Starting phenix.real_space_refine
on Sun Apr  5 05:49:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9m0z_63566/04_2026/9m0z_63566.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9m0z_63566/04_2026/9m0z_63566.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9m0z_63566/04_2026/9m0z_63566.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9m0z_63566/04_2026/9m0z_63566.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9m0z_63566/04_2026/9m0z_63566.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9m0z_63566/04_2026/9m0z_63566.cif"
  }
  resolution = 2.74
  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=   0.002 sd=   0.031
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      61      5.16       5
     C    5375      2.51       5
     N    1452      2.21       5
     O    1572      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8460
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2524
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2524
          Classifications: {'peptide': 316}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 303}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "C"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 967
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
    Chain: "A"
      Number of atoms: 1926
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1926
          Classifications: {'peptide': 235}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 228}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "R"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 7
          Unusual residues: {'N2P': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.96, per 1000 atoms: 0.23
  Number of scatterers: 8460
  At special positions: 0
  Unit cell: (76.544, 99.84, 138.944, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      61     16.00
     O    1572      8.00
     N    1452      7.00
     C    5375      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  14 " - pdb=" SG  CYS R  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  22 " - pdb=" SG  CYS R 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 105 " - pdb=" SG  CYS R 190 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03

  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: 0.82
  Conformation dependent library (CDL) restraints added in 221.2 milliseconds
  

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2020

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 10 sheets defined
      44.0% alpha, 19.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'R' and resid 28 through 60
    Processing helix  chain 'R' and resid 61 through 64
    Processing helix  chain 'R' and resid 65 through 85
      removed outlier: 3.816A  pdb=" N   LEU R  70 " --> pdb=" O   THR R  66 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 85 through 96
    Processing helix  chain 'R' and resid 100 through 136
      removed outlier: 4.054A  pdb=" N   PHE R 104 " --> pdb=" O   TYR R 100 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 139 through 144
    Processing helix  chain 'R' and resid 145 through 168
    Processing helix  chain 'R' and resid 169 through 171
      No H-bonds generated for 'chain 'R' and resid 169 through 171'
    Processing helix  chain 'R' and resid 177 through 184
    Processing helix  chain 'R' and resid 195 through 233
      removed outlier: 4.839A  pdb=" N   LEU R 209 " --> pdb=" O   ILE R 205 " (cutoff:3.500A)
      Proline residue:  R 210  - end of helix
    Processing helix  chain 'R' and resid 250 through 279
      removed outlier: 3.992A  pdb=" N   PHE R 265 " --> pdb=" O   VAL R 261 " (cutoff:3.500A)
      Proline residue:  R 271  - end of helix
    Processing helix  chain 'R' and resid 280 through 282
      No H-bonds generated for 'chain 'R' and resid 280 through 282'
    Processing helix  chain 'R' and resid 287 through 309
      removed outlier: 3.639A  pdb=" N   SER R 302 " --> pdb=" O   GLY R 298 " (cutoff:3.500A)
      Proline residue:  R 306  - end of helix
    Processing helix  chain 'R' and resid 313 through 325
    Processing helix  chain 'R' and resid 326 through 330
      removed outlier: 3.567A  pdb=" N   PHE R 329 " --> pdb=" O   ARG R 326 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 332 through 336
      removed outlier: 4.111A  pdb=" N   ASP R 335 " --> pdb=" O   ASN R 332 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ILE R 336 " --> pdb=" O   SER R 333 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 332 through 336'
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 7 through 24
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 45 through 48
      removed outlier: 3.556A  pdb=" N   ASP C  48 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 45 through 48'
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.536A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 12 through 36
    Processing helix  chain 'A' and resid 52 through 60
      removed outlier: 3.567A  pdb=" N   MET A  60 " --> pdb=" O   ILE A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 101
      removed outlier: 3.507A  pdb=" N   PHE A 100 " --> pdb=" O   ILE A  97 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   ASN A 101 " --> pdb=" O   GLN A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 131
    Processing helix  chain 'A' and resid 145 through 156
    Processing helix  chain 'A' and resid 159 through 164
      removed outlier: 4.340A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 170
      removed outlier: 3.669A  pdb=" N   ALA A 168 " --> pdb=" O   PRO A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 205
      removed outlier: 3.980A  pdb=" N   ILE A 200 " --> pdb=" O   GLU A 196 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   SER A 204 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 243
    Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 52
      removed outlier: 5.734A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.007A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.167A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.372A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.765A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.687A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.934A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.149A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.798A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.029A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.648A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.978A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.439A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.076A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.938A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.400A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.540A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.587A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.041A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.944A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.586A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AA9, first strand: chain 'N' and resid 11 through 12
      removed outlier: 6.817A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 69 through 75
      removed outlier: 4.646A  pdb=" N   VAL A  86 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 9.360A  pdb=" N   ALA A 105 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 105 " (cutoff:3.500A)
      removed outlier: 7.926A  pdb=" N   ILE A 107 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
      removed outlier: 7.537A  pdb=" N   VAL A 109 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
      removed outlier: 8.602A  pdb=" N   ASP A 111 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   ILE A 106 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   PHE A 142 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   PHE A 108 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   ASN A 144 " --> pdb=" O   PHE A 108 " (cutoff:3.500A)
      removed outlier: 5.724A  pdb=" N   VAL A 110 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)

    434 hydrogen bonds defined for protein.
    1242 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.26

  Time building geometry restraints manager: 1.00 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2753
        1.34 -     1.46: 1967
        1.46 -     1.58: 3832
        1.58 -     1.70: 0
        1.70 -     1.81: 90
  Bond restraints: 8642
  Sorted by residual:
  bond pdb=" N   ILE R 124 "
       pdb=" CA  ILE R 124 "
    ideal  model  delta    sigma   weight residual
    1.461  1.497 -0.036 1.19e-02 7.06e+03 9.29e+00
  bond pdb=" N   HIS B 225 "
       pdb=" CA  HIS B 225 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.036 1.18e-02 7.18e+03 9.26e+00
  bond pdb=" N   ILE R 155 "
       pdb=" CA  ILE R 155 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.30e-02 5.92e+03 8.97e+00
  bond pdb=" N   MET B 262 "
       pdb=" CA  MET B 262 "
    ideal  model  delta    sigma   weight residual
    1.454  1.492 -0.038 1.29e-02 6.01e+03 8.68e+00
  bond pdb=" N   ASP B 163 "
       pdb=" CA  ASP B 163 "
    ideal  model  delta    sigma   weight residual
    1.455  1.492 -0.037 1.25e-02 6.40e+03 8.62e+00
  ... (remaining 8637 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.23: 11152
        1.23 -     2.46: 415
        2.46 -     3.68: 113
        3.68 -     4.91: 29
        4.91 -     6.14: 5
  Bond angle restraints: 11714
  Sorted by residual:
  angle pdb=" CA  THR B 223 "
        pdb=" C   THR B 223 "
        pdb=" O   THR B 223 "
      ideal   model   delta    sigma   weight residual
     122.37  118.05    4.32 1.15e+00 7.56e-01 1.41e+01
  angle pdb=" C   ARG R  92 "
        pdb=" CA  ARG R  92 "
        pdb=" CB  ARG R  92 "
      ideal   model   delta    sigma   weight residual
     110.85  104.71    6.14 1.70e+00 3.46e-01 1.30e+01
  angle pdb=" N   ILE R 274 "
        pdb=" CA  ILE R 274 "
        pdb=" C   ILE R 274 "
      ideal   model   delta    sigma   weight residual
     110.42  106.98    3.44 9.60e-01 1.09e+00 1.28e+01
  angle pdb=" N   GLU A  20 "
        pdb=" CA  GLU A  20 "
        pdb=" CB  GLU A  20 "
      ideal   model   delta    sigma   weight residual
     110.28  115.71   -5.43 1.55e+00 4.16e-01 1.23e+01
  angle pdb=" N   ASP B 163 "
        pdb=" CA  ASP B 163 "
        pdb=" C   ASP B 163 "
      ideal   model   delta    sigma   weight residual
     112.93  109.38    3.55 1.12e+00 7.97e-01 1.01e+01
  ... (remaining 11709 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.23: 4628
       16.23 -    32.46: 394
       32.46 -    48.69: 89
       48.69 -    64.92: 15
       64.92 -    81.15: 10
  Dihedral angle restraints: 5136
    sinusoidal: 2010
      harmonic: 3126
  Sorted by residual:
  dihedral pdb=" CB  CYS R  22 "
           pdb=" SG  CYS R  22 "
           pdb=" SG  CYS R 186 "
           pdb=" CB  CYS R 186 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -134.09   48.09     1      1.00e+01 1.00e-02 3.19e+01
  dihedral pdb=" CA  CYS R  22 "
           pdb=" CB  CYS R  22 "
           pdb=" SG  CYS R  22 "
           pdb=" SG  CYS R 186 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00    3.00  -76.00     1      2.00e+01 2.50e-03 1.82e+01
  dihedral pdb=" CD  ARG A 241 "
           pdb=" NE  ARG A 241 "
           pdb=" CZ  ARG A 241 "
           pdb=" NH1 ARG A 241 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   31.59  -31.59     1      1.00e+01 1.00e-02 1.42e+01
  ... (remaining 5133 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 963
       0.046 -    0.092: 261
       0.092 -    0.139: 81
       0.139 -    0.185: 8
       0.185 -    0.231: 5
  Chirality restraints: 1318
  Sorted by residual:
  chirality pdb=" CA  ILE B  58 "
            pdb=" N   ILE B  58 "
            pdb=" C   ILE B  58 "
            pdb=" CB  ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.23 2.00e-01 2.50e+01 1.33e+00
  chirality pdb=" CA  ILE R 274 "
            pdb=" N   ILE R 274 "
            pdb=" C   ILE R 274 "
            pdb=" CB  ILE R 274 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CA  ILE R 338 "
            pdb=" N   ILE R 338 "
            pdb=" C   ILE R 338 "
            pdb=" CB  ILE R 338 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.19 2.00e-01 2.50e+01 9.47e-01
  ... (remaining 1315 not shown)

  Planarity restraints: 1492
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 241 "   -0.570 9.50e-02 1.11e+02   2.56e-01 3.99e+01
        pdb=" NE  ARG A 241 "    0.033 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 241 "    0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 241 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 241 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG R  92 "    0.398 9.50e-02 1.11e+02   1.79e-01 1.96e+01
        pdb=" NE  ARG R  92 "   -0.022 2.00e-02 2.50e+03
        pdb=" CZ  ARG R  92 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG R  92 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG R  92 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  52 "   -0.370 9.50e-02 1.11e+02   1.66e-01 1.69e+01
        pdb=" NE  ARG B  52 "    0.022 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  52 "    0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  52 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  52 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1489 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 893
        2.75 -     3.29: 8421
        3.29 -     3.82: 14666
        3.82 -     4.36: 17502
        4.36 -     4.90: 30390
  Nonbonded interactions: 71872
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   VAL B 187 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" OD1 ASP N  50 "
            pdb=" OG  SER N  59 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" OG  SER R  93 "
            pdb=" OE1 GLU R 292 "
     model   vdw
     2.306 3.040
  ... (remaining 71867 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:             1.060
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.140
  Find NCS groups from input model:        0.040
  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:6.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
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      :  0.004   0.068   8647  Z= 0.253
  Angle     :  0.600   6.138  11724  Z= 0.381
  Chirality :  0.047   0.231   1318
  Planarity :  0.010   0.256   1492
  Dihedral  : 12.899  81.149   3101
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  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:  0.85 (0.26), residues: 1059
  helix:  2.04 (0.26), residues: 416
  sheet: -0.08 (0.35), residues: 204
  loop : -0.51 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  21 
 TYR   0.017   0.001   TYR R 165 
 PHE   0.016   0.001   PHE R  15 
 TRP   0.013   0.001   TRP R 315 
 HIS   0.005   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 8642)
  covalent geometry    : angle       0.59951 (11714)
  SS BOND              : bond        0.00245 (    5)
  SS BOND              : angle       0.76538 (   10)
  hydrogen bonds       : bond        0.15681 (  434)
  hydrogen bonds       : angle       6.81181 ( 1242)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 254
  time to evaluate  : 0.309 
Fit side-chains
REVERT: R  312 PHE cc_start: 0.8398 (t80) cc_final: 0.8039 (t80)
REVERT: B   38 ASP cc_start: 0.7609 (m-30) cc_final: 0.7390 (m-30)
REVERT: B  254 ASP cc_start: 0.7173 (t70) cc_final: 0.6955 (t70)
REVERT: B  291 ASP cc_start: 0.7701 (p0) cc_final: 0.7408 (p0)
REVERT: A  159 LYS cc_start: 0.7536 (mmmm) cc_final: 0.7100 (mmmm)
  outliers start: 0
  outliers final: 1
  residues processed: 254
  average time/residue: 0.5583
  time to fit residues: 150.6877
Evaluate side-chains
  225 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 224
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  177 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    0.0050
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   chunk 100 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   overall best weight:    1.0998

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

Flipped N/Q/H residues before XYZ refinement:
R  32 GLN
R 275 ASN
R 283 ASN
** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  17 GLN
B 259 GLN
B 268 ASN
B 340 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.123197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.110927 restraints weight = 11762.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 1.78
r_work: 0.3388 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3242 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.1352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8647  Z= 0.200
  Angle     :  0.532   6.120  11724  Z= 0.286
  Chirality :  0.044   0.141   1318
  Planarity :  0.005   0.056   1492
  Dihedral  :  4.307  44.317   1175
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 11.53 %
    Favored  : 86.29 %
  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:  1.08 (0.26), residues: 1059
  helix:  2.24 (0.26), residues: 416
  sheet: -0.24 (0.32), residues: 237
  loop : -0.23 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  19 
 TYR   0.023   0.002   TYR R  36 
 PHE   0.021   0.002   PHE B 234 
 TRP   0.016   0.002   TRP B 169 
 HIS   0.004   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 8642)
  covalent geometry    : angle       0.53163 (11714)
  SS BOND              : bond        0.00347 (    5)
  SS BOND              : angle       1.09068 (   10)
  hydrogen bonds       : bond        0.04475 (  434)
  hydrogen bonds       : angle       5.10071 ( 1242)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 246
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   86 MET cc_start: 0.8203 (mtt) cc_final: 0.7999 (mmm)
REVERT: R   99 TYR cc_start: 0.7847 (m-80) cc_final: 0.7527 (m-80)
REVERT: B   38 ASP cc_start: 0.8413 (m-30) cc_final: 0.8152 (m-30)
REVERT: B  212 ASP cc_start: 0.8252 (t0) cc_final: 0.7957 (t0)
REVERT: B  291 ASP cc_start: 0.8047 (p0) cc_final: 0.7757 (p0)
REVERT: N   52 SER cc_start: 0.8404 (m) cc_final: 0.8069 (p)
REVERT: A   61 ARG cc_start: 0.7067 (mpp80) cc_final: 0.6713 (mpp80)
REVERT: A  159 LYS cc_start: 0.7853 (mmmm) cc_final: 0.7350 (mmmm)
REVERT: A  208 ARG cc_start: 0.8155 (mtp85) cc_final: 0.7848 (mmt-90)
  outliers start: 20
  outliers final: 10
  residues processed: 251
  average time/residue: 0.5267
  time to fit residues: 141.2222
Evaluate side-chains
  248 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 238
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   83 LEU
Chi-restraints excluded: chain R residue  103 THR
Chi-restraints excluded: chain R residue  110 SER
Chi-restraints excluded: chain R residue  177 LEU
Chi-restraints excluded: chain R residue  191 THR
Chi-restraints excluded: chain R residue  200 VAL
Chi-restraints excluded: chain R residue  267 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain A residue   20 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 95 optimal weight:    4.9990
   chunk 92 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   chunk 86 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 81 optimal weight:   10.0000
   chunk 55 optimal weight:    0.4980
   chunk 103 optimal weight:    0.9990
   chunk 82 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
R 275 ASN
R 301 ASN
B  17 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN
B 340 ASN
A 131 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.123817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.111692 restraints weight = 11695.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 1.79
r_work: 0.3405 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3255 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.1621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8647  Z= 0.150
  Angle     :  0.496   5.895  11724  Z= 0.264
  Chirality :  0.042   0.143   1318
  Planarity :  0.004   0.046   1492
  Dihedral  :  4.209  43.388   1175
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 13.93 %
    Favored  : 83.68 %
  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:  1.09 (0.26), residues: 1059
  helix:  2.27 (0.26), residues: 416
  sheet: -0.23 (0.32), residues: 235
  loop : -0.25 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  19 
 TYR   0.013   0.001   TYR R  36 
 PHE   0.017   0.001   PHE B 234 
 TRP   0.014   0.002   TRP A  96 
 HIS   0.003   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 8642)
  covalent geometry    : angle       0.49520 (11714)
  SS BOND              : bond        0.00261 (    5)
  SS BOND              : angle       0.84264 (   10)
  hydrogen bonds       : bond        0.03985 (  434)
  hydrogen bonds       : angle       4.85661 ( 1242)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 239
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: R   39 LEU cc_start: 0.8774 (mp) cc_final: 0.8538 (mm)
REVERT: R   99 TYR cc_start: 0.7753 (m-80) cc_final: 0.7547 (m-80)
REVERT: R  148 VAL cc_start: 0.8136 (OUTLIER) cc_final: 0.7832 (t)
REVERT: B   38 ASP cc_start: 0.8410 (m-30) cc_final: 0.8155 (m-30)
REVERT: B   49 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.6466 (mpt180)
REVERT: B  212 ASP cc_start: 0.8167 (t0) cc_final: 0.7841 (t0)
REVERT: B  221 THR cc_start: 0.8709 (t) cc_final: 0.8423 (p)
REVERT: B  258 ASP cc_start: 0.7905 (t70) cc_final: 0.7578 (t70)
REVERT: B  291 ASP cc_start: 0.8074 (p0) cc_final: 0.7759 (p0)
REVERT: N   52 SER cc_start: 0.8369 (m) cc_final: 0.8022 (p)
REVERT: A   61 ARG cc_start: 0.7087 (mpp80) cc_final: 0.6740 (mpp80)
REVERT: A   93 ARG cc_start: 0.8514 (ptp-170) cc_final: 0.8308 (ptm-80)
REVERT: A  159 LYS cc_start: 0.7899 (mmmm) cc_final: 0.7401 (mmmm)
REVERT: A  166 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7573 (mm-30)
REVERT: A  169 ARG cc_start: 0.8029 (mtt180) cc_final: 0.7812 (mtm110)
REVERT: A  170 TYR cc_start: 0.8827 (t80) cc_final: 0.8561 (t80)
REVERT: A  195 ASP cc_start: 0.7949 (m-30) cc_final: 0.7667 (m-30)
REVERT: A  208 ARG cc_start: 0.8205 (mtp85) cc_final: 0.7930 (mmt-90)
  outliers start: 22
  outliers final: 12
  residues processed: 246
  average time/residue: 0.5001
  time to fit residues: 131.8325
Evaluate side-chains
  249 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 235
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  103 THR
Chi-restraints excluded: chain R residue  110 SER
Chi-restraints excluded: chain R residue  148 VAL
Chi-restraints excluded: chain R residue  177 LEU
Chi-restraints excluded: chain R residue  191 THR
Chi-restraints excluded: chain R residue  267 MET
Chi-restraints excluded: chain B residue   49 ARG
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain A residue   24 MET
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  222 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 90 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 86 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   chunk 83 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
R 275 ASN
R 301 ASN
B  17 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN
B 340 ASN
A  80 ASN
A 131 ASN
A 144 ASN
A 223 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.123356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.111146 restraints weight = 11905.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 1.80
r_work: 0.3386 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3238 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.1827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8647  Z= 0.165
  Angle     :  0.494   6.236  11724  Z= 0.262
  Chirality :  0.042   0.142   1318
  Planarity :  0.004   0.045   1492
  Dihedral  :  4.211  43.458   1175
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 15.13 %
    Favored  : 81.61 %
  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:  1.08 (0.26), residues: 1059
  helix:  2.25 (0.26), residues: 416
  sheet: -0.29 (0.32), residues: 237
  loop : -0.20 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  19 
 TYR   0.010   0.001   TYR R 165 
 PHE   0.015   0.001   PHE B 234 
 TRP   0.015   0.002   TRP A  96 
 HIS   0.004   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 8642)
  covalent geometry    : angle       0.49389 (11714)
  SS BOND              : bond        0.00261 (    5)
  SS BOND              : angle       0.87090 (   10)
  hydrogen bonds       : bond        0.03890 (  434)
  hydrogen bonds       : angle       4.76359 ( 1242)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 250
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: R   39 LEU cc_start: 0.8798 (mp) cc_final: 0.8567 (mm)
REVERT: R  148 VAL cc_start: 0.8143 (OUTLIER) cc_final: 0.7806 (t)
REVERT: B   38 ASP cc_start: 0.8383 (m-30) cc_final: 0.8151 (m-30)
REVERT: B   49 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.6476 (mpt180)
REVERT: B  212 ASP cc_start: 0.8176 (t0) cc_final: 0.7866 (t0)
REVERT: B  221 THR cc_start: 0.8682 (t) cc_final: 0.8369 (p)
REVERT: B  258 ASP cc_start: 0.7967 (t70) cc_final: 0.7432 (t0)
REVERT: B  291 ASP cc_start: 0.8070 (p0) cc_final: 0.7768 (p0)
REVERT: B  313 ASN cc_start: 0.8624 (t0) cc_final: 0.8352 (t0)
REVERT: N   52 SER cc_start: 0.8367 (m) cc_final: 0.8018 (p)
REVERT: A  159 LYS cc_start: 0.7907 (mmmm) cc_final: 0.7418 (mmmm)
REVERT: A  166 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7581 (mm-30)
REVERT: A  169 ARG cc_start: 0.8027 (mtt180) cc_final: 0.7827 (mtm110)
REVERT: A  170 TYR cc_start: 0.8857 (t80) cc_final: 0.8580 (t80)
REVERT: A  195 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7670 (m-30)
REVERT: A  208 ARG cc_start: 0.8161 (mtp85) cc_final: 0.7862 (mmt-90)
  outliers start: 30
  outliers final: 17
  residues processed: 259
  average time/residue: 0.5176
  time to fit residues: 143.4288
Evaluate side-chains
  255 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 235
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   23 LEU
Chi-restraints excluded: chain R residue  103 THR
Chi-restraints excluded: chain R residue  110 SER
Chi-restraints excluded: chain R residue  148 VAL
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  177 LEU
Chi-restraints excluded: chain R residue  191 THR
Chi-restraints excluded: chain R residue  267 MET
Chi-restraints excluded: chain R residue  305 ASN
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   49 ARG
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain A residue   20 GLU
Chi-restraints excluded: chain A residue   24 MET
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  195 ASP
Chi-restraints excluded: chain A residue  222 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 16 optimal weight:    0.0870
   chunk 59 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 9 optimal weight:    6.9990
   chunk 78 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 79 optimal weight:    0.1980
   chunk 0 optimal weight:    6.9990
   chunk 44 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.6564

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

Flipped N/Q/H residues before XYZ refinement:
R 301 ASN
B  16 ASN
B  17 GLN
B  35 ASN
B 125 ASN
B 259 GLN
A 131 ASN
A 144 ASN
A 223 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.123736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.111735 restraints weight = 11836.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 1.77
r_work: 0.3400 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3255 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.1922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8647  Z= 0.136
  Angle     :  0.476   5.818  11724  Z= 0.255
  Chirality :  0.041   0.140   1318
  Planarity :  0.004   0.045   1492
  Dihedral  :  4.153  42.345   1175
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 16.43 %
    Favored  : 80.09 %
  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:  1.14 (0.26), residues: 1059
  helix:  2.31 (0.26), residues: 416
  sheet: -0.12 (0.32), residues: 233
  loop : -0.27 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  61 
 TYR   0.010   0.001   TYR R  36 
 PHE   0.013   0.001   PHE B 234 
 TRP   0.014   0.001   TRP B 169 
 HIS   0.003   0.001   HIS R 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 8642)
  covalent geometry    : angle       0.47608 (11714)
  SS BOND              : bond        0.00201 (    5)
  SS BOND              : angle       0.73625 (   10)
  hydrogen bonds       : bond        0.03714 (  434)
  hydrogen bonds       : angle       4.67648 ( 1242)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 239
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
REVERT: R  148 VAL cc_start: 0.8098 (OUTLIER) cc_final: 0.7740 (t)
REVERT: R  309 TYR cc_start: 0.8633 (m-80) cc_final: 0.8413 (m-80)
REVERT: B   38 ASP cc_start: 0.8372 (m-30) cc_final: 0.8141 (m-30)
REVERT: B   49 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.6469 (mpt180)
REVERT: B  197 ARG cc_start: 0.8040 (mtp85) cc_final: 0.7792 (mtp85)
REVERT: B  212 ASP cc_start: 0.8139 (t0) cc_final: 0.7870 (t0)
REVERT: B  258 ASP cc_start: 0.7884 (t70) cc_final: 0.7349 (t0)
REVERT: B  291 ASP cc_start: 0.8072 (p0) cc_final: 0.7775 (p0)
REVERT: B  304 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7991 (ttm170)
REVERT: N   29 PHE cc_start: 0.8666 (t80) cc_final: 0.8444 (t80)
REVERT: N   52 SER cc_start: 0.8348 (m) cc_final: 0.8035 (p)
REVERT: A  159 LYS cc_start: 0.7896 (mmmm) cc_final: 0.7406 (mmmm)
REVERT: A  169 ARG cc_start: 0.8002 (mtt180) cc_final: 0.7801 (mtm110)
REVERT: A  170 TYR cc_start: 0.8850 (t80) cc_final: 0.8581 (t80)
REVERT: A  188 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7539 (ttt180)
REVERT: A  195 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7650 (m-30)
REVERT: A  208 ARG cc_start: 0.8150 (mtp85) cc_final: 0.7861 (mmt-90)
  outliers start: 32
  outliers final: 17
  residues processed: 251
  average time/residue: 0.4952
  time to fit residues: 133.2068
Evaluate side-chains
  256 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 234
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   23 LEU
Chi-restraints excluded: chain R residue  103 THR
Chi-restraints excluded: chain R residue  110 SER
Chi-restraints excluded: chain R residue  148 VAL
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  177 LEU
Chi-restraints excluded: chain R residue  191 THR
Chi-restraints excluded: chain R residue  267 MET
Chi-restraints excluded: chain R residue  305 ASN
Chi-restraints excluded: chain B residue   49 ARG
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  304 ARG
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain A residue   20 GLU
Chi-restraints excluded: chain A residue   24 MET
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  188 ARG
Chi-restraints excluded: chain A residue  195 ASP
Chi-restraints excluded: chain A residue  222 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 95 optimal weight:    4.9990
   chunk 103 optimal weight:    0.8980
   chunk 81 optimal weight:    9.9990
   chunk 25 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
R 301 ASN
B  17 GLN
B 259 GLN
B 268 ASN
C  24 ASN
A 223 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.123003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.111011 restraints weight = 11699.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 1.75
r_work: 0.3394 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3246 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.1986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8647  Z= 0.172
  Angle     :  0.496   5.680  11724  Z= 0.265
  Chirality :  0.043   0.146   1318
  Planarity :  0.004   0.044   1492
  Dihedral  :  4.194  42.860   1175
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 16.65 %
    Favored  : 79.87 %
  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:  1.09 (0.26), residues: 1059
  helix:  2.25 (0.26), residues: 416
  sheet: -0.14 (0.32), residues: 233
  loop : -0.29 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B  19 
 TYR   0.010   0.001   TYR B  59 
 PHE   0.016   0.001   PHE R 136 
 TRP   0.016   0.002   TRP A  96 
 HIS   0.003   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 8642)
  covalent geometry    : angle       0.49545 (11714)
  SS BOND              : bond        0.00258 (    5)
  SS BOND              : angle       0.75823 (   10)
  hydrogen bonds       : bond        0.03859 (  434)
  hydrogen bonds       : angle       4.71292 ( 1242)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 245
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
REVERT: R  148 VAL cc_start: 0.8073 (OUTLIER) cc_final: 0.7757 (t)
REVERT: R  309 TYR cc_start: 0.8623 (m-80) cc_final: 0.8376 (m-80)
REVERT: B   38 ASP cc_start: 0.8402 (m-30) cc_final: 0.8180 (m-30)
REVERT: B   49 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.6409 (mpt180)
REVERT: B  176 GLN cc_start: 0.8882 (mt0) cc_final: 0.8631 (mt0)
REVERT: B  197 ARG cc_start: 0.8073 (mtp85) cc_final: 0.7772 (mtp85)
REVERT: B  212 ASP cc_start: 0.8180 (t0) cc_final: 0.7882 (t0)
REVERT: B  258 ASP cc_start: 0.7905 (t70) cc_final: 0.7348 (t0)
REVERT: B  277 SER cc_start: 0.8585 (p) cc_final: 0.8231 (m)
REVERT: B  291 ASP cc_start: 0.8086 (p0) cc_final: 0.7804 (p0)
REVERT: B  304 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8006 (ttm170)
REVERT: N   52 SER cc_start: 0.8349 (m) cc_final: 0.8034 (p)
REVERT: A  159 LYS cc_start: 0.7901 (mmmm) cc_final: 0.7400 (mmmm)
REVERT: A  170 TYR cc_start: 0.8867 (t80) cc_final: 0.8587 (t80)
REVERT: A  188 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7522 (ttt180)
REVERT: A  195 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7613 (m-30)
REVERT: A  208 ARG cc_start: 0.8154 (mtp85) cc_final: 0.7864 (mmt-90)
  outliers start: 32
  outliers final: 18
  residues processed: 255
  average time/residue: 0.4965
  time to fit residues: 135.4055
Evaluate side-chains
  265 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 242
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   23 LEU
Chi-restraints excluded: chain R residue  103 THR
Chi-restraints excluded: chain R residue  110 SER
Chi-restraints excluded: chain R residue  148 VAL
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  177 LEU
Chi-restraints excluded: chain R residue  191 THR
Chi-restraints excluded: chain R residue  267 MET
Chi-restraints excluded: chain R residue  305 ASN
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   49 ARG
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  304 ARG
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain A residue   20 GLU
Chi-restraints excluded: chain A residue   24 MET
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  188 ARG
Chi-restraints excluded: chain A residue  195 ASP
Chi-restraints excluded: chain A residue  222 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 75 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   chunk 78 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
R 301 ASN
B  17 GLN
B 259 GLN
B 268 ASN
B 340 ASN
A  80 ASN
A 131 ASN
A 144 ASN
A 223 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.122596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.110435 restraints weight = 11869.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 1.78
r_work: 0.3385 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.2029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8647  Z= 0.197
  Angle     :  0.512   6.345  11724  Z= 0.273
  Chirality :  0.043   0.144   1318
  Planarity :  0.004   0.044   1492
  Dihedral  :  4.263  43.505   1175
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 17.63 %
    Favored  : 78.67 %
  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:  1.05 (0.26), residues: 1059
  helix:  2.18 (0.26), residues: 416
  sheet: -0.16 (0.32), residues: 239
  loop : -0.26 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  19 
 TYR   0.011   0.001   TYR A 115 
 PHE   0.014   0.001   PHE B 234 
 TRP   0.017   0.002   TRP A  96 
 HIS   0.003   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 8642)
  covalent geometry    : angle       0.51146 (11714)
  SS BOND              : bond        0.00270 (    5)
  SS BOND              : angle       0.78880 (   10)
  hydrogen bonds       : bond        0.03984 (  434)
  hydrogen bonds       : angle       4.75974 ( 1242)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 239
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
REVERT: R  148 VAL cc_start: 0.8151 (OUTLIER) cc_final: 0.7844 (t)
REVERT: R  309 TYR cc_start: 0.8628 (m-80) cc_final: 0.8383 (m-80)
REVERT: B   38 ASP cc_start: 0.8404 (m-30) cc_final: 0.8192 (m-30)
REVERT: B   49 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.6460 (mpt180)
REVERT: B   50 THR cc_start: 0.8252 (m) cc_final: 0.8052 (t)
REVERT: B  176 GLN cc_start: 0.8889 (mt0) cc_final: 0.8643 (mt0)
REVERT: B  197 ARG cc_start: 0.8084 (mtp85) cc_final: 0.7813 (mtp85)
REVERT: B  212 ASP cc_start: 0.8159 (t0) cc_final: 0.7870 (t0)
REVERT: B  221 THR cc_start: 0.8680 (t) cc_final: 0.8362 (p)
REVERT: B  258 ASP cc_start: 0.7934 (t70) cc_final: 0.7398 (t0)
REVERT: B  277 SER cc_start: 0.8572 (p) cc_final: 0.8253 (m)
REVERT: B  304 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8027 (ttm170)
REVERT: N   52 SER cc_start: 0.8359 (m) cc_final: 0.8046 (p)
REVERT: A  159 LYS cc_start: 0.7903 (mmmm) cc_final: 0.7411 (mmmm)
REVERT: A  170 TYR cc_start: 0.8872 (t80) cc_final: 0.8575 (t80)
REVERT: A  188 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7585 (ttt180)
REVERT: A  195 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7619 (m-30)
REVERT: A  208 ARG cc_start: 0.8162 (mtp85) cc_final: 0.7892 (mmt-90)
  outliers start: 34
  outliers final: 20
  residues processed: 252
  average time/residue: 0.4912
  time to fit residues: 132.5205
Evaluate side-chains
  257 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 232
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   23 LEU
Chi-restraints excluded: chain R residue  103 THR
Chi-restraints excluded: chain R residue  110 SER
Chi-restraints excluded: chain R residue  148 VAL
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  177 LEU
Chi-restraints excluded: chain R residue  191 THR
Chi-restraints excluded: chain R residue  231 ILE
Chi-restraints excluded: chain R residue  267 MET
Chi-restraints excluded: chain R residue  305 ASN
Chi-restraints excluded: chain B residue   49 ARG
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  304 ARG
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain A residue   20 GLU
Chi-restraints excluded: chain A residue   24 MET
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  152 LYS
Chi-restraints excluded: chain A residue  188 ARG
Chi-restraints excluded: chain A residue  195 ASP
Chi-restraints excluded: chain A residue  222 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 36 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 71 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
R 301 ASN
B  17 GLN
B 259 GLN
B 268 ASN
B 340 ASN
A 131 ASN
A 144 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.122628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.110724 restraints weight = 11662.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 1.75
r_work: 0.3391 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3243 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.2081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8647  Z= 0.184
  Angle     :  0.509   5.692  11724  Z= 0.273
  Chirality :  0.043   0.173   1318
  Planarity :  0.004   0.047   1492
  Dihedral  :  4.281  43.158   1175
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 18.28 %
    Favored  : 78.13 %
  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:  0.99 (0.26), residues: 1059
  helix:  2.16 (0.26), residues: 416
  sheet: -0.19 (0.32), residues: 235
  loop : -0.33 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  61 
 TYR   0.011   0.001   TYR R 100 
 PHE   0.017   0.001   PHE R 136 
 TRP   0.016   0.002   TRP A  96 
 HIS   0.003   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 8642)
  covalent geometry    : angle       0.50918 (11714)
  SS BOND              : bond        0.00261 (    5)
  SS BOND              : angle       0.75184 (   10)
  hydrogen bonds       : bond        0.03978 (  434)
  hydrogen bonds       : angle       4.76740 ( 1242)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 239
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
REVERT: R  148 VAL cc_start: 0.8083 (OUTLIER) cc_final: 0.7776 (t)
REVERT: R  309 TYR cc_start: 0.8626 (m-80) cc_final: 0.8375 (m-80)
REVERT: B   38 ASP cc_start: 0.8416 (m-30) cc_final: 0.8209 (m-30)
REVERT: B   49 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.6442 (mpt180)
REVERT: B  176 GLN cc_start: 0.8872 (mt0) cc_final: 0.8619 (mt0)
REVERT: B  197 ARG cc_start: 0.8056 (mtp85) cc_final: 0.7773 (mtp85)
REVERT: B  212 ASP cc_start: 0.8162 (t0) cc_final: 0.7875 (t0)
REVERT: B  258 ASP cc_start: 0.7898 (t70) cc_final: 0.7355 (t0)
REVERT: B  277 SER cc_start: 0.8559 (p) cc_final: 0.8251 (m)
REVERT: B  303 ASP cc_start: 0.7517 (m-30) cc_final: 0.7249 (m-30)
REVERT: B  304 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8016 (ttm170)
REVERT: B  340 ASN cc_start: 0.7208 (t0) cc_final: 0.6970 (t0)
REVERT: N   52 SER cc_start: 0.8340 (m) cc_final: 0.8024 (p)
REVERT: A   80 ASN cc_start: 0.8311 (m-40) cc_final: 0.8098 (m-40)
REVERT: A  132 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7857 (ttt90)
REVERT: A  159 LYS cc_start: 0.7879 (mmmm) cc_final: 0.7399 (mmmm)
REVERT: A  170 TYR cc_start: 0.8876 (t80) cc_final: 0.8573 (t80)
REVERT: A  188 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7539 (ttt180)
REVERT: A  195 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7608 (m-30)
REVERT: A  208 ARG cc_start: 0.8165 (mtp85) cc_final: 0.7892 (mmt-90)
  outliers start: 33
  outliers final: 20
  residues processed: 250
  average time/residue: 0.4833
  time to fit residues: 129.2774
Evaluate side-chains
  260 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 234
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   23 LEU
Chi-restraints excluded: chain R residue  103 THR
Chi-restraints excluded: chain R residue  110 SER
Chi-restraints excluded: chain R residue  148 VAL
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  177 LEU
Chi-restraints excluded: chain R residue  191 THR
Chi-restraints excluded: chain R residue  267 MET
Chi-restraints excluded: chain R residue  305 ASN
Chi-restraints excluded: chain R residue  338 ILE
Chi-restraints excluded: chain B residue   49 ARG
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  304 ARG
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain A residue   20 GLU
Chi-restraints excluded: chain A residue   24 MET
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  132 ARG
Chi-restraints excluded: chain A residue  152 LYS
Chi-restraints excluded: chain A residue  188 ARG
Chi-restraints excluded: chain A residue  195 ASP
Chi-restraints excluded: chain A residue  222 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 53 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 52 optimal weight:    4.9990
   chunk 71 optimal weight:    0.7980
   chunk 102 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
R 301 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN
A 131 ASN
A 223 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.123461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.111450 restraints weight = 11731.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 1.77
r_work: 0.3400 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.2118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8647  Z= 0.150
  Angle     :  0.499   7.457  11724  Z= 0.267
  Chirality :  0.042   0.159   1318
  Planarity :  0.004   0.044   1492
  Dihedral  :  4.202  41.838   1175
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 19.59 %
    Favored  : 77.69 %
  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:  1.02 (0.26), residues: 1059
  helix:  2.19 (0.26), residues: 414
  sheet: -0.16 (0.32), residues: 235
  loop : -0.32 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  19 
 TYR   0.008   0.001   TYR R  36 
 PHE   0.011   0.001   PHE B 234 
 TRP   0.015   0.002   TRP A  96 
 HIS   0.003   0.001   HIS R 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 8642)
  covalent geometry    : angle       0.49890 (11714)
  SS BOND              : bond        0.00214 (    5)
  SS BOND              : angle       0.68336 (   10)
  hydrogen bonds       : bond        0.03803 (  434)
  hydrogen bonds       : angle       4.72255 ( 1242)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 245
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
REVERT: R  148 VAL cc_start: 0.8063 (OUTLIER) cc_final: 0.7745 (t)
REVERT: R  309 TYR cc_start: 0.8608 (m-80) cc_final: 0.8364 (m-80)
REVERT: B   38 ASP cc_start: 0.8377 (m-30) cc_final: 0.8172 (m-30)
REVERT: B   49 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.6522 (mpt180)
REVERT: B  114 CYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8197 (p)
REVERT: B  176 GLN cc_start: 0.8872 (mt0) cc_final: 0.8615 (mt0)
REVERT: B  197 ARG cc_start: 0.8047 (mtp85) cc_final: 0.7816 (mtp85)
REVERT: B  212 ASP cc_start: 0.8159 (t0) cc_final: 0.7870 (t0)
REVERT: B  258 ASP cc_start: 0.7866 (t70) cc_final: 0.7307 (t0)
REVERT: B  277 SER cc_start: 0.8567 (p) cc_final: 0.8204 (m)
REVERT: B  291 ASP cc_start: 0.8085 (p0) cc_final: 0.7785 (p0)
REVERT: B  304 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7983 (ttm170)
REVERT: N   52 SER cc_start: 0.8331 (m) cc_final: 0.8011 (p)
REVERT: A  132 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7861 (ttt90)
REVERT: A  159 LYS cc_start: 0.7866 (mmmm) cc_final: 0.7388 (mmmm)
REVERT: A  170 TYR cc_start: 0.8858 (t80) cc_final: 0.8549 (t80)
REVERT: A  188 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7549 (ttt180)
REVERT: A  195 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7603 (m-30)
REVERT: A  208 ARG cc_start: 0.8139 (mtp85) cc_final: 0.7850 (mtt-85)
  outliers start: 25
  outliers final: 17
  residues processed: 253
  average time/residue: 0.5431
  time to fit residues: 146.4054
Evaluate side-chains
  261 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 237
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   23 LEU
Chi-restraints excluded: chain R residue  103 THR
Chi-restraints excluded: chain R residue  110 SER
Chi-restraints excluded: chain R residue  148 VAL
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  177 LEU
Chi-restraints excluded: chain R residue  191 THR
Chi-restraints excluded: chain R residue  231 ILE
Chi-restraints excluded: chain R residue  267 MET
Chi-restraints excluded: chain R residue  338 ILE
Chi-restraints excluded: chain B residue   49 ARG
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  304 ARG
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain A residue   20 GLU
Chi-restraints excluded: chain A residue   24 MET
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  132 ARG
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  188 ARG
Chi-restraints excluded: chain A residue  195 ASP
Chi-restraints excluded: chain A residue  222 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 102 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
R 301 ASN
** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN
B 340 ASN
A  80 ASN
A 131 ASN
A 144 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.122961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.111109 restraints weight = 11736.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 1.75
r_work: 0.3399 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.2164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8647  Z= 0.162
  Angle     :  0.512   8.989  11724  Z= 0.274
  Chirality :  0.043   0.154   1318
  Planarity :  0.004   0.046   1492
  Dihedral  :  4.212  41.155   1175
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 19.80 %
    Favored  : 77.48 %
  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:  0.99 (0.26), residues: 1059
  helix:  2.14 (0.26), residues: 414
  sheet: -0.16 (0.32), residues: 235
  loop : -0.31 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B  19 
 TYR   0.010   0.001   TYR A 115 
 PHE   0.017   0.001   PHE R 136 
 TRP   0.015   0.002   TRP A  96 
 HIS   0.003   0.001   HIS R 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 8642)
  covalent geometry    : angle       0.51166 (11714)
  SS BOND              : bond        0.00231 (    5)
  SS BOND              : angle       0.71924 (   10)
  hydrogen bonds       : bond        0.03856 (  434)
  hydrogen bonds       : angle       4.73399 ( 1242)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 235
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: R  148 VAL cc_start: 0.8063 (OUTLIER) cc_final: 0.7748 (t)
REVERT: R  177 LEU cc_start: 0.8308 (mm) cc_final: 0.8020 (mp)
REVERT: R  309 TYR cc_start: 0.8601 (m-80) cc_final: 0.8362 (m-80)
REVERT: B   49 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.6524 (mpt180)
REVERT: B  114 CYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8194 (p)
REVERT: B  176 GLN cc_start: 0.8871 (mt0) cc_final: 0.8616 (mt0)
REVERT: B  197 ARG cc_start: 0.8042 (mtp85) cc_final: 0.7795 (mtp85)
REVERT: B  212 ASP cc_start: 0.8172 (t0) cc_final: 0.7873 (t0)
REVERT: B  258 ASP cc_start: 0.7859 (t70) cc_final: 0.7313 (t0)
REVERT: B  277 SER cc_start: 0.8585 (p) cc_final: 0.8258 (m)
REVERT: B  291 ASP cc_start: 0.8093 (p0) cc_final: 0.7802 (p0)
REVERT: B  303 ASP cc_start: 0.7430 (m-30) cc_final: 0.7190 (m-30)
REVERT: B  304 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8012 (ttm170)
REVERT: B  340 ASN cc_start: 0.7369 (t0) cc_final: 0.7122 (t0)
REVERT: N   52 SER cc_start: 0.8337 (m) cc_final: 0.8022 (p)
REVERT: A  132 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7846 (ttt90)
REVERT: A  159 LYS cc_start: 0.7871 (mmmm) cc_final: 0.7399 (mmmm)
REVERT: A  170 TYR cc_start: 0.8858 (t80) cc_final: 0.8549 (t80)
REVERT: A  188 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7514 (ttt180)
REVERT: A  195 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7620 (m-30)
REVERT: A  208 ARG cc_start: 0.8124 (mtp85) cc_final: 0.7837 (mtt-85)
  outliers start: 25
  outliers final: 17
  residues processed: 242
  average time/residue: 0.5139
  time to fit residues: 132.9644
Evaluate side-chains
  257 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 233
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   23 LEU
Chi-restraints excluded: chain R residue  103 THR
Chi-restraints excluded: chain R residue  110 SER
Chi-restraints excluded: chain R residue  148 VAL
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  191 THR
Chi-restraints excluded: chain R residue  231 ILE
Chi-restraints excluded: chain R residue  267 MET
Chi-restraints excluded: chain R residue  338 ILE
Chi-restraints excluded: chain B residue   49 ARG
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  304 ARG
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain A residue   20 GLU
Chi-restraints excluded: chain A residue   24 MET
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  132 ARG
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  188 ARG
Chi-restraints excluded: chain A residue  195 ASP
Chi-restraints excluded: chain A residue  222 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 83 optimal weight:    4.9990
   chunk 18 optimal weight:    0.7980
   chunk 62 optimal weight:    4.9990
   chunk 14 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 52 optimal weight:    4.9990
   chunk 44 optimal weight:    0.5980
   chunk 34 optimal weight:    0.2980
   chunk 32 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
R 301 ASN
** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN
A 131 ASN
A 144 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.123613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.111728 restraints weight = 11701.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 1.75
r_work: 0.3408 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3260 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.2198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8647  Z= 0.144
  Angle     :  0.505   8.454  11724  Z= 0.269
  Chirality :  0.042   0.150   1318
  Planarity :  0.004   0.044   1492
  Dihedral  :  4.095  39.896   1173
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 20.02 %
    Favored  : 77.15 %
  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:  1.16 (0.26), residues: 1059
  helix:  2.33 (0.26), residues: 407
  sheet: -0.08 (0.32), residues: 233
  loop : -0.23 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B  19 
 TYR   0.008   0.001   TYR A 115 
 PHE   0.011   0.001   PHE B 234 
 TRP   0.015   0.001   TRP A  96 
 HIS   0.003   0.001   HIS R 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 8642)
  covalent geometry    : angle       0.50486 (11714)
  SS BOND              : bond        0.00215 (    5)
  SS BOND              : angle       0.69381 (   10)
  hydrogen bonds       : bond        0.03759 (  434)
  hydrogen bonds       : angle       4.69070 ( 1242)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3627.33 seconds
wall clock time: 62 minutes 25.82 seconds (3745.82 seconds total)