Starting phenix.real_space_refine
on Fri Mar 14 01:00:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5k0z_8191/03_2025/5k0z_8191.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5k0z_8191/03_2025/5k0z_8191.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5k0z_8191/03_2025/5k0z_8191.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5k0z_8191/03_2025/5k0z_8191.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5k0z_8191/03_2025/5k0z_8191.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5k0z_8191/03_2025/5k0z_8191.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    6196      2.51       5
     N    1636      2.21       5
     O    1865      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9749
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2427
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 317, 2427
          Classifications: {'peptide': 317}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 307}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 10
          Classifications: {'water': 10}
          Link IDs: {None: 9}
    Chain: "B"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 11
          Classifications: {'water': 11}
          Link IDs: {None: 10}
    Chain: "C"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 10
          Classifications: {'water': 10}
          Link IDs: {None: 9}
    Chain: "D"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 10
          Classifications: {'water': 10}
          Link IDs: {None: 9}
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 4.44, per 1000 atoms: 0.46
  Number of scatterers: 9749
  At special positions: 0
  Unit cell: (73.755, 97.515, 83.655, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      52     16.00
     O    1865      8.00
     N    1636      7.00
     C    6196      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: 2.31
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2352

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 12 sheets defined
      46.4% alpha, 17.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 7
    Processing helix  chain 'A' and resid 30 through 41
    Processing helix  chain 'A' and resid 54 through 66
      removed outlier: 3.673A  pdb=" N   LYS A  58 " --> pdb=" O   GLU A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 71
    Processing helix  chain 'A' and resid 109 through 127
      removed outlier: 3.501A  pdb=" N   ASN A 114 " --> pdb=" O   GLN A 110 " (cutoff:3.500A)
      Proline residue:  A 121  - end of helix
      removed outlier: 3.595A  pdb=" N   TYR A 126 " --> pdb=" O   GLN A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 149
    Processing helix  chain 'A' and resid 153 through 155
      No H-bonds generated for 'chain 'A' and resid 153 through 155'
    Processing helix  chain 'A' and resid 162 through 176
    Processing helix  chain 'A' and resid 210 through 214
    Processing helix  chain 'A' and resid 226 through 245
      removed outlier: 3.999A  pdb=" N   HIS A 230 " --> pdb=" O   TRP A 226 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ALA A 237 " --> pdb=" O   VAL A 233 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   TYR A 238 " --> pdb=" O   VAL A 234 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LEU A 243 " --> pdb=" O   GLU A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 264
    Processing helix  chain 'A' and resid 308 through 327
      removed outlier: 3.760A  pdb=" N   ILE A 325 " --> pdb=" O   THR A 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 7
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 54 through 66
      removed outlier: 3.673A  pdb=" N   LYS B  58 " --> pdb=" O   GLU B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 71
    Processing helix  chain 'B' and resid 109 through 127
      removed outlier: 3.501A  pdb=" N   ASN B 114 " --> pdb=" O   GLN B 110 " (cutoff:3.500A)
      Proline residue:  B 121  - end of helix
      removed outlier: 3.595A  pdb=" N   TYR B 126 " --> pdb=" O   GLN B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 149
    Processing helix  chain 'B' and resid 153 through 155
      No H-bonds generated for 'chain 'B' and resid 153 through 155'
    Processing helix  chain 'B' and resid 162 through 176
    Processing helix  chain 'B' and resid 210 through 214
    Processing helix  chain 'B' and resid 226 through 245
      removed outlier: 4.000A  pdb=" N   HIS B 230 " --> pdb=" O   TRP B 226 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ALA B 237 " --> pdb=" O   VAL B 233 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   TYR B 238 " --> pdb=" O   VAL B 234 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LEU B 243 " --> pdb=" O   GLU B 239 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 264
    Processing helix  chain 'B' and resid 308 through 327
      removed outlier: 3.760A  pdb=" N   ILE B 325 " --> pdb=" O   THR B 321 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2 through 7
    Processing helix  chain 'C' and resid 30 through 41
    Processing helix  chain 'C' and resid 54 through 66
      removed outlier: 3.672A  pdb=" N   LYS C  58 " --> pdb=" O   GLU C  54 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 71
    Processing helix  chain 'C' and resid 109 through 127
      removed outlier: 3.501A  pdb=" N   ASN C 114 " --> pdb=" O   GLN C 110 " (cutoff:3.500A)
      Proline residue:  C 121  - end of helix
      removed outlier: 3.595A  pdb=" N   TYR C 126 " --> pdb=" O   GLN C 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 138 through 149
    Processing helix  chain 'C' and resid 153 through 155
      No H-bonds generated for 'chain 'C' and resid 153 through 155'
    Processing helix  chain 'C' and resid 162 through 176
    Processing helix  chain 'C' and resid 210 through 214
    Processing helix  chain 'C' and resid 226 through 245
      removed outlier: 4.000A  pdb=" N   HIS C 230 " --> pdb=" O   TRP C 226 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ALA C 237 " --> pdb=" O   VAL C 233 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   TYR C 238 " --> pdb=" O   VAL C 234 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LEU C 243 " --> pdb=" O   GLU C 239 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 248 through 264
    Processing helix  chain 'C' and resid 308 through 327
      removed outlier: 3.760A  pdb=" N   ILE C 325 " --> pdb=" O   THR C 321 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 2 through 7
    Processing helix  chain 'D' and resid 30 through 41
    Processing helix  chain 'D' and resid 54 through 66
      removed outlier: 3.673A  pdb=" N   LYS D  58 " --> pdb=" O   GLU D  54 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 67 through 71
    Processing helix  chain 'D' and resid 109 through 127
      removed outlier: 3.502A  pdb=" N   ASN D 114 " --> pdb=" O   GLN D 110 " (cutoff:3.500A)
      Proline residue:  D 121  - end of helix
      removed outlier: 3.595A  pdb=" N   TYR D 126 " --> pdb=" O   GLN D 122 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 138 through 149
    Processing helix  chain 'D' and resid 153 through 155
      No H-bonds generated for 'chain 'D' and resid 153 through 155'
    Processing helix  chain 'D' and resid 162 through 176
    Processing helix  chain 'D' and resid 210 through 214
    Processing helix  chain 'D' and resid 226 through 245
      removed outlier: 3.999A  pdb=" N   HIS D 230 " --> pdb=" O   TRP D 226 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ALA D 237 " --> pdb=" O   VAL D 233 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   TYR D 238 " --> pdb=" O   VAL D 234 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LEU D 243 " --> pdb=" O   GLU D 239 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 248 through 264
    Processing helix  chain 'D' and resid 308 through 327
      removed outlier: 3.760A  pdb=" N   ILE D 325 " --> pdb=" O   THR D 321 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 10
      removed outlier: 6.580A  pdb=" N   VAL C 293 " --> pdb=" O   THR C 300 " (cutoff:3.500A)
      removed outlier: 4.830A  pdb=" N   VAL C 302 " --> pdb=" O   PRO C 291 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 78
      removed outlier: 5.923A  pdb=" N   LEU A  47 " --> pdb=" O   VAL A  77 " (cutoff:3.500A)
      removed outlier: 5.681A  pdb=" N   ILE A 132 " --> pdb=" O   ILE A 158 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 184 through 190
      removed outlier: 10.027A  pdb=" N   HIS A 185 " --> pdb=" O   SER A 201 " (cutoff:3.500A)
      removed outlier: 8.100A  pdb=" N   SER A 201 " --> pdb=" O   HIS A 185 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   TRP A 187 " --> pdb=" O   VAL A 199 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 268 through 275
      removed outlier: 4.830A  pdb=" N   VAL A 302 " --> pdb=" O   PRO A 291 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   VAL A 293 " --> pdb=" O   THR A 300 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 8 through 10
      removed outlier: 6.579A  pdb=" N   VAL D 293 " --> pdb=" O   THR D 300 " (cutoff:3.500A)
      removed outlier: 4.830A  pdb=" N   VAL D 302 " --> pdb=" O   PRO D 291 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 75 through 78
      removed outlier: 5.923A  pdb=" N   LEU B  47 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
      removed outlier: 5.680A  pdb=" N   ILE B 132 " --> pdb=" O   ILE B 158 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 184 through 190
      removed outlier: 10.027A  pdb=" N   HIS B 185 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
      removed outlier: 8.100A  pdb=" N   SER B 201 " --> pdb=" O   HIS B 185 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   TRP B 187 " --> pdb=" O   VAL B 199 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 268 through 275
      removed outlier: 4.830A  pdb=" N   VAL B 302 " --> pdb=" O   PRO B 291 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   VAL B 293 " --> pdb=" O   THR B 300 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 75 through 78
      removed outlier: 5.924A  pdb=" N   LEU C  47 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
      removed outlier: 5.681A  pdb=" N   ILE C 132 " --> pdb=" O   ILE C 158 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 184 through 190
      removed outlier: 10.027A  pdb=" N   HIS C 185 " --> pdb=" O   SER C 201 " (cutoff:3.500A)
      removed outlier: 8.100A  pdb=" N   SER C 201 " --> pdb=" O   HIS C 185 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   TRP C 187 " --> pdb=" O   VAL C 199 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 75 through 78
      removed outlier: 5.923A  pdb=" N   LEU D  47 " --> pdb=" O   VAL D  77 " (cutoff:3.500A)
      removed outlier: 5.681A  pdb=" N   ILE D 132 " --> pdb=" O   ILE D 158 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 184 through 190
      removed outlier: 10.027A  pdb=" N   HIS D 185 " --> pdb=" O   SER D 201 " (cutoff:3.500A)
      removed outlier: 8.100A  pdb=" N   SER D 201 " --> pdb=" O   HIS D 185 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   TRP D 187 " --> pdb=" O   VAL D 199 " (cutoff:3.500A)

    464 hydrogen bonds defined for protein.
    1332 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: 2.80

  Time building geometry restraints manager: 2.66 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2690
        1.33 -     1.45: 1393
        1.45 -     1.57: 5705
        1.57 -     1.68: 0
        1.68 -     1.80: 76
  Bond restraints: 9864
  Sorted by residual:
  bond pdb=" CB  CYS B 184 "
       pdb=" SG  CYS B 184 "
    ideal  model  delta    sigma   weight residual
    1.808  1.745  0.063 3.30e-02 9.18e+02 3.66e+00
  bond pdb=" CB  CYS A 184 "
       pdb=" SG  CYS A 184 "
    ideal  model  delta    sigma   weight residual
    1.808  1.745  0.063 3.30e-02 9.18e+02 3.62e+00
  bond pdb=" CB  CYS C 184 "
       pdb=" SG  CYS C 184 "
    ideal  model  delta    sigma   weight residual
    1.808  1.745  0.063 3.30e-02 9.18e+02 3.59e+00
  bond pdb=" CB  CYS D 184 "
       pdb=" SG  CYS D 184 "
    ideal  model  delta    sigma   weight residual
    1.808  1.745  0.063 3.30e-02 9.18e+02 3.59e+00
  bond pdb=" CG  LEU D 263 "
       pdb=" CD1 LEU D 263 "
    ideal  model  delta    sigma   weight residual
    1.521  1.459  0.062 3.30e-02 9.18e+02 3.49e+00
  ... (remaining 9859 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 12500
        1.89 -     3.78: 768
        3.78 -     5.67: 88
        5.67 -     7.56: 16
        7.56 -     9.46: 12
  Bond angle restraints: 13384
  Sorted by residual:
  angle pdb=" C   TYR D 126 "
        pdb=" N   SER D 127 "
        pdb=" CA  SER D 127 "
      ideal   model   delta    sigma   weight residual
     122.74  119.03    3.71 1.06e+00 8.90e-01 1.23e+01
  angle pdb=" C   TYR B 126 "
        pdb=" N   SER B 127 "
        pdb=" CA  SER B 127 "
      ideal   model   delta    sigma   weight residual
     122.74  119.05    3.69 1.06e+00 8.90e-01 1.21e+01
  angle pdb=" C   TYR A 126 "
        pdb=" N   SER A 127 "
        pdb=" CA  SER A 127 "
      ideal   model   delta    sigma   weight residual
     122.74  119.07    3.67 1.06e+00 8.90e-01 1.20e+01
  angle pdb=" C   TYR C 126 "
        pdb=" N   SER C 127 "
        pdb=" CA  SER C 127 "
      ideal   model   delta    sigma   weight residual
     122.74  119.08    3.66 1.06e+00 8.90e-01 1.19e+01
  angle pdb=" CA  GLN B 326 "
        pdb=" CB  GLN B 326 "
        pdb=" CG  GLN B 326 "
      ideal   model   delta    sigma   weight residual
     114.10  120.89   -6.79 2.00e+00 2.50e-01 1.15e+01
  ... (remaining 13379 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.61: 5704
       17.61 -    35.22: 180
       35.22 -    52.84: 20
       52.84 -    70.45: 8
       70.45 -    88.06: 12
  Dihedral angle restraints: 5924
    sinusoidal: 2284
      harmonic: 3640
  Sorted by residual:
  dihedral pdb=" CA  GLY D 298 "
           pdb=" C   GLY D 298 "
           pdb=" N   LEU D 299 "
           pdb=" CA  LEU D 299 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.61   21.39     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  GLY A 298 "
           pdb=" C   GLY A 298 "
           pdb=" N   LEU A 299 "
           pdb=" CA  LEU A 299 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.62   21.38     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  GLY C 298 "
           pdb=" C   GLY C 298 "
           pdb=" N   LEU C 299 "
           pdb=" CA  LEU C 299 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.63   21.37     0      5.00e+00 4.00e-02 1.83e+01
  ... (remaining 5921 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 924
       0.044 -    0.087: 505
       0.087 -    0.131: 146
       0.131 -    0.175: 39
       0.175 -    0.218: 18
  Chirality restraints: 1632
  Sorted by residual:
  chirality pdb=" CA  ASN D 225 "
            pdb=" N   ASN D 225 "
            pdb=" C   ASN D 225 "
            pdb=" CB  ASN D 225 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CA  ASN C 225 "
            pdb=" N   ASN C 225 "
            pdb=" C   ASN C 225 "
            pdb=" CB  ASN C 225 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CA  ASN A 225 "
            pdb=" N   ASN A 225 "
            pdb=" C   ASN A 225 "
            pdb=" CB  ASN A 225 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 1629 not shown)

  Planarity restraints: 1652
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D 118 "    0.023 2.00e-02 2.50e+03   1.81e-02 5.75e+00
        pdb=" CG  PHE D 118 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 PHE D 118 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE D 118 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE D 118 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE D 118 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE D 118 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 118 "    0.023 2.00e-02 2.50e+03   1.80e-02 5.67e+00
        pdb=" CG  PHE C 118 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 118 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 118 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 118 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 118 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 118 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 118 "   -0.023 2.00e-02 2.50e+03   1.80e-02 5.66e+00
        pdb=" CG  PHE A 118 "    0.041 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 118 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 118 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 118 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 118 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 118 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1649 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.62: 143
        2.62 -     3.19: 9617
        3.19 -     3.76: 15515
        3.76 -     4.33: 23988
        4.33 -     4.90: 37950
  Nonbonded interactions: 87213
  Sorted by model distance:
  nonbonded pdb=" O   THR B  16 "
            pdb=" CG2 VAL B  17 "
     model   vdw
     2.056 3.460
  nonbonded pdb=" O   THR D  16 "
            pdb=" CG2 VAL D  17 "
     model   vdw
     2.056 3.460
  nonbonded pdb=" O   THR C  16 "
            pdb=" CG2 VAL C  17 "
     model   vdw
     2.056 3.460
  nonbonded pdb=" O   THR A  16 "
            pdb=" CG2 VAL A  17 "
     model   vdw
     2.056 3.460
  nonbonded pdb=" NZ  LYS B  21 "
            pdb=" O   VAL B  84 "
     model   vdw
     2.089 3.120
  ... (remaining 87208 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.330
  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:          0.480
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     22.810
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5940
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      :  0.011   0.063   9864  Z= 0.728
  Angle     :  1.038   9.456  13384  Z= 0.572
  Chirality :  0.059   0.218   1632
  Planarity :  0.006   0.052   1652
  Dihedral  : 10.637  88.059   3572
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 18.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.11 (0.17), residues: 1244
  helix: -3.65 (0.13), residues: 536
  sheet: -2.52 (0.31), residues: 164
  loop : -1.53 (0.20), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.005   TRP C 147 
 HIS   0.010   0.003   HIS C 180 
 PHE   0.041   0.008   PHE D 118 
 TYR   0.022   0.003   TYR D  82 
 ARG   0.007   0.001   ARG B 242 

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  518 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 518
  time to evaluate  : 1.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 ASP cc_start: 0.5770 (p0) cc_final: 0.5431 (p0)
REVERT: A  328 ASP cc_start: 0.6820 (p0) cc_final: 0.6499 (p0)
REVERT: B   55 ASP cc_start: 0.5735 (p0) cc_final: 0.5448 (p0)
REVERT: B  268 ARG cc_start: 0.6675 (mtp180) cc_final: 0.6461 (mtm180)
REVERT: B  328 ASP cc_start: 0.6840 (p0) cc_final: 0.6517 (p0)
REVERT: C   55 ASP cc_start: 0.5777 (p0) cc_final: 0.5481 (p0)
REVERT: C  328 ASP cc_start: 0.6801 (p0) cc_final: 0.6481 (p0)
REVERT: D   55 ASP cc_start: 0.5785 (p0) cc_final: 0.5490 (p0)
REVERT: D  328 ASP cc_start: 0.6820 (p0) cc_final: 0.6501 (p0)
  outliers start: 0
  outliers final: 1
  residues processed: 518
  average time/residue: 0.9522
  time to fit residues: 535.5455
Evaluate side-chains
  324 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 323
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    6.9990
   chunk 93 optimal weight:    6.9990
   chunk 52 optimal weight:   20.0000
   chunk 32 optimal weight:    7.9990
   chunk 63 optimal weight:    0.8980
   chunk 50 optimal weight:    7.9990
   chunk 97 optimal weight:    9.9990
   chunk 37 optimal weight:    8.9990
   chunk 59 optimal weight:    7.9990
   chunk 72 optimal weight:    9.9990
   chunk 112 optimal weight:   10.0000
   overall best weight:    6.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 163 ASN
A 304 ASN
B 163 ASN
B 304 ASN
C 163 ASN
C 304 ASN
D 304 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.105238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.083409 restraints weight = 24613.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 5.08
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.4959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   9864  Z= 0.309
  Angle     :  0.882   8.958  13384  Z= 0.463
  Chirality :  0.049   0.197   1632
  Planarity :  0.006   0.036   1652
  Dihedral  :  5.461  24.747   1318
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 23.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 22.64 %
    Favored  : 74.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.20), residues: 1244
  helix: -1.17 (0.20), residues: 512
  sheet: -2.00 (0.31), residues: 168
  loop : -0.71 (0.24), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 249 
 HIS   0.005   0.002   HIS C 185 
 PHE   0.019   0.003   PHE D 116 
 TYR   0.027   0.003   TYR C 171 
 ARG   0.007   0.002   ARG A 111 

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  453 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 418
  time to evaluate  : 1.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.8721 (ttp) cc_final: 0.8476 (ttp)
REVERT: A   75 LYS cc_start: 0.9101 (tppp) cc_final: 0.8879 (tppp)
REVERT: A  133 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9099 (tm)
REVERT: A  170 ARG cc_start: 0.9055 (mtt180) cc_final: 0.8830 (mtt90)
REVERT: A  171 TYR cc_start: 0.9145 (t80) cc_final: 0.8838 (t80)
REVERT: A  188 ILE cc_start: 0.9118 (mp) cc_final: 0.8838 (mp)
REVERT: A  232 GLN cc_start: 0.9291 (tp-100) cc_final: 0.8970 (tp-100)
REVERT: A  249 TRP cc_start: 0.8152 (m-90) cc_final: 0.7935 (m-90)
REVERT: A  268 ARG cc_start: 0.8627 (mtm180) cc_final: 0.8016 (ttp80)
REVERT: A  310 ASP cc_start: 0.9251 (p0) cc_final: 0.8531 (p0)
REVERT: B   61 MET cc_start: 0.8765 (ttp) cc_final: 0.8556 (ttp)
REVERT: B   75 LYS cc_start: 0.9106 (tppp) cc_final: 0.8867 (tppp)
REVERT: B  170 ARG cc_start: 0.9055 (mtt180) cc_final: 0.8835 (mtt90)
REVERT: B  171 TYR cc_start: 0.9162 (t80) cc_final: 0.8856 (t80)
REVERT: B  188 ILE cc_start: 0.9099 (mp) cc_final: 0.8827 (mp)
REVERT: B  232 GLN cc_start: 0.9341 (tp-100) cc_final: 0.9021 (tp-100)
REVERT: B  249 TRP cc_start: 0.8203 (m-90) cc_final: 0.7967 (m-90)
REVERT: B  257 GLU cc_start: 0.8438 (tp30) cc_final: 0.8049 (tm-30)
REVERT: B  294 LEU cc_start: 0.9122 (mp) cc_final: 0.8642 (tm)
REVERT: B  310 ASP cc_start: 0.9206 (p0) cc_final: 0.8605 (p0)
REVERT: B  311 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8514 (mt-10)
REVERT: C   61 MET cc_start: 0.8743 (ttp) cc_final: 0.8495 (ttp)
REVERT: C   75 LYS cc_start: 0.9064 (tppp) cc_final: 0.8860 (tppp)
REVERT: C  170 ARG cc_start: 0.9072 (mtt180) cc_final: 0.8848 (mtt90)
REVERT: C  171 TYR cc_start: 0.9147 (t80) cc_final: 0.8867 (t80)
REVERT: C  188 ILE cc_start: 0.9109 (mp) cc_final: 0.8828 (mp)
REVERT: C  232 GLN cc_start: 0.9315 (tp-100) cc_final: 0.8983 (tp-100)
REVERT: C  249 TRP cc_start: 0.8144 (m-90) cc_final: 0.7934 (m-90)
REVERT: C  268 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7961 (ttp80)
REVERT: C  310 ASP cc_start: 0.9295 (p0) cc_final: 0.8589 (p0)
REVERT: D   61 MET cc_start: 0.8814 (ttp) cc_final: 0.8561 (ttp)
REVERT: D   75 LYS cc_start: 0.9075 (tppp) cc_final: 0.8869 (tppp)
REVERT: D  170 ARG cc_start: 0.9054 (mtt180) cc_final: 0.8827 (mtt90)
REVERT: D  171 TYR cc_start: 0.9154 (t80) cc_final: 0.8870 (t80)
REVERT: D  188 ILE cc_start: 0.9104 (mp) cc_final: 0.8825 (mp)
REVERT: D  232 GLN cc_start: 0.9322 (tp-100) cc_final: 0.8996 (tp-100)
REVERT: D  249 TRP cc_start: 0.8135 (m-90) cc_final: 0.7932 (m-90)
REVERT: D  268 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7731 (ttp80)
REVERT: D  310 ASP cc_start: 0.9285 (p0) cc_final: 0.8583 (p0)
  outliers start: 35
  outliers final: 5
  residues processed: 426
  average time/residue: 0.9607
  time to fit residues: 444.5816
Evaluate side-chains
  341 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 333
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain B residue  293 VAL
Chi-restraints excluded: chain C residue  268 ARG
Chi-restraints excluded: chain C residue  293 VAL
Chi-restraints excluded: chain D residue  268 ARG
Chi-restraints excluded: chain D residue  293 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 1 optimal weight:   30.0000
   chunk 13 optimal weight:   20.0000
   chunk 4 optimal weight:    5.9990
   chunk 7 optimal weight:    7.9990
   chunk 118 optimal weight:   10.0000
   chunk 27 optimal weight:    8.9990
   chunk 10 optimal weight:    7.9990
   chunk 33 optimal weight:   20.0000
   chunk 76 optimal weight:    9.9990
   chunk 113 optimal weight:   30.0000
   chunk 109 optimal weight:   30.0000
   overall best weight:    8.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 305 GLN
C 305 GLN
D 305 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.100148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.080228 restraints weight = 26140.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 4.88
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8554
moved from start:          0.5714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069   9864  Z= 0.331
  Angle     :  0.849   9.222  13384  Z= 0.437
  Chirality :  0.052   0.282   1632
  Planarity :  0.005   0.041   1652
  Dihedral  :  5.228  13.446   1316
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 22.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 25.27 %
    Favored  : 70.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.86 (0.22), residues: 1244
  helix: -0.29 (0.21), residues: 524
  sheet: -1.84 (0.32), residues: 168
  loop : -0.20 (0.25), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 249 
 HIS   0.005   0.001   HIS C 230 
 PHE   0.018   0.003   PHE A 169 
 TYR   0.022   0.003   TYR A 126 
 ARG   0.006   0.002   ARG C 176 

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  415 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 365
  time to evaluate  : 1.075 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.8954 (ttp) cc_final: 0.8729 (ttp)
REVERT: A  170 ARG cc_start: 0.9079 (mtt180) cc_final: 0.8758 (mtt-85)
REVERT: A  171 TYR cc_start: 0.9180 (t80) cc_final: 0.8732 (t80)
REVERT: A  172 LEU cc_start: 0.9105 (mt) cc_final: 0.8850 (mt)
REVERT: A  242 ARG cc_start: 0.8784 (ttp-110) cc_final: 0.8345 (ptt-90)
REVERT: A  264 LYS cc_start: 0.9079 (mmmm) cc_final: 0.8869 (mtpt)
REVERT: A  268 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8187 (ttp80)
REVERT: A  311 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8569 (mt-10)
REVERT: B   61 MET cc_start: 0.8977 (ttp) cc_final: 0.8600 (ttp)
REVERT: B   65 GLN cc_start: 0.9003 (mt0) cc_final: 0.8723 (pm20)
REVERT: B  170 ARG cc_start: 0.9079 (mtt180) cc_final: 0.8777 (mtt-85)
REVERT: B  171 TYR cc_start: 0.9170 (t80) cc_final: 0.8706 (t80)
REVERT: B  172 LEU cc_start: 0.9115 (mt) cc_final: 0.8836 (mt)
REVERT: B  232 GLN cc_start: 0.9256 (tp-100) cc_final: 0.8948 (tp-100)
REVERT: B  257 GLU cc_start: 0.8588 (tp30) cc_final: 0.8182 (tm-30)
REVERT: B  268 ARG cc_start: 0.8989 (ttp-110) cc_final: 0.8784 (ttp80)
REVERT: C   61 MET cc_start: 0.8982 (ttp) cc_final: 0.8744 (ttp)
REVERT: C   75 LYS cc_start: 0.9010 (tppp) cc_final: 0.8704 (tppp)
REVERT: C  170 ARG cc_start: 0.9064 (mtt180) cc_final: 0.8754 (mtt-85)
REVERT: C  171 TYR cc_start: 0.9158 (t80) cc_final: 0.8722 (t80)
REVERT: C  232 GLN cc_start: 0.9248 (tp-100) cc_final: 0.8912 (tp-100)
REVERT: C  268 ARG cc_start: 0.8555 (mtm180) cc_final: 0.8223 (ttp80)
REVERT: C  311 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8581 (mt-10)
REVERT: D   61 MET cc_start: 0.8949 (ttp) cc_final: 0.8701 (ttp)
REVERT: D   75 LYS cc_start: 0.9006 (tppp) cc_final: 0.8716 (tppp)
REVERT: D  170 ARG cc_start: 0.9082 (mtt180) cc_final: 0.8770 (mtt-85)
REVERT: D  171 TYR cc_start: 0.9166 (t80) cc_final: 0.8707 (t80)
REVERT: D  172 LEU cc_start: 0.9086 (mt) cc_final: 0.8820 (mt)
REVERT: D  232 GLN cc_start: 0.9241 (tp-100) cc_final: 0.9019 (tp-100)
REVERT: D  311 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8574 (mt-10)
  outliers start: 50
  outliers final: 15
  residues processed: 380
  average time/residue: 1.1176
  time to fit residues: 458.2356
Evaluate side-chains
  321 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 305
  time to evaluate  : 1.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  268 ARG
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain C residue  255 VAL
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  300 THR
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain D residue  255 VAL
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  300 THR
Chi-restraints excluded: chain D residue  324 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 80 optimal weight:   20.0000
   chunk 49 optimal weight:    3.9990
   chunk 47 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0010
   chunk 115 optimal weight:   20.0000
   chunk 54 optimal weight:   10.0000
   chunk 87 optimal weight:    7.9990
   chunk 114 optimal weight:   30.0000
   chunk 11 optimal weight:    9.9990
   chunk 40 optimal weight:   20.0000
   overall best weight:    3.5192

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

Flipped N/Q/H residues before XYZ refinement:
** A  20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.104417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.082677 restraints weight = 25642.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 5.49
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.6434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9864  Z= 0.239
  Angle     :  0.796   9.532  13384  Z= 0.402
  Chirality :  0.049   0.207   1632
  Planarity :  0.004   0.036   1652
  Dihedral  :  5.134  16.440   1316
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 17.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 28.36 %
    Favored  : 66.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.24), residues: 1244
  helix:  0.17 (0.23), residues: 516
  sheet: -1.43 (0.41), residues: 132
  loop :  0.25 (0.26), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D 249 
 HIS   0.004   0.001   HIS C 230 
 PHE   0.021   0.003   PHE B  70 
 TYR   0.018   0.002   TYR B 126 
 ARG   0.007   0.001   ARG D 168 

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  417 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 365
  time to evaluate  : 1.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.8933 (ttp) cc_final: 0.8681 (ttp)
REVERT: A   75 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8578 (ttpp)
REVERT: A  170 ARG cc_start: 0.8918 (mtt180) cc_final: 0.8464 (mtt-85)
REVERT: A  171 TYR cc_start: 0.9220 (t80) cc_final: 0.8943 (t80)
REVERT: A  217 MET cc_start: 0.6824 (ptm) cc_final: 0.6480 (ptm)
REVERT: A  232 GLN cc_start: 0.9303 (tp-100) cc_final: 0.9070 (tp-100)
REVERT: A  257 GLU cc_start: 0.8217 (tp30) cc_final: 0.7594 (tp30)
REVERT: B   61 MET cc_start: 0.8971 (ttp) cc_final: 0.8754 (ttp)
REVERT: B  170 ARG cc_start: 0.8943 (mtt180) cc_final: 0.8717 (mtt180)
REVERT: B  171 TYR cc_start: 0.9226 (t80) cc_final: 0.8917 (t80)
REVERT: B  217 MET cc_start: 0.6822 (ptm) cc_final: 0.6352 (ptm)
REVERT: B  232 GLN cc_start: 0.9139 (tp-100) cc_final: 0.8875 (tp-100)
REVERT: B  257 GLU cc_start: 0.8610 (tp30) cc_final: 0.8186 (tm-30)
REVERT: B  294 LEU cc_start: 0.9149 (mp) cc_final: 0.8781 (tm)
REVERT: B  311 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8636 (mt-10)
REVERT: C   61 MET cc_start: 0.8922 (ttp) cc_final: 0.8715 (ttp)
REVERT: C  170 ARG cc_start: 0.8966 (mtt180) cc_final: 0.8698 (mtt180)
REVERT: C  171 TYR cc_start: 0.9190 (t80) cc_final: 0.8888 (t80)
REVERT: C  232 GLN cc_start: 0.9171 (tp-100) cc_final: 0.8840 (tp-100)
REVERT: C  235 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8614 (pt0)
REVERT: C  239 GLU cc_start: 0.8461 (mp0) cc_final: 0.8234 (mp0)
REVERT: C  257 GLU cc_start: 0.8133 (tp30) cc_final: 0.7600 (tp30)
REVERT: D   61 MET cc_start: 0.8922 (ttp) cc_final: 0.8649 (ttp)
REVERT: D  170 ARG cc_start: 0.9007 (mtt180) cc_final: 0.8500 (mtt-85)
REVERT: D  171 TYR cc_start: 0.9217 (t80) cc_final: 0.8960 (t80)
REVERT: D  217 MET cc_start: 0.6811 (ptm) cc_final: 0.6509 (ptt)
REVERT: D  232 GLN cc_start: 0.9233 (tp-100) cc_final: 0.8894 (tp-100)
REVERT: D  235 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8611 (pt0)
REVERT: D  239 GLU cc_start: 0.8417 (mp0) cc_final: 0.8206 (mp0)
REVERT: D  257 GLU cc_start: 0.8224 (tp30) cc_final: 0.6866 (tm-30)
REVERT: D  268 ARG cc_start: 0.8588 (ttp80) cc_final: 0.7060 (ttm170)
  outliers start: 52
  outliers final: 22
  residues processed: 394
  average time/residue: 1.0239
  time to fit residues: 437.9398
Evaluate side-chains
  335 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 312
  time to evaluate  : 1.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   75 LYS
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain B residue   62 MET
Chi-restraints excluded: chain B residue  251 ILE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain C residue   43 LEU
Chi-restraints excluded: chain C residue  251 ILE
Chi-restraints excluded: chain C residue  255 VAL
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain D residue   43 LEU
Chi-restraints excluded: chain D residue   49 LEU
Chi-restraints excluded: chain D residue  251 ILE
Chi-restraints excluded: chain D residue  255 VAL
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  324 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 121 optimal weight:    6.9990
   chunk 120 optimal weight:   10.0000
   chunk 43 optimal weight:    1.9990
   chunk 60 optimal weight:    8.9990
   chunk 109 optimal weight:    6.9990
   chunk 59 optimal weight:    5.9990
   chunk 7 optimal weight:   30.0000
   chunk 38 optimal weight:    9.9990
   chunk 55 optimal weight:    5.9990
   chunk 17 optimal weight:    6.9990
   chunk 16 optimal weight:    6.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  20 ASN
A 155 HIS
B 155 HIS
C 155 HIS
D 155 HIS
D 163 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.100769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.079028 restraints weight = 25736.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 5.02
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.6641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   9864  Z= 0.276
  Angle     :  0.817   9.334  13384  Z= 0.413
  Chirality :  0.049   0.261   1632
  Planarity :  0.005   0.056   1652
  Dihedral  :  5.022  16.369   1316
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 19.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 31.82 %
    Favored  : 64.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.25), residues: 1244
  helix:  0.42 (0.23), residues: 516
  sheet: -1.33 (0.43), residues: 132
  loop :  0.49 (0.28), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D 249 
 HIS   0.004   0.001   HIS A 180 
 PHE   0.016   0.003   PHE B  70 
 TYR   0.018   0.002   TYR A 126 
 ARG   0.004   0.001   ARG A 268 

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  405 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 359
  time to evaluate  : 1.027 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 ILE cc_start: 0.8961 (mt) cc_final: 0.8673 (pt)
REVERT: A   61 MET cc_start: 0.8946 (ttp) cc_final: 0.8552 (ttp)
REVERT: A  170 ARG cc_start: 0.8972 (mtt180) cc_final: 0.8722 (mtt180)
REVERT: A  171 TYR cc_start: 0.9202 (t80) cc_final: 0.8881 (t80)
REVERT: A  232 GLN cc_start: 0.9218 (tp-100) cc_final: 0.8935 (tp-100)
REVERT: A  235 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8767 (pt0)
REVERT: A  257 GLU cc_start: 0.8018 (tp30) cc_final: 0.7719 (tp30)
REVERT: A  311 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8640 (mt-10)
REVERT: B   61 MET cc_start: 0.9042 (ttp) cc_final: 0.8707 (ttp)
REVERT: B  170 ARG cc_start: 0.9011 (mtt180) cc_final: 0.8783 (mtt180)
REVERT: B  171 TYR cc_start: 0.9211 (t80) cc_final: 0.8910 (t80)
REVERT: B  232 GLN cc_start: 0.9185 (tp-100) cc_final: 0.8874 (tp-100)
REVERT: B  235 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8715 (pt0)
REVERT: B  316 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8818 (mtpp)
REVERT: B  328 ASP cc_start: 0.9013 (p0) cc_final: 0.8670 (p0)
REVERT: C   56 LYS cc_start: 0.9237 (tppt) cc_final: 0.8987 (tppt)
REVERT: C  170 ARG cc_start: 0.8974 (mtt180) cc_final: 0.8722 (mtt180)
REVERT: C  171 TYR cc_start: 0.9157 (t80) cc_final: 0.8834 (t80)
REVERT: C  232 GLN cc_start: 0.9161 (tp-100) cc_final: 0.8874 (tp-100)
REVERT: C  235 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8740 (pt0)
REVERT: C  257 GLU cc_start: 0.8142 (tp30) cc_final: 0.7251 (tp30)
REVERT: C  311 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8647 (mt-10)
REVERT: D  170 ARG cc_start: 0.9036 (mtt180) cc_final: 0.8746 (mtt180)
REVERT: D  171 TYR cc_start: 0.9197 (t80) cc_final: 0.8889 (t80)
REVERT: D  232 GLN cc_start: 0.9182 (tp-100) cc_final: 0.8863 (tp-100)
REVERT: D  235 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8627 (pt0)
REVERT: D  249 TRP cc_start: 0.7929 (m-90) cc_final: 0.7387 (m-90)
REVERT: D  311 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8657 (mt-10)
  outliers start: 46
  outliers final: 23
  residues processed: 381
  average time/residue: 0.9720
  time to fit residues: 402.6010
Evaluate side-chains
  322 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 298
  time to evaluate  : 1.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 MET
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  173 MET
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  316 LYS
Chi-restraints excluded: chain C residue   43 LEU
Chi-restraints excluded: chain C residue  173 MET
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  239 GLU
Chi-restraints excluded: chain C residue  251 ILE
Chi-restraints excluded: chain C residue  255 VAL
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain D residue   43 LEU
Chi-restraints excluded: chain D residue  173 MET
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  255 VAL
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  303 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 121 optimal weight:    9.9990
   chunk 3 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   chunk 95 optimal weight:   20.0000
   chunk 27 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 32 optimal weight:   30.0000
   chunk 99 optimal weight:    0.7980
   chunk 98 optimal weight:    9.9990
   chunk 33 optimal weight:    9.9990
   chunk 45 optimal weight:   40.0000
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 214 ASN
A 314 GLN
B 214 ASN
B 314 GLN
C  20 ASN
D  20 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.104856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.083304 restraints weight = 25587.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 5.45
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.7089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9864  Z= 0.248
  Angle     :  0.859  10.828  13384  Z= 0.430
  Chirality :  0.049   0.256   1632
  Planarity :  0.005   0.051   1652
  Dihedral  :  5.032  17.033   1316
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 18.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 33.36 %
    Favored  : 62.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.25), residues: 1244
  helix:  0.57 (0.23), residues: 512
  sheet: -0.20 (0.54), residues: 92
  loop :  0.38 (0.27), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 249 
 HIS   0.003   0.001   HIS D 180 
 PHE   0.023   0.003   PHE D  70 
 TYR   0.022   0.002   TYR B 126 
 ARG   0.007   0.001   ARG B 168 

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  398 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 353
  time to evaluate  : 1.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 ILE cc_start: 0.8942 (mt) cc_final: 0.8637 (pt)
REVERT: A   61 MET cc_start: 0.8882 (ttp) cc_final: 0.8536 (ttp)
REVERT: A  170 ARG cc_start: 0.8915 (mtt180) cc_final: 0.8492 (mtt-85)
REVERT: A  232 GLN cc_start: 0.9154 (tp-100) cc_final: 0.8873 (tp-100)
REVERT: A  235 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8704 (pt0)
REVERT: A  257 GLU cc_start: 0.8109 (tp30) cc_final: 0.7896 (tp30)
REVERT: A  262 MET cc_start: 0.8660 (mmm) cc_final: 0.7336 (mmm)
REVERT: A  294 LEU cc_start: 0.8949 (mp) cc_final: 0.8423 (tp)
REVERT: A  311 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8587 (mt-10)
REVERT: A  328 ASP cc_start: 0.8963 (p0) cc_final: 0.8610 (p0)
REVERT: B   61 MET cc_start: 0.8881 (ttp) cc_final: 0.8498 (ttp)
REVERT: B  170 ARG cc_start: 0.9000 (mtt180) cc_final: 0.8591 (mtt-85)
REVERT: B  171 TYR cc_start: 0.9197 (t80) cc_final: 0.8951 (t80)
REVERT: B  232 GLN cc_start: 0.9211 (tp-100) cc_final: 0.8922 (tp-100)
REVERT: B  235 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8741 (pt0)
REVERT: B  311 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8622 (mt-10)
REVERT: B  317 LYS cc_start: 0.9232 (mtmm) cc_final: 0.8923 (mptt)
REVERT: C   61 MET cc_start: 0.8802 (ttp) cc_final: 0.8554 (tpp)
REVERT: C  170 ARG cc_start: 0.8955 (mtt180) cc_final: 0.8480 (mtt-85)
REVERT: C  171 TYR cc_start: 0.9143 (t80) cc_final: 0.8879 (t80)
REVERT: C  232 GLN cc_start: 0.9206 (tp-100) cc_final: 0.8916 (tp-100)
REVERT: C  235 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8701 (pt0)
REVERT: C  257 GLU cc_start: 0.8205 (tp30) cc_final: 0.7483 (tp30)
REVERT: C  264 LYS cc_start: 0.8747 (mmmm) cc_final: 0.8476 (mtpt)
REVERT: C  294 LEU cc_start: 0.8986 (mp) cc_final: 0.8473 (tp)
REVERT: C  311 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8598 (mt-10)
REVERT: D   61 MET cc_start: 0.8888 (ttp) cc_final: 0.8566 (tpp)
REVERT: D  170 ARG cc_start: 0.9037 (mtt180) cc_final: 0.8790 (mtt180)
REVERT: D  171 TYR cc_start: 0.9173 (t80) cc_final: 0.8943 (t80)
REVERT: D  232 GLN cc_start: 0.9218 (tp-100) cc_final: 0.8892 (tp-100)
REVERT: D  235 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8613 (pt0)
REVERT: D  257 GLU cc_start: 0.8412 (tm-30) cc_final: 0.7698 (tp30)
REVERT: D  294 LEU cc_start: 0.8937 (mp) cc_final: 0.8518 (tp)
REVERT: D  311 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8636 (mt-10)
  outliers start: 45
  outliers final: 28
  residues processed: 375
  average time/residue: 1.0194
  time to fit residues: 413.9952
Evaluate side-chains
  331 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 303
  time to evaluate  : 1.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue  173 MET
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain B residue  173 MET
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain C residue   32 MET
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue  173 MET
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  239 GLU
Chi-restraints excluded: chain C residue  255 VAL
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain D residue   32 MET
Chi-restraints excluded: chain D residue   43 LEU
Chi-restraints excluded: chain D residue  173 MET
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  255 VAL
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  324 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 122 optimal weight:   50.0000
   chunk 118 optimal weight:    9.9990
   chunk 18 optimal weight:    7.9990
   chunk 64 optimal weight:    7.9990
   chunk 38 optimal weight:   30.0000
   chunk 68 optimal weight:   10.0000
   chunk 47 optimal weight:   20.0000
   chunk 30 optimal weight:    4.9990
   chunk 1 optimal weight:   40.0000
   chunk 22 optimal weight:    9.9990
   chunk 84 optimal weight:   40.0000
   overall best weight:    8.1990

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

Flipped N/Q/H residues before XYZ refinement:
** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 284 ASN
D 314 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.098623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.075657 restraints weight = 26883.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 5.42
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.7220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   9864  Z= 0.326
  Angle     :  0.909  12.287  13384  Z= 0.451
  Chirality :  0.050   0.246   1632
  Planarity :  0.006   0.073   1652
  Dihedral  :  5.084  18.828   1316
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 22.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 34.45 %
    Favored  : 60.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.26), residues: 1244
  helix:  0.63 (0.23), residues: 516
  sheet: -1.30 (0.43), residues: 132
  loop :  0.75 (0.29), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 249 
 HIS   0.006   0.001   HIS C 180 
 PHE   0.030   0.004   PHE D  70 
 TYR   0.036   0.003   TYR A 171 
 ARG   0.011   0.002   ARG C 168 

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  390 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 335
  time to evaluate  : 1.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 ILE cc_start: 0.9009 (mt) cc_final: 0.8720 (pt)
REVERT: A   56 LYS cc_start: 0.9355 (tppp) cc_final: 0.9138 (tppt)
REVERT: A   61 MET cc_start: 0.8828 (ttp) cc_final: 0.8559 (ttp)
REVERT: A   79 ASP cc_start: 0.8382 (p0) cc_final: 0.7596 (p0)
REVERT: A  170 ARG cc_start: 0.8890 (mtt180) cc_final: 0.8416 (mtt-85)
REVERT: A  232 GLN cc_start: 0.9247 (tp-100) cc_final: 0.8989 (tp-100)
REVERT: A  235 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8903 (pt0)
REVERT: A  249 TRP cc_start: 0.7857 (m-90) cc_final: 0.7444 (m-90)
REVERT: A  311 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8677 (mt-10)
REVERT: A  328 ASP cc_start: 0.8960 (p0) cc_final: 0.8597 (p0)
REVERT: B   65 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8604 (pm20)
REVERT: B  170 ARG cc_start: 0.9022 (mtt180) cc_final: 0.8518 (mtt-85)
REVERT: B  171 TYR cc_start: 0.9260 (t80) cc_final: 0.9052 (t80)
REVERT: B  217 MET cc_start: 0.6708 (ptt) cc_final: 0.6449 (pmm)
REVERT: B  232 GLN cc_start: 0.9226 (tp-100) cc_final: 0.8939 (tp-100)
REVERT: B  235 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8806 (pt0)
REVERT: B  294 LEU cc_start: 0.9078 (mp) cc_final: 0.8501 (tp)
REVERT: B  311 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8689 (mt-10)
REVERT: B  316 LYS cc_start: 0.9376 (OUTLIER) cc_final: 0.9107 (mtpp)
REVERT: B  328 ASP cc_start: 0.8992 (p0) cc_final: 0.8645 (p0)
REVERT: C   61 MET cc_start: 0.8854 (ttp) cc_final: 0.8448 (tpp)
REVERT: C  170 ARG cc_start: 0.8983 (mtt180) cc_final: 0.8734 (mtt180)
REVERT: C  232 GLN cc_start: 0.9255 (tp-100) cc_final: 0.8963 (tp-100)
REVERT: C  235 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8907 (pt0)
REVERT: C  249 TRP cc_start: 0.7826 (m-90) cc_final: 0.7517 (m-90)
REVERT: C  257 GLU cc_start: 0.7987 (tp30) cc_final: 0.7772 (tp30)
REVERT: C  294 LEU cc_start: 0.9095 (mp) cc_final: 0.8466 (tp)
REVERT: C  311 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8637 (mt-10)
REVERT: C  328 ASP cc_start: 0.9009 (p0) cc_final: 0.8660 (p0)
REVERT: D   61 MET cc_start: 0.8825 (ttp) cc_final: 0.8426 (tpp)
REVERT: D   79 ASP cc_start: 0.8469 (p0) cc_final: 0.7708 (p0)
REVERT: D  170 ARG cc_start: 0.9048 (mtt180) cc_final: 0.8549 (mtt-85)
REVERT: D  232 GLN cc_start: 0.9248 (tp-100) cc_final: 0.8952 (tp-100)
REVERT: D  235 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8827 (pt0)
REVERT: D  294 LEU cc_start: 0.9059 (mp) cc_final: 0.8516 (tp)
REVERT: D  311 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8657 (mt-10)
REVERT: D  328 ASP cc_start: 0.8974 (p0) cc_final: 0.8620 (p0)
  outliers start: 55
  outliers final: 32
  residues processed: 362
  average time/residue: 1.2370
  time to fit residues: 486.5520
Evaluate side-chains
  328 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 294
  time to evaluate  : 1.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 MET
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  204 ASN
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain B residue   65 GLN
Chi-restraints excluded: chain B residue  173 MET
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  239 GLU
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  316 LYS
Chi-restraints excluded: chain C residue   32 MET
Chi-restraints excluded: chain C residue   62 MET
Chi-restraints excluded: chain C residue   87 ASN
Chi-restraints excluded: chain C residue  173 MET
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  192 HIS
Chi-restraints excluded: chain C residue  239 GLU
Chi-restraints excluded: chain C residue  251 ILE
Chi-restraints excluded: chain C residue  255 VAL
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain D residue   32 MET
Chi-restraints excluded: chain D residue   43 LEU
Chi-restraints excluded: chain D residue  173 MET
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  255 VAL
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  303 ILE
Chi-restraints excluded: chain D residue  324 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 80 optimal weight:   30.0000
   chunk 78 optimal weight:    5.9990
   chunk 108 optimal weight:    6.9990
   chunk 109 optimal weight:    6.9990
   chunk 38 optimal weight:    9.9990
   chunk 15 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9980
   chunk 74 optimal weight:    9.9990
   chunk 106 optimal weight:    5.9990
   overall best weight:    4.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 163 ASN
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 214 ASN
C 232 GLN
D 232 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.102558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.081138 restraints weight = 26212.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 5.29
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.7444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9864  Z= 0.289
  Angle     :  0.948  12.558  13384  Z= 0.465
  Chirality :  0.052   0.281   1632
  Planarity :  0.005   0.056   1652
  Dihedral  :  5.092  18.253   1316
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 22.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 35.91 %
    Favored  : 59.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.25), residues: 1244
  helix:  0.46 (0.23), residues: 516
  sheet: -1.31 (0.43), residues: 132
  loop :  0.72 (0.29), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 226 
 HIS   0.005   0.001   HIS B  66 
 PHE   0.027   0.005   PHE C  70 
 TYR   0.044   0.002   TYR A 171 
 ARG   0.010   0.002   ARG C 168 

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  379 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 327
  time to evaluate  : 1.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.8765 (ttp) cc_final: 0.8473 (ttp)
REVERT: A  170 ARG cc_start: 0.8742 (mtt180) cc_final: 0.8518 (mtt180)
REVERT: A  232 GLN cc_start: 0.9210 (tp-100) cc_final: 0.8971 (tp-100)
REVERT: A  235 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8905 (pt0)
REVERT: A  294 LEU cc_start: 0.9001 (mp) cc_final: 0.8470 (tp)
REVERT: A  311 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8641 (mt-10)
REVERT: B   65 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8494 (pm20)
REVERT: B  170 ARG cc_start: 0.8999 (mtt180) cc_final: 0.8598 (mtt-85)
REVERT: B  171 TYR cc_start: 0.9227 (t80) cc_final: 0.9019 (t80)
REVERT: B  232 GLN cc_start: 0.9187 (tp-100) cc_final: 0.8912 (tp-100)
REVERT: B  235 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8760 (pt0)
REVERT: B  294 LEU cc_start: 0.9062 (mp) cc_final: 0.8518 (tp)
REVERT: B  311 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8654 (mt-10)
REVERT: B  316 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8932 (mtpp)
REVERT: C   65 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8638 (pm20)
REVERT: C  170 ARG cc_start: 0.8818 (mtt180) cc_final: 0.8412 (mtt-85)
REVERT: C  171 TYR cc_start: 0.9124 (t80) cc_final: 0.8923 (t80)
REVERT: C  232 GLN cc_start: 0.9270 (tp40) cc_final: 0.8968 (tp-100)
REVERT: C  235 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8907 (pt0)
REVERT: C  257 GLU cc_start: 0.8097 (tp30) cc_final: 0.7856 (tp30)
REVERT: C  294 LEU cc_start: 0.9057 (mp) cc_final: 0.8468 (tp)
REVERT: C  311 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8609 (mt-10)
REVERT: D   61 MET cc_start: 0.8867 (ttp) cc_final: 0.8518 (tpp)
REVERT: D  170 ARG cc_start: 0.8917 (mtt180) cc_final: 0.8398 (mtt-85)
REVERT: D  232 GLN cc_start: 0.9251 (tp40) cc_final: 0.8973 (tp-100)
REVERT: D  294 LEU cc_start: 0.9003 (mp) cc_final: 0.8493 (tp)
REVERT: D  311 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8646 (mt-10)
  outliers start: 52
  outliers final: 32
  residues processed: 351
  average time/residue: 1.0589
  time to fit residues: 403.7893
Evaluate side-chains
  343 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 308
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 MET
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  204 ASN
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain B residue   65 GLN
Chi-restraints excluded: chain B residue  173 MET
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  239 GLU
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  316 LYS
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain C residue   32 MET
Chi-restraints excluded: chain C residue   43 LEU
Chi-restraints excluded: chain C residue   65 GLN
Chi-restraints excluded: chain C residue  173 MET
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  192 HIS
Chi-restraints excluded: chain C residue  239 GLU
Chi-restraints excluded: chain C residue  255 VAL
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain D residue   32 MET
Chi-restraints excluded: chain D residue   65 GLN
Chi-restraints excluded: chain D residue  173 MET
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  255 VAL
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  303 ILE
Chi-restraints excluded: chain D residue  324 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 92 optimal weight:    8.9990
   chunk 62 optimal weight:    2.9990
   chunk 108 optimal weight:    8.9990
   chunk 93 optimal weight:   30.0000
   chunk 52 optimal weight:   40.0000
   chunk 18 optimal weight:    2.9990
   chunk 41 optimal weight:    7.9990
   chunk 110 optimal weight:    5.9990
   chunk 102 optimal weight:    2.9990
   chunk 45 optimal weight:    8.9990
   chunk 27 optimal weight:    7.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  20 ASN
C 284 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.103336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.081478 restraints weight = 26327.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 5.48
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.7719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9864  Z= 0.293
  Angle     :  0.991  13.096  13384  Z= 0.485
  Chirality :  0.053   0.309   1632
  Planarity :  0.005   0.053   1652
  Dihedral  :  5.179  20.494   1316
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 22.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 36.09 %
    Favored  : 59.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.25), residues: 1244
  helix: -0.00 (0.22), residues: 544
  sheet: -0.12 (0.54), residues: 92
  loop :  0.33 (0.28), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C 226 
 HIS   0.006   0.001   HIS B  66 
 PHE   0.026   0.005   PHE C  70 
 TYR   0.040   0.003   TYR D 171 
 ARG   0.014   0.002   ARG B 168 

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  377 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 324
  time to evaluate  : 1.012 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 ILE cc_start: 0.8970 (mt) cc_final: 0.8663 (pt)
REVERT: A   61 MET cc_start: 0.8797 (ttp) cc_final: 0.8518 (ttp)
REVERT: A   79 ASP cc_start: 0.8250 (p0) cc_final: 0.7447 (p0)
REVERT: A  170 ARG cc_start: 0.8670 (mtt180) cc_final: 0.8461 (mtt180)
REVERT: A  232 GLN cc_start: 0.9186 (tp-100) cc_final: 0.8785 (tp-100)
REVERT: A  275 LEU cc_start: 0.8389 (mt) cc_final: 0.8026 (mt)
REVERT: A  294 LEU cc_start: 0.8964 (mp) cc_final: 0.8437 (tp)
REVERT: A  328 ASP cc_start: 0.8828 (p0) cc_final: 0.8453 (p0)
REVERT: B   61 MET cc_start: 0.8871 (ttp) cc_final: 0.8620 (tpp)
REVERT: B   65 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8278 (pm20)
REVERT: B  170 ARG cc_start: 0.8975 (mtt180) cc_final: 0.8585 (mtt-85)
REVERT: B  217 MET cc_start: 0.6730 (pmm) cc_final: 0.6465 (mpp)
REVERT: B  232 GLN cc_start: 0.9202 (tp-100) cc_final: 0.8952 (tp-100)
REVERT: B  294 LEU cc_start: 0.9044 (mp) cc_final: 0.8490 (tp)
REVERT: B  311 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8603 (mt-10)
REVERT: C   65 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8440 (pm20)
REVERT: C  170 ARG cc_start: 0.8778 (mtt180) cc_final: 0.8367 (mtt-85)
REVERT: C  232 GLN cc_start: 0.9285 (tp40) cc_final: 0.8980 (tp-100)
REVERT: C  249 TRP cc_start: 0.7803 (m-90) cc_final: 0.7455 (m-90)
REVERT: C  257 GLU cc_start: 0.7995 (tp30) cc_final: 0.7783 (tp30)
REVERT: C  294 LEU cc_start: 0.9029 (mp) cc_final: 0.8473 (tp)
REVERT: D   65 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8532 (pm20)
REVERT: D  170 ARG cc_start: 0.8758 (mtt180) cc_final: 0.8437 (mtt-85)
REVERT: D  294 LEU cc_start: 0.8993 (mp) cc_final: 0.8526 (tp)
REVERT: D  311 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8637 (mt-10)
  outliers start: 53
  outliers final: 28
  residues processed: 350
  average time/residue: 0.8711
  time to fit residues: 335.1729
Evaluate side-chains
  311 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 280
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 MET
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain B residue   65 GLN
Chi-restraints excluded: chain B residue  173 MET
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain B residue  204 ASN
Chi-restraints excluded: chain B residue  239 GLU
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain C residue   32 MET
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue   65 GLN
Chi-restraints excluded: chain C residue  173 MET
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  255 VAL
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain D residue   32 MET
Chi-restraints excluded: chain D residue   62 MET
Chi-restraints excluded: chain D residue   65 GLN
Chi-restraints excluded: chain D residue  173 MET
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  255 VAL
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  303 ILE
Chi-restraints excluded: chain D residue  324 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 117 optimal weight:    7.9990
   chunk 14 optimal weight:   30.0000
   chunk 38 optimal weight:    5.9990
   chunk 105 optimal weight:   20.0000
   chunk 73 optimal weight:    8.9990
   chunk 81 optimal weight:   20.0000
   chunk 45 optimal weight:   30.0000
   chunk 21 optimal weight:    5.9990
   chunk 86 optimal weight:    7.9990
   chunk 59 optimal weight:    6.9990
   chunk 18 optimal weight:    7.9990
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  20 ASN
A 163 ASN
** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  20 ASN
** C  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.102432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.080900 restraints weight = 26549.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 5.32
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.7749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   9864  Z= 0.334
  Angle     :  1.059  13.786  13384  Z= 0.524
  Chirality :  0.054   0.306   1632
  Planarity :  0.005   0.052   1652
  Dihedral  :  5.363  17.228   1316
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 25.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 38.36 %
    Favored  : 57.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.25), residues: 1244
  helix: -0.15 (0.23), residues: 544
  sheet: -1.17 (0.46), residues: 124
  loop :  0.26 (0.28), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP C 226 
 HIS   0.005   0.001   HIS C 180 
 PHE   0.029   0.005   PHE D 287 
 TYR   0.043   0.003   TYR C 171 
 ARG   0.011   0.002   ARG B 168 

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  348 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 303
  time to evaluate  : 1.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 ILE cc_start: 0.8994 (mt) cc_final: 0.8687 (pt)
REVERT: A  170 ARG cc_start: 0.8641 (mtt180) cc_final: 0.8439 (mtt180)
REVERT: A  294 LEU cc_start: 0.9049 (mp) cc_final: 0.8444 (tp)
REVERT: A  311 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8672 (mt-10)
REVERT: B   65 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8550 (pm20)
REVERT: B  170 ARG cc_start: 0.8915 (mtt180) cc_final: 0.8548 (mtt-85)
REVERT: B  294 LEU cc_start: 0.9070 (mp) cc_final: 0.8480 (tp)
REVERT: B  311 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8612 (mt-10)
REVERT: C  217 MET cc_start: 0.6724 (pmm) cc_final: 0.6480 (mpp)
REVERT: C  232 GLN cc_start: 0.9304 (tp40) cc_final: 0.9014 (tp-100)
REVERT: C  235 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8878 (pt0)
REVERT: C  257 GLU cc_start: 0.7992 (tp30) cc_final: 0.7697 (tp30)
REVERT: C  294 LEU cc_start: 0.9085 (mp) cc_final: 0.8428 (tp)
REVERT: C  311 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8580 (mt-10)
REVERT: D   61 MET cc_start: 0.8877 (ttp) cc_final: 0.8599 (tpp)
REVERT: D   65 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8442 (pm20)
REVERT: D  170 ARG cc_start: 0.8736 (mtt180) cc_final: 0.8381 (mtt-85)
REVERT: D  294 LEU cc_start: 0.9060 (mp) cc_final: 0.8528 (tp)
REVERT: D  311 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8640 (mt-10)
  outliers start: 45
  outliers final: 32
  residues processed: 321
  average time/residue: 0.9669
  time to fit residues: 337.2937
Evaluate side-chains
  318 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 284
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  173 MET
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  204 ASN
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain B residue   65 GLN
Chi-restraints excluded: chain B residue  173 MET
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain B residue  204 ASN
Chi-restraints excluded: chain B residue  239 GLU
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain C residue   32 MET
Chi-restraints excluded: chain C residue  173 MET
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  255 VAL
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain D residue   32 MET
Chi-restraints excluded: chain D residue   43 LEU
Chi-restraints excluded: chain D residue   65 GLN
Chi-restraints excluded: chain D residue  173 MET
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  255 VAL
Chi-restraints excluded: chain D residue  263 LEU
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  303 ILE
Chi-restraints excluded: chain D residue  324 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 90 optimal weight:   30.0000
   chunk 69 optimal weight:    5.9990
   chunk 16 optimal weight:    9.9990
   chunk 118 optimal weight:    9.9990
   chunk 81 optimal weight:    7.9990
   chunk 75 optimal weight:    7.9990
   chunk 119 optimal weight:   40.0000
   chunk 3 optimal weight:    6.9990
   chunk 102 optimal weight:   40.0000
   chunk 67 optimal weight:   10.0000
   chunk 120 optimal weight:    6.9990
   overall best weight:    7.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B  20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.100845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.080050 restraints weight = 26761.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 5.26
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.7879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   9864  Z= 0.348
  Angle     :  1.093  13.630  13384  Z= 0.540
  Chirality :  0.055   0.305   1632
  Planarity :  0.006   0.055   1652
  Dihedral  :  5.439  18.983   1316
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 26.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 38.91 %
    Favored  : 57.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.25), residues: 1244
  helix: -0.22 (0.23), residues: 544
  sheet: -0.19 (0.55), residues: 92
  loop : -0.02 (0.27), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP C 226 
 HIS   0.007   0.002   HIS A  66 
 PHE   0.030   0.005   PHE D 287 
 TYR   0.040   0.002   TYR B 171 
 ARG   0.010   0.002   ARG B 168 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7988.97 seconds
wall clock time: 140 minutes 44.86 seconds (8444.86 seconds total)