Starting phenix.real_space_refine
on Wed Mar 12 03:43:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8umc_42375/03_2025/8umc_42375.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8umc_42375/03_2025/8umc_42375.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8umc_42375/03_2025/8umc_42375.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8umc_42375/03_2025/8umc_42375.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8umc_42375/03_2025/8umc_42375.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8umc_42375/03_2025/8umc_42375.cif"
  }
  resolution = 2.5
  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=   0.021
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Mn      2      7.51       5
     S      54      5.16       5
     C    4564      2.51       5
     N    1270      2.21       5
     O    1308      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7198
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2630
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 322, 2630
          Classifications: {'peptide': 322}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 307}
    Chain: "B"
      Number of atoms: 968
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 968
          Classifications: {'peptide': 123}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 114}
    Chain: "C"
      Number of atoms: 2630
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 322, 2630
          Classifications: {'peptide': 322}
          Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 307}
    Chain: "D"
      Number of atoms: 968
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 968
          Classifications: {'peptide': 123}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 114}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MN': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.71, per 1000 atoms: 0.65
  Number of scatterers: 7198
  At special positions: 0
  Unit cell: (107.06, 80.8, 82.82, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Mn      2     24.99
     S      54     16.00
     O    1308      8.00
     N    1270      7.00
     C    4564      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: 1.75
  Conformation dependent library (CDL) restraints added in 940.6 milliseconds
  

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1644

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 9 sheets defined
      43.5% alpha, 17.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 21
    Processing helix  chain 'A' and resid 25 through 36
    Processing helix  chain 'A' and resid 44 through 49
    Processing helix  chain 'A' and resid 56 through 71
    Processing helix  chain 'A' and resid 92 through 111
      removed outlier: 3.563A  pdb=" N   GLU A  98 " --> pdb=" O   ASP A  94 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ASP A 103 " --> pdb=" O   SER A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 129
    Processing helix  chain 'A' and resid 129 through 137
    Processing helix  chain 'A' and resid 152 through 164
      removed outlier: 3.770A  pdb=" N   ARG A 164 " --> pdb=" O   GLU A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 180
      removed outlier: 3.860A  pdb=" N   THR A 180 " --> pdb=" O   GLY A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 194
    Processing helix  chain 'A' and resid 197 through 210
    Processing helix  chain 'A' and resid 213 through 225
    Processing helix  chain 'A' and resid 227 through 240
      removed outlier: 4.030A  pdb=" N   LEU A 237 " --> pdb=" O   ALA A 233 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   ARG A 238 " --> pdb=" O   ALA A 234 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   HIS A 239 " --> pdb=" O   GLU A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 250
    Processing helix  chain 'A' and resid 279 through 286
    Processing helix  chain 'A' and resid 309 through 325
    Processing helix  chain 'B' and resid 34 through 36
      No H-bonds generated for 'chain 'B' and resid 34 through 36'
    Processing helix  chain 'B' and resid 49 through 51
      No H-bonds generated for 'chain 'B' and resid 49 through 51'
    Processing helix  chain 'B' and resid 65 through 69
      removed outlier: 4.367A  pdb=" N   ASP B  68 " --> pdb=" O   ALA B  65 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 15 through 21
    Processing helix  chain 'C' and resid 25 through 37
    Processing helix  chain 'C' and resid 44 through 49
    Processing helix  chain 'C' and resid 56 through 71
      removed outlier: 3.658A  pdb=" N   TYR C  60 " --> pdb=" O   ASP C  56 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ASP C  61 " --> pdb=" O   ASP C  57 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 111
      removed outlier: 3.659A  pdb=" N   ASP C 103 " --> pdb=" O   SER C  99 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ARG C 109 " --> pdb=" O   ARG C 105 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 122 through 129
    Processing helix  chain 'C' and resid 129 through 137
      removed outlier: 3.685A  pdb=" N   SER C 136 " --> pdb=" O   HIS C 132 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 152 through 162
    Processing helix  chain 'C' and resid 176 through 179
    Processing helix  chain 'C' and resid 184 through 194
    Processing helix  chain 'C' and resid 197 through 211
    Processing helix  chain 'C' and resid 213 through 224
    Processing helix  chain 'C' and resid 227 through 240
      removed outlier: 3.996A  pdb=" N   LEU C 237 " --> pdb=" O   ALA C 233 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   ARG C 238 " --> pdb=" O   ALA C 234 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   HIS C 239 " --> pdb=" O   GLU C 235 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 244 through 250
      removed outlier: 3.526A  pdb=" N   GLU C 250 " --> pdb=" O   ARG C 247 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 251 through 255
    Processing helix  chain 'C' and resid 279 through 287
    Processing helix  chain 'C' and resid 298 through 303
    Processing helix  chain 'C' and resid 309 through 325
    Processing helix  chain 'D' and resid 49 through 51
      No H-bonds generated for 'chain 'D' and resid 49 through 51'
    Processing helix  chain 'D' and resid 65 through 67
      No H-bonds generated for 'chain 'D' and resid 65 through 67'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 170 through 174
      removed outlier: 6.093A  pdb=" N   ILE A 115 " --> pdb=" O   GLY A 141 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   GLU A 143 " --> pdb=" O   ILE A 115 " (cutoff:3.500A)
      removed outlier: 7.458A  pdb=" N   VAL A 117 " --> pdb=" O   GLU A 143 " (cutoff:3.500A)
      removed outlier: 9.727A  pdb=" N   VAL A 114 " --> pdb=" O   VAL A  73 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   VAL A  75 " --> pdb=" O   VAL A 114 " (cutoff:3.500A)
      removed outlier: 7.609A  pdb=" N   ARG A 116 " --> pdb=" O   VAL A  75 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   HIS A  77 " --> pdb=" O   ARG A 116 " (cutoff:3.500A)
      removed outlier: 7.353A  pdb=" N   ILE A  41 " --> pdb=" O   VAL A  75 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   HIS A  77 " --> pdb=" O   ILE A  41 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   SER A  43 " --> pdb=" O   HIS A  77 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   GLY A  40 " --> pdb=" O   ARG A   8 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   LYS A   7 " --> pdb=" O   LEU A 292 " (cutoff:3.500A)
      removed outlier: 7.364A  pdb=" N   SER A 294 " --> pdb=" O   LYS A   7 " (cutoff:3.500A)
      removed outlier: 7.612A  pdb=" N   GLY A   9 " --> pdb=" O   SER A 294 " (cutoff:3.500A)
      removed outlier: 8.388A  pdb=" N   TYR A 296 " --> pdb=" O   GLY A   9 " (cutoff:3.500A)
      removed outlier: 8.631A  pdb=" N   SER A  11 " --> pdb=" O   TYR A 296 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   VAL A 258 " --> pdb=" O   ALA A 293 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   GLU A 295 " --> pdb=" O   VAL A 258 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   ALA A 260 " --> pdb=" O   GLU A 295 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 13 through 15
    Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 23
    Processing sheet with id=AA4, first strand: chain 'B' and resid 31 through 32
    Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 48
      removed outlier: 4.707A  pdb=" N   VAL B  41 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   GLY B  94 " --> pdb=" O   LEU B 123 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 170 through 174
      removed outlier: 6.707A  pdb=" N   LEU C 140 " --> pdb=" O   GLY C 171 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   ILE C 173 " --> pdb=" O   LEU C 140 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   LEU C 142 " --> pdb=" O   ILE C 173 " (cutoff:3.500A)
      removed outlier: 5.957A  pdb=" N   ILE C 115 " --> pdb=" O   GLY C 141 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   GLU C 143 " --> pdb=" O   ILE C 115 " (cutoff:3.500A)
      removed outlier: 7.402A  pdb=" N   VAL C 117 " --> pdb=" O   GLU C 143 " (cutoff:3.500A)
      removed outlier: 7.338A  pdb=" N   ILE C  41 " --> pdb=" O   VAL C  75 " (cutoff:3.500A)
      removed outlier: 6.120A  pdb=" N   HIS C  77 " --> pdb=" O   ILE C  41 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   SER C  43 " --> pdb=" O   HIS C  77 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   GLY C  40 " --> pdb=" O   ARG C   8 " (cutoff:3.500A)
      removed outlier: 6.993A  pdb=" N   LYS C   7 " --> pdb=" O   LEU C 292 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   SER C 294 " --> pdb=" O   LYS C   7 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   GLY C   9 " --> pdb=" O   SER C 294 " (cutoff:3.500A)
      removed outlier: 8.371A  pdb=" N   TYR C 296 " --> pdb=" O   GLY C   9 " (cutoff:3.500A)
      removed outlier: 8.331A  pdb=" N   SER C  11 " --> pdb=" O   TYR C 296 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 13 through 15
      removed outlier: 3.543A  pdb=" N   THR D  84 " --> pdb=" O   THR D  54 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 31 through 32
    Processing sheet with id=AA9, first strand: chain 'D' and resid 46 through 47
      removed outlier: 3.529A  pdb=" N   GLU D  46 " --> pdb=" O   VAL D  43 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL D  43 " --> pdb=" O   GLU D  46 " (cutoff:3.500A)

    305 hydrogen bonds defined for protein.
    834 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.78

  Time building geometry restraints manager: 2.07 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2438
        1.34 -     1.46: 1331
        1.46 -     1.57: 3499
        1.57 -     1.69: 0
        1.69 -     1.81: 100
  Bond restraints: 7368
  Sorted by residual:
  bond pdb=" N   VAL A 101 "
       pdb=" CA  VAL A 101 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.036 1.19e-02 7.06e+03 9.01e+00
  bond pdb=" N   ILE A 104 "
       pdb=" CA  ILE A 104 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.17e-02 7.31e+03 7.76e+00
  bond pdb=" N   ASP A 266 "
       pdb=" CA  ASP A 266 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.036 1.34e-02 5.57e+03 7.07e+00
  bond pdb=" N   GLN C 268 "
       pdb=" CA  GLN C 268 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.18e-02 7.18e+03 6.98e+00
  bond pdb=" N   HIS A 145 "
       pdb=" CA  HIS A 145 "
    ideal  model  delta    sigma   weight residual
    1.454  1.485 -0.031 1.18e-02 7.18e+03 6.86e+00
  ... (remaining 7363 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.26: 9339
        1.26 -     2.53: 487
        2.53 -     3.79: 104
        3.79 -     5.05: 21
        5.05 -     6.32: 3
  Bond angle restraints: 9954
  Sorted by residual:
  angle pdb=" N   PRO A 147 "
        pdb=" CA  PRO A 147 "
        pdb=" CB  PRO A 147 "
      ideal   model   delta    sigma   weight residual
     103.25   96.93    6.32 1.05e+00 9.07e-01 3.62e+01
  angle pdb=" CA  ILE A 302 "
        pdb=" C   ILE A 302 "
        pdb=" O   ILE A 302 "
      ideal   model   delta    sigma   weight residual
     122.63  118.54    4.09 8.70e-01 1.32e+00 2.21e+01
  angle pdb=" N   MET C 320 "
        pdb=" CA  MET C 320 "
        pdb=" C   MET C 320 "
      ideal   model   delta    sigma   weight residual
     111.14  106.07    5.07 1.08e+00 8.57e-01 2.20e+01
  angle pdb=" CA  ASP C 266 "
        pdb=" C   ASP C 266 "
        pdb=" O   ASP C 266 "
      ideal   model   delta    sigma   weight residual
     122.01  118.23    3.78 1.05e+00 9.07e-01 1.30e+01
  angle pdb=" CA  ASP A 266 "
        pdb=" C   ASP A 266 "
        pdb=" O   ASP A 266 "
      ideal   model   delta    sigma   weight residual
     122.01  118.28    3.73 1.05e+00 9.07e-01 1.26e+01
  ... (remaining 9949 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.28: 4078
       26.28 -    52.56: 288
       52.56 -    78.84: 47
       78.84 -   105.12: 10
      105.12 -   131.40: 1
  Dihedral angle restraints: 4424
    sinusoidal: 1862
      harmonic: 2562
  Sorted by residual:
  dihedral pdb=" CA  ALA A 146 "
           pdb=" C   ALA A 146 "
           pdb=" N   PRO A 147 "
           pdb=" CA  PRO A 147 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   48.60  131.40     0      5.00e+00 4.00e-02 6.91e+02
  dihedral pdb=" CA  ARG C 193 "
           pdb=" C   ARG C 193 "
           pdb=" N   GLN C 194 "
           pdb=" CA  GLN C 194 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.55   18.45     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  ARG C 105 "
           pdb=" C   ARG C 105 "
           pdb=" N   HIS C 106 "
           pdb=" CA  HIS C 106 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.20   17.80     0      5.00e+00 4.00e-02 1.27e+01
  ... (remaining 4421 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 801
       0.049 -    0.098: 192
       0.098 -    0.147: 55
       0.147 -    0.197: 6
       0.197 -    0.246: 2
  Chirality restraints: 1056
  Sorted by residual:
  chirality pdb=" CA  MET C 320 "
            pdb=" N   MET C 320 "
            pdb=" C   MET C 320 "
            pdb=" CB  MET C 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.51e+00
  chirality pdb=" CA  ARG A 102 "
            pdb=" N   ARG A 102 "
            pdb=" C   ARG A 102 "
            pdb=" CB  ARG A 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CA  VAL B  15 "
            pdb=" N   VAL B  15 "
            pdb=" C   VAL B  15 "
            pdb=" CB  VAL B  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 8.17e-01
  ... (remaining 1053 not shown)

  Planarity restraints: 1310
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 210 "    0.313 9.50e-02 1.11e+02   1.40e-01 1.21e+01
        pdb=" NE  ARG A 210 "   -0.020 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 210 "    0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 210 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 210 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 254 "    0.248 9.50e-02 1.11e+02   1.11e-01 7.56e+00
        pdb=" NE  ARG A 254 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 254 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 254 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 254 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 270 "    0.178 9.50e-02 1.11e+02   7.99e-02 4.29e+00
        pdb=" NE  ARG A 270 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 270 "    0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 270 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 270 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1307 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.62: 113
        2.62 -     3.19: 6478
        3.19 -     3.76: 11573
        3.76 -     4.33: 17203
        4.33 -     4.90: 27913
  Nonbonded interactions: 63280
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  27 "
            pdb=" OH  TYR B 108 "
     model   vdw
     2.045 3.040
  nonbonded pdb=" OH  TYR D  28 "
            pdb=" OH  TYR D 108 "
     model   vdw
     2.048 3.040
  nonbonded pdb=" OE1 GLU A 295 "
            pdb="MN    MN A 401 "
     model   vdw
     2.101 2.320
  nonbonded pdb=" OE1 GLU C 295 "
            pdb="MN    MN C 401 "
     model   vdw
     2.115 2.320
  nonbonded pdb=" O   LYS C 261 "
            pdb=" OH  TYR C 276 "
     model   vdw
     2.133 3.040
  ... (remaining 63275 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = 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=0.00 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:             0.810
  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:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     19.890
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  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:10.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
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      :  0.005   0.039   7368  Z= 0.334
  Angle     :  0.683   6.318   9954  Z= 0.420
  Chirality :  0.048   0.246   1056
  Planarity :  0.007   0.140   1310
  Dihedral  : 17.532 131.399   2780
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.95 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 19.51 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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: -0.80 (0.28), residues: 882
  helix:  0.14 (0.28), residues: 344
  sheet: -1.05 (0.42), residues: 154
  loop : -0.79 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 242 
 HIS   0.006   0.001   HIS C 257 
 PHE   0.012   0.002   PHE C  20 
 TYR   0.014   0.001   TYR A  13 
 ARG   0.011   0.001   ARG A 270 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 214
  time to evaluate  : 0.824 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  241 ASN cc_start: 0.8181 (p0) cc_final: 0.7918 (p0)
  outliers start: 9
  outliers final: 5
  residues processed: 221
  average time/residue: 1.3534
  time to fit residues: 313.1360
Evaluate side-chains
  214 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 209
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   27 GLU
Chi-restraints excluded: chain C residue   54 ASN
Chi-restraints excluded: chain D residue   62 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 22 optimal weight:    0.3980
   chunk 44 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  96 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.131999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.122606 restraints weight = 8877.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3653 rms_B_bonded: 1.28
r_work: 0.3562 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3432 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.1197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   7368  Z= 0.392
  Angle     :  0.642   6.255   9954  Z= 0.335
  Chirality :  0.047   0.170   1056
  Planarity :  0.005   0.056   1310
  Dihedral  :  5.930  68.780   1004
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 19.77 %
    Favored  : 76.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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: -0.48 (0.28), residues: 882
  helix:  0.50 (0.28), residues: 334
  sheet: -1.12 (0.43), residues: 150
  loop : -0.57 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 242 
 HIS   0.005   0.001   HIS A 149 
 PHE   0.016   0.002   PHE C  20 
 TYR   0.012   0.002   TYR A  13 
 ARG   0.007   0.001   ARG A 270 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 218
  time to evaluate  : 0.868 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ASP cc_start: 0.7095 (p0) cc_final: 0.6520 (p0)
REVERT: A   61 ASP cc_start: 0.7490 (m-30) cc_final: 0.7225 (m-30)
REVERT: A   91 MET cc_start: 0.8111 (mtm) cc_final: 0.7901 (ttm)
REVERT: C  278 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7292 (mm-30)
REVERT: C  284 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8632 (mttp)
  outliers start: 31
  outliers final: 14
  residues processed: 232
  average time/residue: 1.3304
  time to fit residues: 325.1691
Evaluate side-chains
  221 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 205
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain B residue   19 VAL
Chi-restraints excluded: chain B residue   44 ASP
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  231 ILE
Chi-restraints excluded: chain C residue  278 GLU
Chi-restraints excluded: chain C residue  284 LYS
Chi-restraints excluded: chain C residue  289 SER
Chi-restraints excluded: chain C residue  303 GLN
Chi-restraints excluded: chain D residue   40 ASP
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue   62 VAL
Chi-restraints excluded: chain D residue  111 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 85 optimal weight:    0.7980
   chunk 76 optimal weight:    0.8980
   chunk 64 optimal weight:    0.6980
   chunk 59 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 66 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  96 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.132735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.123390 restraints weight = 8982.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 1.30
r_work: 0.3573 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.3444 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7368  Z= 0.277
  Angle     :  0.584   5.770   9954  Z= 0.303
  Chirality :  0.045   0.164   1056
  Planarity :  0.005   0.103   1310
  Dihedral  :  5.504  59.833    999
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 20.28 %
    Favored  : 75.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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: -0.26 (0.29), residues: 882
  helix:  0.71 (0.28), residues: 334
  sheet: -1.02 (0.44), residues: 150
  loop : -0.46 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  63 
 HIS   0.003   0.001   HIS A 182 
 PHE   0.014   0.002   PHE C  20 
 TYR   0.016   0.002   TYR A  13 
 ARG   0.007   0.000   ARG A 270 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 213
  time to evaluate  : 0.759 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ASP cc_start: 0.7498 (m-30) cc_final: 0.7273 (m-30)
REVERT: C  241 ASN cc_start: 0.8137 (p0) cc_final: 0.7868 (p0)
REVERT: C  278 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7282 (mm-30)
  outliers start: 33
  outliers final: 15
  residues processed: 230
  average time/residue: 1.3057
  time to fit residues: 314.7533
Evaluate side-chains
  225 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 209
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain B residue   19 VAL
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  243 SER
Chi-restraints excluded: chain C residue  278 GLU
Chi-restraints excluded: chain C residue  289 SER
Chi-restraints excluded: chain C residue  303 GLN
Chi-restraints excluded: chain D residue   40 ASP
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   62 VAL
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  111 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 50 optimal weight:    0.3980
   chunk 17 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 11 optimal weight:    0.3980
   chunk 10 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 76 optimal weight:    0.6980
   chunk 46 optimal weight:    0.4980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 241 ASN
C  96 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.133668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.124216 restraints weight = 8985.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 1.30
r_work: 0.3585 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3456 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.1701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7368  Z= 0.236
  Angle     :  0.560   5.480   9954  Z= 0.290
  Chirality :  0.044   0.159   1056
  Planarity :  0.005   0.107   1310
  Dihedral  :  5.297  55.115    999
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 21.83 %
    Favored  : 73.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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: -0.10 (0.29), residues: 882
  helix:  0.83 (0.28), residues: 334
  sheet: -0.93 (0.44), residues: 154
  loop : -0.35 (0.33), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  63 
 HIS   0.003   0.001   HIS A 158 
 PHE   0.013   0.002   PHE C  59 
 TYR   0.010   0.001   TYR C  13 
 ARG   0.005   0.000   ARG A 102 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 221
  time to evaluate  : 0.745 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 LYS cc_start: 0.8162 (mptt) cc_final: 0.7932 (mttp)
REVERT: A   61 ASP cc_start: 0.7523 (m-30) cc_final: 0.7262 (m-30)
REVERT: A  193 ARG cc_start: 0.8284 (ptp90) cc_final: 0.8067 (ptp90)
REVERT: C   49 MET cc_start: 0.8467 (mtt) cc_final: 0.7902 (mtt)
REVERT: C  241 ASN cc_start: 0.8139 (p0) cc_final: 0.7883 (p0)
REVERT: C  278 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7225 (mm-30)
  outliers start: 33
  outliers final: 20
  residues processed: 239
  average time/residue: 1.2792
  time to fit residues: 320.5438
Evaluate side-chains
  239 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 218
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue  158 HIS
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   19 VAL
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   44 ASP
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   56 ASP
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  243 SER
Chi-restraints excluded: chain C residue  278 GLU
Chi-restraints excluded: chain C residue  289 SER
Chi-restraints excluded: chain C residue  303 GLN
Chi-restraints excluded: chain D residue   40 ASP
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue   62 VAL
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  123 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 84 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 30 optimal weight:    0.4980
   chunk 27 optimal weight:    0.0370
   chunk 54 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0050
   chunk 36 optimal weight:    0.0870
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.2650

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
A 241 ASN
C  96 GLN
C 313 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.135701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.126385 restraints weight = 8909.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.3703 rms_B_bonded: 1.30
r_work: 0.3614 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.3487 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.1990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7368  Z= 0.174
  Angle     :  0.544   6.077   9954  Z= 0.281
  Chirality :  0.043   0.164   1056
  Planarity :  0.005   0.104   1310
  Dihedral  :  5.013  50.003    999
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 22.22 %
    Favored  : 74.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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:  0.10 (0.29), residues: 882
  helix:  1.02 (0.29), residues: 334
  sheet: -1.02 (0.43), residues: 166
  loop : -0.12 (0.34), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  63 
 HIS   0.005   0.001   HIS A 301 
 PHE   0.011   0.001   PHE C 172 
 TYR   0.017   0.001   TYR A  13 
 ARG   0.006   0.000   ARG A 102 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 215
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 LYS cc_start: 0.8122 (mptt) cc_final: 0.7895 (mttp)
REVERT: A   61 ASP cc_start: 0.7496 (m-30) cc_final: 0.7241 (m-30)
REVERT: A  252 MET cc_start: 0.8350 (mmp) cc_final: 0.7882 (mmp)
REVERT: B   29 ARG cc_start: 0.8667 (ptt90) cc_final: 0.8290 (ptt-90)
REVERT: C  232 ARG cc_start: 0.8296 (ttp80) cc_final: 0.8046 (ttm110)
REVERT: C  236 MET cc_start: 0.8808 (mtt) cc_final: 0.8373 (mtt)
REVERT: C  241 ASN cc_start: 0.8089 (p0) cc_final: 0.7872 (p0)
  outliers start: 28
  outliers final: 18
  residues processed: 232
  average time/residue: 1.3870
  time to fit residues: 336.3892
Evaluate side-chains
  230 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 212
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  158 HIS
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   56 ASP
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  289 SER
Chi-restraints excluded: chain C residue  303 GLN
Chi-restraints excluded: chain D residue   38 THR
Chi-restraints excluded: chain D residue   40 ASP
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  123 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 83 optimal weight:    0.8980
   chunk 73 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   chunk 11 optimal weight:    0.1980
   chunk 61 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 1 optimal weight:    0.4980
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
A 199 HIS
A 207 GLN
C  96 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.134220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.124721 restraints weight = 8975.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3680 rms_B_bonded: 1.31
r_work: 0.3589 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3461 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.2029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7368  Z= 0.270
  Angle     :  0.587   6.383   9954  Z= 0.303
  Chirality :  0.045   0.169   1056
  Planarity :  0.005   0.095   1310
  Dihedral  :  5.126  48.786    998
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 24.03 %
    Favored  : 72.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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:  0.10 (0.30), residues: 882
  helix:  1.03 (0.29), residues: 334
  sheet: -1.04 (0.43), residues: 168
  loop : -0.12 (0.34), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  63 
 HIS   0.005   0.001   HIS A 158 
 PHE   0.016   0.002   PHE C  20 
 TYR   0.012   0.001   TYR C  13 
 ARG   0.006   0.001   ARG A 102 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 204
  time to evaluate  : 0.837 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 LYS cc_start: 0.8176 (mptt) cc_final: 0.7933 (mttp)
REVERT: A   61 ASP cc_start: 0.7515 (m-30) cc_final: 0.7260 (m-30)
REVERT: B   29 ARG cc_start: 0.8643 (ptt90) cc_final: 0.8431 (ptm-80)
REVERT: C  203 TYR cc_start: 0.8206 (t80) cc_final: 0.7892 (t80)
REVERT: C  232 ARG cc_start: 0.8315 (ttp80) cc_final: 0.8027 (ttm110)
REVERT: C  241 ASN cc_start: 0.8116 (p0) cc_final: 0.7888 (p0)
  outliers start: 25
  outliers final: 17
  residues processed: 219
  average time/residue: 1.3818
  time to fit residues: 316.4474
Evaluate side-chains
  219 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 202
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  158 HIS
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   56 ASP
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  289 SER
Chi-restraints excluded: chain C residue  303 GLN
Chi-restraints excluded: chain D residue   38 THR
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  123 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 68 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0870
   chunk 43 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.7762

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
A 145 HIS
A 207 GLN
A 241 ASN
C  96 GLN
C 241 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.133480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.124099 restraints weight = 8877.976|
|-----------------------------------------------------------------------------|
r_work (start): 0.3668 rms_B_bonded: 1.29
r_work: 0.3578 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.3449 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.2030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   7368  Z= 0.316
  Angle     :  0.610   6.886   9954  Z= 0.315
  Chirality :  0.045   0.181   1056
  Planarity :  0.005   0.089   1310
  Dihedral  :  5.261  48.781    998
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 23.64 %
    Favored  : 72.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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:  0.06 (0.30), residues: 882
  helix:  0.99 (0.29), residues: 334
  sheet: -1.06 (0.43), residues: 168
  loop : -0.13 (0.34), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A  63 
 HIS   0.005   0.001   HIS C 145 
 PHE   0.017   0.002   PHE C  20 
 TYR   0.019   0.002   TYR A  13 
 ARG   0.007   0.001   ARG A 102 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 208
  time to evaluate  : 0.779 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 ASP cc_start: 0.7498 (m-30) cc_final: 0.7224 (m-30)
REVERT: A  246 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7740 (mmm160)
REVERT: C  187 MET cc_start: 0.8163 (mtt) cc_final: 0.7837 (mtp)
REVERT: C  203 TYR cc_start: 0.8228 (t80) cc_final: 0.7929 (t80)
REVERT: C  241 ASN cc_start: 0.8102 (p0) cc_final: 0.7893 (p0)
REVERT: C  278 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7227 (mm-30)
  outliers start: 27
  outliers final: 22
  residues processed: 223
  average time/residue: 1.4170
  time to fit residues: 331.0741
Evaluate side-chains
  229 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 205
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  158 HIS
Chi-restraints excluded: chain A residue  246 ARG
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   54 ASN
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  126 MET
Chi-restraints excluded: chain C residue  278 GLU
Chi-restraints excluded: chain C residue  289 SER
Chi-restraints excluded: chain C residue  303 GLN
Chi-restraints excluded: chain D residue   38 THR
Chi-restraints excluded: chain D residue   40 ASP
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  123 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 72 optimal weight:    0.3980
   chunk 67 optimal weight:    0.1980
   chunk 28 optimal weight:    0.8980
   chunk 45 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
A 145 HIS
A 207 GLN
A 240 ASN
A 244 ASN
C  96 GLN
C 313 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.134533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.125131 restraints weight = 9002.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.3685 rms_B_bonded: 1.31
r_work: 0.3594 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3467 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7368  Z= 0.240
  Angle     :  0.584   7.336   9954  Z= 0.302
  Chirality :  0.044   0.182   1056
  Planarity :  0.005   0.087   1310
  Dihedral  :  5.100  44.229    998
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 23.90 %
    Favored  : 72.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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 (0.30), residues: 882
  helix:  1.05 (0.29), residues: 334
  sheet: -1.05 (0.43), residues: 168
  loop : -0.11 (0.34), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  63 
 HIS   0.005   0.001   HIS A 158 
 PHE   0.013   0.002   PHE C  20 
 TYR   0.017   0.001   TYR D 108 
 ARG   0.008   0.001   ARG A 102 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 205
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 LYS cc_start: 0.8163 (mptt) cc_final: 0.7917 (mttp)
REVERT: A   61 ASP cc_start: 0.7507 (m-30) cc_final: 0.7248 (m-30)
REVERT: A  300 ARG cc_start: 0.8035 (ptp-170) cc_final: 0.7804 (ptp-170)
REVERT: B   29 ARG cc_start: 0.8619 (ptt90) cc_final: 0.8409 (ptm-80)
REVERT: C  161 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7872 (t80)
REVERT: C  187 MET cc_start: 0.8163 (mtt) cc_final: 0.7802 (mtp)
REVERT: C  203 TYR cc_start: 0.8195 (t80) cc_final: 0.7863 (t80)
  outliers start: 31
  outliers final: 19
  residues processed: 223
  average time/residue: 1.6425
  time to fit residues: 384.2993
Evaluate side-chains
  226 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 206
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  158 HIS
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   56 ASP
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  161 PHE
Chi-restraints excluded: chain C residue  289 SER
Chi-restraints excluded: chain D residue   38 THR
Chi-restraints excluded: chain D residue   40 ASP
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  123 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9980
   chunk 54 optimal weight:    0.1980
   chunk 70 optimal weight:    0.7980
   chunk 50 optimal weight:    0.5980
   chunk 17 optimal weight:    0.4980
   chunk 72 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
A 145 HIS
A 207 GLN
A 303 GLN
C  96 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.134695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.125288 restraints weight = 8941.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3687 rms_B_bonded: 1.31
r_work: 0.3598 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.3472 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.2296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7368  Z= 0.249
  Angle     :  0.605   7.827   9954  Z= 0.311
  Chirality :  0.044   0.191   1056
  Planarity :  0.005   0.083   1310
  Dihedral  :  5.077  44.082    998
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 25.19 %
    Favored  : 71.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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 (0.30), residues: 882
  helix:  1.07 (0.29), residues: 334
  sheet: -1.06 (0.42), residues: 168
  loop : -0.14 (0.34), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  63 
 HIS   0.005   0.001   HIS A 158 
 PHE   0.013   0.002   PHE C  20 
 TYR   0.019   0.002   TYR A  13 
 ARG   0.008   0.001   ARG A 102 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 210
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 LYS cc_start: 0.8154 (mptt) cc_final: 0.7911 (mttp)
REVERT: A   61 ASP cc_start: 0.7506 (m-30) cc_final: 0.7243 (m-30)
REVERT: A  247 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8089 (tpm170)
REVERT: C   48 MET cc_start: 0.8584 (mtt) cc_final: 0.8270 (mtt)
REVERT: C  187 MET cc_start: 0.8143 (mtt) cc_final: 0.7814 (mtp)
REVERT: C  203 TYR cc_start: 0.8231 (t80) cc_final: 0.7951 (t80)
REVERT: C  232 ARG cc_start: 0.8323 (ttp80) cc_final: 0.8111 (ttm110)
  outliers start: 26
  outliers final: 21
  residues processed: 227
  average time/residue: 1.4873
  time to fit residues: 352.5062
Evaluate side-chains
  229 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 207
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  158 HIS
Chi-restraints excluded: chain A residue  247 ARG
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   56 ASP
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  161 PHE
Chi-restraints excluded: chain C residue  289 SER
Chi-restraints excluded: chain D residue   38 THR
Chi-restraints excluded: chain D residue   40 ASP
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  123 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 87 optimal weight:    0.8980
   chunk 85 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 35 optimal weight:    0.4980
   chunk 69 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 75 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
A 145 HIS
A 207 GLN
A 244 ASN
C  96 GLN
C 241 ASN
C 313 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.134052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.124597 restraints weight = 9102.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3674 rms_B_bonded: 1.32
r_work: 0.3582 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3454 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   7368  Z= 0.316
  Angle     :  0.642   7.811   9954  Z= 0.329
  Chirality :  0.046   0.178   1056
  Planarity :  0.005   0.082   1310
  Dihedral  :  5.246  44.386    998
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 25.32 %
    Favored  : 70.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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:  0.05 (0.30), residues: 882
  helix:  1.05 (0.29), residues: 334
  sheet: -1.06 (0.43), residues: 168
  loop : -0.21 (0.34), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  63 
 HIS   0.006   0.001   HIS A 158 
 PHE   0.018   0.002   PHE A  80 
 TYR   0.020   0.002   TYR D 108 
 ARG   0.009   0.001   ARG A 102 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 208
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6873 (tm-30)
REVERT: A   61 ASP cc_start: 0.7494 (m-30) cc_final: 0.7228 (m-30)
REVERT: A  247 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8143 (tpm170)
REVERT: C   48 MET cc_start: 0.8595 (mtt) cc_final: 0.8286 (mtt)
REVERT: C  187 MET cc_start: 0.8171 (mtt) cc_final: 0.7858 (mtm)
REVERT: C  203 TYR cc_start: 0.8253 (t80) cc_final: 0.7963 (t80)
  outliers start: 29
  outliers final: 23
  residues processed: 226
  average time/residue: 1.8768
  time to fit residues: 443.7472
Evaluate side-chains
  232 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 207
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   42 GLU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  158 HIS
Chi-restraints excluded: chain A residue  247 ARG
Chi-restraints excluded: chain B residue   19 VAL
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   44 ASP
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   56 ASP
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   83 THR
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  289 SER
Chi-restraints excluded: chain D residue   38 THR
Chi-restraints excluded: chain D residue   40 ASP
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  123 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 78 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 61 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 76 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   chunk 60 optimal weight:    0.0870
   chunk 17 optimal weight:    0.0170
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
A 145 HIS
** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 244 ASN
C  96 GLN
C 313 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.135702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.126236 restraints weight = 9017.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3695 rms_B_bonded: 1.33
r_work: 0.3606 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3479 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.2437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7368  Z= 0.234
  Angle     :  0.607   7.784   9954  Z= 0.314
  Chirality :  0.044   0.172   1056
  Planarity :  0.005   0.083   1310
  Dihedral  :  5.088  43.847    998
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 26.36 %
    Favored  : 70.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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 (0.30), residues: 882
  helix:  1.24 (0.29), residues: 332
  sheet: -1.02 (0.43), residues: 168
  loop : -0.12 (0.34), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  63 
 HIS   0.005   0.001   HIS A 158 
 PHE   0.017   0.002   PHE A  80 
 TYR   0.022   0.002   TYR A  13 
 ARG   0.014   0.001   ARG A 102 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7415.89 seconds
wall clock time: 130 minutes 42.05 seconds (7842.05 seconds total)