Starting phenix.real_space_refine
on Tue Mar  3 16:25:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xn6_33312/03_2026/7xn6_33312.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xn6_33312/03_2026/7xn6_33312.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.45
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xn6_33312/03_2026/7xn6_33312.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xn6_33312/03_2026/7xn6_33312.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xn6_33312/03_2026/7xn6_33312.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xn6_33312/03_2026/7xn6_33312.cif"
  }
  resolution = 3.45
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      38      5.16       5
     C    4346      2.51       5
     N    1211      2.21       5
     O    1277      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6874
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1714
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1714
          Classifications: {'peptide': 211}
          Link IDs: {'PTRANS': 6, 'TRANS': 204}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 3256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 422, 3256
          Classifications: {'peptide': 422}
          Link IDs: {'PTRANS': 13, 'TRANS': 408}
    Chain: "C"
      Number of atoms: 1394
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 170, 1394
          Classifications: {'peptide': 170}
          Link IDs: {'PTRANS': 6, 'TRANS': 163}
          Chain breaks: 5
    Chain: "D"
      Number of atoms: 466
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 466
          Classifications: {'peptide': 58}
          Link IDs: {'TRANS': 57}
    Chain: "A"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'APR': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Unusual residues: {'NCA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.60, per 1000 atoms: 0.23
  Number of scatterers: 6874
  At special positions: 0
  Unit cell: (107.776, 96.83, 76.622, 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      38     16.00
     P       2     15.00
     O    1277      8.00
     N    1211      7.00
     C    4346      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.79
  Conformation dependent library (CDL) restraints added in 270.0 milliseconds
  

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1606

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 5 sheets defined
      42.3% alpha, 8.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 67 through 80
    Processing helix  chain 'A' and resid 92 through 105
    Processing helix  chain 'A' and resid 136 through 141
      removed outlier: 3.541A  pdb=" N   THR A 140 " --> pdb=" O   LEU A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 144
      No H-bonds generated for 'chain 'A' and resid 142 through 144'
    Processing helix  chain 'A' and resid 214 through 226
      removed outlier: 4.355A  pdb=" N   CYS A 220 " --> pdb=" O   ILE A 216 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   GLN A 225 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 229
      No H-bonds generated for 'chain 'A' and resid 227 through 229'
    Processing helix  chain 'A' and resid 231 through 243
    Processing helix  chain 'B' and resid 52 through 74
      removed outlier: 4.209A  pdb=" N   PHE B  58 " --> pdb=" O   LYS B  54 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LYS B  61 " --> pdb=" O   ALA B  57 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLN B  66 " --> pdb=" O   ALA B  62 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   SER B  67 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   LEU B  70 " --> pdb=" O   GLN B  66 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   MET B  71 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 82
      removed outlier: 3.547A  pdb=" N   GLU B  79 " --> pdb=" O   GLY B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 114
      removed outlier: 3.927A  pdb=" N   LEU B  99 " --> pdb=" O   ALA B  95 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   VAL B 110 " --> pdb=" O   ASN B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 128
    Processing helix  chain 'B' and resid 153 through 158
    Processing helix  chain 'B' and resid 171 through 176
      removed outlier: 3.568A  pdb=" N   LEU B 175 " --> pdb=" O   GLY B 171 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LEU B 176 " --> pdb=" O   ASP B 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 171 through 176'
    Processing helix  chain 'B' and resid 218 through 222
      removed outlier: 3.570A  pdb=" N   CYS B 221 " --> pdb=" O   LEU B 218 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ARG B 222 " --> pdb=" O   PRO B 219 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 218 through 222'
    Processing helix  chain 'B' and resid 244 through 251
      removed outlier: 3.715A  pdb=" N   VAL B 248 " --> pdb=" O   HIS B 244 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 256
      removed outlier: 4.035A  pdb=" N   GLY B 255 " --> pdb=" O   PHE B 251 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ALA B 256 " --> pdb=" O   PRO B 252 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 251 through 256'
    Processing helix  chain 'B' and resid 280 through 292
      removed outlier: 4.028A  pdb=" N   ALA B 284 " --> pdb=" O   LYS B 280 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLU B 289 " --> pdb=" O   LEU B 285 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 302
      removed outlier: 3.882A  pdb=" N   TYR B 302 " --> pdb=" O   ALA B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 322
      removed outlier: 3.800A  pdb=" N   SER B 320 " --> pdb=" O   ARG B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 346 through 353
    Processing helix  chain 'B' and resid 355 through 363
      removed outlier: 3.821A  pdb=" N   GLY B 361 " --> pdb=" O   PRO B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 378
      removed outlier: 4.148A  pdb=" N   THR B 371 " --> pdb=" O   GLY B 367 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ASP B 378 " --> pdb=" O   TRP B 374 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 392
    Processing helix  chain 'B' and resid 409 through 414
    Processing helix  chain 'B' and resid 420 through 431
    Processing helix  chain 'B' and resid 447 through 456
    Processing helix  chain 'B' and resid 457 through 468
    Processing helix  chain 'C' and resid 69 through 80
      removed outlier: 3.783A  pdb=" N   GLU C  76 " --> pdb=" O   ALA C  72 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 94 through 105
    Processing helix  chain 'C' and resid 107 through 111
      removed outlier: 4.015A  pdb=" N   LYS C 110 " --> pdb=" O   ASP C 107 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 136 through 141
    Processing helix  chain 'C' and resid 142 through 144
      No H-bonds generated for 'chain 'C' and resid 142 through 144'
    Processing helix  chain 'C' and resid 213 through 226
    Processing helix  chain 'C' and resid 231 through 246
    Processing helix  chain 'D' and resid 86 through 91
    Processing helix  chain 'D' and resid 102 through 112
      removed outlier: 3.628A  pdb=" N   THR D 110 " --> pdb=" O   ARG D 106 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ASN D 111 " --> pdb=" O   HIS D 107 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 117 through 128
      removed outlier: 4.042A  pdb=" N   GLU D 123 " --> pdb=" O   GLU D 119 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 89
      removed outlier: 6.208A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 115 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   VAL A 117 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   ILE A  48 " --> pdb=" O   VAL A 117 " (cutoff:3.500A)
      removed outlier: 7.552A  pdb=" N   LEU A 119 " --> pdb=" O   ILE A  48 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   ILE A  50 " --> pdb=" O   LEU A 119 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   PHE A 114 " --> pdb=" O   LEU A 157 " (cutoff:3.500A)
      removed outlier: 8.262A  pdb=" N   ILE A 159 " --> pdb=" O   PHE A 114 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   CYS A 116 " --> pdb=" O   ILE A 159 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   LYS A 156 " --> pdb=" O   LEU A 194 " (cutoff:3.500A)
      removed outlier: 7.803A  pdb=" N   ALA A 196 " --> pdb=" O   LYS A 156 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   PHE A 158 " --> pdb=" O   ALA A 196 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 128
    Processing sheet with id=AA3, first strand: chain 'B' and resid 225 through 227
    Processing sheet with id=AA4, first strand: chain 'B' and resid 149 through 152
    Processing sheet with id=AA5, first strand: chain 'C' and resid 84 through 87
      removed outlier: 7.079A  pdb=" N   CYS C  47 " --> pdb=" O   ARG C  86 " (cutoff:3.500A)
      removed outlier: 5.849A  pdb=" N   LEU C  46 " --> pdb=" O   VAL C 115 " (cutoff:3.500A)
      removed outlier: 7.877A  pdb=" N   VAL C 117 " --> pdb=" O   LEU C  46 " (cutoff:3.500A)
      removed outlier: 6.085A  pdb=" N   ILE C  48 " --> pdb=" O   VAL C 117 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   LEU C 119 " --> pdb=" O   ILE C  48 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   ILE C  50 " --> pdb=" O   LEU C 119 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU C 194 " --> pdb=" O   LYS C 156 " (cutoff:3.500A)

    227 hydrogen bonds defined for protein.
    654 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: 0.93

  Time building geometry restraints manager: 0.97 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1150
        1.29 -     1.42: 1879
        1.42 -     1.55: 3918
        1.55 -     1.68: 6
        1.68 -     1.81: 64
  Bond restraints: 7017
  Sorted by residual:
  bond pdb=" C2D APR A1001 "
       pdb=" O2D APR A1001 "
    ideal  model  delta    sigma   weight residual
    1.397  1.573 -0.176 2.00e-02 2.50e+03 7.77e+01
  bond pdb=" CA  TYR B  68 "
       pdb=" C   TYR B  68 "
    ideal  model  delta    sigma   weight residual
    1.522  1.413  0.109 1.34e-02 5.57e+03 6.65e+01
  bond pdb=" C1D APR A1001 "
       pdb=" C2D APR A1001 "
    ideal  model  delta    sigma   weight residual
    1.529  1.675 -0.146 2.00e-02 2.50e+03 5.36e+01
  bond pdb=" CA  ALA B 141 "
       pdb=" C   ALA B 141 "
    ideal  model  delta    sigma   weight residual
    1.528  1.449  0.080 1.39e-02 5.18e+03 3.28e+01
  bond pdb=" CA  SER B 139 "
       pdb=" C   SER B 139 "
    ideal  model  delta    sigma   weight residual
    1.522  1.453  0.070 1.23e-02 6.61e+03 3.20e+01
  ... (remaining 7012 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.61: 9408
        4.61 -     9.23: 28
        9.23 -    13.84: 4
       13.84 -    18.46: 3
       18.46 -    23.07: 4
  Bond angle restraints: 9447
  Sorted by residual:
  angle pdb=" O3A APR A1001 "
        pdb=" PB  APR A1001 "
        pdb=" O5D APR A1001 "
      ideal   model   delta    sigma   weight residual
     101.31  124.38  -23.07 3.00e+00 1.11e-01 5.91e+01
  angle pdb=" C1D APR A1001 "
        pdb=" C2D APR A1001 "
        pdb=" O2D APR A1001 "
      ideal   model   delta    sigma   weight residual
     110.00   87.63   22.37 3.00e+00 1.11e-01 5.56e+01
  angle pdb=" N   TYR B  68 "
        pdb=" CA  TYR B  68 "
        pdb=" C   TYR B  68 "
      ideal   model   delta    sigma   weight residual
     113.38  105.51    7.87 1.23e+00 6.61e-01 4.09e+01
  angle pdb=" C5D APR A1001 "
        pdb=" C4D APR A1001 "
        pdb=" O4D APR A1001 "
      ideal   model   delta    sigma   weight residual
     111.97  130.75  -18.78 3.00e+00 1.11e-01 3.92e+01
  angle pdb=" O3A APR A1001 "
        pdb=" PA  APR A1001 "
        pdb=" O5' APR A1001 "
      ideal   model   delta    sigma   weight residual
     102.36  121.10  -18.74 3.00e+00 1.11e-01 3.90e+01
  ... (remaining 9442 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 3681
       17.82 -    35.64: 426
       35.64 -    53.46: 89
       53.46 -    71.28: 11
       71.28 -    89.09: 10
  Dihedral angle restraints: 4217
    sinusoidal: 1729
      harmonic: 2488
  Sorted by residual:
  dihedral pdb=" CA  GLU D 140 "
           pdb=" C   GLU D 140 "
           pdb=" N   PHE D 141 "
           pdb=" CA  PHE D 141 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.49  -27.51     0      5.00e+00 4.00e-02 3.03e+01
  dihedral pdb=" CA  LYS B 300 "
           pdb=" C   LYS B 300 "
           pdb=" N   ALA B 301 "
           pdb=" CA  ALA B 301 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.71  -25.29     0      5.00e+00 4.00e-02 2.56e+01
  dihedral pdb=" C   ASN B 355 "
           pdb=" N   ASN B 355 "
           pdb=" CA  ASN B 355 "
           pdb=" CB  ASN B 355 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -110.04  -12.56     0      2.50e+00 1.60e-01 2.52e+01
  ... (remaining 4214 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.185: 1002
       0.185 -    0.370: 5
       0.370 -    0.556: 1
       0.556 -    0.741: 0
       0.741 -    0.926: 2
  Chirality restraints: 1010
  Sorted by residual:
  chirality pdb=" C2D APR A1001 "
            pdb=" C1D APR A1001 "
            pdb=" C3D APR A1001 "
            pdb=" O2D APR A1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -3.38    0.93 2.00e-01 2.50e+01 2.14e+01
  chirality pdb=" C3D APR A1001 "
            pdb=" C2D APR A1001 "
            pdb=" C4D APR A1001 "
            pdb=" O3D APR A1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.71   -1.96   -0.75 2.00e-01 2.50e+01 1.40e+01
  chirality pdb=" C4D APR A1001 "
            pdb=" C3D APR A1001 "
            pdb=" C5D APR A1001 "
            pdb=" O4D APR A1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.04   -0.45 2.00e-01 2.50e+01 5.05e+00
  ... (remaining 1007 not shown)

  Planarity restraints: 1221
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' APR A1001 "   -0.124 2.00e-02 2.50e+03   5.80e-02 9.25e+01
        pdb=" C2  APR A1001 "    0.007 2.00e-02 2.50e+03
        pdb=" C4  APR A1001 "    0.060 2.00e-02 2.50e+03
        pdb=" C5  APR A1001 "    0.057 2.00e-02 2.50e+03
        pdb=" C6  APR A1001 "   -0.001 2.00e-02 2.50e+03
        pdb=" C8  APR A1001 "    0.016 2.00e-02 2.50e+03
        pdb=" N1  APR A1001 "   -0.024 2.00e-02 2.50e+03
        pdb=" N3  APR A1001 "    0.051 2.00e-02 2.50e+03
        pdb=" N6  APR A1001 "   -0.095 2.00e-02 2.50e+03
        pdb=" N7  APR A1001 "    0.046 2.00e-02 2.50e+03
        pdb=" N9  APR A1001 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B  66 "    0.024 2.00e-02 2.50e+03   4.77e-02 2.27e+01
        pdb=" C   GLN B  66 "   -0.082 2.00e-02 2.50e+03
        pdb=" O   GLN B  66 "    0.030 2.00e-02 2.50e+03
        pdb=" N   SER B  67 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 443 "   -0.016 2.00e-02 2.50e+03   3.08e-02 9.48e+00
        pdb=" C   ASN B 443 "    0.053 2.00e-02 2.50e+03
        pdb=" O   ASN B 443 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   SER B 444 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1218 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.26: 4
        2.26 -     2.92: 2852
        2.92 -     3.58: 9411
        3.58 -     4.24: 15202
        4.24 -     4.90: 26010
  Nonbonded interactions: 53479
  Sorted by model distance:
  nonbonded pdb=" NE  ARG A 207 "
            pdb=" C1D APR A1001 "
     model   vdw
     1.596 3.550
  nonbonded pdb=" C3D APR A1001 "
            pdb=" O5D APR A1001 "
     model   vdw
     2.029 2.776
  nonbonded pdb=" CZ  ARG A 207 "
            pdb=" C1D APR A1001 "
     model   vdw
     2.227 2.960
  nonbonded pdb=" OH  TYR A  37 "
            pdb=" O   GLY A 153 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" O   PHE B  72 "
            pdb=" N   LEU B  85 "
     model   vdw
     2.261 3.120
  ... (remaining 53474 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.960
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.176   7018  Z= 0.402
  Angle     :  0.965  23.071   9447  Z= 0.518
  Chirality :  0.061   0.926   1010
  Planarity :  0.006   0.069   1221
  Dihedral  : 15.940  89.095   2611
  Min Nonbonded Distance : 1.596

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.58 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  0.98 %
    Favored  : 98.33 %
  Cbeta Deviations :  0.25 %
  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: -3.19 (0.27), residues: 839
  helix: -0.96 (0.28), residues: 342
  sheet: -2.81 (0.47), residues: 119
  loop : -2.98 (0.28), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  75 
 TYR   0.016   0.001   TYR B  68 
 PHE   0.007   0.001   PHE A  78 
 TRP   0.033   0.002   TRP B 261 
 HIS   0.007   0.001   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00664 ( 7017)
  covalent geometry    : angle       0.96466 ( 9447)
  hydrogen bonds       : bond        0.16424 (  227)
  hydrogen bonds       : angle       6.52226 (  654)
  Misc. bond           : bond        0.03089 (    1)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 130
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
REVERT: B  306 GLN cc_start: 0.6926 (pp30) cc_final: 0.6716 (pp30)
REVERT: B  332 MET cc_start: 0.8470 (tmm) cc_final: 0.8254 (tmm)
REVERT: C   89 ASN cc_start: 0.7856 (p0) cc_final: 0.7637 (p0)
REVERT: C  102 ASP cc_start: 0.7464 (m-30) cc_final: 0.6305 (m-30)
  outliers start: 5
  outliers final: 2
  residues processed: 135
  average time/residue: 0.0762
  time to fit residues: 13.9181
Evaluate side-chains
  106 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 104
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ARG
Chi-restraints excluded: chain B residue  139 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.3980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  56 HIS
A 121 HIS
A 208 ASN
A 217 GLN
B 140 ASN
B 200 HIS
B 210 ASN
B 309 GLN
B 443 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.139495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.111984 restraints weight = 12343.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 2.93
r_work: 0.3353 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.1249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7018  Z= 0.134
  Angle     :  0.577   5.906   9447  Z= 0.307
  Chirality :  0.042   0.152   1010
  Planarity :  0.005   0.065   1221
  Dihedral  :  8.001  78.876    986
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.10 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  :  8.51 %
    Favored  : 89.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.73 (0.28), residues: 839
  helix: -0.58 (0.28), residues: 342
  sheet: -2.70 (0.47), residues: 120
  loop : -2.66 (0.29), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  75 
 TYR   0.017   0.001   TYR A  37 
 PHE   0.029   0.001   PHE A 247 
 TRP   0.019   0.001   TRP B 261 
 HIS   0.004   0.001   HIS B 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 7017)
  covalent geometry    : angle       0.57692 ( 9447)
  hydrogen bonds       : bond        0.03764 (  227)
  hydrogen bonds       : angle       4.93669 (  654)
  Misc. bond           : bond        0.00044 (    1)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 TRP cc_start: 0.4520 (OUTLIER) cc_final: 0.4020 (m100)
REVERT: B  302 TYR cc_start: 0.7612 (t80) cc_final: 0.7132 (t80)
REVERT: C   89 ASN cc_start: 0.8171 (p0) cc_final: 0.7937 (p0)
REVERT: D  140 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7722 (mm-30)
  outliers start: 11
  outliers final: 8
  residues processed: 116
  average time/residue: 0.0829
  time to fit residues: 12.8396
Evaluate side-chains
  117 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  192 ASP
Chi-restraints excluded: chain A residue  206 TRP
Chi-restraints excluded: chain A residue  207 ARG
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  231 GLU
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  210 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 60 optimal weight:    0.0970
   chunk 77 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 32 optimal weight:    8.9990
   chunk 18 optimal weight:    1.9990
   chunk 56 optimal weight:    0.4980
   chunk 20 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 121 HIS
** B  66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 210 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.137015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.110653 restraints weight = 12247.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 2.88
r_work: 0.3316 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.1604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   7018  Z= 0.191
  Angle     :  0.603   6.208   9447  Z= 0.320
  Chirality :  0.043   0.137   1010
  Planarity :  0.005   0.062   1221
  Dihedral  :  7.922  78.509    985
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 13.11 %
    Favored  : 85.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.74 (0.28), residues: 839
  helix: -0.72 (0.27), residues: 357
  sheet: -2.61 (0.46), residues: 120
  loop : -2.62 (0.30), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 149 
 TYR   0.022   0.002   TYR A  37 
 PHE   0.012   0.001   PHE B 299 
 TRP   0.026   0.002   TRP B 261 
 HIS   0.006   0.001   HIS B 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 7017)
  covalent geometry    : angle       0.60306 ( 9447)
  hydrogen bonds       : bond        0.03679 (  227)
  hydrogen bonds       : angle       4.88770 (  654)
  Misc. bond           : bond        0.00035 (    1)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 111
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 TRP cc_start: 0.4482 (OUTLIER) cc_final: 0.3963 (m100)
REVERT: C   89 ASN cc_start: 0.8131 (p0) cc_final: 0.7826 (p0)
REVERT: C  107 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8116 (p0)
REVERT: C  233 MET cc_start: 0.7927 (mmp) cc_final: 0.7686 (mmm)
REVERT: D  140 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7548 (mm-30)
  outliers start: 13
  outliers final: 11
  residues processed: 116
  average time/residue: 0.0814
  time to fit residues: 12.5941
Evaluate side-chains
  118 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 HIS
Chi-restraints excluded: chain A residue  128 PHE
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  192 ASP
Chi-restraints excluded: chain A residue  206 TRP
Chi-restraints excluded: chain A residue  207 ARG
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  231 GLU
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  210 ASN
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue  107 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 2 optimal weight:    0.0970
   chunk 78 optimal weight:    0.9990
   chunk 52 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 36 optimal weight:    0.1980
   chunk 41 optimal weight:    0.7980
   chunk 76 optimal weight:    3.9990
   chunk 60 optimal weight:    0.0470
   chunk 23 optimal weight:    0.9990
   chunk 79 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.3676

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

Flipped N/Q/H residues before XYZ refinement:
A 121 HIS
** B  66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 210 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.140065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.113622 restraints weight = 12476.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 2.75
r_work: 0.3396 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7018  Z= 0.105
  Angle     :  0.532   4.813   9447  Z= 0.285
  Chirality :  0.041   0.136   1010
  Planarity :  0.004   0.056   1221
  Dihedral  :  7.389  75.806    985
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 13.11 %
    Favored  : 84.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.52 (0.28), residues: 839
  helix: -0.49 (0.28), residues: 356
  sheet: -2.45 (0.46), residues: 120
  loop : -2.58 (0.30), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 149 
 TYR   0.017   0.001   TYR A  37 
 PHE   0.010   0.001   PHE A 247 
 TRP   0.015   0.001   TRP B 261 
 HIS   0.005   0.001   HIS B 327 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 7017)
  covalent geometry    : angle       0.53192 ( 9447)
  hydrogen bonds       : bond        0.03017 (  227)
  hydrogen bonds       : angle       4.58009 (  654)
  Misc. bond           : bond        0.00035 (    1)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 TRP cc_start: 0.4481 (OUTLIER) cc_final: 0.3958 (m100)
REVERT: A  228 ASP cc_start: 0.8279 (p0) cc_final: 0.7808 (p0)
REVERT: B  467 HIS cc_start: 0.8371 (OUTLIER) cc_final: 0.8090 (m-70)
REVERT: C   89 ASN cc_start: 0.8135 (p0) cc_final: 0.7830 (p0)
REVERT: C   98 GLU cc_start: 0.8045 (tp30) cc_final: 0.7499 (tp30)
REVERT: C  107 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8011 (p0)
REVERT: D  140 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7482 (mm-30)
  outliers start: 15
  outliers final: 10
  residues processed: 118
  average time/residue: 0.0759
  time to fit residues: 12.1257
Evaluate side-chains
  117 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  128 PHE
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  192 ASP
Chi-restraints excluded: chain A residue  206 TRP
Chi-restraints excluded: chain A residue  207 ARG
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  231 GLU
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  467 HIS
Chi-restraints excluded: chain C residue  107 ASP
Chi-restraints excluded: chain D residue   89 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   chunk 50 optimal weight:    0.2980
   chunk 25 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 68 optimal weight:    4.9990
   chunk 79 optimal weight:    0.5980
   chunk 3 optimal weight:    3.9990
   chunk 49 optimal weight:    0.0980
   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 121 HIS
** B  66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.140169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.113817 restraints weight = 12600.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 2.71
r_work: 0.3408 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7018  Z= 0.109
  Angle     :  0.527   6.761   9447  Z= 0.279
  Chirality :  0.041   0.133   1010
  Planarity :  0.004   0.054   1221
  Dihedral  :  7.171  71.276    985
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.15 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 14.64 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.36 (0.29), residues: 839
  helix: -0.39 (0.28), residues: 360
  sheet: -2.35 (0.47), residues: 122
  loop : -2.48 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 149 
 TYR   0.016   0.001   TYR A  37 
 PHE   0.008   0.001   PHE C 193 
 TRP   0.012   0.001   TRP B 261 
 HIS   0.004   0.001   HIS B 327 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 7017)
  covalent geometry    : angle       0.52720 ( 9447)
  hydrogen bonds       : bond        0.02883 (  227)
  hydrogen bonds       : angle       4.45752 (  654)
  Misc. bond           : bond        0.00031 (    1)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 LYS cc_start: 0.8997 (mmmt) cc_final: 0.8567 (pttt)
REVERT: B  467 HIS cc_start: 0.8362 (OUTLIER) cc_final: 0.8117 (m-70)
REVERT: C   76 GLU cc_start: 0.8187 (pm20) cc_final: 0.7911 (pm20)
REVERT: C   89 ASN cc_start: 0.8129 (p0) cc_final: 0.7827 (p0)
REVERT: C  107 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.8035 (p0)
REVERT: C  233 MET cc_start: 0.7708 (mmp) cc_final: 0.7451 (mmm)
REVERT: D  110 THR cc_start: 0.6944 (p) cc_final: 0.6649 (p)
REVERT: D  118 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8286 (p0)
  outliers start: 20
  outliers final: 15
  residues processed: 115
  average time/residue: 0.0758
  time to fit residues: 11.8815
Evaluate side-chains
  121 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  121 HIS
Chi-restraints excluded: chain A residue  128 PHE
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  192 ASP
Chi-restraints excluded: chain A residue  206 TRP
Chi-restraints excluded: chain A residue  207 ARG
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  231 GLU
Chi-restraints excluded: chain B residue  139 SER
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  467 HIS
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue  107 ASP
Chi-restraints excluded: chain D residue   89 PHE
Chi-restraints excluded: chain D residue  118 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 65 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0670
   chunk 78 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 43 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
** B  66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.140328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.112696 restraints weight = 12580.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 2.93
r_work: 0.3384 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.1979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7018  Z= 0.117
  Angle     :  0.530   6.094   9447  Z= 0.280
  Chirality :  0.041   0.172   1010
  Planarity :  0.004   0.055   1221
  Dihedral  :  7.152  69.993    985
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 15.48 %
    Favored  : 82.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.28 (0.29), residues: 839
  helix: -0.36 (0.28), residues: 366
  sheet: -2.28 (0.47), residues: 122
  loop : -2.44 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 106 
 TYR   0.016   0.001   TYR A  37 
 PHE   0.027   0.001   PHE A 247 
 TRP   0.011   0.001   TRP B 261 
 HIS   0.009   0.001   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 7017)
  covalent geometry    : angle       0.53040 ( 9447)
  hydrogen bonds       : bond        0.02799 (  227)
  hydrogen bonds       : angle       4.42907 (  654)
  Misc. bond           : bond        0.00027 (    1)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  467 HIS cc_start: 0.8385 (OUTLIER) cc_final: 0.8142 (m-70)
REVERT: C   89 ASN cc_start: 0.8149 (p0) cc_final: 0.7855 (p0)
REVERT: C  107 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8156 (p0)
REVERT: C  233 MET cc_start: 0.7709 (mmp) cc_final: 0.7458 (mmm)
REVERT: D  110 THR cc_start: 0.6890 (p) cc_final: 0.6605 (p)
REVERT: D  118 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8252 (p0)
  outliers start: 18
  outliers final: 14
  residues processed: 113
  average time/residue: 0.0771
  time to fit residues: 11.9707
Evaluate side-chains
  115 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 HIS
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  128 PHE
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  192 ASP
Chi-restraints excluded: chain A residue  206 TRP
Chi-restraints excluded: chain A residue  207 ARG
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  231 GLU
Chi-restraints excluded: chain B residue  139 SER
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  467 HIS
Chi-restraints excluded: chain C residue  107 ASP
Chi-restraints excluded: chain D residue   89 PHE
Chi-restraints excluded: chain D residue  118 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 80 optimal weight:    8.9990
   chunk 36 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0470
   chunk 73 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
A 121 HIS
** B  66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.138835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.109791 restraints weight = 12342.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 2.90
r_work: 0.3359 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7018  Z= 0.124
  Angle     :  0.543   6.557   9447  Z= 0.286
  Chirality :  0.041   0.132   1010
  Planarity :  0.004   0.055   1221
  Dihedral  :  7.162  68.443    985
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 15.06 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.18 (0.29), residues: 839
  helix: -0.31 (0.28), residues: 366
  sheet: -2.18 (0.48), residues: 122
  loop : -2.36 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 106 
 TYR   0.017   0.001   TYR A  37 
 PHE   0.018   0.001   PHE A 247 
 TRP   0.012   0.001   TRP B 261 
 HIS   0.004   0.001   HIS B 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 7017)
  covalent geometry    : angle       0.54289 ( 9447)
  hydrogen bonds       : bond        0.02810 (  227)
  hydrogen bonds       : angle       4.40096 (  654)
  Misc. bond           : bond        0.00030 (    1)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 LYS cc_start: 0.8868 (mmmt) cc_final: 0.8209 (pttt)
REVERT: B  173 LYS cc_start: 0.6410 (mttt) cc_final: 0.5066 (mmtt)
REVERT: B  467 HIS cc_start: 0.8396 (OUTLIER) cc_final: 0.8191 (m-70)
REVERT: C   89 ASN cc_start: 0.8146 (p0) cc_final: 0.7849 (p0)
REVERT: C  107 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8223 (p0)
REVERT: D  110 THR cc_start: 0.6872 (p) cc_final: 0.6628 (p)
REVERT: D  118 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8350 (p0)
  outliers start: 22
  outliers final: 15
  residues processed: 113
  average time/residue: 0.0778
  time to fit residues: 11.8949
Evaluate side-chains
  121 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 HIS
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  128 PHE
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  192 ASP
Chi-restraints excluded: chain A residue  206 TRP
Chi-restraints excluded: chain A residue  207 ARG
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  231 GLU
Chi-restraints excluded: chain B residue  139 SER
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  467 HIS
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue  107 ASP
Chi-restraints excluded: chain D residue   89 PHE
Chi-restraints excluded: chain D residue  118 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 67 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 46 optimal weight:    6.9990
   chunk 41 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 52 optimal weight:    0.5980
   chunk 31 optimal weight:    0.4980
   chunk 7 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 42 optimal weight:    0.2980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** B  66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.138854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.110004 restraints weight = 12389.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 2.87
r_work: 0.3359 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.2139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7018  Z= 0.122
  Angle     :  0.551   9.347   9447  Z= 0.288
  Chirality :  0.041   0.131   1010
  Planarity :  0.004   0.056   1221
  Dihedral  :  7.129  66.987    985
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 16.04 %
    Favored  : 81.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.17 (0.29), residues: 839
  helix: -0.35 (0.28), residues: 372
  sheet: -2.09 (0.48), residues: 122
  loop : -2.37 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 106 
 TYR   0.016   0.001   TYR A  37 
 PHE   0.014   0.001   PHE A 247 
 TRP   0.011   0.001   TRP B 261 
 HIS   0.004   0.001   HIS B 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 7017)
  covalent geometry    : angle       0.55054 ( 9447)
  hydrogen bonds       : bond        0.02910 (  227)
  hydrogen bonds       : angle       4.35223 (  654)
  Misc. bond           : bond        0.00031 (    1)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 LYS cc_start: 0.8900 (mmmt) cc_final: 0.8296 (pttt)
REVERT: B  173 LYS cc_start: 0.6409 (mttt) cc_final: 0.5066 (mmtt)
REVERT: C   89 ASN cc_start: 0.8128 (p0) cc_final: 0.7848 (p0)
REVERT: C  107 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8257 (p0)
REVERT: D  110 THR cc_start: 0.6834 (p) cc_final: 0.6600 (p)
REVERT: D  118 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8390 (p0)
  outliers start: 18
  outliers final: 14
  residues processed: 115
  average time/residue: 0.0725
  time to fit residues: 11.4000
Evaluate side-chains
  123 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 HIS
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  128 PHE
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  192 ASP
Chi-restraints excluded: chain A residue  207 ARG
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  231 GLU
Chi-restraints excluded: chain B residue  139 SER
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue  107 ASP
Chi-restraints excluded: chain D residue  118 ASP
Chi-restraints excluded: chain D residue  141 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 15 optimal weight:    8.9990
   chunk 64 optimal weight:    3.9990
   chunk 25 optimal weight:    0.1980
   chunk 9 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0270
   chunk 72 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 57 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   overall best weight:    1.0040

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

Flipped N/Q/H residues before XYZ refinement:
** B  66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 467 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.137402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.108169 restraints weight = 12453.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 3.04
r_work: 0.3324 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.2236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7018  Z= 0.157
  Angle     :  0.591  11.323   9447  Z= 0.308
  Chirality :  0.042   0.133   1010
  Planarity :  0.004   0.055   1221
  Dihedral  :  7.394  68.340    985
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.34 %
    Favored  : 91.66 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 15.76 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.24 (0.29), residues: 839
  helix: -0.43 (0.28), residues: 374
  sheet: -2.13 (0.48), residues: 122
  loop : -2.38 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 106 
 TYR   0.018   0.001   TYR A  37 
 PHE   0.013   0.001   PHE A 247 
 TRP   0.014   0.001   TRP B 261 
 HIS   0.005   0.001   HIS B 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 7017)
  covalent geometry    : angle       0.59122 ( 9447)
  hydrogen bonds       : bond        0.03187 (  227)
  hydrogen bonds       : angle       4.46115 (  654)
  Misc. bond           : bond        0.00035 (    1)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 LYS cc_start: 0.9000 (mmmt) cc_final: 0.8518 (pttt)
REVERT: B  173 LYS cc_start: 0.6438 (mttt) cc_final: 0.5104 (mmtt)
REVERT: B  302 TYR cc_start: 0.7847 (t80) cc_final: 0.7382 (t80)
REVERT: C   89 ASN cc_start: 0.8102 (p0) cc_final: 0.7839 (p0)
REVERT: C  107 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8340 (p0)
REVERT: D  110 THR cc_start: 0.6876 (p) cc_final: 0.6624 (p)
  outliers start: 21
  outliers final: 16
  residues processed: 121
  average time/residue: 0.0803
  time to fit residues: 13.0982
Evaluate side-chains
  125 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 HIS
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  128 PHE
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  192 ASP
Chi-restraints excluded: chain A residue  207 ARG
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  231 GLU
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  467 HIS
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue  107 ASP
Chi-restraints excluded: chain D residue  141 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 56 optimal weight:    0.5980
   chunk 59 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   chunk 69 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0040
   chunk 16 optimal weight:    0.9990
   chunk 84 optimal weight:    6.9990
   overall best weight:    0.5992

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

Flipped N/Q/H residues before XYZ refinement:
** B  66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.138731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.110955 restraints weight = 12500.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 2.92
r_work: 0.3377 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7018  Z= 0.127
  Angle     :  0.597  12.702   9447  Z= 0.312
  Chirality :  0.042   0.204   1010
  Planarity :  0.004   0.056   1221
  Dihedral  :  7.286  66.798    985
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 17.29 %
    Favored  : 80.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.20 (0.29), residues: 839
  helix: -0.38 (0.28), residues: 374
  sheet: -2.08 (0.49), residues: 122
  loop : -2.38 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 106 
 TYR   0.017   0.001   TYR A  37 
 PHE   0.012   0.001   PHE A 247 
 TRP   0.012   0.001   TRP A 214 
 HIS   0.004   0.001   HIS B 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 7017)
  covalent geometry    : angle       0.59743 ( 9447)
  hydrogen bonds       : bond        0.03051 (  227)
  hydrogen bonds       : angle       4.37638 (  654)
  Misc. bond           : bond        0.00040 (    1)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 LYS cc_start: 0.8804 (mmmt) cc_final: 0.8132 (pttm)
REVERT: B  173 LYS cc_start: 0.6424 (mttt) cc_final: 0.5116 (mmtt)
REVERT: B  302 TYR cc_start: 0.7786 (t80) cc_final: 0.7358 (t80)
REVERT: C   76 GLU cc_start: 0.8171 (pm20) cc_final: 0.7892 (pm20)
REVERT: C   89 ASN cc_start: 0.8120 (p0) cc_final: 0.7867 (p0)
REVERT: C  107 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.8303 (p0)
REVERT: C  271 LYS cc_start: 0.8183 (mttt) cc_final: 0.7954 (mttm)
REVERT: D  110 THR cc_start: 0.6907 (p) cc_final: 0.6666 (p)
  outliers start: 16
  outliers final: 15
  residues processed: 116
  average time/residue: 0.0795
  time to fit residues: 12.5751
Evaluate side-chains
  123 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 HIS
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  128 PHE
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  192 ASP
Chi-restraints excluded: chain A residue  207 ARG
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  231 GLU
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  467 HIS
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue  107 ASP
Chi-restraints excluded: chain D residue  141 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 70 optimal weight:    8.9990
   chunk 31 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 81 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   overall best weight:    1.2982

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

Flipped N/Q/H residues before XYZ refinement:
** B  66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 467 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.136553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.109971 restraints weight = 12575.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 2.83
r_work: 0.3326 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.2344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   7018  Z= 0.192
  Angle     :  0.644  12.835   9447  Z= 0.334
  Chirality :  0.043   0.141   1010
  Planarity :  0.005   0.056   1221
  Dihedral  :  7.739  74.034    985
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.82 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 17.71 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.34 (0.29), residues: 839
  helix: -0.52 (0.27), residues: 375
  sheet: -2.20 (0.49), residues: 122
  loop : -2.40 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 106 
 TYR   0.021   0.002   TYR A  37 
 PHE   0.011   0.002   PHE B  78 
 TRP   0.016   0.002   TRP B 261 
 HIS   0.006   0.001   HIS B 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 7017)
  covalent geometry    : angle       0.64355 ( 9447)
  hydrogen bonds       : bond        0.03409 (  227)
  hydrogen bonds       : angle       4.62809 (  654)
  Misc. bond           : bond        0.00047 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1491.70 seconds
wall clock time: 26 minutes 18.77 seconds (1578.77 seconds total)