Starting phenix.real_space_refine
on Thu Jul  2 22:12:06 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7v9x_31829/07_2026/7v9x_31829.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v9x_31829/07_2026/7v9x_31829.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.82
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v9x_31829/07_2026/7v9x_31829.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v9x_31829/07_2026/7v9x_31829.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v9x_31829/07_2026/7v9x_31829.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v9x_31829/07_2026/7v9x_31829.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7v9x_31829/07_2026/7v9x_31829.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7v9x_31829/07_2026/7v9x_31829.cif"
  }
  resolution = 2.82
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.071
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     210      5.49       5
     S      23      5.16       5
     C    5946      2.51       5
     N    1901      2.21       5
     O    2470      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 10550
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 2518
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 314, 2518
          Classifications: {'peptide': 314}
          Link IDs: {'PTRANS': 12, 'TRANS': 301}
    Chain: "C"
      Number of atoms: 1096
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 1096
          Classifications: {'peptide': 132}
          Link IDs: {'PTRANS': 2, 'TRANS': 129}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 808
          Classifications: {'DNA': 39}
          Link IDs: {'rna3p': 38}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 1225
          Classifications: {'RNA': 58}
          Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 20, 'rna3p_pyr': 23}
          Link IDs: {'rna2p': 15, 'rna3p': 42}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 176
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 176
          Classifications: {'RNA': 8}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2}
          Link IDs: {'rna3p': 7}
    Chain: "B"
      Number of atoms: 2518
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 314, 2518
          Classifications: {'peptide': 314}
          Link IDs: {'PTRANS': 12, 'TRANS': 301}
    Chain: "G"
      Number of atoms: 808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 808
          Classifications: {'DNA': 39}
          Link IDs: {'rna3p': 38}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 1225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 1225
          Classifications: {'RNA': 58}
          Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 20, 'rna3p_pyr': 23}
          Link IDs: {'rna2p': 15, 'rna3p': 42}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 176
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 176
          Classifications: {'RNA': 8}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2}
          Link IDs: {'rna3p': 7}
  Time building chain proxies: 2.04, per 1000 atoms: 0.19
  Number of scatterers: 10550
  At special positions: 0
  Unit cell: (94.35, 129.2, 155.55, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      23     16.00
     P     210     15.00
     O    2470      8.00
     N    1901      7.00
     C    5946      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.62
  Conformation dependent library (CDL) restraints added in 165.9 milliseconds
  

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1434

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 8 sheets defined
      60.5% alpha, 10.9% beta
      64 base pairs and 116 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 14
      removed outlier: 3.633A  pdb=" N   LEU A   7 " --> pdb=" O   SER A   3 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ASN A   8 " --> pdb=" O   ALA A   4 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   PHE A  10 " --> pdb=" O   TYR A   6 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 22 through 31
    Processing helix  chain 'A' and resid 33 through 44
      removed outlier: 3.581A  pdb=" N   TYR A  42 " --> pdb=" O   ARG A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 83
      removed outlier: 3.733A  pdb=" N   LEU A  75 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 87
    Processing helix  chain 'A' and resid 102 through 107
    Processing helix  chain 'A' and resid 108 through 110
      No H-bonds generated for 'chain 'A' and resid 108 through 110'
    Processing helix  chain 'A' and resid 122 through 127
      removed outlier: 3.691A  pdb=" N   LEU A 127 " --> pdb=" O   PHE A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 139
      removed outlier: 3.756A  pdb=" N   VAL A 135 " --> pdb=" O   LYS A 131 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LEU A 139 " --> pdb=" O   VAL A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 154
    Processing helix  chain 'A' and resid 165 through 174
    Processing helix  chain 'A' and resid 174 through 188
      removed outlier: 4.625A  pdb=" N   SER A 187 " --> pdb=" O   GLY A 183 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   ARG A 188 " --> pdb=" O   TYR A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 220
      removed outlier: 3.606A  pdb=" N   VAL A 209 " --> pdb=" O   SER A 205 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   SER A 218 " --> pdb=" O   ASP A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 224
    Processing helix  chain 'A' and resid 256 through 272
    Processing helix  chain 'A' and resid 277 through 292
      removed outlier: 3.655A  pdb=" N   VAL A 281 " --> pdb=" O   GLU A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 311
    Processing helix  chain 'C' and resid 8 through 19
      removed outlier: 3.766A  pdb=" N   GLN C  12 " --> pdb=" O   GLU C   8 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LYS C  19 " --> pdb=" O   GLY C  15 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 202 through 213
      Proline residue:  C 208  - end of helix
    Processing helix  chain 'C' and resid 217 through 230
    Processing helix  chain 'C' and resid 236 through 250
    Processing helix  chain 'C' and resid 263 through 274
    Processing helix  chain 'C' and resid 277 through 292
      removed outlier: 3.575A  pdb=" N   ARG C 283 " --> pdb=" O   LEU C 279 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ARG C 292 " --> pdb=" O   ASN C 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 15
      removed outlier: 3.937A  pdb=" N   ASN B   8 " --> pdb=" O   ALA B   4 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   PHE B  10 " --> pdb=" O   TYR B   6 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   LEU B  15 " --> pdb=" O   ARG B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 31
    Processing helix  chain 'B' and resid 33 through 43
    Processing helix  chain 'B' and resid 44 through 46
      No H-bonds generated for 'chain 'B' and resid 44 through 46'
    Processing helix  chain 'B' and resid 69 through 83
      removed outlier: 3.615A  pdb=" N   LEU B  75 " --> pdb=" O   GLU B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 87
    Processing helix  chain 'B' and resid 102 through 107
    Processing helix  chain 'B' and resid 108 through 110
      No H-bonds generated for 'chain 'B' and resid 108 through 110'
    Processing helix  chain 'B' and resid 123 through 127
    Processing helix  chain 'B' and resid 128 through 139
      removed outlier: 4.060A  pdb=" N   VAL B 132 " --> pdb=" O   THR B 128 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   LEU B 139 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 154
    Processing helix  chain 'B' and resid 165 through 174
    Processing helix  chain 'B' and resid 175 through 188
      removed outlier: 4.232A  pdb=" N   SER B 187 " --> pdb=" O   GLY B 183 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   ARG B 188 " --> pdb=" O   TYR B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 220
      removed outlier: 3.664A  pdb=" N   VAL B 209 " --> pdb=" O   SER B 205 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   SER B 218 " --> pdb=" O   ASP B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 224
    Processing helix  chain 'B' and resid 256 through 273
      removed outlier: 3.619A  pdb=" N   TYR B 260 " --> pdb=" O   GLY B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 277 through 292
    Processing helix  chain 'B' and resid 292 through 310
      removed outlier: 3.679A  pdb=" N   LYS B 308 " --> pdb=" O   SER B 304 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   LYS B 309 " --> pdb=" O   LYS B 305 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 53
      removed outlier: 3.643A  pdb=" N   ARG A  63 " --> pdb=" O   VAL A  53 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 195
    Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 243
    Processing sheet with id=AA4, first strand: chain 'C' and resid 253 through 256
    Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 53
      removed outlier: 3.979A  pdb=" N   ARG B  63 " --> pdb=" O   VAL B  53 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 194
      removed outlier: 3.543A  pdb=" N   PHE B 114 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   VAL B 226 " --> pdb=" O   GLU B 121 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 194
      removed outlier: 3.543A  pdb=" N   PHE B 114 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 242 through 243

    332 hydrogen bonds defined for protein.
    948 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      161 hydrogen bonds
      290 hydrogen bond angles
      0 basepair planarities
      64 basepair parallelities
      116 stacking parallelities
  Total time for adding SS restraints: 1.68

  Time building geometry restraints manager: 0.92 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: 1841
        1.33 -     1.45: 3746
        1.45 -     1.57: 5159
        1.57 -     1.69: 410
        1.69 -     1.81: 34
  Bond restraints: 11190
  Sorted by residual:
  bond pdb=" C3'  DT G  17 "
       pdb=" C2'  DT G  17 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.20e+01
  bond pdb=" C3'  DT D  17 "
       pdb=" C2'  DT D  17 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 9.32e+00
  bond pdb=" C1'  DC D  75 "
       pdb=" N1   DC D  75 "
    ideal  model  delta    sigma   weight residual
    1.468  1.508 -0.040 1.40e-02 5.10e+03 8.25e+00
  bond pdb=" C3'  DA D  10 "
       pdb=" C2'  DA D  10 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 8.00e-03 1.56e+04 7.69e+00
  bond pdb=" C3'  DC D  75 "
       pdb=" C2'  DC D  75 "
    ideal  model  delta    sigma   weight residual
    1.516  1.537 -0.021 8.00e-03 1.56e+04 7.11e+00
  ... (remaining 11185 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 15694
        2.10 -     4.20: 327
        4.20 -     6.30: 26
        6.30 -     8.40: 3
        8.40 -    10.50: 1
  Bond angle restraints: 16051
  Sorted by residual:
  angle pdb=" O4'  DT D  82 "
        pdb=" C4'  DT D  82 "
        pdb=" C3'  DT D  82 "
      ideal   model   delta    sigma   weight residual
     106.00  102.75    3.25 6.00e-01 2.78e+00 2.94e+01
  angle pdb=" O4'  DC D  83 "
        pdb=" C4'  DC D  83 "
        pdb=" C3'  DC D  83 "
      ideal   model   delta    sigma   weight residual
     106.00  103.03    2.97 6.00e-01 2.78e+00 2.44e+01
  angle pdb=" O4'  DC G  83 "
        pdb=" C4'  DC G  83 "
        pdb=" C3'  DC G  83 "
      ideal   model   delta    sigma   weight residual
     106.00  103.14    2.86 6.00e-01 2.78e+00 2.28e+01
  angle pdb=" O4'  DG G  85 "
        pdb=" C4'  DG G  85 "
        pdb=" C3'  DG G  85 "
      ideal   model   delta    sigma   weight residual
     106.00  103.29    2.71 6.00e-01 2.78e+00 2.04e+01
  angle pdb=" O4'  DG D  85 "
        pdb=" C4'  DG D  85 "
        pdb=" C3'  DG D  85 "
      ideal   model   delta    sigma   weight residual
     106.00  103.30    2.70 6.00e-01 2.78e+00 2.03e+01
  ... (remaining 16046 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.67: 5853
       35.67 -    71.33: 416
       71.33 -   107.00: 7
      107.00 -   142.67: 5
      142.67 -   178.33: 17
  Dihedral angle restraints: 6298
    sinusoidal: 4073
      harmonic: 2225
  Sorted by residual:
  dihedral pdb=" O4'   U H  68 "
           pdb=" C1'   U H  68 "
           pdb=" N1    U H  68 "
           pdb=" C2    U H  68 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   23.34  176.66     1      1.50e+01 4.44e-03 8.53e+01
  dihedral pdb=" O4'   U E  68 "
           pdb=" C1'   U E  68 "
           pdb=" N1    U E  68 "
           pdb=" C2    U E  68 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   43.99  156.01     1      1.50e+01 4.44e-03 8.16e+01
  dihedral pdb=" O4'   C H  65 "
           pdb=" C1'   C H  65 "
           pdb=" N1    C H  65 "
           pdb=" C2    C H  65 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   71.06  128.94     1      1.50e+01 4.44e-03 6.95e+01
  ... (remaining 6295 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1400
       0.040 -    0.079: 369
       0.079 -    0.119: 120
       0.119 -    0.159: 22
       0.159 -    0.198: 5
  Chirality restraints: 1916
  Sorted by residual:
  chirality pdb=" C3'   A E  66 "
            pdb=" C4'   A E  66 "
            pdb=" O3'   A E  66 "
            pdb=" C2'   A E  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.55   -0.20 2.00e-01 2.50e+01 9.85e-01
  chirality pdb=" C1'   C H  65 "
            pdb=" O4'   C H  65 "
            pdb=" C2'   C H  65 "
            pdb=" N1    C H  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.27    0.19 2.00e-01 2.50e+01 9.29e-01
  chirality pdb=" C3'  DC G  12 "
            pdb=" C4'  DC G  12 "
            pdb=" O3'  DC G  12 "
            pdb=" C2'  DC G  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.54   -0.19 2.00e-01 2.50e+01 8.96e-01
  ... (remaining 1913 not shown)

  Planarity restraints: 1259
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A E  17 "   -0.023 2.00e-02 2.50e+03   1.08e-02 3.19e+00
        pdb=" N9    A E  17 "    0.026 2.00e-02 2.50e+03
        pdb=" C8    A E  17 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    A E  17 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5    A E  17 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    A E  17 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6    A E  17 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    A E  17 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    A E  17 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    A E  17 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    A E  17 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B  80 "    0.008 2.00e-02 2.50e+03   1.62e-02 2.62e+00
        pdb=" C   LEU B  80 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   LEU B  80 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ARG B  81 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA D   6 "   -0.018 2.00e-02 2.50e+03   8.09e-03 1.80e+00
        pdb=" N9   DA D   6 "    0.018 2.00e-02 2.50e+03
        pdb=" C8   DA D   6 "   -0.000 2.00e-02 2.50e+03
        pdb=" N7   DA D   6 "    0.001 2.00e-02 2.50e+03
        pdb=" C5   DA D   6 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DA D   6 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6   DA D   6 "   -0.005 2.00e-02 2.50e+03
        pdb=" N1   DA D   6 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DA D   6 "    0.000 2.00e-02 2.50e+03
        pdb=" N3   DA D   6 "    0.005 2.00e-02 2.50e+03
        pdb=" C4   DA D   6 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1256 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1933
        2.77 -     3.30: 8918
        3.30 -     3.84: 18963
        3.84 -     4.37: 23081
        4.37 -     4.90: 35214
  Nonbonded interactions: 88109
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B   8 "
            pdb=" NH2 ARG B  11 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" O   TYR C 211 "
            pdb=" NH2 ARG B  31 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" O   LEU A  39 "
            pdb=" OG1 THR A  43 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" NZ  LYS B  60 "
            pdb=" OE2 GLU B 121 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" O   PHE B 287 "
            pdb=" OG  SER B 290 "
     model   vdw
     2.276 3.040
  ... (remaining 88104 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'I'
}

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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.450
  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:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.680
  Find NCS groups from input model:        0.100
  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:5.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
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   0.040  11190  Z= 0.352
  Angle     :  0.679  10.501  16051  Z= 0.460
  Chirality :  0.042   0.198   1916
  Planarity :  0.004   0.045   1259
  Dihedral  : 21.309 178.334   4864
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.30), residues: 750
  helix:  0.89 (0.27), residues: 394
  sheet:  1.50 (0.64), residues: 62
  loop : -1.26 (0.33), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 188 
 TYR   0.013   0.001   TYR B 179 
 PHE   0.013   0.002   PHE B  92 
 TRP   0.007   0.002   TRP B 284 
 HIS   0.005   0.001   HIS B 280 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00505 /  0.35 (11190)
  covalent geometry    : angle       0.67946 /  0.46 (16051)
  hydrogen bonds       : bond        0.12453 /  8.38 (  484)
  hydrogen bonds       : angle       4.54192 /  3.17 ( 1238)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A   45 ASP cc_start: 0.7618 (m-30) cc_final: 0.7343 (m-30)
REVERT: A  231 LYS cc_start: 0.6377 (mptt) cc_final: 0.6076 (mptt)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.5143
  time to fit residues: 49.2375
Evaluate side-chains
  63 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    8.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:   20.0000
   chunk 74 optimal weight:    0.0970
   overall best weight:    2.0186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 228 ASN
B 104 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.147037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.098858 restraints weight = 14739.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 1.75
r_work: 0.3133 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.3007 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.0563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11190  Z= 0.186
  Angle     :  0.648   8.874  16051  Z= 0.354
  Chirality :  0.043   0.222   1916
  Planarity :  0.005   0.040   1259
  Dihedral  : 23.329 178.868   3317
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  7.92 %
    Favored  : 90.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.30), residues: 750
  helix:  0.90 (0.26), residues: 400
  sheet:  2.00 (0.62), residues: 58
  loop : -1.46 (0.33), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 246 
 TYR   0.013   0.001   TYR B 179 
 PHE   0.014   0.002   PHE B  92 
 TRP   0.007   0.001   TRP B 284 
 HIS   0.004   0.001   HIS B 280 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00391 /  0.19 (11190)
  covalent geometry    : angle       0.64779 /  0.35 (16051)
  hydrogen bonds       : bond        0.05484 /  3.54 (  484)
  hydrogen bonds       : angle       3.81523 /  2.67 ( 1238)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 ASP cc_start: 0.8053 (m-30) cc_final: 0.7669 (m-30)
REVERT: A   62 MET cc_start: 0.7389 (pmm) cc_final: 0.6641 (ppp)
REVERT: A  119 ASP cc_start: 0.8792 (OUTLIER) cc_final: 0.8460 (m-30)
REVERT: A  231 LYS cc_start: 0.6082 (mptt) cc_final: 0.5788 (mptt)
REVERT: B  251 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7663 (mm-30)
  outliers start: 8
  outliers final: 4
  residues processed: 67
  average time/residue: 0.4864
  time to fit residues: 35.1788
Evaluate side-chains
  71 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain C residue  242 SER
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain B residue  251 GLU
Chi-restraints excluded: chain B residue  300 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 36 optimal weight:    9.9990
   chunk 16 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 84 optimal weight:   20.0000
   overall best weight:    1.7988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 228 ASN
B 296 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.147382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.099231 restraints weight = 14835.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 1.76
r_work: 0.3142 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.3016 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.0761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  11190  Z= 0.170
  Angle     :  0.612   7.205  16051  Z= 0.336
  Chirality :  0.042   0.220   1916
  Planarity :  0.004   0.036   1259
  Dihedral  : 23.326 178.866   3317
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  :  9.97 %
    Favored  : 88.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.30), residues: 750
  helix:  1.00 (0.26), residues: 400
  sheet:  1.98 (0.61), residues: 58
  loop : -1.47 (0.33), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 246 
 TYR   0.013   0.001   TYR B 179 
 PHE   0.012   0.002   PHE B  92 
 TRP   0.005   0.001   TRP B 284 
 HIS   0.005   0.001   HIS A 280 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.17 (11190)
  covalent geometry    : angle       0.61184 /  0.34 (16051)
  hydrogen bonds       : bond        0.05117 /  3.30 (  484)
  hydrogen bonds       : angle       3.64594 /  2.57 ( 1238)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 ASP cc_start: 0.8001 (m-30) cc_final: 0.7685 (m-30)
REVERT: A   62 MET cc_start: 0.7365 (pmm) cc_final: 0.6649 (ppp)
REVERT: A  119 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.8425 (m-30)
REVERT: A  231 LYS cc_start: 0.6079 (mptt) cc_final: 0.5781 (mptt)
REVERT: B  251 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7678 (mm-30)
REVERT: B  282 ARG cc_start: 0.8150 (ttm110) cc_final: 0.7839 (ttp-170)
  outliers start: 10
  outliers final: 5
  residues processed: 69
  average time/residue: 0.4999
  time to fit residues: 37.2001
Evaluate side-chains
  71 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain C residue  242 SER
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain B residue  251 GLU
Chi-restraints excluded: chain B residue  300 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 61 optimal weight:    7.9990
   chunk 41 optimal weight:    7.9990
   chunk 69 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 83 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   chunk 46 optimal weight:   20.0000
   chunk 82 optimal weight:    6.9990
   chunk 67 optimal weight:    0.2980
   chunk 47 optimal weight:    9.9990
   overall best weight:    1.9984

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.146947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.098733 restraints weight = 14825.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 1.76
r_work: 0.3133 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.3007 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
moved from start:          0.0847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  11190  Z= 0.179
  Angle     :  0.615   6.524  16051  Z= 0.336
  Chirality :  0.042   0.229   1916
  Planarity :  0.004   0.037   1259
  Dihedral  : 23.338 179.236   3317
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 11.00 %
    Favored  : 87.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.30), residues: 750
  helix:  1.09 (0.26), residues: 402
  sheet:  1.93 (0.61), residues: 58
  loop : -1.46 (0.33), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 246 
 TYR   0.013   0.001   TYR B 179 
 PHE   0.012   0.002   PHE B  92 
 TRP   0.005   0.001   TRP A  78 
 HIS   0.005   0.001   HIS A 280 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00377 /  0.18 (11190)
  covalent geometry    : angle       0.61468 /  0.34 (16051)
  hydrogen bonds       : bond        0.05162 /  3.33 (  484)
  hydrogen bonds       : angle       3.61164 /  2.55 ( 1238)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 ASP cc_start: 0.7946 (m-30) cc_final: 0.7613 (m-30)
REVERT: A   62 MET cc_start: 0.7402 (pmm) cc_final: 0.6669 (ppp)
REVERT: A  119 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8411 (m-30)
REVERT: A  231 LYS cc_start: 0.6100 (mptt) cc_final: 0.5786 (mptt)
REVERT: B  251 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7664 (mm-30)
REVERT: B  282 ARG cc_start: 0.8176 (ttm110) cc_final: 0.7870 (ttp-170)
  outliers start: 13
  outliers final: 6
  residues processed: 70
  average time/residue: 0.4802
  time to fit residues: 36.4834
Evaluate side-chains
  72 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain C residue  242 SER
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  296 THR
Chi-restraints excluded: chain B residue  251 GLU
Chi-restraints excluded: chain B residue  300 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 77 optimal weight:    4.9990
   chunk 65 optimal weight:    0.6980
   chunk 42 optimal weight:    6.9990
   chunk 41 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 38 optimal weight:    0.4980
   chunk 12 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0770
   chunk 90 optimal weight:   10.0000
   chunk 0 optimal weight:    6.9990
   chunk 67 optimal weight:    0.8980
   overall best weight:    0.6138

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 240 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.149040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.101165 restraints weight = 14822.047|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 1.73
r_work: 0.3181 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.1008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  11190  Z= 0.125
  Angle     :  0.576   6.547  16051  Z= 0.316
  Chirality :  0.039   0.194   1916
  Planarity :  0.003   0.031   1259
  Dihedral  : 23.327 179.283   3317
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 12.17 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.30), residues: 750
  helix:  1.26 (0.27), residues: 400
  sheet:  2.07 (0.62), residues: 58
  loop : -1.39 (0.33), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 246 
 TYR   0.011   0.001   TYR B 179 
 PHE   0.012   0.001   PHE B  92 
 TRP   0.005   0.001   TRP A  78 
 HIS   0.004   0.001   HIS A 280 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00214 /  0.13 (11190)
  covalent geometry    : angle       0.57565 /  0.32 (16051)
  hydrogen bonds       : bond        0.04405 /  2.83 (  484)
  hydrogen bonds       : angle       3.47144 /  2.45 ( 1238)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 ASP cc_start: 0.7881 (m-30) cc_final: 0.7620 (m-30)
REVERT: A   62 MET cc_start: 0.7424 (pmm) cc_final: 0.6709 (ppp)
REVERT: A  119 ASP cc_start: 0.8715 (OUTLIER) cc_final: 0.8370 (m-30)
REVERT: A  207 LYS cc_start: 0.8224 (ptmm) cc_final: 0.7915 (pttp)
REVERT: A  231 LYS cc_start: 0.6048 (mptt) cc_final: 0.5612 (mptt)
REVERT: C  249 ASN cc_start: 0.7911 (OUTLIER) cc_final: 0.7636 (m-40)
REVERT: B  251 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7663 (mm-30)
REVERT: B  282 ARG cc_start: 0.8132 (ttm110) cc_final: 0.7837 (ttp-170)
  outliers start: 10
  outliers final: 4
  residues processed: 72
  average time/residue: 0.4723
  time to fit residues: 36.6610
Evaluate side-chains
  72 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain C residue  242 SER
Chi-restraints excluded: chain C residue  249 ASN
Chi-restraints excluded: chain B residue  251 GLU
Chi-restraints excluded: chain B residue  300 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 68 optimal weight:    0.3980
   chunk 23 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 89 optimal weight:   10.0000
   chunk 19 optimal weight:    4.9990
   chunk 79 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 57 optimal weight:    0.0470
   chunk 88 optimal weight:    9.9990
   chunk 12 optimal weight:    1.9990
   chunk 36 optimal weight:   10.0000
   overall best weight:    0.8682

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.149764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.102009 restraints weight = 14847.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 1.74
r_work: 0.3186 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.3061 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.1159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  11190  Z= 0.128
  Angle     :  0.564   6.535  16051  Z= 0.309
  Chirality :  0.039   0.197   1916
  Planarity :  0.003   0.030   1259
  Dihedral  : 23.280 179.967   3317
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 12.32 %
    Favored  : 85.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.62 (0.31), residues: 750
  helix:  1.43 (0.27), residues: 399
  sheet:  0.96 (0.60), residues: 72
  loop : -1.25 (0.35), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 246 
 TYR   0.010   0.001   TYR B 179 
 PHE   0.011   0.001   PHE B  92 
 TRP   0.004   0.001   TRP A  78 
 HIS   0.004   0.001   HIS A 280 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00233 /  0.13 (11190)
  covalent geometry    : angle       0.56446 /  0.31 (16051)
  hydrogen bonds       : bond        0.04344 /  2.79 (  484)
  hydrogen bonds       : angle       3.35167 /  2.38 ( 1238)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 ASP cc_start: 0.7853 (m-30) cc_final: 0.7629 (m-30)
REVERT: A  119 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.8298 (m-30)
REVERT: A  207 LYS cc_start: 0.8207 (ptmm) cc_final: 0.7903 (pttp)
REVERT: A  231 LYS cc_start: 0.6006 (mptt) cc_final: 0.5571 (mptt)
REVERT: B  251 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7678 (mm-30)
REVERT: B  282 ARG cc_start: 0.8115 (ttm110) cc_final: 0.7811 (ttp-170)
  outliers start: 13
  outliers final: 5
  residues processed: 73
  average time/residue: 0.4942
  time to fit residues: 39.0243
Evaluate side-chains
  74 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain C residue  207 LEU
Chi-restraints excluded: chain C residue  242 SER
Chi-restraints excluded: chain B residue   59 GLU
Chi-restraints excluded: chain B residue  251 GLU
Chi-restraints excluded: chain B residue  300 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 55 optimal weight:    4.9990
   chunk 35 optimal weight:    8.9990
   chunk 43 optimal weight:   10.0000
   chunk 45 optimal weight:   20.0000
   chunk 90 optimal weight:   10.0000
   chunk 14 optimal weight:    0.7980
   chunk 75 optimal weight:    6.9990
   chunk 5 optimal weight:    0.6980
   chunk 76 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   overall best weight:    1.6382

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.148345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.100165 restraints weight = 14755.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 1.76
r_work: 0.3154 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.3028 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.1126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11190  Z= 0.158
  Angle     :  0.589   8.119  16051  Z= 0.320
  Chirality :  0.040   0.217   1916
  Planarity :  0.004   0.035   1259
  Dihedral  : 23.280 179.377   3317
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 12.61 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.31), residues: 750
  helix:  1.38 (0.27), residues: 402
  sheet:  1.39 (0.59), residues: 68
  loop : -1.28 (0.34), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 246 
 TYR   0.012   0.001   TYR B 179 
 PHE   0.012   0.001   PHE B  92 
 TRP   0.004   0.001   TRP A  78 
 HIS   0.005   0.001   HIS A 280 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.16 (11190)
  covalent geometry    : angle       0.58877 /  0.32 (16051)
  hydrogen bonds       : bond        0.04717 /  3.04 (  484)
  hydrogen bonds       : angle       3.40887 /  2.42 ( 1238)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 ASP cc_start: 0.7865 (m-30) cc_final: 0.7609 (m-30)
REVERT: A   62 MET cc_start: 0.7358 (pmm) cc_final: 0.5850 (ttp)
REVERT: A  119 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8318 (m-30)
REVERT: A  207 LYS cc_start: 0.8254 (ptmm) cc_final: 0.7947 (pttp)
REVERT: A  231 LYS cc_start: 0.6053 (mptt) cc_final: 0.5616 (mptt)
REVERT: C  241 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7235 (tpm-80)
REVERT: B  251 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7704 (mm-30)
REVERT: B  282 ARG cc_start: 0.8168 (ttm110) cc_final: 0.7856 (ttp-170)
  outliers start: 15
  outliers final: 7
  residues processed: 75
  average time/residue: 0.4968
  time to fit residues: 40.2556
Evaluate side-chains
  75 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 SER
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain C residue  207 LEU
Chi-restraints excluded: chain C residue  241 ARG
Chi-restraints excluded: chain C residue  242 SER
Chi-restraints excluded: chain B residue   59 GLU
Chi-restraints excluded: chain B residue  251 GLU
Chi-restraints excluded: chain B residue  300 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 75 optimal weight:    7.9990
   chunk 89 optimal weight:   10.0000
   chunk 4 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 82 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 16 optimal weight:    3.9990
   chunk 85 optimal weight:   30.0000
   chunk 50 optimal weight:   10.0000
   chunk 81 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   overall best weight:    3.1588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 261 GLN
B 240 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.145391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.096862 restraints weight = 14703.859|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 1.78
r_work: 0.3110 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.2986 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
moved from start:          0.1080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  11190  Z= 0.243
  Angle     :  0.675   7.763  16051  Z= 0.364
  Chirality :  0.045   0.276   1916
  Planarity :  0.005   0.046   1259
  Dihedral  : 23.355 179.902   3317
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 12.32 %
    Favored  : 85.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.30), residues: 750
  helix:  1.11 (0.27), residues: 396
  sheet:  1.16 (0.57), residues: 68
  loop : -1.48 (0.33), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  70 
 TYR   0.017   0.002   TYR B 179 
 PHE   0.013   0.002   PHE B  92 
 TRP   0.006   0.002   TRP B 284 
 HIS   0.006   0.001   HIS A 280 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00542 /  0.24 (11190)
  covalent geometry    : angle       0.67519 /  0.36 (16051)
  hydrogen bonds       : bond        0.05975 /  3.85 (  484)
  hydrogen bonds       : angle       3.64185 /  2.59 ( 1238)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 ASP cc_start: 0.7928 (m-30) cc_final: 0.7645 (m-30)
REVERT: A  119 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.8373 (m-30)
REVERT: A  231 LYS cc_start: 0.6149 (mptt) cc_final: 0.5815 (mptt)
REVERT: C  241 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7292 (tpm-80)
REVERT: C  249 ASN cc_start: 0.7941 (OUTLIER) cc_final: 0.7638 (m-40)
REVERT: B  251 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7694 (mm-30)
REVERT: B  282 ARG cc_start: 0.8228 (ttm110) cc_final: 0.7897 (ttp-170)
  outliers start: 15
  outliers final: 9
  residues processed: 71
  average time/residue: 0.5187
  time to fit residues: 39.7134
Evaluate side-chains
  77 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 SER
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain C residue  207 LEU
Chi-restraints excluded: chain C residue  241 ARG
Chi-restraints excluded: chain C residue  242 SER
Chi-restraints excluded: chain C residue  249 ASN
Chi-restraints excluded: chain C residue  257 THR
Chi-restraints excluded: chain C residue  296 THR
Chi-restraints excluded: chain B residue   59 GLU
Chi-restraints excluded: chain B residue  251 GLU
Chi-restraints excluded: chain B residue  300 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 84 optimal weight:   20.0000
   chunk 44 optimal weight:    9.9990
   chunk 41 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   overall best weight:    1.5786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 240 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.147247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.098738 restraints weight = 14762.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 1.82
r_work: 0.3143 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.1078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11190  Z= 0.162
  Angle     :  0.619   7.649  16051  Z= 0.338
  Chirality :  0.042   0.222   1916
  Planarity :  0.004   0.034   1259
  Dihedral  : 23.355 179.672   3317
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 12.90 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.30), residues: 750
  helix:  1.19 (0.27), residues: 400
  sheet:  1.25 (0.58), residues: 68
  loop : -1.45 (0.34), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 180 
 TYR   0.014   0.001   TYR B 179 
 PHE   0.013   0.001   PHE B  92 
 TRP   0.005   0.001   TRP A  78 
 HIS   0.005   0.001   HIS A 280 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.16 (11190)
  covalent geometry    : angle       0.61877 /  0.34 (16051)
  hydrogen bonds       : bond        0.05020 /  3.24 (  484)
  hydrogen bonds       : angle       3.52299 /  2.50 ( 1238)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 ASP cc_start: 0.7906 (m-30) cc_final: 0.7651 (m-30)
REVERT: A  119 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8303 (m-30)
REVERT: A  207 LYS cc_start: 0.8249 (ptmm) cc_final: 0.7914 (pttp)
REVERT: A  231 LYS cc_start: 0.6157 (mptt) cc_final: 0.5831 (mptt)
REVERT: C  241 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7265 (tpm-80)
REVERT: B  251 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7666 (mm-30)
REVERT: B  282 ARG cc_start: 0.8188 (ttm110) cc_final: 0.7869 (ttp-170)
  outliers start: 12
  outliers final: 8
  residues processed: 69
  average time/residue: 0.5097
  time to fit residues: 37.9318
Evaluate side-chains
  75 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 SER
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain C residue  207 LEU
Chi-restraints excluded: chain C residue  241 ARG
Chi-restraints excluded: chain C residue  242 SER
Chi-restraints excluded: chain C residue  257 THR
Chi-restraints excluded: chain B residue   59 GLU
Chi-restraints excluded: chain B residue  251 GLU
Chi-restraints excluded: chain B residue  300 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 44 optimal weight:   10.0000
   chunk 18 optimal weight:    0.7980
   chunk 72 optimal weight:    4.9990
   chunk 58 optimal weight:    0.0370
   chunk 34 optimal weight:    3.9990
   chunk 82 optimal weight:    4.9990
   chunk 76 optimal weight:    4.9990
   chunk 46 optimal weight:   20.0000
   chunk 54 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 87 optimal weight:   20.0000
   overall best weight:    1.7262

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.147361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.098929 restraints weight = 14659.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 1.80
r_work: 0.3146 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.3025 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8498
moved from start:          0.1103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11190  Z= 0.168
  Angle     :  0.614   7.448  16051  Z= 0.334
  Chirality :  0.042   0.228   1916
  Planarity :  0.004   0.035   1259
  Dihedral  : 23.355 179.561   3317
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 12.90 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.30), residues: 750
  helix:  1.20 (0.27), residues: 400
  sheet:  1.21 (0.58), residues: 68
  loop : -1.44 (0.34), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 180 
 TYR   0.012   0.001   TYR B 179 
 PHE   0.013   0.002   PHE B  92 
 TRP   0.004   0.001   TRP A  78 
 HIS   0.005   0.001   HIS A 280 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00352 /  0.17 (11190)
  covalent geometry    : angle       0.61373 /  0.33 (16051)
  hydrogen bonds       : bond        0.05001 /  3.22 (  484)
  hydrogen bonds       : angle       3.49402 /  2.49 ( 1238)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 ASP cc_start: 0.7908 (m-30) cc_final: 0.7645 (m-30)
REVERT: A  119 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8306 (m-30)
REVERT: A  231 LYS cc_start: 0.6152 (mptt) cc_final: 0.5825 (mptt)
REVERT: C  241 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7259 (tpm-80)
REVERT: B  251 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7675 (mm-30)
REVERT: B  282 ARG cc_start: 0.8220 (ttm110) cc_final: 0.7904 (ttp-170)
  outliers start: 13
  outliers final: 9
  residues processed: 69
  average time/residue: 0.5353
  time to fit residues: 39.8948
Evaluate side-chains
  74 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 SER
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain C residue  207 LEU
Chi-restraints excluded: chain C residue  241 ARG
Chi-restraints excluded: chain C residue  242 SER
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  257 THR
Chi-restraints excluded: chain B residue   59 GLU
Chi-restraints excluded: chain B residue  251 GLU
Chi-restraints excluded: chain B residue  300 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 46 optimal weight:   20.0000
   chunk 88 optimal weight:   10.0000
   chunk 49 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 31 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   chunk 45 optimal weight:   20.0000
   overall best weight:    2.3588

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.146292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.097907 restraints weight = 14795.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 1.78
r_work: 0.3128 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.3002 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.1112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11190  Z= 0.196
  Angle     :  0.634   7.591  16051  Z= 0.344
  Chirality :  0.043   0.243   1916
  Planarity :  0.004   0.036   1259
  Dihedral  : 23.363 179.937   3317
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 13.05 %
    Favored  : 85.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.25 (0.30), residues: 750
  helix:  1.12 (0.27), residues: 400
  sheet:  1.16 (0.57), residues: 68
  loop : -1.50 (0.33), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  70 
 TYR   0.014   0.001   TYR B 179 
 PHE   0.013   0.002   PHE B  92 
 TRP   0.004   0.001   TRP A  78 
 HIS   0.005   0.001   HIS A 280 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00424 /  0.20 (11190)
  covalent geometry    : angle       0.63424 /  0.34 (16051)
  hydrogen bonds       : bond        0.05343 /  3.44 (  484)
  hydrogen bonds       : angle       3.54772 /  2.52 ( 1238)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3194.33 seconds
wall clock time: 55 minutes 8.55 seconds (3308.55 seconds total)