Starting phenix.real_space_refine
on Sat Jul 26 07:17:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6oya_20223/07_2025/6oya_20223.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6oya_20223/07_2025/6oya_20223.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6oya_20223/07_2025/6oya_20223.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6oya_20223/07_2025/6oya_20223.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6oya_20223/07_2025/6oya_20223.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6oya_20223/07_2025/6oya_20223.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.023 sd=   0.464
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      67      5.16       5
     C    5312      2.51       5
     N    1389      2.21       5
     O    1553      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 49 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8321
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1655
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 205, 1655
          Classifications: {'peptide': 205}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 202}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "B"
      Number of atoms: 2592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2592
          Classifications: {'peptide': 337}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
    Chain: "G"
      Number of atoms: 495
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 495
          Classifications: {'peptide': 60}
          Link IDs: {'PTRANS': 3, 'TRANS': 56}
    Chain: "N"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 967
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "R"
      Number of atoms: 2592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 326, 2592
          Classifications: {'peptide': 326}
          Link IDs: {'PTRANS': 18, 'TRANS': 307}
    Chain: "R"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 20
          Unusual residues: {'RET': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 7.35, per 1000 atoms: 0.88
  Number of scatterers: 8321
  At special positions: 0
  Unit cell: (85.86, 117.66, 113.42, 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      67     16.00
     O    1553      8.00
     N    1389      7.00
     C    5312      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 149 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 110 " - pdb=" SG  CYS R 187 " 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.89
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1964

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 13 sheets defined
      36.6% alpha, 13.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 27
      removed outlier: 3.752A  pdb=" N   GLU A  24 " --> pdb=" O   LYS A  20 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   LYS A  25 " --> pdb=" O   GLU A  21 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ASP A  26 " --> pdb=" O   ASP A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 46
      removed outlier: 3.609A  pdb=" N   ILE A  45 " --> pdb=" O   GLY A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 3.521A  pdb=" N   CYS A 210 " --> pdb=" O   TRP A 207 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   PHE A 211 " --> pdb=" O   ILE A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 250
      removed outlier: 3.566A  pdb=" N   MET A 243 " --> pdb=" O   MET A 239 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   SER A 248 " --> pdb=" O   ASN A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 274
      removed outlier: 4.122A  pdb=" N   GLU A 272 " --> pdb=" O   ASP A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 304
    Processing helix  chain 'A' and resid 326 through 348
      removed outlier: 3.670A  pdb=" N   ASP A 337 " --> pdb=" O   ASP A 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 26
      removed outlier: 3.863A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.767A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 25
    Processing helix  chain 'G' and resid 32 through 47
      removed outlier: 3.672A  pdb=" N   ARG G  47 " --> pdb=" O   TYR G  43 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 48 through 51
      removed outlier: 3.897A  pdb=" N   ASP G  51 " --> pdb=" O   SER G  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 48 through 51'
    Processing helix  chain 'R' and resid 14 through 18
      removed outlier: 4.172A  pdb=" N   THR R  17 " --> pdb=" O   SER R  14 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 27 through 31
      removed outlier: 4.548A  pdb=" N   TYR R  30 " --> pdb=" O   PRO R  27 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 33 through 65
      Proline residue:  R  53  - end of helix
      removed outlier: 4.382A  pdb=" N   THR R  58 " --> pdb=" O   ILE R  54 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   LEU R  59 " --> pdb=" O   ASN R  55 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 73 through 89
    Processing helix  chain 'R' and resid 89 through 101
      removed outlier: 4.260A  pdb=" N   THR R  93 " --> pdb=" O   GLY R  89 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 106 through 140
    Processing helix  chain 'R' and resid 149 through 169
      removed outlier: 3.704A  pdb=" N   ALA R 153 " --> pdb=" O   GLY R 149 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   ILE R 154 " --> pdb=" O   GLU R 150 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   MET R 155 " --> pdb=" O   ASN R 151 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ALA R 169 " --> pdb=" O   LEU R 165 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 199 through 211
    Processing helix  chain 'R' and resid 212 through 235
      removed outlier: 3.673A  pdb=" N   ALA R 233 " --> pdb=" O   THR R 229 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 242 through 263
      removed outlier: 3.856A  pdb=" N   LYS R 248 " --> pdb=" O   GLN R 244 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   GLU R 249 " --> pdb=" O   LYS R 245 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 265 through 278
      removed outlier: 3.966A  pdb=" N   ALA R 269 " --> pdb=" O   TRP R 265 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 284 through 307
      removed outlier: 3.904A  pdb=" N   ILE R 290 " --> pdb=" O   ILE R 286 " (cutoff:3.500A)
      Proline residue:  R 291  - end of helix
      removed outlier: 3.615A  pdb=" N   SER R 298 " --> pdb=" O   PHE R 294 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   ALA R 299 " --> pdb=" O   ALA R 295 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   VAL R 300 " --> pdb=" O   LYS R 296 " (cutoff:3.500A)
      Proline residue:  R 303  - end of helix
    Processing helix  chain 'R' and resid 312 through 322
      removed outlier: 3.856A  pdb=" N   CYS R 316 " --> pdb=" O   GLN R 312 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 31
      removed outlier: 7.047A  pdb=" N   VAL A  30 " --> pdb=" O   ARG A 193 " (cutoff:3.500A)
      removed outlier: 8.195A  pdb=" N   PHE A 195 " --> pdb=" O   VAL A  30 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   THR A 183 " --> pdb=" O   MET A 194 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 34
      removed outlier: 6.712A  pdb=" N   LEU A  33 " --> pdb=" O   ILE A 218 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   ILE A 217 " --> pdb=" O   ILE A 261 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.953A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.859A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 61
      removed outlier: 7.262A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   MET B  61 " --> pdb=" O   LEU B  71 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   LEU B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.810A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105
      removed outlier: 6.698A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.086A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.899A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.527A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.781A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ALA B 203 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 5.003A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 233 through 234
      removed outlier: 6.899A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.622A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 277
      removed outlier: 3.576A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12
      removed outlier: 3.623A  pdb=" N   VAL N  12 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'N' and resid 45 through 51
      removed outlier: 6.340A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 5.962A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'R' and resid 4 through 5

    327 hydrogen bonds defined for protein.
    936 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.76

  Time building geometry restraints manager: 3.37 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2672
        1.35 -     1.47: 2121
        1.47 -     1.59: 3609
        1.59 -     1.71: 0
        1.71 -     1.84: 99
  Bond restraints: 8501
  Sorted by residual:
  bond pdb=" CB  ASP A 189 "
       pdb=" CG  ASP A 189 "
    ideal  model  delta    sigma   weight residual
    1.516  1.561 -0.045 2.50e-02 1.60e+03 3.25e+00
  bond pdb=" C   ILE R 214 "
       pdb=" N   PRO R 215 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.23e-02 6.61e+03 2.20e+00
  bond pdb=" C   ILE R 290 "
       pdb=" N   PRO R 291 "
    ideal  model  delta    sigma   weight residual
    1.336  1.353 -0.018 1.23e-02 6.61e+03 2.12e+00
  bond pdb=" CA  ASP A 189 "
       pdb=" CB  ASP A 189 "
    ideal  model  delta    sigma   weight residual
    1.532  1.554 -0.022 1.56e-02 4.11e+03 2.00e+00
  bond pdb=" N   LYS B 127 "
       pdb=" CA  LYS B 127 "
    ideal  model  delta    sigma   weight residual
    1.460  1.479 -0.020 1.42e-02 4.96e+03 1.91e+00
  ... (remaining 8496 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.19: 11183
        2.19 -     4.38: 261
        4.38 -     6.57: 35
        6.57 -     8.76: 18
        8.76 -    10.96: 5
  Bond angle restraints: 11502
  Sorted by residual:
  angle pdb=" C   ASN R 310 "
        pdb=" N   LYS R 311 "
        pdb=" CA  LYS R 311 "
      ideal   model   delta    sigma   weight residual
     121.54  129.49   -7.95 1.91e+00 2.74e-01 1.73e+01
  angle pdb=" CA  ASP A 189 "
        pdb=" CB  ASP A 189 "
        pdb=" CG  ASP A 189 "
      ideal   model   delta    sigma   weight residual
     112.60  116.47   -3.87 1.00e+00 1.00e+00 1.50e+01
  angle pdb=" N   PRO R 170 "
        pdb=" CA  PRO R 170 "
        pdb=" C   PRO R 170 "
      ideal   model   delta    sigma   weight residual
     110.70  115.28   -4.58 1.22e+00 6.72e-01 1.41e+01
  angle pdb=" N   ALA R 169 "
        pdb=" CA  ALA R 169 "
        pdb=" C   ALA R 169 "
      ideal   model   delta    sigma   weight residual
     109.81  118.10   -8.29 2.21e+00 2.05e-01 1.41e+01
  angle pdb=" C   LEU B 126 "
        pdb=" N   LYS B 127 "
        pdb=" CA  LYS B 127 "
      ideal   model   delta    sigma   weight residual
     122.82  127.91   -5.09 1.42e+00 4.96e-01 1.28e+01
  ... (remaining 11497 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.68: 4436
       17.68 -    35.36: 499
       35.36 -    53.04: 74
       53.04 -    70.72: 21
       70.72 -    88.40: 9
  Dihedral angle restraints: 5039
    sinusoidal: 1986
      harmonic: 3053
  Sorted by residual:
  dihedral pdb=" CB  CYS B 121 "
           pdb=" SG  CYS B 121 "
           pdb=" SG  CYS B 149 "
           pdb=" CB  CYS B 149 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  163.25  -70.25     1      1.00e+01 1.00e-02 6.36e+01
  dihedral pdb=" CB  CYS R 110 "
           pdb=" SG  CYS R 110 "
           pdb=" SG  CYS R 187 "
           pdb=" CB  CYS R 187 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -132.79   46.79     1      1.00e+01 1.00e-02 3.03e+01
  dihedral pdb=" CA  CYS B 166 "
           pdb=" C   CYS B 166 "
           pdb=" N   ALA B 167 "
           pdb=" CA  ALA B 167 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.45  -23.55     0      5.00e+00 4.00e-02 2.22e+01
  ... (remaining 5036 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 957
       0.054 -    0.108: 247
       0.108 -    0.161: 59
       0.161 -    0.215: 10
       0.215 -    0.269: 3
  Chirality restraints: 1276
  Sorted by residual:
  chirality pdb=" CB  THR N  28 "
            pdb=" CA  THR N  28 "
            pdb=" OG1 THR N  28 "
            pdb=" CG2 THR N  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.28    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CA  ASP A 189 "
            pdb=" N   ASP A 189 "
            pdb=" C   ASP A 189 "
            pdb=" CB  ASP A 189 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CB  ILE B  80 "
            pdb=" CA  ILE B  80 "
            pdb=" CG1 ILE B  80 "
            pdb=" CG2 ILE B  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.31e+00
  ... (remaining 1273 not shown)

  Planarity restraints: 1468
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO R 170 "    0.062 5.00e-02 4.00e+02   9.36e-02 1.40e+01
        pdb=" N   PRO R 171 "   -0.162 5.00e-02 4.00e+02
        pdb=" CA  PRO R 171 "    0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO R 171 "    0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR R  70 "    0.044 5.00e-02 4.00e+02   6.71e-02 7.19e+00
        pdb=" N   PRO R  71 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO R  71 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO R  71 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 283 "   -0.039 5.00e-02 4.00e+02   5.90e-02 5.58e+00
        pdb=" N   PRO A 284 "    0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO A 284 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 284 "   -0.033 5.00e-02 4.00e+02
  ... (remaining 1465 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.84: 2821
        2.84 -     3.36: 7395
        3.36 -     3.87: 13818
        3.87 -     4.39: 15242
        4.39 -     4.90: 26585
  Nonbonded interactions: 65861
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 320 "
            pdb=" OD2 ASP A 324 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" O   SER B  67 "
            pdb=" OG  SER B  67 "
     model   vdw
     2.331 3.040
  nonbonded pdb=" OE1 GLU B 226 "
            pdb=" OH  TYR N  32 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" O   SER B  84 "
            pdb=" OG  SER B  84 "
     model   vdw
     2.347 3.040
  nonbonded pdb=" NZ  LYS A 341 "
            pdb=" OG1 THR R 243 "
     model   vdw
     2.351 3.120
  ... (remaining 65856 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:             1.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     27.570
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:5.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
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   0.096   8505  Z= 0.219
  Angle     :  0.877  10.956  11508  Z= 0.470
  Chirality :  0.054   0.269   1276
  Planarity :  0.007   0.094   1468
  Dihedral  : 15.281  88.402   3066
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  : 10.19 %
    Favored  : 89.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.69 (0.20), residues: 1042
  helix: -2.67 (0.19), residues: 369
  sheet: -2.86 (0.31), residues: 206
  loop : -3.55 (0.22), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 209 
 PHE   0.024   0.002   PHE B 151 
 TYR   0.025   0.002   TYR R 301 
 ARG   0.004   0.000   ARG N  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15123 (  327)
  hydrogen bonds       : angle       7.11329 (  936)
  SS BOND              : bond        0.00527 (    3)
  SS BOND              : angle       1.29584 (    6)
  covalent geometry    : bond        0.00402 ( 8501)
  covalent geometry    : angle       0.87669 (11502)
  Misc. bond           : bond        0.09587 (    1)

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

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

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 269
  time to evaluate  : 1.614 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.8849 (tt0) cc_final: 0.8580 (tt0)
REVERT: A  212 GLU cc_start: 0.8663 (tt0) cc_final: 0.8406 (tm-30)
REVERT: A  240 GLN cc_start: 0.9210 (tp-100) cc_final: 0.8953 (tp-100)
REVERT: A  267 LYS cc_start: 0.7444 (mmpt) cc_final: 0.7015 (ttpt)
REVERT: A  302 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8825 (mm110)
REVERT: A  326 GLN cc_start: 0.8268 (mm110) cc_final: 0.7871 (mm110)
REVERT: A  337 ASP cc_start: 0.8694 (t0) cc_final: 0.8387 (t0)
REVERT: B  125 ASN cc_start: 0.8847 (t0) cc_final: 0.8483 (t0)
REVERT: B  264 TYR cc_start: 0.8696 (m-80) cc_final: 0.8465 (m-10)
REVERT: B  289 TYR cc_start: 0.8239 (m-10) cc_final: 0.7900 (m-10)
REVERT: B  308 LEU cc_start: 0.9212 (mm) cc_final: 0.8645 (mt)
REVERT: B  333 ASP cc_start: 0.7945 (p0) cc_final: 0.7723 (p0)
REVERT: B  337 LYS cc_start: 0.8604 (mttt) cc_final: 0.8246 (mmtm)
REVERT: B  339 TRP cc_start: 0.8548 (m100) cc_final: 0.8082 (m100)
REVERT: G   51 ASP cc_start: 0.7973 (t0) cc_final: 0.7268 (t70)
REVERT: G   65 LYS cc_start: 0.8080 (mttt) cc_final: 0.7872 (mttm)
REVERT: N    6 GLU cc_start: 0.7804 (mp0) cc_final: 0.7425 (mp0)
REVERT: N   22 CYS cc_start: 0.7485 (t) cc_final: 0.7184 (t)
REVERT: N   76 LYS cc_start: 0.8751 (mmmt) cc_final: 0.8253 (mptt)
REVERT: N   77 ASN cc_start: 0.7865 (t0) cc_final: 0.7376 (t0)
REVERT: N  112 SER cc_start: 0.8901 (m) cc_final: 0.8679 (m)
REVERT: N  123 GLN cc_start: 0.8761 (tp-100) cc_final: 0.8281 (tp40)
REVERT: R   44 MET cc_start: 0.8555 (mmp) cc_final: 0.7571 (mmm)
REVERT: R   60 TYR cc_start: 0.8569 (t80) cc_final: 0.8301 (t80)
REVERT: R   78 ASN cc_start: 0.9040 (t0) cc_final: 0.8721 (t0)
REVERT: R  134 GLU cc_start: 0.8259 (pt0) cc_final: 0.7944 (pt0)
REVERT: R  147 ARG cc_start: 0.8304 (mmm-85) cc_final: 0.8092 (mmm-85)
REVERT: R  155 MET cc_start: 0.8488 (ttt) cc_final: 0.8274 (ttm)
REVERT: R  183 MET cc_start: 0.8629 (mmm) cc_final: 0.8298 (mmt)
REVERT: R  236 GLN cc_start: 0.8324 (mm-40) cc_final: 0.8092 (mm110)
REVERT: R  308 MET cc_start: 0.8655 (mmm) cc_final: 0.8046 (mmm)
REVERT: R  310 ASN cc_start: 0.8921 (t0) cc_final: 0.8233 (t0)
REVERT: R  317 MET cc_start: 0.8656 (mtp) cc_final: 0.8413 (mtp)
  outliers start: 1
  outliers final: 0
  residues processed: 269
  average time/residue: 0.2769
  time to fit residues: 100.9494
Evaluate side-chains
  205 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 1.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0980
   chunk 52 optimal weight:    0.9990
   chunk 41 optimal weight:    0.6980
   chunk 80 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   chunk 60 optimal weight:    3.9990
   chunk 93 optimal weight:    4.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 200 GLN
** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 318 HIS
B   6 GLN
B  13 GLN
B  62 HIS
B  91 HIS
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 HIS
B 268 ASN
R  73 ASN
R 310 ASN
R 312 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.111774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.095237 restraints weight = 16532.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 3.54
r_work: 0.3207 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.1700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8505  Z= 0.137
  Angle     :  0.625   8.557  11508  Z= 0.325
  Chirality :  0.042   0.180   1276
  Planarity :  0.004   0.050   1468
  Dihedral  :  5.769  69.617   1145
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 16.83 %
    Favored  : 81.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.08 (0.23), residues: 1042
  helix: -0.71 (0.26), residues: 360
  sheet: -2.27 (0.34), residues: 200
  loop : -3.01 (0.24), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 318 
 PHE   0.013   0.001   PHE B 151 
 TYR   0.019   0.002   TYR R 301 
 ARG   0.004   0.000   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03442 (  327)
  hydrogen bonds       : angle       4.88542 (  936)
  SS BOND              : bond        0.00241 (    3)
  SS BOND              : angle       1.30751 (    6)
  covalent geometry    : bond        0.00305 ( 8501)
  covalent geometry    : angle       0.62471 (11502)
  Misc. bond           : bond        0.00025 (    1)

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

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

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 232
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.9089 (tt0) cc_final: 0.8822 (tt0)
REVERT: A  182 GLU cc_start: 0.8466 (tt0) cc_final: 0.8236 (tp30)
REVERT: A  194 MET cc_start: 0.8871 (mtt) cc_final: 0.8182 (mtp)
REVERT: A  212 GLU cc_start: 0.9031 (tt0) cc_final: 0.8793 (tm-30)
REVERT: A  240 GLN cc_start: 0.8695 (tp-100) cc_final: 0.8315 (tp40)
REVERT: A  268 ASP cc_start: 0.7000 (m-30) cc_final: 0.6357 (p0)
REVERT: A  302 GLN cc_start: 0.9385 (mm-40) cc_final: 0.8907 (mm110)
REVERT: A  326 GLN cc_start: 0.8682 (mm110) cc_final: 0.8273 (mm110)
REVERT: A  337 ASP cc_start: 0.9341 (t0) cc_final: 0.8965 (t0)
REVERT: B   17 GLN cc_start: 0.7813 (mt0) cc_final: 0.7554 (tm-30)
REVERT: B   19 ARG cc_start: 0.7826 (tmt-80) cc_final: 0.6996 (ttm-80)
REVERT: B  101 MET cc_start: 0.9032 (mmm) cc_final: 0.8767 (mmm)
REVERT: B  125 ASN cc_start: 0.8941 (t0) cc_final: 0.8497 (t0)
REVERT: B  186 ASP cc_start: 0.8299 (p0) cc_final: 0.7922 (p0)
REVERT: B  228 ASP cc_start: 0.8825 (m-30) cc_final: 0.8096 (m-30)
REVERT: B  235 PHE cc_start: 0.8987 (t80) cc_final: 0.8628 (t80)
REVERT: B  262 MET cc_start: 0.8611 (mmm) cc_final: 0.8367 (mmt)
REVERT: B  293 ASN cc_start: 0.7761 (t0) cc_final: 0.7356 (t0)
REVERT: B  308 LEU cc_start: 0.9322 (mm) cc_final: 0.8960 (mp)
REVERT: B  337 LYS cc_start: 0.8323 (mttt) cc_final: 0.8099 (mmtm)
REVERT: B  339 TRP cc_start: 0.8875 (m100) cc_final: 0.8417 (m100)
REVERT: G   65 LYS cc_start: 0.7868 (mttt) cc_final: 0.7634 (mttm)
REVERT: N   22 CYS cc_start: 0.7783 (t) cc_final: 0.7471 (t)
REVERT: N   76 LYS cc_start: 0.8892 (mmmt) cc_final: 0.8239 (mptt)
REVERT: N   77 ASN cc_start: 0.8243 (t0) cc_final: 0.7706 (t0)
REVERT: N  123 GLN cc_start: 0.8981 (tp-100) cc_final: 0.8419 (tp-100)
REVERT: R   60 TYR cc_start: 0.8604 (t80) cc_final: 0.8351 (t80)
REVERT: R   78 ASN cc_start: 0.9099 (t0) cc_final: 0.8743 (t0)
REVERT: R  147 ARG cc_start: 0.8862 (mmm-85) cc_final: 0.8251 (tpp80)
REVERT: R  155 MET cc_start: 0.8714 (ttt) cc_final: 0.8412 (ttm)
REVERT: R  183 MET cc_start: 0.8696 (mmm) cc_final: 0.8366 (tpp)
REVERT: R  287 PHE cc_start: 0.9099 (t80) cc_final: 0.8853 (t80)
REVERT: R  308 MET cc_start: 0.8807 (mmm) cc_final: 0.8254 (mmm)
REVERT: R  310 ASN cc_start: 0.9270 (t0) cc_final: 0.8467 (t0)
REVERT: R  317 MET cc_start: 0.8894 (mtp) cc_final: 0.8617 (mtp)
  outliers start: 16
  outliers final: 8
  residues processed: 243
  average time/residue: 0.2020
  time to fit residues: 66.6818
Evaluate side-chains
  213 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 205
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain R residue   11 VAL
Chi-restraints excluded: chain R residue   64 GLN
Chi-restraints excluded: chain R residue   85 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 61 optimal weight:    5.9990
   chunk 94 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0980
   chunk 62 optimal weight:    0.9990
   chunk 97 optimal weight:    2.9990
   chunk 86 optimal weight:    0.0050
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 236 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.115647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.099858 restraints weight = 16670.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 3.39
r_work: 0.3345 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.2114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8505  Z= 0.114
  Angle     :  0.604   9.432  11508  Z= 0.307
  Chirality :  0.042   0.166   1276
  Planarity :  0.004   0.046   1468
  Dihedral  :  5.069  56.989   1145
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 17.28 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.32 (0.25), residues: 1042
  helix:  0.09 (0.27), residues: 367
  sheet: -1.87 (0.35), residues: 198
  loop : -2.74 (0.25), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 278 
 PHE   0.028   0.001   PHE R 293 
 TYR   0.019   0.001   TYR R 178 
 ARG   0.003   0.000   ARG A 201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03052 (  327)
  hydrogen bonds       : angle       4.46999 (  936)
  SS BOND              : bond        0.00498 (    3)
  SS BOND              : angle       1.68011 (    6)
  covalent geometry    : bond        0.00261 ( 8501)
  covalent geometry    : angle       0.60263 (11502)
  Misc. bond           : bond        0.00011 (    1)

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

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

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 212
  time to evaluate  : 1.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.9070 (tt0) cc_final: 0.8807 (tt0)
REVERT: A   24 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7567 (pp20)
REVERT: A  194 MET cc_start: 0.8927 (mtt) cc_final: 0.8726 (ttm)
REVERT: A  202 ASP cc_start: 0.8738 (t0) cc_final: 0.8484 (t0)
REVERT: A  212 GLU cc_start: 0.8998 (tt0) cc_final: 0.8795 (tm-30)
REVERT: A  240 GLN cc_start: 0.8874 (tp-100) cc_final: 0.8490 (tp-100)
REVERT: A  267 LYS cc_start: 0.8234 (mmtm) cc_final: 0.7968 (mmtm)
REVERT: A  268 ASP cc_start: 0.6941 (m-30) cc_final: 0.6427 (p0)
REVERT: A  302 GLN cc_start: 0.9332 (mm-40) cc_final: 0.8886 (mm-40)
REVERT: A  319 MET cc_start: 0.7685 (mmm) cc_final: 0.7385 (mmm)
REVERT: A  326 GLN cc_start: 0.8600 (mm110) cc_final: 0.8129 (mm110)
REVERT: A  337 ASP cc_start: 0.9242 (t0) cc_final: 0.8953 (t0)
REVERT: B   17 GLN cc_start: 0.7711 (mt0) cc_final: 0.7510 (tm-30)
REVERT: B   19 ARG cc_start: 0.7709 (tmt-80) cc_final: 0.6960 (ttm-80)
REVERT: B  125 ASN cc_start: 0.8959 (t0) cc_final: 0.8492 (t0)
REVERT: B  186 ASP cc_start: 0.8344 (p0) cc_final: 0.8013 (p0)
REVERT: B  220 GLN cc_start: 0.8568 (mt0) cc_final: 0.8160 (tt0)
REVERT: B  228 ASP cc_start: 0.8752 (m-30) cc_final: 0.8131 (m-30)
REVERT: B  261 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9098 (mm)
REVERT: B  293 ASN cc_start: 0.7835 (t0) cc_final: 0.7481 (t0)
REVERT: B  308 LEU cc_start: 0.9289 (mm) cc_final: 0.8827 (mp)
REVERT: B  333 ASP cc_start: 0.8486 (p0) cc_final: 0.8059 (p0)
REVERT: B  339 TRP cc_start: 0.8890 (m100) cc_final: 0.8508 (m100)
REVERT: N   32 TYR cc_start: 0.8422 (m-10) cc_final: 0.8111 (m-10)
REVERT: N   76 LYS cc_start: 0.8850 (mmmt) cc_final: 0.8255 (mptt)
REVERT: N   77 ASN cc_start: 0.8190 (t0) cc_final: 0.7683 (t0)
REVERT: N  108 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.8048 (m-80)
REVERT: N  123 GLN cc_start: 0.9017 (tp-100) cc_final: 0.8492 (tp40)
REVERT: R   60 TYR cc_start: 0.8652 (t80) cc_final: 0.8442 (t80)
REVERT: R   78 ASN cc_start: 0.9154 (t0) cc_final: 0.8778 (t0)
REVERT: R   86 MET cc_start: 0.8707 (mtp) cc_final: 0.8500 (mtp)
REVERT: R  147 ARG cc_start: 0.8832 (mmm-85) cc_final: 0.8305 (tpp80)
REVERT: R  155 MET cc_start: 0.8687 (ttt) cc_final: 0.8247 (mtp)
REVERT: R  183 MET cc_start: 0.8791 (mmm) cc_final: 0.8444 (tpp)
REVERT: R  308 MET cc_start: 0.8823 (mmm) cc_final: 0.8318 (mmm)
REVERT: R  310 ASN cc_start: 0.9242 (t0) cc_final: 0.8458 (t0)
REVERT: R  317 MET cc_start: 0.8819 (mtp) cc_final: 0.8590 (mtp)
  outliers start: 21
  outliers final: 13
  residues processed: 227
  average time/residue: 0.2807
  time to fit residues: 86.3151
Evaluate side-chains
  213 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 198
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain R residue    1 MET
Chi-restraints excluded: chain R residue   22 SER
Chi-restraints excluded: chain R residue   64 GLN
Chi-restraints excluded: chain R residue   70 THR
Chi-restraints excluded: chain R residue   85 PHE
Chi-restraints excluded: chain R residue  163 MET
Chi-restraints excluded: chain R residue  307 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   chunk 95 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 72 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9990
   chunk 81 optimal weight:    0.6980
   chunk 87 optimal weight:    8.9990
   chunk 16 optimal weight:    8.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 209 HIS
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN
R 278 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.115550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.099002 restraints weight = 16795.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 3.43
r_work: 0.3331 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.2403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8505  Z= 0.119
  Angle     :  0.588   7.336  11508  Z= 0.300
  Chirality :  0.042   0.162   1276
  Planarity :  0.004   0.045   1468
  Dihedral  :  4.841  56.103   1145
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 19.16 %
    Favored  : 77.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.91 (0.26), residues: 1042
  helix:  0.44 (0.28), residues: 374
  sheet: -1.59 (0.36), residues: 197
  loop : -2.59 (0.27), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.006   0.001   HIS R 278 
 PHE   0.020   0.001   PHE R 287 
 TYR   0.017   0.001   TYR R 301 
 ARG   0.003   0.000   ARG A 201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02965 (  327)
  hydrogen bonds       : angle       4.28384 (  936)
  SS BOND              : bond        0.00362 (    3)
  SS BOND              : angle       1.86850 (    6)
  covalent geometry    : bond        0.00272 ( 8501)
  covalent geometry    : angle       0.58646 (11502)
  Misc. bond           : bond        0.00020 (    1)

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

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

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 214
  time to evaluate  : 2.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.9067 (tt0) cc_final: 0.8809 (tt0)
REVERT: A   24 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7609 (pp20)
REVERT: A   25 LYS cc_start: 0.8941 (mmmt) cc_final: 0.8712 (mtmm)
REVERT: A  194 MET cc_start: 0.8979 (mtt) cc_final: 0.8691 (ttm)
REVERT: A  202 ASP cc_start: 0.8816 (t0) cc_final: 0.8531 (t0)
REVERT: A  212 GLU cc_start: 0.9029 (tt0) cc_final: 0.8803 (tm-30)
REVERT: A  240 GLN cc_start: 0.8908 (tp-100) cc_final: 0.8358 (tp-100)
REVERT: A  268 ASP cc_start: 0.7009 (m-30) cc_final: 0.6512 (p0)
REVERT: A  302 GLN cc_start: 0.9310 (mm-40) cc_final: 0.8863 (mm110)
REVERT: A  326 GLN cc_start: 0.8660 (mm110) cc_final: 0.8190 (mm110)
REVERT: B   19 ARG cc_start: 0.7756 (tmt-80) cc_final: 0.7002 (ttm-80)
REVERT: B  125 ASN cc_start: 0.9023 (t0) cc_final: 0.8473 (t0)
REVERT: B  293 ASN cc_start: 0.7927 (t0) cc_final: 0.7440 (t0)
REVERT: B  339 TRP cc_start: 0.8910 (m100) cc_final: 0.7511 (m-90)
REVERT: G   42 ASP cc_start: 0.8618 (m-30) cc_final: 0.8318 (m-30)
REVERT: G   46 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8251 (tp30)
REVERT: N    6 GLU cc_start: 0.7684 (mp0) cc_final: 0.7015 (mm-30)
REVERT: N   22 CYS cc_start: 0.8028 (t) cc_final: 0.7793 (t)
REVERT: N   76 LYS cc_start: 0.8841 (mmmt) cc_final: 0.8255 (mptt)
REVERT: N   77 ASN cc_start: 0.8265 (t0) cc_final: 0.7727 (t0)
REVERT: N  108 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.8097 (m-80)
REVERT: N  123 GLN cc_start: 0.8968 (tp-100) cc_final: 0.8460 (tp40)
REVERT: R   60 TYR cc_start: 0.8649 (t80) cc_final: 0.8411 (t80)
REVERT: R   78 ASN cc_start: 0.9141 (t0) cc_final: 0.8772 (t0)
REVERT: R   86 MET cc_start: 0.8691 (mtp) cc_final: 0.8490 (mtp)
REVERT: R  147 ARG cc_start: 0.8869 (mmm-85) cc_final: 0.8336 (tpp80)
REVERT: R  155 MET cc_start: 0.8769 (ttt) cc_final: 0.8322 (mtp)
REVERT: R  183 MET cc_start: 0.8793 (mmm) cc_final: 0.8430 (tpp)
REVERT: R  308 MET cc_start: 0.8855 (mmm) cc_final: 0.8392 (mmm)
REVERT: R  310 ASN cc_start: 0.9276 (t0) cc_final: 0.8457 (t0)
REVERT: R  317 MET cc_start: 0.8826 (mtp) cc_final: 0.8575 (mtp)
  outliers start: 28
  outliers final: 16
  residues processed: 234
  average time/residue: 0.3328
  time to fit residues: 109.7604
Evaluate side-chains
  213 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 196
  time to evaluate  : 2.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   53 GLN
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   11 VAL
Chi-restraints excluded: chain R residue   22 SER
Chi-restraints excluded: chain R residue   64 GLN
Chi-restraints excluded: chain R residue   70 THR
Chi-restraints excluded: chain R residue   85 PHE
Chi-restraints excluded: chain R residue  307 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 23 optimal weight:    8.9990
   chunk 37 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 14 optimal weight:   10.0000
   chunk 61 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 88 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 183 HIS
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 311 HIS
R  28 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.112124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.095715 restraints weight = 16925.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 3.39
r_work: 0.3273 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.2568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8505  Z= 0.173
  Angle     :  0.633   8.427  11508  Z= 0.323
  Chirality :  0.043   0.163   1276
  Planarity :  0.004   0.045   1468
  Dihedral  :  4.899  52.237   1145
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 20.93 %
    Favored  : 75.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.83 (0.26), residues: 1042
  helix:  0.55 (0.28), residues: 380
  sheet: -1.47 (0.36), residues: 197
  loop : -2.66 (0.27), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.006   0.001   HIS B 266 
 PHE   0.020   0.001   PHE R 287 
 TYR   0.022   0.002   TYR A 283 
 ARG   0.007   0.000   ARG A 205 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03146 (  327)
  hydrogen bonds       : angle       4.33980 (  936)
  SS BOND              : bond        0.00451 (    3)
  SS BOND              : angle       1.43193 (    6)
  covalent geometry    : bond        0.00397 ( 8501)
  covalent geometry    : angle       0.63201 (11502)
  Misc. bond           : bond        0.00036 (    1)

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

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

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 198
  time to evaluate  : 1.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.9093 (tt0) cc_final: 0.8851 (tt0)
REVERT: A   24 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7592 (pp20)
REVERT: A   25 LYS cc_start: 0.8992 (mmmt) cc_final: 0.8680 (mtmm)
REVERT: A  202 ASP cc_start: 0.8814 (t0) cc_final: 0.8520 (t0)
REVERT: A  212 GLU cc_start: 0.9108 (tt0) cc_final: 0.8823 (tm-30)
REVERT: A  240 GLN cc_start: 0.8962 (tp-100) cc_final: 0.8354 (tp-100)
REVERT: A  268 ASP cc_start: 0.7000 (m-30) cc_final: 0.6694 (p0)
REVERT: A  302 GLN cc_start: 0.9341 (mm-40) cc_final: 0.8907 (mm110)
REVERT: A  326 GLN cc_start: 0.8696 (mm110) cc_final: 0.8228 (mm110)
REVERT: B   58 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8642 (pt)
REVERT: B  215 GLU cc_start: 0.7487 (pt0) cc_final: 0.7239 (tm-30)
REVERT: B  293 ASN cc_start: 0.7965 (t0) cc_final: 0.7466 (t0)
REVERT: B  339 TRP cc_start: 0.8897 (m100) cc_final: 0.8599 (m100)
REVERT: G   46 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8279 (tp30)
REVERT: N    6 GLU cc_start: 0.7621 (mp0) cc_final: 0.6944 (mp0)
REVERT: N   22 CYS cc_start: 0.8034 (t) cc_final: 0.7819 (t)
REVERT: N   76 LYS cc_start: 0.8877 (mmmt) cc_final: 0.8285 (mptt)
REVERT: N   77 ASN cc_start: 0.8326 (t0) cc_final: 0.7773 (t0)
REVERT: N  123 GLN cc_start: 0.9002 (tp-100) cc_final: 0.8502 (tp-100)
REVERT: R   60 TYR cc_start: 0.8653 (t80) cc_final: 0.8417 (t80)
REVERT: R   78 ASN cc_start: 0.9176 (t0) cc_final: 0.8852 (t0)
REVERT: R  147 ARG cc_start: 0.8902 (mmm-85) cc_final: 0.8339 (tpp80)
REVERT: R  155 MET cc_start: 0.8813 (ttt) cc_final: 0.8512 (ttm)
REVERT: R  183 MET cc_start: 0.8822 (mmm) cc_final: 0.8447 (tpp)
REVERT: R  308 MET cc_start: 0.8891 (mmm) cc_final: 0.8414 (mmm)
REVERT: R  310 ASN cc_start: 0.9313 (t0) cc_final: 0.8501 (t0)
REVERT: R  317 MET cc_start: 0.8817 (mtp) cc_final: 0.8484 (mtp)
  outliers start: 32
  outliers final: 20
  residues processed: 222
  average time/residue: 0.2638
  time to fit residues: 82.1481
Evaluate side-chains
  208 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 187
  time to evaluate  : 1.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   28 LEU
Chi-restraints excluded: chain G residue   65 LYS
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   53 GLN
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   11 VAL
Chi-restraints excluded: chain R residue   22 SER
Chi-restraints excluded: chain R residue   64 GLN
Chi-restraints excluded: chain R residue   85 PHE
Chi-restraints excluded: chain R residue  307 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 70 optimal weight:    0.6980
   chunk 30 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 85 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 12 optimal weight:    4.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B 183 HIS
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.113982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.097577 restraints weight = 16956.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 3.41
r_work: 0.3303 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8505  Z= 0.123
  Angle     :  0.616   9.910  11508  Z= 0.314
  Chirality :  0.042   0.160   1276
  Planarity :  0.004   0.045   1468
  Dihedral  :  4.806  56.254   1145
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 21.48 %
    Favored  : 74.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.26), residues: 1042
  helix:  0.66 (0.27), residues: 383
  sheet: -1.24 (0.37), residues: 197
  loop : -2.44 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.023   0.001   PHE R 293 
 TYR   0.029   0.002   TYR A 283 
 ARG   0.006   0.000   ARG A 205 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03023 (  327)
  hydrogen bonds       : angle       4.25956 (  936)
  SS BOND              : bond        0.00318 (    3)
  SS BOND              : angle       1.12915 (    6)
  covalent geometry    : bond        0.00286 ( 8501)
  covalent geometry    : angle       0.61607 (11502)
  Misc. bond           : bond        0.00015 (    1)

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

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

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 202
  time to evaluate  : 1.771 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.9092 (tt0) cc_final: 0.8846 (tt0)
REVERT: A   24 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7594 (pp20)
REVERT: A   25 LYS cc_start: 0.8959 (mmmt) cc_final: 0.8656 (mtmm)
REVERT: A  202 ASP cc_start: 0.8844 (t0) cc_final: 0.8504 (t0)
REVERT: A  212 GLU cc_start: 0.9064 (tt0) cc_final: 0.8798 (tm-30)
REVERT: A  240 GLN cc_start: 0.8980 (tp-100) cc_final: 0.8354 (tp-100)
REVERT: A  268 ASP cc_start: 0.6988 (m-30) cc_final: 0.6767 (p0)
REVERT: A  302 GLN cc_start: 0.9310 (mm-40) cc_final: 0.8866 (mm110)
REVERT: A  319 MET cc_start: 0.8108 (mmm) cc_final: 0.7859 (tpp)
REVERT: A  326 GLN cc_start: 0.8728 (mm110) cc_final: 0.8268 (mm110)
REVERT: B   57 LYS cc_start: 0.8981 (ptpp) cc_final: 0.8570 (ptmm)
REVERT: B   58 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8571 (pt)
REVERT: B  215 GLU cc_start: 0.7396 (pt0) cc_final: 0.7186 (tm-30)
REVERT: B  220 GLN cc_start: 0.8565 (mt0) cc_final: 0.8154 (tt0)
REVERT: B  228 ASP cc_start: 0.8834 (m-30) cc_final: 0.8248 (m-30)
REVERT: B  264 TYR cc_start: 0.8900 (m-10) cc_final: 0.8621 (m-10)
REVERT: B  289 TYR cc_start: 0.8047 (m-10) cc_final: 0.7350 (m-10)
REVERT: B  293 ASN cc_start: 0.7987 (t0) cc_final: 0.7360 (t0)
REVERT: B  339 TRP cc_start: 0.8905 (m100) cc_final: 0.8601 (m100)
REVERT: G   42 ASP cc_start: 0.8605 (m-30) cc_final: 0.8291 (m-30)
REVERT: G   46 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8310 (tp30)
REVERT: N   73 ASP cc_start: 0.6747 (t0) cc_final: 0.6320 (t0)
REVERT: N   76 LYS cc_start: 0.8842 (mmmt) cc_final: 0.8020 (mppt)
REVERT: N   77 ASN cc_start: 0.8329 (t0) cc_final: 0.7797 (t0)
REVERT: N  108 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.8115 (m-80)
REVERT: R   30 TYR cc_start: 0.8181 (p90) cc_final: 0.7849 (p90)
REVERT: R   60 TYR cc_start: 0.8637 (t80) cc_final: 0.8430 (t80)
REVERT: R   78 ASN cc_start: 0.9154 (t0) cc_final: 0.8809 (t0)
REVERT: R  147 ARG cc_start: 0.8881 (mmm-85) cc_final: 0.8240 (tpp80)
REVERT: R  155 MET cc_start: 0.8736 (ttt) cc_final: 0.8390 (ttm)
REVERT: R  183 MET cc_start: 0.8782 (mmm) cc_final: 0.8384 (tpp)
REVERT: R  308 MET cc_start: 0.8861 (mmm) cc_final: 0.8410 (mmm)
REVERT: R  310 ASN cc_start: 0.9271 (t0) cc_final: 0.8536 (t0)
REVERT: R  317 MET cc_start: 0.8827 (mtp) cc_final: 0.8494 (mtp)
  outliers start: 33
  outliers final: 22
  residues processed: 226
  average time/residue: 0.2265
  time to fit residues: 72.9020
Evaluate side-chains
  216 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 192
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   28 LEU
Chi-restraints excluded: chain G residue   65 LYS
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   53 GLN
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue   11 VAL
Chi-restraints excluded: chain R residue   22 SER
Chi-restraints excluded: chain R residue   64 GLN
Chi-restraints excluded: chain R residue   70 THR
Chi-restraints excluded: chain R residue   85 PHE
Chi-restraints excluded: chain R residue  104 VAL
Chi-restraints excluded: chain R residue  307 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 14 optimal weight:    9.9990
   chunk 71 optimal weight:    3.9990
   chunk 102 optimal weight:    3.9990
   chunk 46 optimal weight:    0.2980
   chunk 30 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.8588

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

Flipped N/Q/H residues before XYZ refinement:
** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   9 GLN
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.110647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.094351 restraints weight = 17201.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 3.40
r_work: 0.3254 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.2840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8505  Z= 0.191
  Angle     :  0.674   9.183  11508  Z= 0.344
  Chirality :  0.044   0.168   1276
  Planarity :  0.004   0.044   1468
  Dihedral  :  4.879  50.525   1145
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.29 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 21.71 %
    Favored  : 74.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.56 (0.27), residues: 1042
  helix:  0.76 (0.28), residues: 381
  sheet: -1.40 (0.36), residues: 207
  loop : -2.46 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.009   0.001   HIS B 183 
 PHE   0.026   0.002   PHE B 235 
 TYR   0.027   0.002   TYR A 283 
 ARG   0.006   0.000   ARG A 205 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03344 (  327)
  hydrogen bonds       : angle       4.39451 (  936)
  SS BOND              : bond        0.00412 (    3)
  SS BOND              : angle       1.21359 (    6)
  covalent geometry    : bond        0.00438 ( 8501)
  covalent geometry    : angle       0.67353 (11502)
  Misc. bond           : bond        0.00044 (    1)

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

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

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 194
  time to evaluate  : 1.022 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.9112 (tt0) cc_final: 0.8904 (tt0)
REVERT: A   24 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7630 (pp20)
REVERT: A  202 ASP cc_start: 0.8898 (t0) cc_final: 0.8512 (t0)
REVERT: A  212 GLU cc_start: 0.9140 (tt0) cc_final: 0.8758 (tm-30)
REVERT: A  240 GLN cc_start: 0.9031 (tp-100) cc_final: 0.8400 (tp-100)
REVERT: A  268 ASP cc_start: 0.7135 (m-30) cc_final: 0.6810 (p0)
REVERT: A  298 TYR cc_start: 0.8864 (t80) cc_final: 0.8443 (t80)
REVERT: A  326 GLN cc_start: 0.8773 (mm110) cc_final: 0.8301 (mm110)
REVERT: B   19 ARG cc_start: 0.7755 (tmt-80) cc_final: 0.7091 (ttm110)
REVERT: B   58 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8688 (pt)
REVERT: B  228 ASP cc_start: 0.8903 (m-30) cc_final: 0.8345 (m-30)
REVERT: B  264 TYR cc_start: 0.8940 (m-10) cc_final: 0.8654 (m-10)
REVERT: B  293 ASN cc_start: 0.8079 (t0) cc_final: 0.7610 (t0)
REVERT: B  339 TRP cc_start: 0.8910 (m100) cc_final: 0.8645 (m100)
REVERT: N   76 LYS cc_start: 0.8879 (mmmt) cc_final: 0.8188 (mptt)
REVERT: N   77 ASN cc_start: 0.8471 (t0) cc_final: 0.7906 (t0)
REVERT: N  123 GLN cc_start: 0.9096 (tp-100) cc_final: 0.8672 (tp40)
REVERT: R   60 TYR cc_start: 0.8636 (t80) cc_final: 0.8385 (t80)
REVERT: R   69 ARG cc_start: 0.8992 (mtm-85) cc_final: 0.8571 (mtm-85)
REVERT: R   78 ASN cc_start: 0.9182 (t0) cc_final: 0.8914 (t0)
REVERT: R  147 ARG cc_start: 0.8892 (mmm-85) cc_final: 0.8341 (tpp80)
REVERT: R  155 MET cc_start: 0.8844 (ttt) cc_final: 0.8518 (ttm)
REVERT: R  183 MET cc_start: 0.8795 (mmm) cc_final: 0.8382 (tpp)
REVERT: R  308 MET cc_start: 0.8947 (mmm) cc_final: 0.8462 (mmm)
REVERT: R  310 ASN cc_start: 0.9302 (t0) cc_final: 0.8527 (t0)
REVERT: R  317 MET cc_start: 0.8851 (mtp) cc_final: 0.8516 (mtp)
  outliers start: 34
  outliers final: 23
  residues processed: 217
  average time/residue: 0.2507
  time to fit residues: 74.8627
Evaluate side-chains
  205 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 181
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   28 LEU
Chi-restraints excluded: chain G residue   65 LYS
Chi-restraints excluded: chain G residue   67 LEU
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   53 GLN
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue   11 VAL
Chi-restraints excluded: chain R residue   22 SER
Chi-restraints excluded: chain R residue   64 GLN
Chi-restraints excluded: chain R residue   85 PHE
Chi-restraints excluded: chain R residue  104 VAL
Chi-restraints excluded: chain R residue  307 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 3 optimal weight:    0.0170
   chunk 30 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 78 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 91 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 72 optimal weight:    0.0170
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.9460

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.113353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.097001 restraints weight = 16964.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 3.41
r_work: 0.3295 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.2947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8505  Z= 0.133
  Angle     :  0.657   9.105  11508  Z= 0.333
  Chirality :  0.043   0.160   1276
  Planarity :  0.004   0.042   1468
  Dihedral  :  4.841  55.873   1145
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 23.59 %
    Favored  : 73.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.27), residues: 1042
  helix:  0.87 (0.28), residues: 372
  sheet: -1.17 (0.37), residues: 201
  loop : -2.21 (0.28), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP N  47 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.026   0.001   PHE B 235 
 TYR   0.025   0.002   TYR A 283 
 ARG   0.005   0.000   ARG A 205 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03153 (  327)
  hydrogen bonds       : angle       4.31473 (  936)
  SS BOND              : bond        0.00302 (    3)
  SS BOND              : angle       0.93915 (    6)
  covalent geometry    : bond        0.00313 ( 8501)
  covalent geometry    : angle       0.65666 (11502)
  Misc. bond           : bond        0.00020 (    1)

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

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

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 197
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.9106 (tt0) cc_final: 0.8897 (tt0)
REVERT: A   24 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7542 (pp20)
REVERT: A  202 ASP cc_start: 0.8888 (t0) cc_final: 0.8537 (t0)
REVERT: A  212 GLU cc_start: 0.9065 (tt0) cc_final: 0.8749 (tm-30)
REVERT: A  240 GLN cc_start: 0.8985 (tp-100) cc_final: 0.8343 (tp-100)
REVERT: A  268 ASP cc_start: 0.7111 (m-30) cc_final: 0.6708 (p0)
REVERT: A  298 TYR cc_start: 0.8833 (t80) cc_final: 0.8282 (t80)
REVERT: A  326 GLN cc_start: 0.8823 (mm110) cc_final: 0.8394 (mm110)
REVERT: B   57 LYS cc_start: 0.8890 (ptpp) cc_final: 0.8421 (ptmm)
REVERT: B  228 ASP cc_start: 0.8849 (m-30) cc_final: 0.8345 (m-30)
REVERT: B  264 TYR cc_start: 0.8899 (m-10) cc_final: 0.8628 (m-10)
REVERT: B  289 TYR cc_start: 0.7929 (m-10) cc_final: 0.7253 (m-10)
REVERT: B  293 ASN cc_start: 0.8025 (t0) cc_final: 0.7404 (t0)
REVERT: B  308 LEU cc_start: 0.9102 (mp) cc_final: 0.8828 (mt)
REVERT: B  333 ASP cc_start: 0.8531 (p0) cc_final: 0.8253 (p0)
REVERT: B  339 TRP cc_start: 0.8939 (m100) cc_final: 0.8642 (m100)
REVERT: G   42 ASP cc_start: 0.8648 (m-30) cc_final: 0.8343 (m-30)
REVERT: G   46 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8322 (tp30)
REVERT: N    6 GLU cc_start: 0.7731 (mp0) cc_final: 0.7049 (mp0)
REVERT: N   73 ASP cc_start: 0.6663 (t0) cc_final: 0.6234 (t0)
REVERT: N   76 LYS cc_start: 0.8810 (mmmt) cc_final: 0.8003 (mppt)
REVERT: N   77 ASN cc_start: 0.8425 (t0) cc_final: 0.7897 (t0)
REVERT: N  123 GLN cc_start: 0.9098 (tp-100) cc_final: 0.8681 (tp40)
REVERT: R   60 TYR cc_start: 0.8607 (t80) cc_final: 0.8246 (t80)
REVERT: R   64 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.7793 (mt0)
REVERT: R   69 ARG cc_start: 0.8931 (mtm-85) cc_final: 0.8501 (mtt90)
REVERT: R   78 ASN cc_start: 0.9153 (t0) cc_final: 0.8883 (t0)
REVERT: R  147 ARG cc_start: 0.8863 (mmm-85) cc_final: 0.8209 (tpp80)
REVERT: R  155 MET cc_start: 0.8799 (ttt) cc_final: 0.8461 (ttm)
REVERT: R  183 MET cc_start: 0.8758 (mmm) cc_final: 0.8349 (tpp)
REVERT: R  308 MET cc_start: 0.8942 (mmm) cc_final: 0.8451 (mmm)
REVERT: R  310 ASN cc_start: 0.9291 (t0) cc_final: 0.8518 (t0)
REVERT: R  317 MET cc_start: 0.8867 (mtp) cc_final: 0.8524 (mtp)
  outliers start: 29
  outliers final: 23
  residues processed: 217
  average time/residue: 0.2512
  time to fit residues: 76.5446
Evaluate side-chains
  214 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 190
  time to evaluate  : 1.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   28 LEU
Chi-restraints excluded: chain G residue   65 LYS
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   53 GLN
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue   11 VAL
Chi-restraints excluded: chain R residue   22 SER
Chi-restraints excluded: chain R residue   64 GLN
Chi-restraints excluded: chain R residue   70 THR
Chi-restraints excluded: chain R residue   85 PHE
Chi-restraints excluded: chain R residue  104 VAL
Chi-restraints excluded: chain R residue  307 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 22 optimal weight:    7.9990
   chunk 88 optimal weight:    0.9980
   chunk 96 optimal weight:    0.9990
   chunk 69 optimal weight:    0.0040
   chunk 62 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 26 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   overall best weight:    0.7592

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

Flipped N/Q/H residues before XYZ refinement:
A 302 GLN
B 183 HIS
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.114535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.097984 restraints weight = 17047.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 3.46
r_work: 0.3309 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.3020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8505  Z= 0.126
  Angle     :  0.666   9.233  11508  Z= 0.337
  Chirality :  0.043   0.159   1276
  Planarity :  0.003   0.041   1468
  Dihedral  :  4.767  53.940   1145
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 24.03 %
    Favored  : 72.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.27), residues: 1042
  helix:  0.99 (0.28), residues: 364
  sheet: -1.03 (0.38), residues: 199
  loop : -2.12 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP N  47 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.026   0.001   PHE B 235 
 TYR   0.024   0.002   TYR A 283 
 ARG   0.005   0.000   ARG A 205 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03082 (  327)
  hydrogen bonds       : angle       4.31500 (  936)
  SS BOND              : bond        0.00277 (    3)
  SS BOND              : angle       2.18464 (    6)
  covalent geometry    : bond        0.00293 ( 8501)
  covalent geometry    : angle       0.66433 (11502)
  Misc. bond           : bond        0.00012 (    1)

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

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

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 199
  time to evaluate  : 1.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.9099 (tt0) cc_final: 0.8897 (tt0)
REVERT: A  202 ASP cc_start: 0.8895 (t0) cc_final: 0.8521 (t0)
REVERT: A  212 GLU cc_start: 0.9073 (tt0) cc_final: 0.8766 (tm-30)
REVERT: A  240 GLN cc_start: 0.8961 (tp-100) cc_final: 0.8302 (tp-100)
REVERT: A  268 ASP cc_start: 0.7080 (m-30) cc_final: 0.6724 (p0)
REVERT: A  298 TYR cc_start: 0.8879 (t80) cc_final: 0.8508 (t80)
REVERT: A  326 GLN cc_start: 0.8847 (mm110) cc_final: 0.8404 (mm110)
REVERT: B   57 LYS cc_start: 0.8800 (ptpp) cc_final: 0.8337 (ptmm)
REVERT: B   58 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8639 (pt)
REVERT: B  215 GLU cc_start: 0.8061 (pt0) cc_final: 0.7701 (tm-30)
REVERT: B  220 GLN cc_start: 0.8588 (mt0) cc_final: 0.8114 (tt0)
REVERT: B  228 ASP cc_start: 0.8842 (m-30) cc_final: 0.8342 (m-30)
REVERT: B  264 TYR cc_start: 0.8950 (m-10) cc_final: 0.8633 (m-10)
REVERT: B  289 TYR cc_start: 0.7898 (m-10) cc_final: 0.7190 (m-10)
REVERT: B  293 ASN cc_start: 0.8084 (t0) cc_final: 0.7495 (t0)
REVERT: B  308 LEU cc_start: 0.9108 (mp) cc_final: 0.8814 (mt)
REVERT: B  333 ASP cc_start: 0.8490 (p0) cc_final: 0.8247 (p0)
REVERT: B  339 TRP cc_start: 0.8941 (m100) cc_final: 0.8649 (m100)
REVERT: G   17 MET cc_start: 0.6700 (mmm) cc_final: 0.6397 (mmp)
REVERT: G   46 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8076 (tp30)
REVERT: N   22 CYS cc_start: 0.8152 (t) cc_final: 0.7829 (t)
REVERT: N   27 PHE cc_start: 0.9020 (p90) cc_final: 0.8594 (p90)
REVERT: N   73 ASP cc_start: 0.6682 (t0) cc_final: 0.6247 (t0)
REVERT: N   76 LYS cc_start: 0.8841 (mmmt) cc_final: 0.7972 (mppt)
REVERT: N   77 ASN cc_start: 0.8364 (t0) cc_final: 0.7855 (t0)
REVERT: N  123 GLN cc_start: 0.9014 (tp-100) cc_final: 0.8609 (tp40)
REVERT: R   60 TYR cc_start: 0.8595 (t80) cc_final: 0.8291 (t80)
REVERT: R   64 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.7795 (mt0)
REVERT: R   69 ARG cc_start: 0.8892 (mtm-85) cc_final: 0.8484 (mtt90)
REVERT: R   78 ASN cc_start: 0.9125 (t0) cc_final: 0.8848 (t0)
REVERT: R  147 ARG cc_start: 0.8864 (mmm-85) cc_final: 0.8173 (tpp80)
REVERT: R  155 MET cc_start: 0.8790 (ttt) cc_final: 0.8450 (ttm)
REVERT: R  183 MET cc_start: 0.8747 (mmm) cc_final: 0.8348 (tpp)
REVERT: R  310 ASN cc_start: 0.9252 (t0) cc_final: 0.8502 (t0)
REVERT: R  317 MET cc_start: 0.8899 (mtp) cc_final: 0.8645 (ttp)
  outliers start: 27
  outliers final: 21
  residues processed: 218
  average time/residue: 0.2484
  time to fit residues: 75.9144
Evaluate side-chains
  217 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 194
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   28 LEU
Chi-restraints excluded: chain G residue   65 LYS
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   53 GLN
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue   11 VAL
Chi-restraints excluded: chain R residue   22 SER
Chi-restraints excluded: chain R residue   64 GLN
Chi-restraints excluded: chain R residue   70 THR
Chi-restraints excluded: chain R residue   85 PHE
Chi-restraints excluded: chain R residue  104 VAL
Chi-restraints excluded: chain R residue  307 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 80 optimal weight:    0.0870
   chunk 49 optimal weight:    0.7980
   chunk 39 optimal weight:    0.4980
   chunk 44 optimal weight:    9.9990
   chunk 21 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 24 optimal weight:    0.3980
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 312 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.115427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.098938 restraints weight = 16965.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 3.47
r_work: 0.3328 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.3147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8505  Z= 0.126
  Angle     :  0.719  10.855  11508  Z= 0.358
  Chirality :  0.043   0.159   1276
  Planarity :  0.003   0.041   1468
  Dihedral  :  4.781  55.802   1145
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 24.81 %
    Favored  : 72.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.27), residues: 1042
  helix:  0.97 (0.28), residues: 367
  sheet: -0.94 (0.38), residues: 199
  loop : -2.13 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP N  47 
 HIS   0.005   0.001   HIS B 183 
 PHE   0.025   0.001   PHE B 235 
 TYR   0.023   0.002   TYR A 283 
 ARG   0.005   0.000   ARG A 205 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03204 (  327)
  hydrogen bonds       : angle       4.37653 (  936)
  SS BOND              : bond        0.00299 (    3)
  SS BOND              : angle       1.76610 (    6)
  covalent geometry    : bond        0.00292 ( 8501)
  covalent geometry    : angle       0.71825 (11502)
  Misc. bond           : bond        0.00012 (    1)

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

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

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 197
  time to evaluate  : 0.953 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.9087 (tt0) cc_final: 0.8884 (tt0)
REVERT: A  202 ASP cc_start: 0.8824 (t0) cc_final: 0.8473 (t0)
REVERT: A  212 GLU cc_start: 0.9059 (tt0) cc_final: 0.8745 (tm-30)
REVERT: A  240 GLN cc_start: 0.8934 (tp-100) cc_final: 0.8264 (tp-100)
REVERT: A  252 ASN cc_start: 0.8265 (p0) cc_final: 0.8015 (p0)
REVERT: A  298 TYR cc_start: 0.8867 (t80) cc_final: 0.8591 (t80)
REVERT: A  326 GLN cc_start: 0.8868 (mm110) cc_final: 0.8474 (mm110)
REVERT: B   57 LYS cc_start: 0.8830 (ptpp) cc_final: 0.8408 (ptmm)
REVERT: B   58 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8625 (pt)
REVERT: B  215 GLU cc_start: 0.7990 (pt0) cc_final: 0.7607 (tm-30)
REVERT: B  220 GLN cc_start: 0.8580 (mt0) cc_final: 0.8122 (tt0)
REVERT: B  228 ASP cc_start: 0.8830 (m-30) cc_final: 0.8349 (m-30)
REVERT: B  264 TYR cc_start: 0.8888 (m-10) cc_final: 0.8582 (m-10)
REVERT: B  289 TYR cc_start: 0.7867 (m-10) cc_final: 0.7163 (m-10)
REVERT: B  293 ASN cc_start: 0.8025 (t0) cc_final: 0.7439 (t0)
REVERT: B  308 LEU cc_start: 0.9131 (mp) cc_final: 0.8766 (mt)
REVERT: B  333 ASP cc_start: 0.8416 (p0) cc_final: 0.8203 (p0)
REVERT: B  339 TRP cc_start: 0.8905 (m100) cc_final: 0.8587 (m100)
REVERT: G   17 MET cc_start: 0.6677 (mmm) cc_final: 0.6323 (mmp)
REVERT: G   46 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8103 (tp30)
REVERT: N    6 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7397 (mm-30)
REVERT: N   27 PHE cc_start: 0.8960 (p90) cc_final: 0.8600 (p90)
REVERT: N   73 ASP cc_start: 0.6662 (t0) cc_final: 0.6222 (t0)
REVERT: N   76 LYS cc_start: 0.8790 (mmmt) cc_final: 0.7963 (mppt)
REVERT: N   77 ASN cc_start: 0.8447 (t0) cc_final: 0.7918 (t0)
REVERT: N  123 GLN cc_start: 0.8917 (tp-100) cc_final: 0.8514 (tp-100)
REVERT: R   60 TYR cc_start: 0.8509 (t80) cc_final: 0.8212 (t80)
REVERT: R   64 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.7713 (mt0)
REVERT: R   78 ASN cc_start: 0.9083 (t0) cc_final: 0.8809 (t0)
REVERT: R  147 ARG cc_start: 0.8850 (mmm-85) cc_final: 0.8161 (tpp80)
REVERT: R  155 MET cc_start: 0.8771 (ttt) cc_final: 0.8435 (ttm)
REVERT: R  183 MET cc_start: 0.8746 (mmm) cc_final: 0.8346 (tpp)
REVERT: R  310 ASN cc_start: 0.9184 (t0) cc_final: 0.8446 (t0)
  outliers start: 25
  outliers final: 16
  residues processed: 215
  average time/residue: 0.1905
  time to fit residues: 56.8169
Evaluate side-chains
  209 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 191
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   28 LEU
Chi-restraints excluded: chain G residue   65 LYS
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   53 GLN
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue   11 VAL
Chi-restraints excluded: chain R residue   22 SER
Chi-restraints excluded: chain R residue   64 GLN
Chi-restraints excluded: chain R residue  104 VAL
Chi-restraints excluded: chain R residue  307 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 82 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 91 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9990
   chunk 37 optimal weight:    5.9990
   chunk 92 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   chunk 97 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.114976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.098312 restraints weight = 17210.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 3.48
r_work: 0.3320 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.3214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8505  Z= 0.136
  Angle     :  0.732  12.932  11508  Z= 0.360
  Chirality :  0.043   0.159   1276
  Planarity :  0.004   0.041   1468
  Dihedral  :  4.804  54.220   1145
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 26.25 %
    Favored  : 71.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.27), residues: 1042
  helix:  1.01 (0.28), residues: 366
  sheet: -0.93 (0.38), residues: 199
  loop : -2.12 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP N  47 
 HIS   0.002   0.001   HIS B 225 
 PHE   0.026   0.001   PHE B 235 
 TYR   0.022   0.002   TYR A 283 
 ARG   0.005   0.000   ARG A 205 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03142 (  327)
  hydrogen bonds       : angle       4.42378 (  936)
  SS BOND              : bond        0.00337 (    3)
  SS BOND              : angle       1.63754 (    6)
  covalent geometry    : bond        0.00316 ( 8501)
  covalent geometry    : angle       0.73136 (11502)
  Misc. bond           : bond        0.00021 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4535.76 seconds
wall clock time: 83 minutes 59.82 seconds (5039.82 seconds total)