91 
 HIS   0.001   0.001   HIS D 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (10212)
  covalent geometry    : angle       0.67544 (13828)
  hydrogen bonds       : bond        0.04243 (  587)
  hydrogen bonds       : angle       4.86735 ( 1719)

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 225
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ILE cc_start: 0.9258 (mm) cc_final: 0.8948 (tt)
REVERT: A   91 TRP cc_start: 0.8325 (t-100) cc_final: 0.7987 (t-100)
REVERT: B   93 ASP cc_start: 0.7673 (m-30) cc_final: 0.7307 (m-30)
REVERT: B  133 LEU cc_start: 0.7367 (mt) cc_final: 0.7068 (tt)
REVERT: B  205 GLU cc_start: 0.8536 (mp0) cc_final: 0.7749 (mp0)
REVERT: C   22 LEU cc_start: 0.9201 (tp) cc_final: 0.8371 (tp)
REVERT: C   26 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8253 (mt-10)
REVERT: C  234 ARG cc_start: 0.8555 (mtp-110) cc_final: 0.7895 (mtm110)
REVERT: C  308 LEU cc_start: 0.9180 (mt) cc_final: 0.8646 (mt)
REVERT: D   24 MET cc_start: 0.8858 (mtt) cc_final: 0.8414 (mmm)
REVERT: D   60 MET cc_start: 0.7543 (mtp) cc_final: 0.7340 (mtp)
REVERT: D  190 GLU cc_start: 0.7558 (mt-10) cc_final: 0.6951 (mm-30)
REVERT: D  234 ARG cc_start: 0.8518 (mtp-110) cc_final: 0.8105 (mtm110)
REVERT: D  238 MET cc_start: 0.8200 (ttm) cc_final: 0.7658 (ttm)
  outliers start: 1
  outliers final: 0
  residues processed: 226
  average time/residue: 0.0894
  time to fit residues: 28.6270
Evaluate side-chains
  163 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   chunk 17 optimal weight:    6.9990
   chunk 85 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 62 optimal weight:    7.9990
   chunk 1 optimal weight:    7.9990
   chunk 111 optimal weight:    0.9980
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 181 GLN
A 248 GLN
** B  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 GLN
C  90 GLN
C 223 HIS
** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.088609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.077531 restraints weight = 35029.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.079718 restraints weight = 19630.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.081233 restraints weight = 12599.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.082258 restraints weight = 8886.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.083118 restraints weight = 6829.175|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.4139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10212  Z= 0.157
  Angle     :  0.647  10.863  13828  Z= 0.331
  Chirality :  0.045   0.309   1688
  Planarity :  0.004   0.073   1732
  Dihedral  :  6.247  55.863   1426
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  4.07 %
    Favored  : 95.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.90 (0.24), residues: 1296
  helix:  0.71 (0.19), residues: 784
  sheet: -3.54 (0.34), residues: 102
  loop : -2.34 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 141 
 TYR   0.013   0.002   TYR D 129 
 PHE   0.026   0.002   PHE C 115 
 TRP   0.021   0.001   TRP A  14 
 HIS   0.002   0.001   HIS D   9 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (10212)
  covalent geometry    : angle       0.64670 (13828)
  hydrogen bonds       : bond        0.03912 (  587)
  hydrogen bonds       : angle       4.57231 ( 1719)

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 202
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ILE cc_start: 0.9274 (mm) cc_final: 0.8912 (tt)
REVERT: A  205 GLU cc_start: 0.8634 (mp0) cc_final: 0.8236 (mm-30)
REVERT: A  219 GLN cc_start: 0.8294 (mp10) cc_final: 0.7874 (mp10)
REVERT: A  227 MET cc_start: 0.8971 (mmm) cc_final: 0.8714 (mmm)
REVERT: B   14 TRP cc_start: 0.6514 (m100) cc_final: 0.6173 (m100)
REVERT: B   93 ASP cc_start: 0.7802 (m-30) cc_final: 0.7583 (m-30)
REVERT: B  133 LEU cc_start: 0.7672 (mt) cc_final: 0.7365 (tt)
REVERT: B  205 GLU cc_start: 0.8652 (mp0) cc_final: 0.8362 (mm-30)
REVERT: B  219 GLN cc_start: 0.8314 (mp10) cc_final: 0.7724 (mp10)
REVERT: B  227 MET cc_start: 0.8872 (mmm) cc_final: 0.8496 (mmm)
REVERT: C   22 LEU cc_start: 0.9240 (tp) cc_final: 0.8433 (tp)
REVERT: C   24 MET cc_start: 0.8778 (mtp) cc_final: 0.8402 (mtp)
REVERT: C   26 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8387 (mt-10)
REVERT: C  234 ARG cc_start: 0.8745 (mtp-110) cc_final: 0.8106 (mtm110)
REVERT: C  308 LEU cc_start: 0.9102 (mt) cc_final: 0.8811 (mt)
REVERT: C  359 ILE cc_start: 0.8132 (mp) cc_final: 0.7551 (mm)
REVERT: D   24 MET cc_start: 0.8880 (mtt) cc_final: 0.8566 (mmm)
REVERT: D  190 GLU cc_start: 0.7731 (mt-10) cc_final: 0.6878 (mm-30)
REVERT: D  234 ARG cc_start: 0.8571 (mtp-110) cc_final: 0.8120 (mtm110)
  outliers start: 1
  outliers final: 0
  residues processed: 202
  average time/residue: 0.0875
  time to fit residues: 25.6102
Evaluate side-chains
  163 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 63 optimal weight:   10.0000
   chunk 38 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9990
   chunk 75 optimal weight:    4.9990
   chunk 89 optimal weight:    8.9990
   chunk 50 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 81 optimal weight:    9.9990
   chunk 111 optimal weight:    0.9980
   chunk 71 optimal weight:    7.9990
   chunk 127 optimal weight:    5.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
** B  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 248 GLN
C 134 GLN
C 211 GLN
** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 134 GLN
D 316 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.082040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.071493 restraints weight = 35723.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.073503 restraints weight = 19969.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.074928 restraints weight = 12762.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.075946 restraints weight = 9006.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.076658 restraints weight = 6875.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.5174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.090  10212  Z= 0.232
  Angle     :  0.721   9.083  13828  Z= 0.367
  Chirality :  0.049   0.278   1688
  Planarity :  0.005   0.067   1732
  Dihedral  :  6.044  49.080   1426
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.89 %
    Favored  : 95.93 %
  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 are not related in a simple way.
  whole: -0.43 (0.24), residues: 1296
  helix:  0.93 (0.19), residues: 788
  sheet: -2.54 (0.42), residues: 116
  loop : -2.01 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 241 
 TYR   0.011   0.002   TYR C 129 
 PHE   0.031   0.002   PHE B 272 
 TRP   0.032   0.002   TRP A  14 
 HIS   0.003   0.001   HIS C 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00521 (10212)
  covalent geometry    : angle       0.72113 (13828)
  hydrogen bonds       : bond        0.04078 (  587)
  hydrogen bonds       : angle       4.64555 ( 1719)

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 197
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  205 GLU cc_start: 0.8818 (mp0) cc_final: 0.8521 (mm-30)
REVERT: A  227 MET cc_start: 0.9097 (mmm) cc_final: 0.8805 (mmm)
REVERT: B   14 TRP cc_start: 0.6906 (m100) cc_final: 0.6667 (m100)
REVERT: B  133 LEU cc_start: 0.8058 (mt) cc_final: 0.7749 (tp)
REVERT: B  136 MET cc_start: 0.7838 (ptm) cc_final: 0.7477 (ptm)
REVERT: B  227 MET cc_start: 0.9129 (mmm) cc_final: 0.8790 (mmm)
REVERT: C   24 MET cc_start: 0.8817 (mtp) cc_final: 0.8484 (mtp)
REVERT: C  156 ASP cc_start: 0.7668 (p0) cc_final: 0.7270 (p0)
REVERT: C  157 PHE cc_start: 0.8256 (m-80) cc_final: 0.7972 (m-10)
REVERT: C  190 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7385 (mm-30)
REVERT: C  233 ASP cc_start: 0.8526 (m-30) cc_final: 0.7737 (t70)
REVERT: C  308 LEU cc_start: 0.9320 (mt) cc_final: 0.8862 (mt)
REVERT: D   24 MET cc_start: 0.8932 (mtt) cc_final: 0.8661 (mmm)
  outliers start: 2
  outliers final: 2
  residues processed: 198
  average time/residue: 0.0832
  time to fit residues: 24.2849
Evaluate side-chains
  155 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 153
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 86 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 14 optimal weight:   10.0000
   chunk 91 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 60 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 81 optimal weight:    5.9990
   chunk 8 optimal weight:    7.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 181 GLN
A 218 ASN
** B  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 218 ASN
B 248 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.084224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.073398 restraints weight = 35279.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.075464 restraints weight = 19806.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.076932 restraints weight = 12773.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.077922 restraints weight = 9048.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.078633 restraints weight = 6985.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.5518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10212  Z= 0.134
  Angle     :  0.642   8.178  13828  Z= 0.322
  Chirality :  0.045   0.280   1688
  Planarity :  0.004   0.074   1732
  Dihedral  :  5.838  45.509   1426
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  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 are not related in a simple way.
  whole: -0.15 (0.24), residues: 1296
  helix:  1.11 (0.19), residues: 782
  sheet: -2.22 (0.43), residues: 126
  loop : -1.81 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 241 
 TYR   0.015   0.002   TYR A 144 
 PHE   0.016   0.001   PHE C 115 
 TRP   0.008   0.001   TRP B  91 
 HIS   0.001   0.000   HIS D 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (10212)
  covalent geometry    : angle       0.64248 (13828)
  hydrogen bonds       : bond        0.03796 (  587)
  hydrogen bonds       : angle       4.44648 ( 1719)

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 MET cc_start: 0.8403 (mmm) cc_final: 0.7649 (mmm)
REVERT: A  136 MET cc_start: 0.7661 (ptm) cc_final: 0.7320 (ptm)
REVERT: A  205 GLU cc_start: 0.8705 (mp0) cc_final: 0.7895 (mp0)
REVERT: A  241 ARG cc_start: 0.8311 (tpp80) cc_final: 0.7980 (tpp80)
REVERT: C  190 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7158 (mm-30)
REVERT: C  233 ASP cc_start: 0.8571 (m-30) cc_final: 0.7732 (t70)
REVERT: C  234 ARG cc_start: 0.8865 (mtp-110) cc_final: 0.7817 (mtm110)
REVERT: D   24 MET cc_start: 0.8877 (mtt) cc_final: 0.8656 (mmm)
REVERT: D  308 LEU cc_start: 0.9100 (mt) cc_final: 0.8839 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 192
  average time/residue: 0.0907
  time to fit residues: 25.0557
Evaluate side-chains
  146 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 109 optimal weight:    1.9990
   chunk 96 optimal weight:    5.9990
   chunk 125 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 98 optimal weight:    0.8980
   chunk 103 optimal weight:    0.9990
   chunk 60 optimal weight:    7.9990
   chunk 26 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9990
   chunk 127 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
A  34 GLN
A 181 GLN
** B  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 GLN
B 218 ASN
B 248 GLN
** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.083685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.072887 restraints weight = 36091.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.074948 restraints weight = 20279.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.076390 restraints weight = 13034.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.077374 restraints weight = 9261.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.078159 restraints weight = 7177.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.5797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  10212  Z= 0.139
  Angle     :  0.638   7.726  13828  Z= 0.322
  Chirality :  0.045   0.304   1688
  Planarity :  0.004   0.076   1732
  Dihedral  :  5.737  43.836   1426
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  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 are not related in a simple way.
  whole:  0.08 (0.24), residues: 1296
  helix:  1.19 (0.19), residues: 780
  sheet: -1.69 (0.45), residues: 126
  loop : -1.64 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A 173 
 TYR   0.022   0.002   TYR D 129 
 PHE   0.024   0.001   PHE A 166 
 TRP   0.009   0.001   TRP B  14 
 HIS   0.001   0.000   HIS D   9 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (10212)
  covalent geometry    : angle       0.63767 (13828)
  hydrogen bonds       : bond        0.03679 (  587)
  hydrogen bonds       : angle       4.47202 ( 1719)

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 MET cc_start: 0.7900 (ptm) cc_final: 0.7282 (ptm)
REVERT: A  205 GLU cc_start: 0.8672 (mp0) cc_final: 0.8012 (mm-30)
REVERT: B  119 MET cc_start: 0.8303 (mmm) cc_final: 0.8089 (mmm)
REVERT: C   24 MET cc_start: 0.8684 (mtp) cc_final: 0.8336 (mtp)
REVERT: C  225 LEU cc_start: 0.9302 (mm) cc_final: 0.9029 (mt)
REVERT: C  233 ASP cc_start: 0.8563 (m-30) cc_final: 0.7741 (t70)
REVERT: C  234 ARG cc_start: 0.8858 (mtp-110) cc_final: 0.7890 (mtm110)
REVERT: C  300 MET cc_start: 0.9102 (mmt) cc_final: 0.8563 (mmm)
REVERT: C  308 LEU cc_start: 0.9249 (mt) cc_final: 0.8825 (mt)
REVERT: D   24 MET cc_start: 0.8828 (mtt) cc_final: 0.8607 (mmm)
REVERT: D  190 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7185 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.0787
  time to fit residues: 21.1075
Evaluate side-chains
  147 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 93 optimal weight:    8.9990
   chunk 123 optimal weight:    1.9990
   chunk 113 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 54 optimal weight:    9.9990
   chunk 78 optimal weight:    0.7980
   chunk 76 optimal weight:    6.9990
   chunk 39 optimal weight:    0.1980
   chunk 100 optimal weight:    6.9990
   chunk 95 optimal weight:    2.9990
   chunk 57 optimal weight:    7.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A  34 GLN
A 181 GLN
A 218 ASN
** B  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 218 ASN
** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 211 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.083131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.072736 restraints weight = 35541.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.074774 restraints weight = 19718.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.076182 restraints weight = 12585.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.077088 restraints weight = 8881.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.077816 restraints weight = 6878.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.6068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10212  Z= 0.141
  Angle     :  0.635   7.731  13828  Z= 0.319
  Chirality :  0.045   0.263   1688
  Planarity :  0.004   0.075   1732
  Dihedral  :  5.606  41.341   1426
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  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 are not related in a simple way.
  whole:  0.22 (0.24), residues: 1296
  helix:  1.22 (0.19), residues: 780
  sheet: -0.92 (0.54), residues: 106
  loop : -1.63 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 241 
 TYR   0.029   0.003   TYR D 129 
 PHE   0.021   0.001   PHE B 142 
 TRP   0.011   0.001   TRP B  14 
 HIS   0.001   0.001   HIS D 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (10212)
  covalent geometry    : angle       0.63545 (13828)
  hydrogen bonds       : bond        0.03557 (  587)
  hydrogen bonds       : angle       4.48158 ( 1719)

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 MET cc_start: 0.8550 (mmm) cc_final: 0.7722 (mmm)
REVERT: A  205 GLU cc_start: 0.8680 (mp0) cc_final: 0.8034 (mm-30)
REVERT: B  119 MET cc_start: 0.8274 (mmm) cc_final: 0.7605 (mmm)
REVERT: B  241 ARG cc_start: 0.8367 (mtm110) cc_final: 0.8127 (mtm110)
REVERT: C   24 MET cc_start: 0.8630 (mtp) cc_final: 0.8336 (ttt)
REVERT: C  225 LEU cc_start: 0.9267 (mm) cc_final: 0.8952 (mt)
REVERT: D   24 MET cc_start: 0.8862 (mtt) cc_final: 0.8626 (mmm)
REVERT: D  101 LEU cc_start: 0.8936 (tp) cc_final: 0.8716 (tp)
REVERT: D  190 GLU cc_start: 0.7524 (mt-10) cc_final: 0.6969 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.0847
  time to fit residues: 22.9794
Evaluate side-chains
  141 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 118 optimal weight:    0.0770
   chunk 46 optimal weight:    3.9990
   chunk 114 optimal weight:    0.8980
   chunk 54 optimal weight:   10.0000
   chunk 4 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   overall best weight:    0.7942

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

Flipped N/Q/H residues before XYZ refinement:
A 248 GLN
** B  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 GLN
B 248 GLN
C 211 GLN
** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.083829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.073134 restraints weight = 35924.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.075213 restraints weight = 19971.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.076642 restraints weight = 12780.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.077634 restraints weight = 9076.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.078155 restraints weight = 6993.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.6277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10212  Z= 0.127
  Angle     :  0.654   8.904  13828  Z= 0.324
  Chirality :  0.045   0.239   1688
  Planarity :  0.004   0.074   1732
  Dihedral  :  5.516  39.332   1426
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  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 are not related in a simple way.
  whole:  0.42 (0.24), residues: 1296
  helix:  1.35 (0.19), residues: 780
  sheet: -0.70 (0.55), residues: 106
  loop : -1.54 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 241 
 TYR   0.034   0.003   TYR C 129 
 PHE   0.018   0.001   PHE D 115 
 TRP   0.009   0.001   TRP B  14 
 HIS   0.001   0.000   HIS C 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (10212)
  covalent geometry    : angle       0.65439 (13828)
  hydrogen bonds       : bond        0.03491 (  587)
  hydrogen bonds       : angle       4.46311 ( 1719)

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  205 GLU cc_start: 0.8643 (mp0) cc_final: 0.8069 (mm-30)
REVERT: A  244 LEU cc_start: 0.8848 (tt) cc_final: 0.8509 (tp)
REVERT: A  248 GLN cc_start: 0.8834 (mp10) cc_final: 0.8619 (mp10)
REVERT: B  119 MET cc_start: 0.8148 (mmm) cc_final: 0.7558 (mmm)
REVERT: B  136 MET cc_start: 0.8410 (ptm) cc_final: 0.8202 (ptm)
REVERT: B  241 ARG cc_start: 0.8352 (mtm110) cc_final: 0.8124 (mtm110)
REVERT: C   24 MET cc_start: 0.8672 (mtp) cc_final: 0.8403 (ttt)
REVERT: C  190 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7006 (mm-30)
REVERT: C  225 LEU cc_start: 0.9211 (mm) cc_final: 0.8869 (mt)
REVERT: C  233 ASP cc_start: 0.8557 (m-30) cc_final: 0.7799 (t70)
REVERT: C  300 MET cc_start: 0.9102 (mmt) cc_final: 0.8567 (mmm)
REVERT: C  308 LEU cc_start: 0.9233 (mt) cc_final: 0.8932 (mt)
REVERT: D   24 MET cc_start: 0.8901 (mtt) cc_final: 0.8644 (mmm)
REVERT: D  101 LEU cc_start: 0.8943 (tp) cc_final: 0.8708 (tp)
REVERT: D  190 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7119 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 194
  average time/residue: 0.0831
  time to fit residues: 23.8263
Evaluate side-chains
  152 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 55 optimal weight:    8.9990
   chunk 6 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 102 optimal weight:   10.0000
   chunk 82 optimal weight:    0.9990
   chunk 87 optimal weight:    8.9990
   chunk 73 optimal weight:    0.7980
   chunk 117 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 181 GLN
** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.083811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.073322 restraints weight = 35709.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.075357 restraints weight = 20072.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.076774 restraints weight = 12912.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.077743 restraints weight = 9146.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.078434 restraints weight = 7066.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.6468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  10212  Z= 0.132
  Angle     :  0.659   7.737  13828  Z= 0.331
  Chirality :  0.045   0.249   1688
  Planarity :  0.004   0.074   1732
  Dihedral  :  5.484  38.062   1426
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  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 are not related in a simple way.
  whole:  0.49 (0.24), residues: 1296
  helix:  1.30 (0.19), residues: 790
  sheet: -0.61 (0.56), residues: 106
  loop : -1.35 (0.32), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 241 
 TYR   0.035   0.002   TYR C 129 
 PHE   0.025   0.001   PHE C 115 
 TRP   0.011   0.001   TRP B  14 
 HIS   0.001   0.000   HIS D   9 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (10212)
  covalent geometry    : angle       0.65893 (13828)
  hydrogen bonds       : bond        0.03568 (  587)
  hydrogen bonds       : angle       4.54308 ( 1719)

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 MET cc_start: 0.8326 (mmm) cc_final: 0.7876 (mmm)
REVERT: A  205 GLU cc_start: 0.8619 (mp0) cc_final: 0.8024 (mm-30)
REVERT: A  227 MET cc_start: 0.8601 (tpp) cc_final: 0.8388 (mpp)
REVERT: C   24 MET cc_start: 0.8632 (mtp) cc_final: 0.8340 (ttt)
REVERT: C  190 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7016 (mm-30)
REVERT: C  234 ARG cc_start: 0.8845 (mtp-110) cc_final: 0.8005 (mtm110)
REVERT: C  300 MET cc_start: 0.9084 (mmt) cc_final: 0.8490 (mmm)
REVERT: C  308 LEU cc_start: 0.9251 (mt) cc_final: 0.8878 (mt)
REVERT: D   24 MET cc_start: 0.8919 (mtt) cc_final: 0.8657 (mmm)
REVERT: D  101 LEU cc_start: 0.8966 (tp) cc_final: 0.8730 (tp)
REVERT: D  300 MET cc_start: 0.8989 (mmt) cc_final: 0.8633 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 180
  average time/residue: 0.0883
  time to fit residues: 23.2770
Evaluate side-chains
  151 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 109 optimal weight:    3.9990
   chunk 107 optimal weight:    7.9990
   chunk 120 optimal weight:    8.9990
   chunk 12 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 83 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 117 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
B 181 GLN
** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.083603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.073232 restraints weight = 35560.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.075245 restraints weight = 19788.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.076638 restraints weight = 12712.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.077543 restraints weight = 9042.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.078278 restraints weight = 7034.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.6622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10212  Z= 0.128
  Angle     :  0.669   8.585  13828  Z= 0.336
  Chirality :  0.045   0.235   1688
  Planarity :  0.004   0.073   1732
  Dihedral  :  5.454  36.831   1426
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  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 are not related in a simple way.
  whole:  0.53 (0.24), residues: 1296
  helix:  1.31 (0.19), residues: 790
  sheet: -0.50 (0.56), residues: 106
  loop : -1.29 (0.32), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 241 
 TYR   0.031   0.002   TYR C 129 
 PHE   0.037   0.001   PHE A 166 
 TRP   0.011   0.001   TRP B  14 
 HIS   0.001   0.000   HIS D   9 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (10212)
  covalent geometry    : angle       0.66869 (13828)
  hydrogen bonds       : bond        0.03471 (  587)
  hydrogen bonds       : angle       4.54780 ( 1719)

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 LEU cc_start: 0.8508 (mt) cc_final: 0.8293 (pp)
REVERT: A  119 MET cc_start: 0.8373 (mmm) cc_final: 0.7754 (mmm)
REVERT: A  205 GLU cc_start: 0.8626 (mp0) cc_final: 0.8001 (mm-30)
REVERT: A  227 MET cc_start: 0.8665 (tpp) cc_final: 0.8404 (mpp)
REVERT: B  119 MET cc_start: 0.8040 (mmm) cc_final: 0.7675 (mmm)
REVERT: C  300 MET cc_start: 0.9079 (mmt) cc_final: 0.8508 (mmm)
REVERT: C  308 LEU cc_start: 0.9278 (mt) cc_final: 0.8932 (mt)
REVERT: D  101 LEU cc_start: 0.8970 (tp) cc_final: 0.8746 (tp)
REVERT: D  190 GLU cc_start: 0.7500 (mt-10) cc_final: 0.6957 (mm-30)
REVERT: D  300 MET cc_start: 0.9053 (mmt) cc_final: 0.8705 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.0816
  time to fit residues: 21.8925
Evaluate side-chains
  148 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 60 optimal weight:    0.0570
   chunk 108 optimal weight:    1.9990
   chunk 56 optimal weight:    7.9990
   chunk 15 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 116 optimal weight:    0.5980
   chunk 87 optimal weight:   20.0000
   chunk 124 optimal weight:    3.9990
   chunk 8 optimal weight:    7.9990
   chunk 58 optimal weight:    7.9990
   chunk 67 optimal weight:    4.9990
   overall best weight:    0.8902

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

Flipped N/Q/H residues before XYZ refinement:
C 287 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.083513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.073084 restraints weight = 35404.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.075166 restraints weight = 19471.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.076596 restraints weight = 12295.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.077543 restraints weight = 8604.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.078061 restraints weight = 6608.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.6774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10212  Z= 0.125
  Angle     :  0.649   8.144  13828  Z= 0.326
  Chirality :  0.045   0.313   1688
  Planarity :  0.004   0.073   1732
  Dihedral  :  5.446  35.961   1426
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.24), residues: 1296
  helix:  1.34 (0.19), residues: 788
  sheet: -0.41 (0.57), residues: 106
  loop : -1.22 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 172 
 TYR   0.035   0.002   TYR C 129 
 PHE   0.036   0.001   PHE A 166 
 TRP   0.011   0.001   TRP A  14 
 HIS   0.001   0.000   HIS D 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (10212)
  covalent geometry    : angle       0.64863 (13828)
  hydrogen bonds       : bond        0.03436 (  587)
  hydrogen bonds       : angle       4.51878 ( 1719)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1407.61 seconds
wall clock time: 25 minutes 7.98 seconds (1507.98 seconds total)